Daily Papers

Large Language Models (LLMs) demonstrate human-level or even superior language abilities, effectively modeling syntactic structures, yet the specific computational modules responsible remain unclear. A key question is whether LLM behavioral capabilities stem from mechanisms akin to those in the human brain. To address these questions, we introduce the Hierarchical Frequency Tagging Probe (HFTP), a tool that utilizes frequency-domain analysis to identify neuron-wise components of LLMs (e.g., individual Multilayer Perceptron (MLP) neurons) and cortical regions (via intracranial recordings) encoding syntactic structures. Our results show that models such as GPT-2, Gemma, Gemma 2, Llama 2, Llama 3.1, and GLM-4 process syntax in analogous layers, while the human brain relies on distinct cortical regions for different syntactic levels. Representational similarity analysis reveals a stronger alignment between LLM representations and the left hemisphere of the brain (dominant in language processing). Notably, upgraded models exhibit divergent trends: Gemma 2 shows greater brain similarity than Gemma, while Llama 3.1 shows less alignment with the brain compared to Llama 2. These findings offer new insights into the interpretability of LLM behavioral improvements, raising questions about whether these advancements are driven by human-like or non-human-like mechanisms, and establish HFTP as a valuable tool bridging computational linguistics and cognitive neuroscience. This project is available at https://github.com/LilTiger/HFTP.

Text-guided generative diffusion models unlock powerful image creation and editing tools. While these have been extended to video generation, current approaches that edit the content of existing footage while retaining structure require expensive re-training for every input or rely on error-prone propagation of image edits across frames. In this work, we present a structure and content-guided video diffusion model that edits videos based on visual or textual descriptions of the desired output. Conflicts between user-provided content edits and structure representations occur due to insufficient disentanglement between the two aspects. As a solution, we show that training on monocular depth estimates with varying levels of detail provides control over structure and content fidelity. Our model is trained jointly on images and videos which also exposes explicit control of temporal consistency through a novel guidance method. Our experiments demonstrate a wide variety of successes; fine-grained control over output characteristics, customization based on a few reference images, and a strong user preference towards results by our model.

Extracting tables from documents is a crucial task in any document conversion pipeline. Recently, transformer-based models have demonstrated that table-structure can be recognized with impressive accuracy using Image-to-Markup-Sequence (Im2Seq) approaches. Taking only the image of a table, such models predict a sequence of tokens (e.g. in HTML, LaTeX) which represent the structure of the table. Since the token representation of the table structure has a significant impact on the accuracy and run-time performance of any Im2Seq model, we investigate in this paper how table-structure representation can be optimised. We propose a new, optimised table-structure language (OTSL) with a minimized vocabulary and specific rules. The benefits of OTSL are that it reduces the number of tokens to 5 (HTML needs 28+) and shortens the sequence length to half of HTML on average. Consequently, model accuracy improves significantly, inference time is halved compared to HTML-based models, and the predicted table structures are always syntactically correct. This in turn eliminates most post-processing needs.

Crystal structure generation is a foundational challenge in materials discovery, particularly in designing functional inorganic crystalline materials with desired properties. Most existing diffusion-based generative models for crystals rely on complex, hand-crafted priors and modular architectures to separately model atom types, atomic positions, and lattice parameters. These methods often require customized diffusion processes and conditional denoising, which can introduce additional model complexities and inconsistencies. Here we introduce DiffCrysGen, a fully data-driven, score-based diffusion model that jointly learns the distribution of all structural components in crystalline materials. With crystal structure representation as unified 2D matrices, DiffCrysGen bypasses the need for task-specific priors or decoupled modules, enabling end-to-end generation of atom types, fractional coordinates, and lattice parameters within a single framework. Our model learns crystallographic symmetry and chemical validity directly from large-scale datasets, allowing it to scale to complex materials discovery tasks. As a demonstration, we applied DiffCrysGen to the design of rare-earth-free magnetic materials with high saturation magnetization, showing its effectiveness in generating stable, diverse, and property-aligned candidates for sustainable magnet applications.

Crystalline materials often exhibit a high level of symmetry. However, most generative models do not account for symmetry, but rather model each atom without any constraints on its position or element. We propose a generative model, Wyckoff Diffusion (WyckoffDiff), which generates symmetry-based descriptions of crystals. This is enabled by considering a crystal structure representation that encodes all symmetry, and we design a novel neural network architecture which enables using this representation inside a discrete generative model framework. In addition to respecting symmetry by construction, the discrete nature of our model enables fast generation. We additionally present a new metric, Fr\'echet Wrenformer Distance, which captures the symmetry aspects of the materials generated, and we benchmark WyckoffDiff against recently proposed generative models for crystal generation. Code is available online at https://github.com/httk/wyckoffdiff

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Formulating and answering logical queries is a standard communication interface for knowledge graphs (KGs). Alleviating the notorious incompleteness of real-world KGs, neural methods achieved impressive results in link prediction and complex query answering tasks by learning representations of entities, relations, and queries. Still, most existing query answering methods rely on transductive entity embeddings and cannot generalize to KGs containing new entities without retraining the entity embeddings. In this work, we study the inductive query answering task where inference is performed on a graph containing new entities with queries over both seen and unseen entities. To this end, we devise two mechanisms leveraging inductive node and relational structure representations powered by graph neural networks (GNNs). Experimentally, we show that inductive models are able to perform logical reasoning at inference time over unseen nodes generalizing to graphs up to 500% larger than training ones. Exploring the efficiency--effectiveness trade-off, we find the inductive relational structure representation method generally achieves higher performance, while the inductive node representation method is able to answer complex queries in the inference-only regime without any training on queries and scales to graphs of millions of nodes. Code is available at https://github.com/DeepGraphLearning/InductiveQE.

Dramatic progress has been witnessed in basic vision tasks involving low-level perception, such as object recognition, detection, and tracking. Unfortunately, there is still an enormous performance gap between artificial vision systems and human intelligence in terms of higher-level vision problems, especially ones involving reasoning. Earlier attempts in equipping machines with high-level reasoning have hovered around Visual Question Answering (VQA), one typical task associating vision and language understanding. In this work, we propose a new dataset, built in the context of Raven's Progressive Matrices (RPM) and aimed at lifting machine intelligence by associating vision with structural, relational, and analogical reasoning in a hierarchical representation. Unlike previous works in measuring abstract reasoning using RPM, we establish a semantic link between vision and reasoning by providing structure representation. This addition enables a new type of abstract reasoning by jointly operating on the structure representation. Machine reasoning ability using modern computer vision is evaluated in this newly proposed dataset. Additionally, we also provide human performance as a reference. Finally, we show consistent improvement across all models by incorporating a simple neural module that combines visual understanding and structure reasoning.

Transformer-based pre-training techniques of text and layout have proven effective in a number of document understanding tasks. Despite this success, multimodal pre-training models suffer from very high computational and memory costs. Motivated by human reading strategies, this paper presents Skim-Attention, a new attention mechanism that takes advantage of the structure of the document and its layout. Skim-Attention only attends to the 2-dimensional position of the words in a document. Our experiments show that Skim-Attention obtains a lower perplexity than prior works, while being more computationally efficient. Skim-Attention can be further combined with long-range Transformers to efficiently process long documents. We also show how Skim-Attention can be used off-the-shelf as a mask for any Pre-trained Language Model, allowing to improve their performance while restricting attention. Finally, we show the emergence of a document structure representation in Skim-Attention.

Centred on content modification and style preservation, Scene Text Editing (STE) remains a challenging task despite considerable progress in text-to-image synthesis and text-driven image manipulation recently. GAN-based STE methods generally encounter a common issue of model generalization, while Diffusion-based STE methods suffer from undesired style deviations. To address these problems, we propose TextCtrl, a diffusion-based method that edits text with prior guidance control. Our method consists of two key components: (i) By constructing fine-grained text style disentanglement and robust text glyph structure representation, TextCtrl explicitly incorporates Style-Structure guidance into model design and network training, significantly improving text style consistency and rendering accuracy. (ii) To further leverage the style prior, a Glyph-adaptive Mutual Self-attention mechanism is proposed which deconstructs the implicit fine-grained features of the source image to enhance style consistency and vision quality during inference. Furthermore, to fill the vacancy of the real-world STE evaluation benchmark, we create the first real-world image-pair dataset termed ScenePair for fair comparisons. Experiments demonstrate the effectiveness of TextCtrl compared with previous methods concerning both style fidelity and text accuracy.

Grouping and recognition are important components of visual scene understanding, e.g., for object detection and semantic segmentation. With end-to-end deep learning systems, grouping of image regions usually happens implicitly via top-down supervision from pixel-level recognition labels. Instead, in this paper, we propose to bring back the grouping mechanism into deep networks, which allows semantic segments to emerge automatically with only text supervision. We propose a hierarchical Grouping Vision Transformer (GroupViT), which goes beyond the regular grid structure representation and learns to group image regions into progressively larger arbitrary-shaped segments. We train GroupViT jointly with a text encoder on a large-scale image-text dataset via contrastive losses. With only text supervision and without any pixel-level annotations, GroupViT learns to group together semantic regions and successfully transfers to the task of semantic segmentation in a zero-shot manner, i.e., without any further fine-tuning. It achieves a zero-shot accuracy of 52.3% mIoU on the PASCAL VOC 2012 and 22.4% mIoU on PASCAL Context datasets, and performs competitively to state-of-the-art transfer-learning methods requiring greater levels of supervision. We open-source our code at https://github.com/NVlabs/GroupViT .

Existing visual parsers for molecule diagrams translate pixel-based raster images such as PNGs to chemical structure representations (e.g., SMILES). However, PDFs created by word processors including LaTeX and Word provide explicit locations and shapes for characters, lines, and polygons. We extract symbols from born-digital PDF molecule images and then apply simple graph transformations to capture both visual and chemical structure in editable ChemDraw files (CDXML). Our fast ( PDF rightarrow visual graph rightarrow chemical graph ) pipeline does not require GPUs, Optical Character Recognition (OCR) or vectorization. We evaluate on standard benchmarks using SMILES strings, along with a novel evaluation that provides graph-based metrics and error compilation using LgEval. The geometric information in born-digital PDFs produces a highly accurate parser, motivating generating training data for visual parsers that recognize from raster images, with extracted graphics, visual structure, and chemical structure as annotations. To do this we render SMILES strings in Indigo, parse molecule structure, and then validate recognized structure to select correct files.

Despite much progress, achieving real-time high-fidelity head avatar animation is still difficult and existing methods have to trade-off between speed and quality. 3DMM based methods often fail to model non-facial structures such as eyeglasses and hairstyles, while neural implicit models suffer from deformation inflexibility and rendering inefficiency. Although 3D Gaussian has been demonstrated to possess promising capability for geometry representation and radiance field reconstruction, applying 3D Gaussian in head avatar creation remains a major challenge since it is difficult for 3D Gaussian to model the head shape variations caused by changing poses and expressions. In this paper, we introduce PSAvatar, a novel framework for animatable head avatar creation that utilizes discrete geometric primitive to create a parametric morphable shape model and employs 3D Gaussian for fine detail representation and high fidelity rendering. The parametric morphable shape model is a Point-based Morphable Shape Model (PMSM) which uses points instead of meshes for 3D representation to achieve enhanced representation flexibility. The PMSM first converts the FLAME mesh to points by sampling on the surfaces as well as off the meshes to enable the reconstruction of not only surface-like structures but also complex geometries such as eyeglasses and hairstyles. By aligning these points with the head shape in an analysis-by-synthesis manner, the PMSM makes it possible to utilize 3D Gaussian for fine detail representation and appearance modeling, thus enabling the creation of high-fidelity avatars. We show that PSAvatar can reconstruct high-fidelity head avatars of a variety of subjects and the avatars can be animated in real-time (ge 25 fps at a resolution of 512 times 512 ).

Tabular data is a crucial form of information expression, which can organize data in a standard structure for easy information retrieval and comparison. However, in financial industry and many other fields tables are often disclosed in unstructured digital files, e.g. Portable Document Format (PDF) and images, which are difficult to be extracted directly. In this paper, to facilitate deep learning based table extraction from unstructured digital files, we publish a standard Chinese dataset named FinTab, which contains more than 1,600 financial tables of diverse kinds and their corresponding structure representation in JSON. In addition, we propose a novel graph-based convolutional neural network model named GFTE as a baseline for future comparison. GFTE integrates image feature, position feature and textual feature together for precise edge prediction and reaches overall good results.

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

3D Gaussian Splatting (3DGS) integrates the strengths of primitive-based representations and volumetric rendering techniques, enabling real-time, high-quality rendering. However, 3DGS models typically overfit to single-scene training and are highly sensitive to the initialization of Gaussian ellipsoids, heuristically derived from Structure from Motion (SfM) point clouds, which limits both generalization and practicality. To address these limitations, we propose GS-Net, a generalizable, plug-and-play 3DGS module that densifies Gaussian ellipsoids from sparse SfM point clouds, enhancing geometric structure representation. To the best of our knowledge, GS-Net is the first plug-and-play 3DGS module with cross-scene generalization capabilities. Additionally, we introduce the CARLA-NVS dataset, which incorporates additional camera viewpoints to thoroughly evaluate reconstruction and rendering quality. Extensive experiments demonstrate that applying GS-Net to 3DGS yields a PSNR improvement of 2.08 dB for conventional viewpoints and 1.86 dB for novel viewpoints, confirming the method's effectiveness and robustness.

In this paper, we propose a new mixed-integer linear programming (MILP) model ontology and a novel constraint typology of MILP formulations. MILP is a commonly used mathematical programming technique for modelling and solving real-life scheduling, routing, planning, resource allocation, and timetabling optimization problems providing optimized business solutions for industry sectors such as manufacturing, agriculture, defence, healthcare, medicine, energy, finance, and transportation. Despite the numerous real-life Combinatorial Optimization Problems found and solved and millions yet to be discovered and formulated, the number of types of constraints (the building blocks of a MILP) is relatively small. In the search for a suitable machine-readable knowledge representation structure for MILPs, we propose an optimization modelling tree built based upon an MILP model ontology that can be used as a guide for automated systems to elicit an MILP model from end-users on their combinatorial business optimization problems. Our ultimate aim is to develop a machine-readable knowledge representation for MILP that allows us to map an end-user's natural language description of the business optimization problem to an MILP formal specification as a first step towards automated mathematical modelling.

Representation learning and exploration are among the key challenges for any deep reinforcement learning agent. In this work, we provide a singular value decomposition based method that can be used to obtain representations that preserve the underlying transition structure in the domain. Perhaps interestingly, we show that these representations also capture the relative frequency of state visitations, thereby providing an estimate for pseudo-counts for free. To scale this decomposition method to large-scale domains, we provide an algorithm that never requires building the transition matrix, can make use of deep networks, and also permits mini-batch training. Further, we draw inspiration from predictive state representations and extend our decomposition method to partially observable environments. With experiments on multi-task settings with partially observable domains, we show that the proposed method can not only learn useful representation on DM-Lab-30 environments (that have inputs involving language instructions, pixel images, and rewards, among others) but it can also be effective at hard exploration tasks in DM-Hard-8 environments.

Current vision models typically maintain a fixed correspondence between their representation structure and image space. Each layer comprises a set of tokens arranged "on-the-grid," which biases patches or tokens to encode information at a specific spatio(-temporal) location. In this work we present Moving Off-the-Grid (MooG), a self-supervised video representation model that offers an alternative approach, allowing tokens to move "off-the-grid" to better enable them to represent scene elements consistently, even as they move across the image plane through time. By using a combination of cross-attention and positional embeddings we disentangle the representation structure and image structure. We find that a simple self-supervised objective--next frame prediction--trained on video data, results in a set of latent tokens which bind to specific scene structures and track them as they move. We demonstrate the usefulness of MooG's learned representation both qualitatively and quantitatively by training readouts on top of the learned representation on a variety of downstream tasks. We show that MooG can provide a strong foundation for different vision tasks when compared to "on-the-grid" baselines.

Deep neural networks have reached human-level performance on many computer vision tasks. However, the objectives used to train these networks enforce only that similar images are embedded at similar locations in the representation space, and do not directly constrain the global structure of the resulting space. Here, we explore the impact of supervising this global structure by linearly aligning it with human similarity judgments. We find that a naive approach leads to large changes in local representational structure that harm downstream performance. Thus, we propose a novel method that aligns the global structure of representations while preserving their local structure. This global-local transform considerably improves accuracy across a variety of few-shot learning and anomaly detection tasks. Our results indicate that human visual representations are globally organized in a way that facilitates learning from few examples, and incorporating this global structure into neural network representations improves performance on downstream tasks.

Convolutional neural networks (CNNs) have so far been the de-facto model for visual data. Recent work has shown that (Vision) Transformer models (ViT) can achieve comparable or even superior performance on image classification tasks. This raises a central question: how are Vision Transformers solving these tasks? Are they acting like convolutional networks, or learning entirely different visual representations? Analyzing the internal representation structure of ViTs and CNNs on image classification benchmarks, we find striking differences between the two architectures, such as ViT having more uniform representations across all layers. We explore how these differences arise, finding crucial roles played by self-attention, which enables early aggregation of global information, and ViT residual connections, which strongly propagate features from lower to higher layers. We study the ramifications for spatial localization, demonstrating ViTs successfully preserve input spatial information, with noticeable effects from different classification methods. Finally, we study the effect of (pretraining) dataset scale on intermediate features and transfer learning, and conclude with a discussion on connections to new architectures such as the MLP-Mixer.

Distilled diffusion models suffer from a critical limitation: reduced sample diversity compared to their base counterparts. In this work, we uncover that despite this diversity loss, distilled models retain the fundamental concept representations of base models. We demonstrate control distillation - where control mechanisms like Concept Sliders and LoRAs trained on base models can be seamlessly transferred to distilled models and vice-versa, effectively distilling control without any retraining. This preservation of representational structure prompted our investigation into the mechanisms of diversity collapse during distillation. To understand how distillation affects diversity, we introduce Diffusion Target (DT) Visualization, an analysis and debugging tool that reveals how models predict final outputs at intermediate steps. Through DT-Visualization, we identify generation artifacts, inconsistencies, and demonstrate that initial diffusion timesteps disproportionately determine output diversity, while later steps primarily refine details. Based on these insights, we introduce diversity distillation - a hybrid inference approach that strategically employs the base model for only the first critical timestep before transitioning to the efficient distilled model. Our experiments demonstrate that this simple modification not only restores the diversity capabilities from base to distilled models but surprisingly exceeds it, while maintaining nearly the computational efficiency of distilled inference, all without requiring additional training or model modifications. Our code and data are available at https://distillation.baulab.info

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements and bonds respectively. Although existing deep learning models perform remarkably well at predicting physicochemical properties and binding affinities, the generation of new molecules with optimized properties remains challenging. Inherently, most GNNs perform poorly in whole-graph representation due to the limitations of the message-passing paradigm. Furthermore, step-by-step graph generation frameworks that use reinforcement learning or other sequential processing can be slow and result in a high proportion of invalid molecules with substantial post-processing needed in order to satisfy the principles of stoichiometry. To address these issues, we propose a representation-first approach to molecular graph generation. We guide the latent representation of an autoencoder by capturing graph structure information with the geometric scattering transform and apply penalties that structure the representation also by molecular properties. We show that this highly structured latent space can be directly used for molecular graph generation by the use of a GAN. We demonstrate that our architecture learns meaningful representations of drug datasets and provides a platform for goal-directed drug synthesis.

Compositional understanding is crucial for human intelligence, yet it remains unclear whether contemporary vision models exhibit it. The dominant machine learning paradigm is built on the premise that scaling data and model sizes will improve out-of-distribution performance, including compositional generalization. We test this premise through controlled experiments that systematically vary data scale, concept diversity, and combination coverage. We find that compositional generalization is driven by data diversity, not mere data scale. Increased combinatorial coverage forces models to discover a linearly factored representational structure, where concepts decompose into additive components. We prove this structure is key to efficiency, enabling perfect generalization from few observed combinations. Evaluating pretrained models (DINO, CLIP), we find above-random yet imperfect performance, suggesting partial presence of this structure. Our work motivates stronger emphasis on constructing diverse datasets for compositional generalization, and considering the importance of representational structure that enables efficient compositional learning. Code available at https://github.com/oshapio/visual-compositional-generalization.

We present Seg-TTO, a novel framework for zero-shot, open-vocabulary semantic segmentation (OVSS), designed to excel in specialized domain tasks. While current open vocabulary approaches show impressive performance on standard segmentation benchmarks under zero-shot settings, they fall short of supervised counterparts on highly domain-specific datasets. We focus on segmentation-specific test-time optimization to address this gap. Segmentation requires an understanding of multiple concepts within a single image while retaining the locality and spatial structure of representations. We propose a novel self-supervised objective adhering to these requirements and use it to align the model parameters with input images at test time. In the textual modality, we learn multiple embeddings for each category to capture diverse concepts within an image, while in the visual modality, we calculate pixel-level losses followed by embedding aggregation operations specific to preserving spatial structure. Our resulting framework termed Seg-TTO is a plug-in-play module. We integrate Seg-TTO with three state-of-the-art OVSS approaches and evaluate across 22 challenging OVSS tasks covering a range of specialized domains. Our Seg-TTO demonstrates clear performance improvements across these establishing new state-of-the-art. Code: https://github.com/UlinduP/SegTTO.

The prediction of material degradation is an important problem to solve in many industries. Environmental conditions, such as humidity and temperature, are important drivers of degradation processes, with corrosion being one of the most prominent ones. Quantum machine learning is a promising research field but suffers from well known deficits such as barren plateaus and measurement overheads. To address this problem, recent research has examined quantum reservoir computing to address time-series prediction tasks. Although a promising idea, developing circuits that are expressive enough while respecting the limited depths available on current devices is challenging. In classical reservoir computing, the onion echo state network model (ESN) [https://doi.org/10.1007/978-3-031-72359-9_9] was introduced to increase the interpretability of the representation structure of the embeddings. This onion ESN model utilizes a concatenation of smaller reservoirs that describe different time scales by covering different regions of the eigenvalue spectrum. Here, we use the same idea in the realm of quantum reservoir computing by simultaneously evolving smaller quantum reservoirs to better capture all the relevant time-scales while keeping the circuit depth small. We do this by modifying the rotation angles which we show alters the eigenvalues of the quantum evolution, but also note that modifying the number of mid-circuit measurements accomplishes the same goals of changing the long-term or short-term memory. This onion QRC outperforms a simple model and a single classical reservoir for predicting the degradation of aluminum alloys in different environmental conditions. By combining the onion QRC with an additional classical reservoir layer, the prediction accuracy is further improved.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from the universe of natural protein sequences. Furthermore, structure-based encoders like ProteinMPNN learn the structural information of proteins through Graph Neural Networks. However, whether the incorporation of protein encoders can enhance the protein understanding of LLMs has not been explored. To bridge this gap, we propose EvoLlama, a multimodal framework that connects a structure-based encoder, a sequence-based protein encoder and an LLM for protein understanding. EvoLlama consists of a ProteinMPNN structure encoder, an ESM-2 protein sequence encoder, a multimodal projector to align protein and text representations and a Llama-3 text decoder. To train EvoLlama, we fine-tune it on protein-oriented instructions and protein property prediction datasets verbalized via natural language instruction templates. Our experiments show that EvoLlama's protein understanding capabilities have been significantly enhanced, outperforming other fine-tuned protein-oriented LLMs in zero-shot settings by an average of 1%-8% and surpassing the state-of-the-art baseline with supervised fine-tuning by an average of 6%. On protein property prediction datasets, our approach achieves promising results that are competitive with state-of-the-art task-specific baselines. We will release our code in a future version.

Time series classification is a fundamental task in healthcare and industry, yet the development of time series foundation models (TSFMs) remains limited by the scarcity of publicly available time series datasets. In this work, we propose Time Vision Transformer (TiViT), a framework that converts time series into images to leverage the representational power of frozen Vision Transformers (ViTs) pretrained on large-scale image datasets. First, we theoretically motivate our approach by analyzing the 2D patching of ViTs for time series, showing that it can increase the number of label-relevant tokens and reduce the sample complexity. Second, we empirically demonstrate that TiViT achieves state-of-the-art performance on standard time series classification benchmarks by utilizing the hidden representations of large OpenCLIP models. We explore the structure of TiViT representations and find that intermediate layers with high intrinsic dimension are the most effective for time series classification. Finally, we assess the alignment between TiViT and TSFM representation spaces and identify a strong complementarity, with further performance gains achieved by combining their features. Our findings reveal a new direction for reusing vision representations in a non-visual domain. Code is available at https://github.com/ExplainableML/TiViT.

Syllables are compositional units of spoken language that play a crucial role in human speech perception and production. However, current neural speech representations lack structure, resulting in dense token sequences that are costly to process. To bridge this gap, we propose a new model, Sylber, that produces speech representations with clean and robust syllabic structure. Specifically, we propose a self-supervised model that regresses features on syllabic segments distilled from a teacher model which is an exponential moving average of the model in training. This results in a highly structured representation of speech features, offering three key benefits: 1) a fast, linear-time syllable segmentation algorithm, 2) efficient syllabic tokenization with an average of 4.27 tokens per second, and 3) syllabic units better suited for lexical and syntactic understanding. We also train token-to-speech generative models with our syllabic units and show that fully intelligible speech can be reconstructed from these tokens. Lastly, we observe that categorical perception, a linguistic phenomenon of speech perception, emerges naturally in our model, making the embedding space more categorical and sparse than previous self-supervised learning approaches. Together, we present a novel self-supervised approach for representing speech as syllables, with significant potential for efficient speech tokenization and spoken language modeling.

The use of kernel functions is a common technique to extract important features from data sets. A quantum computer can be used to estimate kernel entries as transition amplitudes of unitary circuits. Quantum kernels exist that, subject to computational hardness assumptions, cannot be computed classically. It is an important challenge to find quantum kernels that provide an advantage in the classification of real-world data. We introduce a class of quantum kernels that can be used for data with a group structure. The kernel is defined in terms of a unitary representation of the group and a fiducial state that can be optimized using a technique called kernel alignment. We apply this method to a learning problem on a coset-space that embodies the structure of many essential learning problems on groups. We implement the learning algorithm with 27 qubits on a superconducting processor.

Representational analysis explores how input data of a neural system are encoded in high dimensional spaces of its distributed neural activations, and how we can compare different systems, for instance, artificial neural networks and brains, on those grounds. While existing methods offer important insights, they typically do not account for local intrinsic geometrical properties within the high-dimensional representation spaces. To go beyond these limitations, we explore Ollivier-Ricci curvature and Ricci flow as tools to study the alignment of representations between humans and artificial neural systems on a geometric level. As a proof-of-principle study, we compared the representations of face stimuli between VGG-Face, a human-aligned version of VGG-Face, and corresponding human similarity judgments from a large online study. Using this discrete geometric framework, we were able to identify local structural similarities and differences by examining the distributions of node and edge curvature and higher-level properties by detecting and comparing community structure in the representational graphs.

We introduce Perceptual-Initialization (PI), a paradigm shift in visual representation learning that incorporates human perceptual structure during the initialization phase rather than as a downstream fine-tuning step. By integrating human-derived triplet embeddings from the NIGHTS dataset to initialize a CLIP vision encoder, followed by self-supervised learning on YFCC15M, our approach demonstrates significant zero-shot performance improvements, without any task-specific fine-tuning, across 29 zero shot classification and 2 retrieval benchmarks. On ImageNet-1K, zero-shot gains emerge after approximately 15 epochs of pretraining. Benefits are observed across datasets of various scales, with improvements manifesting at different stages of the pretraining process depending on dataset characteristics. Our approach consistently enhances zero-shot top-1 accuracy, top-5 accuracy, and retrieval recall (e.g., R@1, R@5) across these diverse evaluation tasks, without requiring any adaptation to target domains. These findings challenge the conventional wisdom of using human-perceptual data primarily for fine-tuning and demonstrate that embedding human perceptual structure during early representation learning yields more capable and vision-language aligned systems that generalize immediately to unseen tasks. Our work shows that "beginning with you", starting with human perception, provides a stronger foundation for general-purpose vision-language intelligence.

Deep neural networks have achieved success across a wide range of applications, including as models of human behavior in vision tasks. However, neural network training and human learning differ in fundamental ways, and neural networks often fail to generalize as robustly as humans do, raising questions regarding the similarity of their underlying representations. What is missing for modern learning systems to exhibit more human-like behavior? We highlight a key misalignment between vision models and humans: whereas human conceptual knowledge is hierarchically organized from fine- to coarse-scale distinctions, model representations do not accurately capture all these levels of abstraction. To address this misalignment, we first train a teacher model to imitate human judgments, then transfer human-like structure from its representations into pretrained state-of-the-art vision foundation models. These human-aligned models more accurately approximate human behavior and uncertainty across a wide range of similarity tasks, including a new dataset of human judgments spanning multiple levels of semantic abstractions. They also perform better on a diverse set of machine learning tasks, increasing generalization and out-of-distribution robustness. Thus, infusing neural networks with additional human knowledge yields a best-of-both-worlds representation that is both more consistent with human cognition and more practically useful, thus paving the way toward more robust, interpretable, and human-like artificial intelligence systems.

Object categories are typically organized into a multi-granularity taxonomic hierarchy. When classifying categories at different hierarchy levels, traditional uni-modal approaches focus primarily on image features, revealing limitations in complex scenarios. Recent studies integrating Vision-Language Models (VLMs) with class hierarchies have shown promise, yet they fall short of fully exploiting the hierarchical relationships. These efforts are constrained by their inability to perform effectively across varied granularity of categories. To tackle this issue, we propose a novel framework (HGCLIP) that effectively combines CLIP with a deeper exploitation of the Hierarchical class structure via Graph representation learning. We explore constructing the class hierarchy into a graph, with its nodes representing the textual or image features of each category. After passing through a graph encoder, the textual features incorporate hierarchical structure information, while the image features emphasize class-aware features derived from prototypes through the attention mechanism. Our approach demonstrates significant improvements on 11 diverse visual recognition benchmarks. Our codes are fully available at https://github.com/richard-peng-xia/HGCLIP.

Learning behavioral patterns from observational data has been a de-facto approach to motion forecasting. Yet, the current paradigm suffers from two shortcomings: brittle under distribution shifts and inefficient for knowledge transfer. In this work, we propose to address these challenges from a causal representation perspective. We first introduce a causal formalism of motion forecasting, which casts the problem as a dynamic process with three groups of latent variables, namely invariant variables, style confounders, and spurious features. We then introduce a learning framework that treats each group separately: (i) unlike the common practice mixing datasets collected from different locations, we exploit their subtle distinctions by means of an invariance loss encouraging the model to suppress spurious correlations; (ii) we devise a modular architecture that factorizes the representations of invariant mechanisms and style confounders to approximate a sparse causal graph; (iii) we introduce a style contrastive loss that not only enforces the structure of style representations but also serves as a self-supervisory signal for test-time refinement on the fly. Experiments on synthetic and real datasets show that our proposed method improves the robustness and reusability of learned motion representations, significantly outperforming prior state-of-the-art motion forecasting models for out-of-distribution generalization and low-shot transfer.

To balance quality and cost, various domain areas of science and engineering run simulations at multiple levels of sophistication. Multi-fidelity active learning aims to learn a direct mapping from input parameters to simulation outputs at the highest fidelity by actively acquiring data from multiple fidelity levels. However, existing approaches based on Gaussian processes are hardly scalable to high-dimensional data. Deep learning-based methods often impose a hierarchical structure in hidden representations, which only supports passing information from low-fidelity to high-fidelity. These approaches can lead to the undesirable propagation of errors from low-fidelity representations to high-fidelity ones. We propose a novel framework called Disentangled Multi-fidelity Deep Bayesian Active Learning (D-MFDAL), which learns the surrogate models conditioned on the distribution of functions at multiple fidelities. On benchmark tasks of learning deep surrogates of partial differential equations including heat equation, Poisson's equation and fluid simulations, our approach significantly outperforms state-of-the-art in prediction accuracy and sample efficiency.

Recently, text-guided image editing has achieved significant success. However, existing methods can only apply simple textures like wood or gold when changing the texture of an object. Complex textures such as cloud or fire pose a challenge. This limitation stems from that the target prompt needs to contain both the input image content and <texture>, restricting the texture representation. In this paper, we propose TextureDiffusion, a tuning-free image editing method applied to various texture transfer. Initially, the target prompt is directly set to "<texture>", making the texture disentangled from the input image content to enhance texture representation. Subsequently, query features in self-attention and features in residual blocks are utilized to preserve the structure of the input image. Finally, to maintain the background, we introduce an edit localization technique which blends the self-attention results and the intermediate latents. Comprehensive experiments demonstrate that TextureDiffusion can harmoniously transfer various textures with excellent structure and background preservation.

Human cognition excels at transcending sensory input and forming latent representations that structure our understanding of the world. Although Large Language Models (LLMs) can produce chain-of-thought reasoning, they lack a principled framework to capture latent structures and model uncertainty, especially in compositional reasoning tasks. We propose Verbalized Probabilistic Graphical Modeling (vPGM), a Bayesian prompting framework that guides LLMs to simulate key principles of Probabilistic Graphical Models (PGMs) in natural language. Unlike many traditional probabilistic methods requiring substantial domain expertise or specialized training, vPGM bypasses expert-driven model design, making it well-suited for scenarios with limited assumptions or scarce data. We evaluated our model on several compositional reasoning tasks, both close-ended and open-ended. Our results indicate that the model effectively enhances confidence calibration and text generation quality.

The large pre-trained BERT has achieved remarkable performance on Natural Language Processing (NLP) tasks but is also computation and memory expensive. As one of the powerful compression approaches, binarization extremely reduces the computation and memory consumption by utilizing 1-bit parameters and bitwise operations. Unfortunately, the full binarization of BERT (i.e., 1-bit weight, embedding, and activation) usually suffer a significant performance drop, and there is rare study addressing this problem. In this paper, with the theoretical justification and empirical analysis, we identify that the severe performance drop can be mainly attributed to the information degradation and optimization direction mismatch respectively in the forward and backward propagation, and propose BiBERT, an accurate fully binarized BERT, to eliminate the performance bottlenecks. Specifically, BiBERT introduces an efficient Bi-Attention structure for maximizing representation information statistically and a Direction-Matching Distillation (DMD) scheme to optimize the full binarized BERT accurately. Extensive experiments show that BiBERT outperforms both the straightforward baseline and existing state-of-the-art quantized BERTs with ultra-low bit activations by convincing margins on the NLP benchmark. As the first fully binarized BERT, our method yields impressive 56.3 times and 31.2 times saving on FLOPs and model size, demonstrating the vast advantages and potential of the fully binarized BERT model in real-world resource-constrained scenarios.

Automatic font generation is an imitation task, which aims to create a font library that mimics the style of reference images while preserving the content from source images. Although existing font generation methods have achieved satisfactory performance, they still struggle with complex characters and large style variations. To address these issues, we propose FontDiffuser, a diffusion-based image-to-image one-shot font generation method, which innovatively models the font imitation task as a noise-to-denoise paradigm. In our method, we introduce a Multi-scale Content Aggregation (MCA) block, which effectively combines global and local content cues across different scales, leading to enhanced preservation of intricate strokes of complex characters. Moreover, to better manage the large variations in style transfer, we propose a Style Contrastive Refinement (SCR) module, which is a novel structure for style representation learning. It utilizes a style extractor to disentangle styles from images, subsequently supervising the diffusion model via a meticulously designed style contrastive loss. Extensive experiments demonstrate FontDiffuser's state-of-the-art performance in generating diverse characters and styles. It consistently excels on complex characters and large style changes compared to previous methods. The code is available at https://github.com/yeungchenwa/FontDiffuser.

Mathematical formulas are a fundamental and widely used component in various scientific fields, serving as a universal language for expressing complex concepts and relationships. While state-of-the-art transformer models excel in processing and understanding natural language, they encounter challenges with mathematical notation, which involves a complex structure and diverse representations. This study focuses on the development of specialized training datasets to enhance the encoding of mathematical content. We introduce Math Mutator (MAMUT), a framework capable of generating equivalent and falsified versions of a given mathematical formula in LaTeX notation, effectively capturing the mathematical variety in notation of the same concept. Based on MAMUT, we have generated four large mathematical datasets containing diverse notation, which can be used to train language models with enhanced mathematical embeddings.

We introduce CDBERT, a new learning paradigm that enhances the semantics understanding ability of the Chinese PLMs with dictionary knowledge and structure of Chinese characters. We name the two core modules of CDBERT as Shuowen and Jiezi, where Shuowen refers to the process of retrieving the most appropriate meaning from Chinese dictionaries and Jiezi refers to the process of enhancing characters' glyph representations with structure understanding. To facilitate dictionary understanding, we propose three pre-training tasks, i.e., Masked Entry Modeling, Contrastive Learning for Synonym and Antonym, and Example Learning. We evaluate our method on both modern Chinese understanding benchmark CLUE and ancient Chinese benchmark CCLUE. Moreover, we propose a new polysemy discrimination task PolyMRC based on the collected dictionary of ancient Chinese. Our paradigm demonstrates consistent improvements on previous Chinese PLMs across all tasks. Moreover, our approach yields significant boosting on few-shot setting of ancient Chinese understanding.

Retrieving relevant documents from a corpus is typically based on the semantic similarity between the document content and query text. The inclusion of structural relationship between documents can benefit the retrieval mechanism by addressing semantic gaps. However, incorporating these relationships requires tractable mechanisms that balance structure with semantics and take advantage of the prevalent pre-train/fine-tune paradigm. We propose here a holistic approach to learning document representations by integrating intra-document content with inter-document relations. Our deep metric learning solution analyzes the complex neighborhood structure in the relationship network to efficiently sample similar/dissimilar document pairs and defines a novel quintuplet loss function that simultaneously encourages document pairs that are semantically relevant to be closer and structurally unrelated to be far apart in the representation space. Furthermore, the separation margins between the documents are varied flexibly to encode the heterogeneity in relationship strengths. The model is fully fine-tunable and natively supports query projection during inference. We demonstrate that it outperforms competing methods on multiple datasets for document retrieval tasks.

The goal of protein representation learning is to extract knowledge from protein databases that can be applied to various protein-related downstream tasks. Although protein sequence, structure, and function are the three key modalities for a comprehensive understanding of proteins, existing methods for protein representation learning have utilized only one or two of these modalities due to the difficulty of capturing the asymmetric interrelationships between them. To account for this asymmetry, we introduce our novel asymmetric multi-modal masked autoencoder (AMMA). AMMA adopts (1) a unified multi-modal encoder to integrate all three modalities into a unified representation space and (2) asymmetric decoders to ensure that sequence latent features reflect structural and functional information. The experiments demonstrate that the proposed AMMA is highly effective in learning protein representations that exhibit well-aligned inter-modal relationships, which in turn makes it effective for various downstream protein-related tasks.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Benefiting from the message passing mechanism, Graph Neural Networks (GNNs) have been successful on flourish tasks over graph data. However, recent studies have shown that attackers can catastrophically degrade the performance of GNNs by maliciously modifying the graph structure. A straightforward solution to remedy this issue is to model the edge weights by learning a metric function between pairwise representations of two end nodes, which attempts to assign low weights to adversarial edges. The existing methods use either raw features or representations learned by supervised GNNs to model the edge weights. However, both strategies are faced with some immediate problems: raw features cannot represent various properties of nodes (e.g., structure information), and representations learned by supervised GNN may suffer from the poor performance of the classifier on the poisoned graph. We need representations that carry both feature information and as mush correct structure information as possible and are insensitive to structural perturbations. To this end, we propose an unsupervised pipeline, named STABLE, to optimize the graph structure. Finally, we input the well-refined graph into a downstream classifier. For this part, we design an advanced GCN that significantly enhances the robustness of vanilla GCN without increasing the time complexity. Extensive experiments on four real-world graph benchmarks demonstrate that STABLE outperforms the state-of-the-art methods and successfully defends against various attacks.

We present Banyan, a model that efficiently learns semantic representations by leveraging explicit hierarchical structure. While transformers excel at scale, they struggle in low-resource settings. Conversely recent structured models have shown promise as efficient learners, but lack performance. Banyan bridges this gap with two key innovations: an entangled hierarchical tree structure and diagonalized message passing, enabling it to outperform larger transformer models with just 14 non-embedding parameters. It excels in low-resource settings, offering a viable alternative for under-represented languages and highlighting its potential for efficient, interpretable NLP in resource-constrained environments.

The utility of a learned neural representation depends on how well its geometry supports performance in downstream tasks. This geometry depends on the structure of the inputs, the structure of the target outputs, and the architecture of the network. By studying the learning dynamics of networks with one hidden layer, we discovered that the network's activation function has an unexpectedly strong impact on the representational geometry: Tanh networks tend to learn representations that reflect the structure of the target outputs, while ReLU networks retain more information about the structure of the raw inputs. This difference is consistently observed across a broad class of parameterized tasks in which we modulated the degree of alignment between the geometry of the task inputs and that of the task labels. We analyzed the learning dynamics in weight space and show how the differences between the networks with Tanh and ReLU nonlinearities arise from the asymmetric asymptotic behavior of ReLU, which leads feature neurons to specialize for different regions of input space. By contrast, feature neurons in Tanh networks tend to inherit the task label structure. Consequently, when the target outputs are low dimensional, Tanh networks generate neural representations that are more disentangled than those obtained with a ReLU nonlinearity. Our findings shed light on the interplay between input-output geometry, nonlinearity, and learned representations in neural networks.

Large-scale vision-language pre-training has achieved significant performance in multi-modal understanding and generation tasks. However, existing methods often perform poorly on image-text matching tasks that require structured representations, i.e., representations of objects, attributes, and relations. As illustrated in Fig.~reffig:case (a), the models cannot make a distinction between ``An astronaut rides a horse" and ``A horse rides an astronaut". This is because they fail to fully leverage structured knowledge when learning representations in multi-modal scenarios. In this paper, we present an end-to-end framework Structure-CLIP, which integrates Scene Graph Knowledge (SGK) to enhance multi-modal structured representations. Firstly, we use scene graphs to guide the construction of semantic negative examples, which results in an increased emphasis on learning structured representations. Moreover, a Knowledge-Enhance Encoder (KEE) is proposed to leverage SGK as input to further enhance structured representations. To verify the effectiveness of the proposed framework, we pre-train our model with the aforementioned approaches and conduct experiments on downstream tasks. Experimental results demonstrate that Structure-CLIP achieves state-of-the-art (SOTA) performance on VG-Attribution and VG-Relation datasets, with 12.5% and 4.1% ahead of the multi-modal SOTA model respectively. Meanwhile, the results on MSCOCO indicate that Structure-CLIP significantly enhances the structured representations while maintaining the ability of general representations. Our code is available at https://github.com/zjukg/Structure-CLIP.

We propose the Signal Dice Similarity Coefficient (SDSC), a structure-aware metric function for time series self-supervised representation learning. Most Self-Supervised Learning (SSL) methods for signals commonly adopt distance-based objectives such as mean squared error (MSE), which are sensitive to amplitude, invariant to waveform polarity, and unbounded in scale. These properties hinder semantic alignment and reduce interpretability. SDSC addresses this by quantifying structural agreement between temporal signals based on the intersection of signed amplitudes, derived from the Dice Similarity Coefficient (DSC).Although SDSC is defined as a structure-aware metric, it can be used as a loss by subtracting from 1 and applying a differentiable approximation of the Heaviside function for gradient-based optimization. A hybrid loss formulation is also proposed to combine SDSC with MSE, improving stability and preserving amplitude where necessary. Experiments on forecasting and classification benchmarks demonstrate that SDSC-based pre-training achieves comparable or improved performance over MSE, particularly in in-domain and low-resource scenarios. The results suggest that structural fidelity in signal representations enhances the semantic representation quality, supporting the consideration of structure-aware metrics as viable alternatives to conventional distance-based methods.

Language models demonstrate fundamental abilities in syntax, semantics, and reasoning, though their performance often depends significantly on the inputs they process. This study introduces TSIS (Simplified TSID) and its variants:TSISD (TSIS with Depth-First Search), TSISO (TSIS in Order), and TSISR (TSIS in Random), as integral components of the t-SMILES framework. These additions complete the framework's design, providing diverse approaches to molecular representation. Through comprehensive analysis and experiments employing deep generative models, including GPT, diffusion models, and reinforcement learning, the findings reveal that the hierarchical structure of t-SMILES is more straightforward to parse than initially anticipated. Furthermore, t-SMILES consistently outperforms other linear representations such as SMILES, SELFIES, and SAFE, demonstrating superior convergence speed and enhanced generalization capabilities.

Since fake news poses a serious threat to society and individuals, numerous studies have been brought by considering text, propagation and user profiles. Due to the data collection problem, these methods based on propagation and user profiles are less applicable in the early stages. A good alternative method is to detect news based on text as soon as they are released, and a lot of text-based methods were proposed, which usually utilized words, sentences or paragraphs as basic units. But, word is a too fine-grained unit to express coherent information well, sentence or paragraph is too coarse to show specific information. Which granularity is better and how to utilize it to enhance text representation for fake news detection are two key problems. In this paper, we introduce Elementary Discourse Unit (EDU) whose granularity is between word and sentence, and propose a multi-EDU-structure awareness model to improve text representation for fake news detection, namely EDU4FD. For the multi-EDU-structure awareness, we build the sequence-based EDU representations and the graph-based EDU representations. The former is gotten by modeling the coherence between consecutive EDUs with TextCNN that reflect the semantic coherence. For the latter, we first extract rhetorical relations to build the EDU dependency graph, which can show the global narrative logic and help deliver the main idea truthfully. Then a Relation Graph Attention Network (RGAT) is set to get the graph-based EDU representation. Finally, the two EDU representations are incorporated as the enhanced text representation for fake news detection, using a gated recursive unit combined with a global attention mechanism. Experiments on four cross-source fake news datasets show that our model outperforms the state-of-the-art text-based methods.

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

Understanding the structure and function of circuits is crucial for electronic design automation (EDA). Circuits can be formulated as And-Inverter graphs (AIGs), enabling efficient implementation of representation learning through graph neural networks (GNNs). Masked modeling paradigms have been proven effective in graph representation learning. However, masking augmentation to original circuits will destroy their logical equivalence, which is unsuitable for circuit representation learning. Moreover, existing masked modeling paradigms often prioritize structural information at the expense of abstract information such as circuit function. To address these limitations, we introduce MGVGA, a novel constrained masked modeling paradigm incorporating masked gate modeling (MGM) and Verilog-AIG alignment (VGA). Specifically, MGM preserves logical equivalence by masking gates in the latent space rather than in the original circuits, subsequently reconstructing the attributes of these masked gates. Meanwhile, large language models (LLMs) have demonstrated an excellent understanding of the Verilog code functionality. Building upon this capability, VGA performs masking operations on original circuits and reconstructs masked gates under the constraints of equivalent Verilog codes, enabling GNNs to learn circuit functions from LLMs. We evaluate MGVGA on various logic synthesis tasks for EDA and show the superior performance of MGVGA compared to previous state-of-the-art methods. Our code is available at https://github.com/wuhy68/MGVGA.

Although many pretrained models exist for text or images, there have been relatively fewer attempts to train representations specifically for dialog understanding. Prior works usually relied on finetuned representations based on generic text representation models like BERT or GPT-2. But such language modeling pretraining objectives do not take the structural information of conversational text into consideration. Although generative dialog models can learn structural features too, we argue that the structure-unaware word-by-word generation is not suitable for effective conversation modeling. We empirically demonstrate that such representations do not perform consistently across various dialog understanding tasks. Hence, we propose a structure-aware Mutual Information based loss-function DMI (Discourse Mutual Information) for training dialog-representation models, that additionally captures the inherent uncertainty in response prediction. Extensive evaluation on nine diverse dialog modeling tasks shows that our proposed DMI-based models outperform strong baselines by significant margins.

All tables can be represented as grids. Based on this observation, we propose GridFormer, a novel approach for interpreting unconstrained table structures by predicting the vertex and edge of a grid. First, we propose a flexible table representation in the form of an MXN grid. In this representation, the vertexes and edges of the grid store the localization and adjacency information of the table. Then, we introduce a DETR-style table structure recognizer to efficiently predict this multi-objective information of the grid in a single shot. Specifically, given a set of learned row and column queries, the recognizer directly outputs the vertexes and edges information of the corresponding rows and columns. Extensive experiments on five challenging benchmarks which include wired, wireless, multi-merge-cell, oriented, and distorted tables demonstrate the competitive performance of our model over other methods.

Open World Object Detection (OWOD) is a challenging and realistic task that extends beyond the scope of standard Object Detection task. It involves detecting both known and unknown objects while integrating learned knowledge for future tasks. However, the level of "unknownness" varies significantly depending on the context. For example, a tree is typically considered part of the background in a self-driving scene, but it may be significant in a household context. We argue that this contextual information should already be embedded within the known classes. In other words, there should be a semantic or latent structure relationship between the known and unknown items to be discovered. Motivated by this observation, we propose Hyp-OW, a method that learns and models hierarchical representation of known items through a SuperClass Regularizer. Leveraging this representation allows us to effectively detect unknown objects using a similarity distance-based relabeling module. Extensive experiments on benchmark datasets demonstrate the effectiveness of Hyp-OW, achieving improvement in both known and unknown detection (up to 6 percent). These findings are particularly pronounced in our newly designed benchmark, where a strong hierarchical structure exists between known and unknown objects. Our code can be found at https://github.com/tldoan/-HYP-OW-AAAI-2024-

Similarity metrics such as representational similarity analysis (RSA) and centered kernel alignment (CKA) have been used to compare layer-wise representations between neural networks. However, these metrics are confounded by the population structure of data items in the input space, leading to spuriously high similarity for even completely random neural networks and inconsistent domain relations in transfer learning. We introduce a simple and generally applicable fix to adjust for the confounder with covariate adjustment regression, which retains the intuitive invariance properties of the original similarity measures. We show that deconfounding the similarity metrics increases the resolution of detecting semantically similar neural networks. Moreover, in real-world applications, deconfounding improves the consistency of representation similarities with domain similarities in transfer learning, and increases correlation with out-of-distribution accuracy.

Artificial neural networks (ANN) were inspired by the architecture and functions of the human brain and have revolutionised the field of artificial intelligence (AI). Inspired by studies on the latent geometry of the brain we posit that an increase in the research and application of hyperbolic geometry in machine learning will lead to increased accuracy, improved feature space representations and more efficient models across a range of tasks. We look at the structure and functions of the human brain, highlighting the alignment between the brain's hierarchical nature and hyperbolic geometry. By examining the brain's complex network of neuron connections and its cognitive processes, we illustrate how hyperbolic geometry plays a pivotal role in human intelligence. Empirical evidence indicates that hyperbolic neural networks outperform Euclidean models for tasks including natural language processing, computer vision and complex network analysis, requiring fewer parameters and exhibiting better generalisation. Despite its nascent adoption, hyperbolic geometry holds promise for improving machine learning models and advancing the field toward AGI.

Neural networks embed the geometric structure of a data manifold lying in a high-dimensional space into latent representations. Ideally, the distribution of the data points in the latent space should depend only on the task, the data, the loss, and other architecture-specific constraints. However, factors such as the random weights initialization, training hyperparameters, or other sources of randomness in the training phase may induce incoherent latent spaces that hinder any form of reuse. Nevertheless, we empirically observe that, under the same data and modeling choices, the angles between the encodings within distinct latent spaces do not change. In this work, we propose the latent similarity between each sample and a fixed set of anchors as an alternative data representation, demonstrating that it can enforce the desired invariances without any additional training. We show how neural architectures can leverage these relative representations to guarantee, in practice, invariance to latent isometries and rescalings, effectively enabling latent space communication: from zero-shot model stitching to latent space comparison between diverse settings. We extensively validate the generalization capability of our approach on different datasets, spanning various modalities (images, text, graphs), tasks (e.g., classification, reconstruction) and architectures (e.g., CNNs, GCNs, transformers).

The generation of plausible crystal structures is often the first step in predicting the structure and properties of a material from its chemical composition. Quickly generating and predicting inorganic crystal structures is important for the discovery of new materials, which can target applications such as energy or electronic devices. However, most current methods for crystal structure prediction are computationally expensive, slowing the pace of innovation. Seeding structure prediction algorithms with quality generated candidates can overcome a major bottleneck. Here, we introduce CrystaLLM, a methodology for the versatile generation of crystal structures, based on the autoregressive large language modeling (LLM) of the Crystallographic Information File (CIF) format. Trained on millions of CIF files, CrystaLLM focuses on modeling crystal structures through text. CrystaLLM can produce plausible crystal structures for a wide range of inorganic compounds unseen in training, as demonstrated by ab initio simulations. The integration with predictors of formation energy permits the use of a Monte Carlo Tree Search algorithm to improve the generation of meaningful structures. Our approach challenges conventional representations of crystals, and demonstrates the potential of LLMs for learning effective 'world models' of crystal chemistry, which will lead to accelerated discovery and innovation in materials science.

From whirling ceiling fans to ticking clocks, the sounds that we hear subtly vary as we move through a scene. We ask whether these ambient sounds convey information about 3D scene structure and, if so, whether they provide a useful learning signal for multimodal models. To study this, we collect a dataset of paired audio and RGB-D recordings from a variety of quiet indoor scenes. We then train models that estimate the distance to nearby walls, given only audio as input. We also use these recordings to learn multimodal representations through self-supervision, by training a network to associate images with their corresponding sounds. These results suggest that ambient sound conveys a surprising amount of information about scene structure, and that it is a useful signal for learning multimodal features.

Following the advent of NeRFs, 3D Gaussian Splatting (3D-GS) has paved the way to real-time neural rendering overcoming the computational burden of volumetric methods. Following the pioneering work of 3D-GS, several methods have attempted to achieve compressible and high-fidelity performance alternatives. However, by employing a geometry-agnostic optimization scheme, these methods neglect the inherent 3D structure of the scene, thereby restricting the expressivity and the quality of the representation, resulting in various floating points and artifacts. In this work, we propose a structure-aware Gaussian Splatting method (SAGS) that implicitly encodes the geometry of the scene, which reflects to state-of-the-art rendering performance and reduced storage requirements on benchmark novel-view synthesis datasets. SAGS is founded on a local-global graph representation that facilitates the learning of complex scenes and enforces meaningful point displacements that preserve the scene's geometry. Additionally, we introduce a lightweight version of SAGS, using a simple yet effective mid-point interpolation scheme, which showcases a compact representation of the scene with up to 24times size reduction without the reliance on any compression strategies. Extensive experiments across multiple benchmark datasets demonstrate the superiority of SAGS compared to state-of-the-art 3D-GS methods under both rendering quality and model size. Besides, we demonstrate that our structure-aware method can effectively mitigate floating artifacts and irregular distortions of previous methods while obtaining precise depth maps. Project page https://eververas.github.io/SAGS/.

Vector graphics are essential in design, providing artists with a versatile medium for creating resolution-independent and highly editable visual content. Recent advancements in vision-language and diffusion models have fueled interest in text-to-vector graphics generation. However, existing approaches often suffer from over-parameterized outputs or treat the layered structure - a core feature of vector graphics - as a secondary goal, diminishing their practical use. Recognizing the importance of layered SVG representations, we propose NeuralSVG, an implicit neural representation for generating vector graphics from text prompts. Inspired by Neural Radiance Fields (NeRFs), NeuralSVG encodes the entire scene into the weights of a small MLP network, optimized using Score Distillation Sampling (SDS). To encourage a layered structure in the generated SVG, we introduce a dropout-based regularization technique that strengthens the standalone meaning of each shape. We additionally demonstrate that utilizing a neural representation provides an added benefit of inference-time control, enabling users to dynamically adapt the generated SVG based on user-provided inputs, all with a single learned representation. Through extensive qualitative and quantitative evaluations, we demonstrate that NeuralSVG outperforms existing methods in generating structured and flexible SVG.

When reading a document, glancing at the spatial layout of a document is an initial step to understand it roughly. Traditional document layout analysis (DLA) methods, however, offer only a superficial parsing of documents, focusing on basic instance detection and often failing to capture the nuanced spatial and logical relations between instances. These limitations hinder DLA-based models from achieving a gradually deeper comprehension akin to human reading. In this work, we propose a novel graph-based Document Structure Analysis (gDSA) task. This task requires that model not only detects document elements but also generates spatial and logical relations in form of a graph structure, allowing to understand documents in a holistic and intuitive manner. For this new task, we construct a relation graph-based document structure analysis dataset (GraphDoc) with 80K document images and 4.13M relation annotations, enabling training models to complete multiple tasks like reading order, hierarchical structures analysis, and complex inter-element relation inference. Furthermore, a document relation graph generator (DRGG) is proposed to address the gDSA task, which achieves performance with 57.6% at [email protected] for a strong benchmark baseline on this novel task and dataset. We hope this graphical representation of document structure can mark an innovative advancement in document structure analysis and understanding. The new dataset and code will be made publicly available at https://yufanchen96.github.io/projects/GraphDoc.

One-shot voice conversion aims to change the timbre of any source speech to match that of the unseen target speaker with only one speech sample. Existing methods face difficulties in satisfactory speech representation disentanglement and suffer from sizable networks as some of them leverage numerous complex modules for disentanglement. In this paper, we propose a model named MAIN-VC to effectively disentangle via a concise neural network. The proposed model utilizes Siamese encoders to learn clean representations, further enhanced by the designed mutual information estimator. The Siamese structure and the newly designed convolution module contribute to the lightweight of our model while ensuring performance in diverse voice conversion tasks. The experimental results show that the proposed model achieves comparable subjective scores and exhibits improvements in objective metrics compared to existing methods in a one-shot voice conversion scenario.

GNN-to-MLP distillation aims to utilize knowledge distillation (KD) to learn computationally-efficient multi-layer perceptron (student MLP) on graph data by mimicking the output representations of teacher GNN. Existing methods mainly make the MLP to mimic the GNN predictions over a few class labels. However, the class space may not be expressive enough for covering numerous diverse local graph structures, thus limiting the performance of knowledge transfer from GNN to MLP. To address this issue, we propose to learn a new powerful graph representation space by directly labeling nodes' diverse local structures for GNN-to-MLP distillation. Specifically, we propose a variant of VQ-VAE to learn a structure-aware tokenizer on graph data that can encode each node's local substructure as a discrete code. The discrete codes constitute a codebook as a new graph representation space that is able to identify different local graph structures of nodes with the corresponding code indices. Then, based on the learned codebook, we propose a new distillation target, namely soft code assignments, to directly transfer the structural knowledge of each node from GNN to MLP. The resulting framework VQGraph achieves new state-of-the-art performance on GNN-to-MLP distillation in both transductive and inductive settings across seven graph datasets. We show that VQGraph with better performance infers faster than GNNs by 828x, and also achieves accuracy improvement over GNNs and stand-alone MLPs by 3.90% and 28.05% on average, respectively. Code: https://github.com/YangLing0818/VQGraph.

Self-supervised learning converts raw perceptual data such as images to a compact space where simple Euclidean distances measure meaningful variations in data. In this paper, we extend this formulation by adding additional geometric structure to the embedding space by enforcing transformations of input space to correspond to simple (i.e., linear) transformations of embedding space. Specifically, in the contrastive learning setting, we introduce an equivariance objective and theoretically prove that its minima forces augmentations on input space to correspond to rotations on the spherical embedding space. We show that merely combining our equivariant loss with a non-collapse term results in non-trivial representations, without requiring invariance to data augmentations. Optimal performance is achieved by also encouraging approximate invariance, where input augmentations correspond to small rotations. Our method, CARE: Contrastive Augmentation-induced Rotational Equivariance, leads to improved performance on downstream tasks, and ensures sensitivity in embedding space to important variations in data (e.g., color) that standard contrastive methods do not achieve. Code is available at https://github.com/Sharut/CARE.

Building a robot that can understand and learn to interact by watching humans has inspired several vision problems. However, despite some successful results on static datasets, it remains unclear how current models can be used on a robot directly. In this paper, we aim to bridge this gap by leveraging videos of human interactions in an environment centric manner. Utilizing internet videos of human behavior, we train a visual affordance model that estimates where and how in the scene a human is likely to interact. The structure of these behavioral affordances directly enables the robot to perform many complex tasks. We show how to seamlessly integrate our affordance model with four robot learning paradigms including offline imitation learning, exploration, goal-conditioned learning, and action parameterization for reinforcement learning. We show the efficacy of our approach, which we call VRB, across 4 real world environments, over 10 different tasks, and 2 robotic platforms operating in the wild. Results, visualizations and videos at https://robo-affordances.github.io/

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

We study offline meta-reinforcement learning, a practical reinforcement learning paradigm that learns from offline data to adapt to new tasks. The distribution of offline data is determined jointly by the behavior policy and the task. Existing offline meta-reinforcement learning algorithms cannot distinguish these factors, making task representations unstable to the change of behavior policies. To address this problem, we propose a contrastive learning framework for task representations that are robust to the distribution mismatch of behavior policies in training and test. We design a bi-level encoder structure, use mutual information maximization to formalize task representation learning, derive a contrastive learning objective, and introduce several approaches to approximate the true distribution of negative pairs. Experiments on a variety of offline meta-reinforcement learning benchmarks demonstrate the advantages of our method over prior methods, especially on the generalization to out-of-distribution behavior policies. The code is available at https://github.com/PKU-AI-Edge/CORRO.

Non-exemplar class-incremental learning is to recognize both the old and new classes when old class samples cannot be saved. It is a challenging task since representation optimization and feature retention can only be achieved under supervision from new classes. To address this problem, we propose a novel self-sustaining representation expansion scheme. Our scheme consists of a structure reorganization strategy that fuses main-branch expansion and side-branch updating to maintain the old features, and a main-branch distillation scheme to transfer the invariant knowledge. Furthermore, a prototype selection mechanism is proposed to enhance the discrimination between the old and new classes by selectively incorporating new samples into the distillation process. Extensive experiments on three benchmarks demonstrate significant incremental performance, outperforming the state-of-the-art methods by a margin of 3%, 3% and 6%, respectively.

Foundation models pre-trained on massive unlabeled datasets have revolutionized natural language and computer vision, exhibiting remarkable generalization capabilities, thus highlighting the importance of pre-training. Yet, efforts in robotics have struggled to achieve similar success, limited by either the need for costly robotic annotations or the lack of representations that effectively model the physical world. In this paper, we introduce ARM4R, an Auto-regressive Robotic Model that leverages low-level 4D Representations learned from human video data to yield a better pre-trained robotic model. Specifically, we focus on utilizing 3D point tracking representations from videos derived by lifting 2D representations into 3D space via monocular depth estimation across time. These 4D representations maintain a shared geometric structure between the points and robot state representations up to a linear transformation, enabling efficient transfer learning from human video data to low-level robotic control. Our experiments show that ARM4R can transfer efficiently from human video data to robotics and consistently improves performance on tasks across various robot environments and configurations.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Recent advancements in neural representations, such as Neural Radiance Fields and 3D Gaussian Splatting, have increased interest in applying style transfer to 3D scenes. While existing methods can transfer style patterns onto 3D-consistent neural representations, they struggle to effectively extract and transfer high-level style semantics from the reference style image. Additionally, the stylized results often lack structural clarity and separation, making it difficult to distinguish between different instances or objects within the 3D scene. To address these limitations, we propose a novel 3D style transfer pipeline that effectively integrates prior knowledge from pretrained 2D diffusion models. Our pipeline consists of two key stages: First, we leverage diffusion priors to generate stylized renderings of key viewpoints. Then, we transfer the stylized key views onto the 3D representation. This process incorporates two innovative designs. The first is cross-view style alignment, which inserts cross-view attention into the last upsampling block of the UNet, allowing feature interactions across multiple key views. This ensures that the diffusion model generates stylized key views that maintain both style fidelity and instance-level consistency. The second is instance-level style transfer, which effectively leverages instance-level consistency across stylized key views and transfers it onto the 3D representation. This results in a more structured, visually coherent, and artistically enriched stylization. Extensive qualitative and quantitative experiments demonstrate that our 3D style transfer pipeline significantly outperforms state-of-the-art methods across a wide range of scenes, from forward-facing to challenging 360-degree environments. Visit our project page https://jm-xu.github.io/SSGaussian for immersive visualization.

Continuous convolution has recently gained prominence due to its ability to handle irregularly sampled data and model long-term dependency. Also, the promising experimental results of using large convolutional kernels have catalyzed the development of continuous convolution since they can construct large kernels very efficiently. Leveraging neural networks, more specifically multilayer perceptrons (MLPs), is by far the most prevalent approach to implementing continuous convolution. However, there are a few drawbacks, such as high computational costs, complex hyperparameter tuning, and limited descriptive power of filters. This paper suggests an alternative approach to building a continuous convolution without neural networks, resulting in more computationally efficient and improved performance. We present self-moving point representations where weight parameters freely move, and interpolation schemes are used to implement continuous functions. When applied to construct convolutional kernels, the experimental results have shown improved performance with drop-in replacement in the existing frameworks. Due to its lightweight structure, we are first to demonstrate the effectiveness of continuous convolution in a large-scale setting, e.g., ImageNet, presenting the improvements over the prior arts. Our code is available on https://github.com/sangnekim/SMPConv

Inferring the structure of 3D scenes from 2D observations is a fundamental challenge in computer vision. Recently popularized approaches based on neural scene representations have achieved tremendous impact and have been applied across a variety of applications. One of the major remaining challenges in this space is training a single model which can provide latent representations which effectively generalize beyond a single scene. Scene Representation Transformer (SRT) has shown promise in this direction, but scaling it to a larger set of diverse scenes is challenging and necessitates accurately posed ground truth data. To address this problem, we propose RUST (Really Unposed Scene representation Transformer), a pose-free approach to novel view synthesis trained on RGB images alone. Our main insight is that one can train a Pose Encoder that peeks at the target image and learns a latent pose embedding which is used by the decoder for view synthesis. We perform an empirical investigation into the learned latent pose structure and show that it allows meaningful test-time camera transformations and accurate explicit pose readouts. Perhaps surprisingly, RUST achieves similar quality as methods which have access to perfect camera pose, thereby unlocking the potential for large-scale training of amortized neural scene representations.

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

Recent multimodal embedding approaches leveraging multimodal large language models (MLLMs) fine-tuned with contrastive learning (CL) have shown promising results, yet the underlying reasons behind their superiority remain underexplored. This work argues that a crucial advantage of MLLM-based approaches stems from implicit cross-modal alignment achieved during generative pretraining, where the language decoder learns to exploit multimodal signals within a shared representation space for generating unimodal outputs. Through analysis of anisotropy and kernel similarity structure, we empirically confirm that latent alignment emerges within MLLM representations, allowing CL to serve as a lightweight refinement stage. Leveraging this insight, we propose a Language-Centric Omnimodal Embedding framework, termed LCO-Emb. Extensive experiments across diverse backbones and benchmarks demonstrate its effectiveness, achieving state-of-the-art performance across modalities. Furthermore, we identify a Generation-Representation Scaling Law (GRSL), showing that the representational capabilities gained through contrastive refinement scales positively with the MLLM's generative capabilities. This suggests that improving generative abilities evolves as an effective paradigm for enhancing representation quality. We provide a theoretical explanation of GRSL, which formally links the MLLM's generative quality to the upper bound on its representation performance, and validate it on a challenging, low-resource visual-document retrieval task, showing that continual generative pretraining before CL can further enhance the potential of a model's embedding capabilities. Codes, models, and resources are available at https://github.com/LCO-Embedding/LCO-Embedding.

We introduce Florence-2, a novel vision foundation model with a unified, prompt-based representation for a variety of computer vision and vision-language tasks. While existing large vision models excel in transfer learning, they struggle to perform a diversity of tasks with simple instructions, a capability that implies handling the complexity of various spatial hierarchy and semantic granularity. Florence-2 was designed to take text-prompt as task instructions and generate desirable results in text forms, whether it be captioning, object detection, grounding or segmentation. This multi-task learning setup demands large-scale, high-quality annotated data. To this end, we co-developed FLD-5B that consists of 5.4 billion comprehensive visual annotations on 126 million images, using an iterative strategy of automated image annotation and model refinement. We adopted a sequence-to-sequence structure to train Florence-2 to perform versatile and comprehensive vision tasks. Extensive evaluations on numerous tasks demonstrated Florence-2 to be a strong vision foundation model contender with unprecedented zero-shot and fine-tuning capabilities.

We study how large language models (LLMs) ``think'' through their representation space. We propose a novel geometric framework that models an LLM's reasoning as flows -- embedding trajectories evolving where logic goes. We disentangle logical structure from semantics by employing the same natural deduction propositions with varied semantic carriers, allowing us to test whether LLMs internalize logic beyond surface form. This perspective connects reasoning with geometric quantities such as position, velocity, and curvature, enabling formal analysis in representation and concept spaces. Our theory establishes: (1) LLM reasoning corresponds to smooth flows in representation space, and (2) logical statements act as local controllers of these flows' velocities. Using learned representation proxies, we design controlled experiments to visualize and quantify reasoning flows, providing empirical validation of our theoretical framework. Our work serves as both a conceptual foundation and practical tools for studying reasoning phenomenon, offering a new lens for interpretability and formal analysis of LLMs' behavior.

3D Gaussian Splatting has recently emerged as a highly promising technique for modeling of static 3D scenes. In contrast to Neural Radiance Fields, it utilizes efficient rasterization allowing for very fast rendering at high-quality. However, the storage size is significantly higher, which hinders practical deployment, e.g.~on resource constrained devices. In this paper, we introduce a compact scene representation organizing the parameters of 3D Gaussian Splatting (3DGS) into a 2D grid with local homogeneity, ensuring a drastic reduction in storage requirements without compromising visual quality during rendering. Central to our idea is the explicit exploitation of perceptual redundancies present in natural scenes. In essence, the inherent nature of a scene allows for numerous permutations of Gaussian parameters to equivalently represent it. To this end, we propose a novel highly parallel algorithm that regularly arranges the high-dimensional Gaussian parameters into a 2D grid while preserving their neighborhood structure. During training, we further enforce local smoothness between the sorted parameters in the grid. The uncompressed Gaussians use the same structure as 3DGS, ensuring a seamless integration with established renderers. Our method achieves a reduction factor of 8x to 26x in size for complex scenes with no increase in training time, marking a substantial leap forward in the domain of 3D scene distribution and consumption. Additional information can be found on our project page: https://fraunhoferhhi.github.io/Self-Organizing-Gaussians/

Recent years have witnessed the success of foundation models pre-trained with self-supervised learning (SSL) in various music informatics understanding tasks, including music tagging, instrument classification, key detection, and more. In this paper, we propose a self-supervised music representation learning model for music understanding. Distinguished from previous studies adopting random projection or existing neural codec, the proposed model, named MuQ, is trained to predict tokens generated by Mel Residual Vector Quantization (Mel-RVQ). Our Mel-RVQ utilizes residual linear projection structure for Mel spectrum quantization to enhance the stability and efficiency of target extraction and lead to better performance. Experiments in a large variety of downstream tasks demonstrate that MuQ outperforms previous self-supervised music representation models with only 0.9K hours of open-source pre-training data. Scaling up the data to over 160K hours and adopting iterative training consistently improve the model performance. To further validate the strength of our model, we present MuQ-MuLan, a joint music-text embedding model based on contrastive learning, which achieves state-of-the-art performance in the zero-shot music tagging task on the MagnaTagATune dataset. Code and checkpoints are open source in https://github.com/tencent-ailab/MuQ.

In theoretical neuroscience, recent work leverages deep learning tools to explore how some network attributes critically influence its learning dynamics. Notably, initial weight distributions with small (resp. large) variance may yield a rich (resp. lazy) regime, where significant (resp. minor) changes to network states and representation are observed over the course of learning. However, in biology, neural circuit connectivity could exhibit a low-rank structure and therefore differs markedly from the random initializations generally used for these studies. As such, here we investigate how the structure of the initial weights -- in particular their effective rank -- influences the network learning regime. Through both empirical and theoretical analyses, we discover that high-rank initializations typically yield smaller network changes indicative of lazier learning, a finding we also confirm with experimentally-driven initial connectivity in recurrent neural networks. Conversely, low-rank initialization biases learning towards richer learning. Importantly, however, as an exception to this rule, we find lazier learning can still occur with a low-rank initialization that aligns with task and data statistics. Our research highlights the pivotal role of initial weight structures in shaping learning regimes, with implications for metabolic costs of plasticity and risks of catastrophic forgetting.

Although Large Language Models achieve strong success in many tasks, they still suffer from hallucinations and knowledge deficiencies in real-world applications. Many knowledge graph-based retrieval-augmented generation (KG-RAG) methods enhance the quality and credibility of LLMs by leveraging structure and semantic information in KGs as external knowledge bases. However, these methods struggle to effectively incorporate structure information, either incurring high computational costs or underutilizing available knowledge. Inspired by smoothing operations in graph representation learning, we propose path pooling, a simple, training-free strategy that introduces structure information through a novel path-centric pooling operation. It seamlessly integrates into existing KG-RAG methods in a plug-and-play manner, enabling richer structure information utilization. Extensive experiments demonstrate that incorporating the path pooling into the state-of-the-art KG-RAG method consistently improves performance across various settings while introducing negligible additional cost.

Understanding the chemical structure from a graphical representation of a molecule is a challenging image caption task that would greatly benefit molecule-centric scientific discovery. Variations in molecular images and caption subtasks pose a significant challenge in both image representation learning and task modeling. Yet, existing methods only focus on a specific caption task that translates a molecular image into its graph structure, i.e., OCSR. In this paper, we propose the Optical Chemical Structure Understanding (OCSU) task, which extends OCSR to molecular image caption from motif level to molecule level and abstract level. We present two approaches for that, including an OCSR-based method and an end-to-end OCSR-free method. The proposed Double-Check achieves SOTA OCSR performance on real-world patent and journal article scenarios via attentive feature enhancement for local ambiguous atoms. Cascading with SMILES-based molecule understanding methods, it can leverage the power of existing task-specific models for OCSU. While Mol-VL is an end-to-end optimized VLM-based model. An OCSU dataset, Vis-CheBI20, is built based on the widely used CheBI20 dataset for training and evaluation. Extensive experimental results on Vis-CheBI20 demonstrate the effectiveness of the proposed approaches. Improving OCSR capability can lead to a better OCSU performance for OCSR-based approach, and the SOTA performance of Mol-VL demonstrates the great potential of end-to-end approach.

Developing meaningful and efficient representations that separate the fundamental structure of the data generation mechanism is crucial in representation learning. However, Disentangled Representation Learning has not fully shown its potential on real images, because of correlated generative factors, their resolution and limited access to ground truth labels. Specifically on the latter, we investigate the possibility of leveraging synthetic data to learn general-purpose disentangled representations applicable to real data, discussing the effect of fine-tuning and what properties of disentanglement are preserved after the transfer. We provide an extensive empirical study to address these issues. In addition, we propose a new interpretable intervention-based metric, to measure the quality of factors encoding in the representation. Our results indicate that some level of disentanglement, transferring a representation from synthetic to real data, is possible and effective.

We present AROMA (Attentive Reduced Order Model with Attention), a framework designed to enhance the modeling of partial differential equations (PDEs) using local neural fields. Our flexible encoder-decoder architecture can obtain smooth latent representations of spatial physical fields from a variety of data types, including irregular-grid inputs and point clouds. This versatility eliminates the need for patching and allows efficient processing of diverse geometries. The sequential nature of our latent representation can be interpreted spatially and permits the use of a conditional transformer for modeling the temporal dynamics of PDEs. By employing a diffusion-based formulation, we achieve greater stability and enable longer rollouts compared to conventional MSE training. AROMA's superior performance in simulating 1D and 2D equations underscores the efficacy of our approach in capturing complex dynamical behaviors.

Identifying the chemical structure from a graphical representation, or image, of a molecule is a challenging pattern recognition task that would greatly benefit drug development. Yet, existing methods for chemical structure recognition do not typically generalize well, and show diminished effectiveness when confronted with domains where data is sparse, or costly to generate, such as hand-drawn molecule images. To address this limitation, we propose a new chemical structure recognition tool that delivers state-of-the-art performance and can adapt to new domains with a limited number of data samples and supervision. Unlike previous approaches, our method provides atom-level localization, and can therefore segment the image into the different atoms and bonds. Our model is the first model to perform OCSR with atom-level entity detection with only SMILES supervision. Through rigorous and extensive benchmarking, we demonstrate the preeminence of our chemical structure recognition approach in terms of data efficiency, accuracy, and atom-level entity prediction.

3D Reconstruction of moving articulated objects without additional information about object structure is a challenging problem. Current methods overcome such challenges by employing category-specific skeletal models. Consequently, they do not generalize well to articulated objects in the wild. We treat an articulated object as an unknown, semi-rigid skeletal structure surrounded by nonrigid material (e.g., skin). Our method simultaneously estimates the visible (explicit) representation (3D shapes, colors, camera parameters) and the implicit skeletal representation, from motion cues in the object video without 3D supervision. Our implicit representation consists of four parts. (1) Skeleton, which specifies how semi-rigid parts are connected. (2) black{Skinning Weights}, which associates each surface vertex with semi-rigid parts with probability. (3) Rigidity Coefficients, specifying the articulation of the local surface. (4) Time-Varying Transformations, which specify the skeletal motion and surface deformation parameters. We introduce an algorithm that uses physical constraints as regularization terms and iteratively estimates both implicit and explicit representations. Our method is category-agnostic, thus eliminating the need for category-specific skeletons, we show that our method outperforms state-of-the-art across standard video datasets.

In this work, we introduce SPFormer, a novel Vision Transformer enhanced by superpixel representation. Addressing the limitations of traditional Vision Transformers' fixed-size, non-adaptive patch partitioning, SPFormer employs superpixels that adapt to the image's content. This approach divides the image into irregular, semantically coherent regions, effectively capturing intricate details and applicable at both initial and intermediate feature levels. SPFormer, trainable end-to-end, exhibits superior performance across various benchmarks. Notably, it exhibits significant improvements on the challenging ImageNet benchmark, achieving a 1.4% increase over DeiT-T and 1.1% over DeiT-S respectively. A standout feature of SPFormer is its inherent explainability. The superpixel structure offers a window into the model's internal processes, providing valuable insights that enhance the model's interpretability. This level of clarity significantly improves SPFormer's robustness, particularly in challenging scenarios such as image rotations and occlusions, demonstrating its adaptability and resilience.

Temporal networks have been widely used to model real-world complex systems such as financial systems and e-commerce systems. In a temporal network, the joint neighborhood of a set of nodes often provides crucial structural information useful for predicting whether they may interact at a certain time. However, recent representation learning methods for temporal networks often fail to extract such information or depend on online construction of structural features, which is time-consuming. To address the issue, this work proposes Neighborhood-Aware Temporal network model (NAT). For each node in the network, NAT abandons the commonly-used one-single-vector-based representation while adopting a novel dictionary-type neighborhood representation. Such a dictionary representation records a downsampled set of the neighboring nodes as keys, and allows fast construction of structural features for a joint neighborhood of multiple nodes. We also design a dedicated data structure termed N-cache to support parallel access and update of those dictionary representations on GPUs. NAT gets evaluated over seven real-world large-scale temporal networks. NAT not only outperforms all cutting-edge baselines by averaged 1.2% and 4.2% in transductive and inductive link prediction accuracy, respectively, but also keeps scalable by achieving a speed-up of 4.1-76.7x against the baselines that adopt joint structural features and achieves a speed-up of 1.6-4.0x against the baselines that cannot adopt those features. The link to the code: https: //github.com/Graph-COM/Neighborhood-Aware-Temporal-Network.

Signed networks allow us to model conflicting relationships and interactions, such as friend/enemy and support/oppose. These signed interactions happen in real-time. Modeling such dynamics of signed networks is crucial to understanding the evolution of polarization in the network and enabling effective prediction of the signed structure (i.e., link signs and signed weights) in the future. However, existing works have modeled either (static) signed networks or dynamic (unsigned) networks but not dynamic signed networks. Since both sign and dynamics inform the graph structure in different ways, it is non-trivial to model how to combine the two features. In this work, we propose a new Graph Neural Network (GNN)-based approach to model dynamic signed networks, named SEMBA: Signed link's Evolution using Memory modules and Balanced Aggregation. Here, the idea is to incorporate the signs of temporal interactions using separate modules guided by balance theory and to evolve the embeddings from a higher-order neighborhood. Experiments on 4 real-world datasets and 4 different tasks demonstrate that SEMBA consistently and significantly outperforms the baselines by up to 80% on the tasks of predicting signs of future links while matching the state-of-the-art performance on predicting the existence of these links in the future. We find that this improvement is due specifically to the superior performance of SEMBA on the minority negative class.

HTML documents are an important medium for disseminating information on the Web for human consumption. An HTML document presents information in multiple text formats including unstructured text, structured key-value pairs, and tables. Effective representation of these documents is essential for machine understanding to enable a wide range of applications, such as Question Answering, Web Search, and Personalization. Existing work has either represented these documents using visual features extracted by rendering them in a browser, which is typically computationally expensive, or has simply treated them as plain text documents, thereby failing to capture useful information presented in their HTML structure. We argue that the text and HTML structure together convey important semantics of the content and therefore warrant a special treatment for their representation learning. In this paper, we introduce a novel representation learning approach for web pages, dubbed DOM-LM, which addresses the limitations of existing approaches by encoding both text and DOM tree structure with a transformer-based encoder and learning generalizable representations for HTML documents via self-supervised pre-training. We evaluate DOM-LM on a variety of webpage understanding tasks, including Attribute Extraction, Open Information Extraction, and Question Answering. Our extensive experiments show that DOM-LM consistently outperforms all baselines designed for these tasks. In particular, DOM-LM demonstrates better generalization performance both in few-shot and zero-shot settings, making it attractive for making it suitable for real-world application settings with limited labeled data.

We create a framework for bootstrapping visual representation learning from a primitive visual grouping capability. We operationalize grouping via a contour detector that partitions an image into regions, followed by merging of those regions into a tree hierarchy. A small supervised dataset suffices for training this grouping primitive. Across a large unlabeled dataset, we apply this learned primitive to automatically predict hierarchical region structure. These predictions serve as guidance for self-supervised contrastive feature learning: we task a deep network with producing per-pixel embeddings whose pairwise distances respect the region hierarchy. Experiments demonstrate that our approach can serve as state-of-the-art generic pre-training, benefiting downstream tasks. We additionally explore applications to semantic region search and video-based object instance tracking.

Siamese networks have become a common structure in various recent models for unsupervised visual representation learning. These models maximize the similarity between two augmentations of one image, subject to certain conditions for avoiding collapsing solutions. In this paper, we report surprising empirical results that simple Siamese networks can learn meaningful representations even using none of the following: (i) negative sample pairs, (ii) large batches, (iii) momentum encoders. Our experiments show that collapsing solutions do exist for the loss and structure, but a stop-gradient operation plays an essential role in preventing collapsing. We provide a hypothesis on the implication of stop-gradient, and further show proof-of-concept experiments verifying it. Our "SimSiam" method achieves competitive results on ImageNet and downstream tasks. We hope this simple baseline will motivate people to rethink the roles of Siamese architectures for unsupervised representation learning. Code will be made available.

We present an unsupervised representation learning approach using videos without semantic labels. We leverage the temporal coherence as a supervisory signal by formulating representation learning as a sequence sorting task. We take temporally shuffled frames (i.e., in non-chronological order) as inputs and train a convolutional neural network to sort the shuffled sequences. Similar to comparison-based sorting algorithms, we propose to extract features from all frame pairs and aggregate them to predict the correct order. As sorting shuffled image sequence requires an understanding of the statistical temporal structure of images, training with such a proxy task allows us to learn rich and generalizable visual representation. We validate the effectiveness of the learned representation using our method as pre-training on high-level recognition problems. The experimental results show that our method compares favorably against state-of-the-art methods on action recognition, image classification and object detection tasks.

Recent progress in using recurrent neural networks (RNNs) for image description has motivated the exploration of their application for video description. However, while images are static, working with videos requires modeling their dynamic temporal structure and then properly integrating that information into a natural language description. In this context, we propose an approach that successfully takes into account both the local and global temporal structure of videos to produce descriptions. First, our approach incorporates a spatial temporal 3-D convolutional neural network (3-D CNN) representation of the short temporal dynamics. The 3-D CNN representation is trained on video action recognition tasks, so as to produce a representation that is tuned to human motion and behavior. Second we propose a temporal attention mechanism that allows to go beyond local temporal modeling and learns to automatically select the most relevant temporal segments given the text-generating RNN. Our approach exceeds the current state-of-art for both BLEU and METEOR metrics on the Youtube2Text dataset. We also present results on a new, larger and more challenging dataset of paired video and natural language descriptions.

Document retrieval is a core component of question-answering systems, as it enables conditioning answer generation on new and large-scale corpora. While effective, the standard practice of encoding documents into high-dimensional embeddings for similarity search entails large memory and compute footprints, and also makes it hard to inspect the inner workings of the system. In this paper, we propose a tree-based method for organizing and representing reference documents at various granular levels, which offers the flexibility to balance cost and utility, and eases the inspection of the corpus content and retrieval operations. Our method, called ReTreever, jointly learns a routing function per internal node of a binary tree such that query and reference documents are assigned to similar tree branches, hence directly optimizing for retrieval performance. Our evaluations show that ReTreever generally preserves full representation accuracy. Its hierarchical structure further provides strong coarse representations and enhances transparency by indirectly learning meaningful semantic groupings. Among hierarchical retrieval methods, ReTreever achieves the best retrieval accuracy at the lowest latency, proving that this family of techniques can be viable in practical applications.

Heterophilic Graph Neural Networks (HGNNs) have shown promising results for semi-supervised learning tasks on graphs. Notably, most real-world heterophilic graphs are composed of a mixture of nodes with different neighbor patterns, exhibiting local node-level homophilic and heterophilic structures. However, existing works are only devoted to designing better HGNN backbones or architectures for node classification tasks on heterophilic and homophilic graph benchmarks simultaneously, and their analyses of HGNN performance with respect to nodes are only based on the determined data distribution without exploring the effect caused by this structural difference between training and testing nodes. How to learn invariant node representations on heterophilic graphs to handle this structure difference or distribution shifts remains unexplored. In this paper, we first discuss the limitations of previous graph-based invariant learning methods from the perspective of data augmentation. Then, we propose HEI, a framework capable of generating invariant node representations through incorporating heterophily information to infer latent environments without augmentation, which are then used for invariant prediction, under heterophilic graph structure distribution shifts. We theoretically show that our proposed method can achieve guaranteed performance under heterophilic graph structure distribution shifts. Extensive experiments on various benchmarks and backbones can also demonstrate the effectiveness of our method compared with existing state-of-the-art baselines.

Both biological and artificial neural networks inherently balance their performance with their operational cost, which balances their computational abilities. Typically, an efficient neuromorphic neural network is one that learns representations that reduce the redundancies and dimensionality of its input. This is for instance achieved in sparse coding, and sparse representations derived from natural images yield representations that are heterogeneous, both in their sampling of input features and in the variance of those features. Here, we investigated the connection between natural images' structure, particularly oriented features, and their corresponding sparse codes. We showed that representations of input features scattered across multiple levels of variance substantially improve the sparseness and resilience of sparse codes, at the cost of reconstruction performance. This echoes the structure of the model's input, allowing to account for the heterogeneously aleatoric structures of natural images. We demonstrate that learning kernel from natural images produces heterogeneity by balancing between approximate and dense representations, which improves all reconstruction metrics. Using a parametrized control of the kernels' heterogeneity used by a convolutional sparse coding algorithm, we show that heterogeneity emphasizes sparseness, while homogeneity improves representation granularity. In a broader context, these encoding strategy can serve as inputs to deep convolutional neural networks. We prove that such variance-encoded sparse image datasets enhance computational efficiency, emphasizing the benefits of kernel heterogeneity to leverage naturalistic and variant input structures and possible applications to improve the throughput of neuromorphic hardware.

Abstract grammatical knowledge - of parts of speech and grammatical patterns - is key to the capacity for linguistic generalization in humans. But how abstract is grammatical knowledge in large language models? In the human literature, compelling evidence for grammatical abstraction comes from structural priming. A sentence that shares the same grammatical structure as a preceding sentence is processed and produced more readily. Because confounds exist when using stimuli in a single language, evidence of abstraction is even more compelling from crosslingual structural priming, where use of a syntactic structure in one language primes an analogous structure in another language. We measure crosslingual structural priming in large language models, comparing model behavior to human experimental results from eight crosslingual experiments covering six languages, and four monolingual structural priming experiments in three non-English languages. We find evidence for abstract monolingual and crosslingual grammatical representations in the models that function similarly to those found in humans. These results demonstrate that grammatical representations in multilingual language models are not only similar across languages, but they can causally influence text produced in different languages.

We present a universal motion representation that encompasses a comprehensive range of motor skills for physics-based humanoid control. Due to the high-dimensionality of humanoid control as well as the inherent difficulties in reinforcement learning, prior methods have focused on learning skill embeddings for a narrow range of movement styles (e.g. locomotion, game characters) from specialized motion datasets. This limited scope hampers its applicability in complex tasks. Our work closes this gap, significantly increasing the coverage of motion representation space. To achieve this, we first learn a motion imitator that can imitate all of human motion from a large, unstructured motion dataset. We then create our motion representation by distilling skills directly from the imitator. This is achieved using an encoder-decoder structure with a variational information bottleneck. Additionally, we jointly learn a prior conditioned on proprioception (humanoid's own pose and velocities) to improve model expressiveness and sampling efficiency for downstream tasks. Sampling from the prior, we can generate long, stable, and diverse human motions. Using this latent space for hierarchical RL, we show that our policies solve tasks using natural and realistic human behavior. We demonstrate the effectiveness of our motion representation by solving generative tasks (e.g. strike, terrain traversal) and motion tracking using VR controllers.

Visual and linguistic concepts naturally organize themselves in a hierarchy, where a textual concept ``dog'' entails all images that contain dogs. Despite being intuitive, current large-scale vision and language models such as CLIP do not explicitly capture such hierarchy. We propose MERU, a contrastive model that yields hyperbolic representations of images and text. Hyperbolic spaces have suitable geometric properties to embed tree-like data, so MERU can better capture the underlying hierarchy in image-text data. Our results show that MERU learns a highly interpretable representation space while being competitive with CLIP's performance on multi-modal tasks like image classification and image-text retrieval.

Polygonal meshes are ubiquitous, but have only played a relatively minor role in the deep learning revolution. State-of-the-art neural generative models for 3D shapes learn implicit functions and generate meshes via expensive iso-surfacing. We overcome these challenges by employing a classical spatial data structure from computer graphics, Binary Space Partitioning (BSP), to facilitate 3D learning. The core operation of BSP involves recursive subdivision of 3D space to obtain convex sets. By exploiting this property, we devise BSP-Net, a network that learns to represent a 3D shape via convex decomposition without supervision. The network is trained to reconstruct a shape using a set of convexes obtained from a BSP-tree built over a set of planes, where the planes and convexes are both defined by learned network weights. BSP-Net directly outputs polygonal meshes from the inferred convexes. The generated meshes are watertight, compact (i.e., low-poly), and well suited to represent sharp geometry. We show that the reconstruction quality by BSP-Net is competitive with those from state-of-the-art methods while using much fewer primitives. We also explore variations to BSP-Net including using a more generic decoder for reconstruction, more general primitives than planes, as well as training a generative model with variational auto-encoders. Code is available at https://github.com/czq142857/BSP-NET-original.

Recently, the retrieval models based on dense representations have been gradually applied in the first stage of the document retrieval tasks, showing better performance than traditional sparse vector space models. To obtain high efficiency, the basic structure of these models is Bi-encoder in most cases. However, this simple structure may cause serious information loss during the encoding of documents since the queries are agnostic. To address this problem, we design a method to mimic the queries on each of the documents by an iterative clustering process and represent the documents by multiple pseudo queries (i.e., the cluster centroids). To boost the retrieval process using approximate nearest neighbor search library, we also optimize the matching function with a two-step score calculation procedure. Experimental results on several popular ranking and QA datasets show that our model can achieve state-of-the-art results.

Topic modeling is used for discovering latent semantic structure, usually referred to as topics, in a large collection of documents. The most widely used methods are Latent Dirichlet Allocation and Probabilistic Latent Semantic Analysis. Despite their popularity they have several weaknesses. In order to achieve optimal results they often require the number of topics to be known, custom stop-word lists, stemming, and lemmatization. Additionally these methods rely on bag-of-words representation of documents which ignore the ordering and semantics of words. Distributed representations of documents and words have gained popularity due to their ability to capture semantics of words and documents. We present top2vec, which leverages joint document and word semantic embedding to find topic vectors. This model does not require stop-word lists, stemming or lemmatization, and it automatically finds the number of topics. The resulting topic vectors are jointly embedded with the document and word vectors with distance between them representing semantic similarity. Our experiments demonstrate that top2vec finds topics which are significantly more informative and representative of the corpus trained on than probabilistic generative models.

Recent studies have shown that code language models at scale demonstrate significant performance gains on downstream tasks, i.e., code generation. However, most of the existing works on code representation learning train models at a hundred million parameter scale using very limited pretraining corpora. In this work, we fuel code representation learning with a vast amount of code data via a two-stage pretraining scheme. We first train the encoders via a mix that leverages both randomness in masking language modeling and the structure aspect of programming language. We then enhance the representations via contrastive learning with hard negative and hard positive constructed in an unsupervised manner. We establish an off-the-shelf encoder model that persistently outperforms the existing models on a wide variety of downstream tasks by large margins. To comprehend the factors contributing to successful code representation learning, we conduct detailed ablations and share our findings on (i) a customized and effective token-level denoising scheme for source code; (ii) the importance of hard negatives and hard positives; (iii) how the proposed bimodal contrastive learning boost the cross-lingual semantic search performance; and (iv) how the pretraining schemes decide the downstream task performance scales with the model size.

The success of powerful open source Large Language Models (LLMs) has enabled the community to create a vast collection of post-trained models adapted to specific tasks and domains. However, navigating and understanding these models remains challenging due to inconsistent metadata and unstructured repositories. We introduce Delta Activations, a method to represent finetuned models as vector embeddings by measuring shifts in their internal activations relative to a base model. This representation allows for effective clustering by domain and task, revealing structure in the model landscape. Delta Activations also demonstrate desirable properties: it is robust across finetuning settings and exhibits an additive property when finetuning datasets are mixed. In addition, we show that Delta Activations can embed tasks via few-shot finetuning, and further explore its use for model selection and merging. We hope Delta Activations can facilitate the practice of reusing publicly available models. Code is available at https://github.com/OscarXZQ/delta_activations.

In recent years, 3D Gaussian splatting has emerged as a powerful technique for 3D reconstruction and generation, known for its fast and high-quality rendering capabilities. To address these shortcomings, this paper introduces a novel diffusion-based framework, GVGEN, designed to efficiently generate 3D Gaussian representations from text input. We propose two innovative techniques:(1) Structured Volumetric Representation. We first arrange disorganized 3D Gaussian points as a structured form GaussianVolume. This transformation allows the capture of intricate texture details within a volume composed of a fixed number of Gaussians. To better optimize the representation of these details, we propose a unique pruning and densifying method named the Candidate Pool Strategy, enhancing detail fidelity through selective optimization. (2) Coarse-to-fine Generation Pipeline. To simplify the generation of GaussianVolume and empower the model to generate instances with detailed 3D geometry, we propose a coarse-to-fine pipeline. It initially constructs a basic geometric structure, followed by the prediction of complete Gaussian attributes. Our framework, GVGEN, demonstrates superior performance in qualitative and quantitative assessments compared to existing 3D generation methods. Simultaneously, it maintains a fast generation speed (sim7 seconds), effectively striking a balance between quality and efficiency.

In this study, we focus on the graph representation learning (a.k.a. network embedding) in attributed graphs. Different from existing embedding methods that treat the incorporation of graph structure and semantic as the simple combination of two optimization objectives, we propose a novel semantic graph representation (SGR) method to formulate the joint optimization of the two heterogeneous sources into a common high-order proximity based framework. Concretely, we first construct an auxiliary weighted graph, where the complex homogeneous and heterogeneous relations among nodes and attributes in the original graph are comprehensively encoded. Conventional embedding methods that consider high-order topology proximities can then be easily applied to the newly constructed graph to learn the representations of both node and attribute while capturing the nonlinear high-order intrinsic correlation inside or among graph structure and semantic. The learned attribute embeddings can also effectively support some semantic-oriented inference tasks (e.g., semantic community detection), helping to reveal the graph's deep semantic. The effectiveness of SGR is further verified on a series of real graphs, where it achieves impressive performance over other baselines.

The rise of deep learning technologies has quickly advanced many fields, including that of generative music systems. There exist a number of systems that allow for the generation of good sounding short snippets, yet, these generated snippets often lack an overarching, longer-term structure. In this work, we propose CM-HRNN: a conditional melody generation model based on a hierarchical recurrent neural network. This model allows us to generate melodies with long-term structures based on given chord accompaniments. We also propose a novel, concise event-based representation to encode musical lead sheets while retaining the notes' relative position within the bar with respect to the musical meter. With this new data representation, the proposed architecture can simultaneously model the rhythmic, as well as the pitch structures in an effective way. Melodies generated by the proposed model were extensively evaluated in quantitative experiments as well as a user study to ensure the musical quality of the output as well as to evaluate if they contain repeating patterns. We also compared the system with the state-of-the-art AttentionRNN. This comparison shows that melodies generated by CM-HRNN contain more repeated patterns (i.e., higher compression ratio) and a lower tonal tension (i.e., more tonally concise). Results from our listening test indicate that CM-HRNN outperforms AttentionRNN in terms of long-term structure and overall rating.

Representation learning on text-attributed graphs (TAGs) integrates structural connectivity with rich textual semantics, enabling applications in diverse domains. Current methods largely rely on contrastive learning to maximize cross-modal similarity, assuming tighter coupling between graph and text representations improves transfer performance. However, our empirical analysis reveals that both natural gap expansion and forced gap reduction result in performance degradation by disrupting pre-trained knowledge structures and impairing generalization. This arises from the geometric incompatibility between encoders, where graph encoders capture topological patterns, while text encoders capture semantic structures. Over-alignment compresses these distinct spaces into shared subspaces, causing structure collapse that diminishes both topological reasoning and semantic understanding. We propose LLM4GTA, a gap-aware alignment framework that preserves representation gaps as geometric necessities for maintaining modality-specific knowledge and improving transfer performance. LLM4GTA includes an adaptive gap preservation module to prevent over-alignment by monitoring similarity evolution and an intra-modal compensation mechanism that boosts discriminative power using auxiliary classifiers in graph space. Extensive experiments show significant improvements over existing methods in zero-shot and few-shot scenarios.

The reversal curse -- a language model's (LM) inability to infer an unseen fact ``B is A'' from a learned fact ``A is B'' -- is widely considered a fundamental limitation. We show that this is not an inherent failure but an artifact of how models encode knowledge. By training LMs from scratch on a synthetic dataset of relational knowledge graphs, we demonstrate that bilinear relational structure emerges in their hidden representations. This structure substantially alleviates the reversal curse, enabling LMs to infer unseen reverse facts. Crucially, we also find that this bilinear structure plays a key role in consistent model editing. When a fact is updated in a LM with this structure, the edit correctly propagates to its reverse and other logically dependent facts. In contrast, models lacking this representation not only suffer from the reversal curse but also fail to generalize edits, further introducing logical inconsistencies. Our results establish that training on a relational knowledge dataset induces the emergence of bilinear internal representations, which in turn enable LMs to behave in a logically consistent manner after editing. This implies that the success of model editing depends critically not just on editing algorithms but on the underlying representational geometry of the knowledge being modified.

Motion trajectories offer reliable references for physics-based motion learning but suffer from sparsity, particularly in regions that lack sufficient data coverage. To address this challenge, we introduce a self-supervised, structured representation and generation method that extracts spatial-temporal relationships in periodic or quasi-periodic motions. The motion dynamics in a continuously parameterized latent space enable our method to enhance the interpolation and generalization capabilities of motion learning algorithms. The motion learning controller, informed by the motion parameterization, operates online tracking of a wide range of motions, including targets unseen during training. With a fallback mechanism, the controller dynamically adapts its tracking strategy and automatically resorts to safe action execution when a potentially risky target is proposed. By leveraging the identified spatial-temporal structure, our work opens new possibilities for future advancements in general motion representation and learning algorithms.

Effective root cause analysis (RCA) is vital for swiftly restoring services, minimizing losses, and ensuring the smooth operation and management of complex systems. Previous data-driven RCA methods, particularly those employing causal discovery techniques, have primarily focused on constructing dependency or causal graphs for backtracking the root causes. However, these methods often fall short as they rely solely on data from a single modality, thereby resulting in suboptimal solutions. In this work, we propose Mulan, a unified multi-modal causal structure learning method for root cause localization. We leverage a log-tailored language model to facilitate log representation learning, converting log sequences into time-series data. To explore intricate relationships across different modalities, we propose a contrastive learning-based approach to extract modality-invariant and modality-specific representations within a shared latent space. Additionally, we introduce a novel key performance indicator-aware attention mechanism for assessing modality reliability and co-learning a final causal graph. Finally, we employ random walk with restart to simulate system fault propagation and identify potential root causes. Extensive experiments on three real-world datasets validate the effectiveness of our proposed framework.

Semi-supervised image segmentation has attracted great attention recently. The key is how to leverage unlabeled images in the training process. Most methods maintain consistent predictions of the unlabeled images under variations (e.g., adding noise/perturbations, or creating alternative versions) in the image and/or model level. In most image-level variation, medical images often have prior structure information, which has not been well explored. In this paper, we propose novel dual structure-aware image filterings (DSAIF) as the image-level variations for semi-supervised medical image segmentation. Motivated by connected filtering that simplifies image via filtering in structure-aware tree-based image representation, we resort to the dual contrast invariant Max-tree and Min-tree representation. Specifically, we propose a novel connected filtering that removes topologically equivalent nodes (i.e. connected components) having no siblings in the Max/Min-tree. This results in two filtered images preserving topologically critical structure. Applying the proposed DSAIF to mutually supervised networks decreases the consensus of their erroneous predictions on unlabeled images. This helps to alleviate the confirmation bias issue of overfitting to noisy pseudo labels of unlabeled images, and thus effectively improves the segmentation performance. Extensive experimental results on three benchmark datasets demonstrate that the proposed method significantly/consistently outperforms some state-of-the-art methods. The source codes will be publicly available.

Contrastive learning models based on Siamese structure have demonstrated remarkable performance in self-supervised learning. Such a success of contrastive learning relies on two conditions, a sufficient number of positive pairs and adequate variations between them. If the conditions are not met, these frameworks will lack semantic contrast and be fragile on overfitting. To address these two issues, we propose Hallucinator that could efficiently generate additional positive samples for further contrast. The Hallucinator is differentiable and creates new data in the feature space. Thus, it is optimized directly with the pre-training task and introduces nearly negligible computation. Moreover, we reduce the mutual information of hallucinated pairs and smooth them through non-linear operations. This process helps avoid over-confident contrastive learning models during the training and achieves more transformation-invariant feature embeddings. Remarkably, we empirically prove that the proposed Hallucinator generalizes well to various contrastive learning models, including MoCoV1&V2, SimCLR and SimSiam. Under the linear classification protocol, a stable accuracy gain is achieved, ranging from 0.3% to 3.0% on CIFAR10&100, Tiny ImageNet, STL-10 and ImageNet. The improvement is also observed in transferring pre-train encoders to the downstream tasks, including object detection and segmentation.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Unsupervised representation learning for dynamic graphs has attracted a lot of research attention in recent years. Compared with static graph, the dynamic graph is a comprehensive embodiment of both the intrinsic stable characteristics of nodes and the time-related dynamic preference. However, existing methods generally mix these two types of information into a single representation space, which may lead to poor explanation, less robustness, and a limited ability when applied to different downstream tasks. To solve the above problems, in this paper, we propose a novel disenTangled representation learning framework for discrete-time Dynamic graphs, namely DyTed. We specially design a temporal-clips contrastive learning task together with a structure contrastive learning to effectively identify the time-invariant and time-varying representations respectively. To further enhance the disentanglement of these two types of representation, we propose a disentanglement-aware discriminator under an adversarial learning framework from the perspective of information theory. Extensive experiments on Tencent and five commonly used public datasets demonstrate that DyTed, as a general framework that can be applied to existing methods, achieves state-of-the-art performance on various downstream tasks, as well as be more robust against noise.

Convolutional recurrent networks (CRN) integrating a convolutional encoder-decoder (CED) structure and a recurrent structure have achieved promising performance for monaural speech enhancement. However, feature representation across frequency context is highly constrained due to limited receptive fields in the convolutions of CED. In this paper, we propose a convolutional recurrent encoder-decoder (CRED) structure to boost feature representation along the frequency axis. The CRED applies frequency recurrence on 3D convolutional feature maps along the frequency axis following each convolution, therefore, it is capable of catching long-range frequency correlations and enhancing feature representations of speech inputs. The proposed frequency recurrence is realized efficiently using a feedforward sequential memory network (FSMN). Besides the CRED, we insert two stacked FSMN layers between the encoder and the decoder to model further temporal dynamics. We name the proposed framework as Frequency Recurrent CRN (FRCRN). We design FRCRN to predict complex Ideal Ratio Mask (cIRM) in complex-valued domain and optimize FRCRN using both time-frequency-domain and time-domain losses. Our proposed approach achieved state-of-the-art performance on wideband benchmark datasets and achieved 2nd place for the real-time fullband track in terms of Mean Opinion Score (MOS) and Word Accuracy (WAcc) in the ICASSP 2022 Deep Noise Suppression (DNS) challenge (https://github.com/alibabasglab/FRCRN).

In this paper, we tackle the problem of learning visual representations from unlabeled scene-centric data. Existing works have demonstrated the potential of utilizing the underlying complex structure within scene-centric data; still, they commonly rely on hand-crafted objectness priors or specialized pretext tasks to build a learning framework, which may harm generalizability. Instead, we propose contrastive learning from data-driven semantic slots, namely SlotCon, for joint semantic grouping and representation learning. The semantic grouping is performed by assigning pixels to a set of learnable prototypes, which can adapt to each sample by attentive pooling over the feature and form new slots. Based on the learned data-dependent slots, a contrastive objective is employed for representation learning, which enhances the discriminability of features, and conversely facilitates grouping semantically coherent pixels together. Compared with previous efforts, by simultaneously optimizing the two coupled objectives of semantic grouping and contrastive learning, our approach bypasses the disadvantages of hand-crafted priors and is able to learn object/group-level representations from scene-centric images. Experiments show our approach effectively decomposes complex scenes into semantic groups for feature learning and significantly benefits downstream tasks, including object detection, instance segmentation, and semantic segmentation. Code is available at: https://github.com/CVMI-Lab/SlotCon.

This paper introduces a novel method for self-supervised video representation learning via feature prediction. In contrast to the previous methods that focus on future feature prediction, we argue that a supervisory signal arising from unobserved past frames is complementary to one that originates from the future frames. The rationale behind our method is to encourage the network to explore the temporal structure of videos by distinguishing between future and past given present observations. We train our model in a contrastive learning framework, where joint encoding of future and past provides us with a comprehensive set of temporal hard negatives via swapping. We empirically show that utilizing both signals enriches the learned representations for the downstream task of action recognition. It outperforms independent prediction of future and past.

Biomedical text mining is becoming increasingly important as the number of biomedical documents and web data rapidly grows. Recently, word representation models such as BERT has gained popularity among researchers. However, it is difficult to estimate their performance on datasets containing biomedical texts as the word distributions of general and biomedical corpora are quite different. Moreover, the medical domain has long-tail concepts and terminologies that are difficult to be learned via language models. For the Chinese biomedical text, it is more difficult due to its complex structure and the variety of phrase combinations. In this paper, we investigate how the recently introduced pre-trained language model BERT can be adapted for Chinese biomedical corpora and propose a novel conceptualized representation learning approach. We also release a new Chinese Biomedical Language Understanding Evaluation benchmark (ChineseBLUE). We examine the effectiveness of Chinese pre-trained models: BERT, BERT-wwm, RoBERTa, and our approach. Experimental results on the benchmark show that our approach could bring significant gain. We release the pre-trained model on GitHub: https://github.com/alibaba-research/ChineseBLUE.

Relational tables on the Web store a vast amount of knowledge. Owing to the wealth of such tables, there has been tremendous progress on a variety of tasks in the area of table understanding. However, existing work generally relies on heavily-engineered task-specific features and model architectures. In this paper, we present TURL, a novel framework that introduces the pre-training/fine-tuning paradigm to relational Web tables. During pre-training, our framework learns deep contextualized representations on relational tables in an unsupervised manner. Its universal model design with pre-trained representations can be applied to a wide range of tasks with minimal task-specific fine-tuning. Specifically, we propose a structure-aware Transformer encoder to model the row-column structure of relational tables, and present a new Masked Entity Recovery (MER) objective for pre-training to capture the semantics and knowledge in large-scale unlabeled data. We systematically evaluate TURL with a benchmark consisting of 6 different tasks for table understanding (e.g., relation extraction, cell filling). We show that TURL generalizes well to all tasks and substantially outperforms existing methods in almost all instances.

We present HERO, a novel framework for large-scale video+language omni-representation learning. HERO encodes multimodal inputs in a hierarchical structure, where local context of a video frame is captured by a Cross-modal Transformer via multimodal fusion, and global video context is captured by a Temporal Transformer. In addition to standard Masked Language Modeling (MLM) and Masked Frame Modeling (MFM) objectives, we design two new pre-training tasks: (i) Video-Subtitle Matching (VSM), where the model predicts both global and local temporal alignment; and (ii) Frame Order Modeling (FOM), where the model predicts the right order of shuffled video frames. HERO is jointly trained on HowTo100M and large-scale TV datasets to gain deep understanding of complex social dynamics with multi-character interactions. Comprehensive experiments demonstrate that HERO achieves new state of the art on multiple benchmarks over Text-based Video/Video-moment Retrieval, Video Question Answering (QA), Video-and-language Inference and Video Captioning tasks across different domains. We also introduce two new challenging benchmarks How2QA and How2R for Video QA and Retrieval, collected from diverse video content over multimodalities.

Recent findings in neuroscience suggest that the human brain represents information in a geometric structure (for instance, through conceptual spaces). In order to communicate, we flatten the complex representation of entities and their attributes into a single word or a sentence. In this paper we use graph convolutional networks to support the evolution of language and cooperation in multi-agent systems. Motivated by an image-based referential game, we propose a graph referential game with varying degrees of complexity, and we provide strong baseline models that exhibit desirable properties in terms of language emergence and cooperation. We show that the emerged communication protocol is robust, that the agents uncover the true factors of variation in the game, and that they learn to generalize beyond the samples encountered during training.

Being able to perceive the semantics and the spatial structure of the environment is essential for visual navigation of a household robot. However, most existing works only employ visual backbones pre-trained either with independent images for classification or with self-supervised learning methods to adapt to the indoor navigation domain, neglecting the spatial relationships that are essential to the learning of navigation. Inspired by the behavior that humans naturally build semantically and spatially meaningful cognitive maps in their brains during navigation, in this paper, we propose a novel navigational-specific visual representation learning method by contrasting the agent's egocentric views and semantic maps (Ego^2-Map). We apply the visual transformer as the backbone encoder and train the model with data collected from the large-scale Habitat-Matterport3D environments. Ego^2-Map learning transfers the compact and rich information from a map, such as objects, structure and transition, to the agent's egocentric representations for navigation. Experiments show that agents using our learned representations on object-goal navigation outperform recent visual pre-training methods. Moreover, our representations significantly improve vision-and-language navigation in continuous environments for both high-level and low-level action spaces, achieving new state-of-the-art results of 47% SR and 41% SPL on the test server.

Music structure analysis (MSA) underpins music understanding and controllable generation, yet progress has been limited by small, inconsistent corpora. We present SongFormer, a scalable framework that learns from heterogeneous supervision. SongFormer (i) fuses short- and long-window self-supervised audio representations to capture both fine-grained and long-range dependencies, and (ii) introduces a learned source embedding to enable training with partial, noisy, and schema-mismatched labels. To support scaling and fair evaluation, we release SongFormDB, the largest MSA corpus to date (over 10k tracks spanning languages and genres), and SongFormBench, a 300-song expert-verified benchmark. On SongFormBench, SongFormer sets a new state of the art in strict boundary detection (HR.5F) and achieves the highest functional label accuracy, while remaining computationally efficient; it surpasses strong baselines and Gemini 2.5 Pro on these metrics and remains competitive under relaxed tolerance (HR3F). Code, datasets, and model are publicly available.

This work explores the hypothesis that subjectively attributed meaning constitutes the phenomenal content of conscious experience. That is, phenomenal content is semantic. This form of subjective meaning manifests as an intrinsic and non-representational character of qualia. Empirically, subjective meaning is ubiquitous in conscious experiences. We point to phenomenological studies that lend evidence to support this. Furthermore, this notion of meaning closely relates to what Frege refers to as "sense", in metaphysics and philosophy of language. It also aligns with Peirce's "interpretant", in semiotics. We discuss how Frege's sense can also be extended to the raw feels of consciousness. Sense and reference both play a role in phenomenal experience. Moreover, within the context of the mind-matter relation, we provide a formalization of subjective meaning associated to one's mental representations. Identifying the precise maps between the physical and mental domains, we argue that syntactic and semantic structures transcend language, and are realized within each of these domains. Formally, meaning is a relational attribute, realized via a map that interprets syntactic structures of a formal system within an appropriate semantic space. The image of this map within the mental domain is what is relevant for experience, and thus comprises the phenomenal content of qualia. We conclude with possible implications this may have for experience-based theories of consciousness.

Visual understanding of the world goes beyond the semantics and flat structure of individual images. In this work, we aim to capture both the 3D structure and dynamics of real-world scenes from monocular real-world videos. Our Dynamic Scene Transformer (DyST) model leverages recent work in neural scene representation to learn a latent decomposition of monocular real-world videos into scene content, per-view scene dynamics, and camera pose. This separation is achieved through a novel co-training scheme on monocular videos and our new synthetic dataset DySO. DyST learns tangible latent representations for dynamic scenes that enable view generation with separate control over the camera and the content of the scene.

Self-supervised learning (SSL) models use only the intrinsic structure of a given signal, independent of its acoustic domain, to extract essential information from the input to an embedding space. This implies that the utility of such representations is not limited to modeling human speech alone. Building on this understanding, this paper explores the cross-transferability of SSL neural representations learned from human speech to analyze bio-acoustic signals. We conduct a caller discrimination analysis and a caller detection study on Marmoset vocalizations using eleven SSL models pre-trained with various pretext tasks. The results show that the embedding spaces carry meaningful caller information and can successfully distinguish the individual identities of Marmoset callers without fine-tuning. This demonstrates that representations pre-trained on human speech can be effectively applied to the bio-acoustics domain, providing valuable insights for future investigations in this field.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

While the successes of transformers across many domains are indisputable, accurate understanding of the learning mechanics is still largely lacking. Their capabilities have been probed on benchmarks which include a variety of structured and reasoning tasks -- but mathematical understanding is lagging substantially behind. Recent lines of work have begun studying representational aspects of this question: that is, the size/depth/complexity of attention-based networks to perform certain tasks. However, there is no guarantee the learning dynamics will converge to the constructions proposed. In our paper, we provide fine-grained mechanistic understanding of how transformers learn "semantic structure", understood as capturing co-occurrence structure of words. Precisely, we show, through a combination of experiments on synthetic data modeled by Latent Dirichlet Allocation (LDA), Wikipedia data, and mathematical analysis that the embedding layer and the self-attention layer encode the topical structure. In the former case, this manifests as higher average inner product of embeddings between same-topic words. In the latter, it manifests as higher average pairwise attention between same-topic words. The mathematical results involve several assumptions to make the analysis tractable, which we verify on data, and might be of independent interest as well.

Tables organize valuable content in a concise and compact representation. This content is extremely valuable for systems such as search engines, Knowledge Graph's, etc, since they enhance their predictive capabilities. Unfortunately, tables come in a large variety of shapes and sizes. Furthermore, they can have complex column/row-header configurations, multiline rows, different variety of separation lines, missing entries, etc. As such, the correct identification of the table-structure from an image is a non-trivial task. In this paper, we present a new table-structure identification model. The latter improves the latest end-to-end deep learning model (i.e. encoder-dual-decoder from PubTabNet) in two significant ways. First, we introduce a new object detection decoder for table-cells. In this way, we can obtain the content of the table-cells from programmatic PDF's directly from the PDF source and avoid the training of the custom OCR decoders. This architectural change leads to more accurate table-content extraction and allows us to tackle non-english tables. Second, we replace the LSTM decoders with transformer based decoders. This upgrade improves significantly the previous state-of-the-art tree-editing-distance-score (TEDS) from 91% to 98.5% on simple tables and from 88.7% to 95% on complex tables.

Gaussian splatting, renowned for its exceptional rendering quality and efficiency, has emerged as a prominent technique in 3D scene representation. However, the substantial data volume of Gaussian splatting impedes its practical utility in real-world applications. Herein, we propose an efficient 3D scene representation, named Compressed Gaussian Splatting (CompGS), which harnesses compact Gaussian primitives for faithful 3D scene modeling with a remarkably reduced data size. To ensure the compactness of Gaussian primitives, we devise a hybrid primitive structure that captures predictive relationships between each other. Then, we exploit a small set of anchor primitives for prediction, allowing the majority of primitives to be encapsulated into highly compact residual forms. Moreover, we develop a rate-constrained optimization scheme to eliminate redundancies within such hybrid primitives, steering our CompGS towards an optimal trade-off between bitrate consumption and representation efficacy. Experimental results show that the proposed CompGS significantly outperforms existing methods, achieving superior compactness in 3D scene representation without compromising model accuracy and rendering quality. Our code will be released on GitHub for further research.

Neural fields excel in computer vision and robotics due to their ability to understand the 3D visual world such as inferring semantics, geometry, and dynamics. Given the capabilities of neural fields in densely representing a 3D scene from 2D images, we ask the question: Can we scale their self-supervised pretraining, specifically using masked autoencoders, to generate effective 3D representations from posed RGB images. Owing to the astounding success of extending transformers to novel data modalities, we employ standard 3D Vision Transformers to suit the unique formulation of NeRFs. We leverage NeRF's volumetric grid as a dense input to the transformer, contrasting it with other 3D representations such as pointclouds where the information density can be uneven, and the representation is irregular. Due to the difficulty of applying masked autoencoders to an implicit representation, such as NeRF, we opt for extracting an explicit representation that canonicalizes scenes across domains by employing the camera trajectory for sampling. Our goal is made possible by masking random patches from NeRF's radiance and density grid and employing a standard 3D Swin Transformer to reconstruct the masked patches. In doing so, the model can learn the semantic and spatial structure of complete scenes. We pretrain this representation at scale on our proposed curated posed-RGB data, totaling over 1.8 million images. Once pretrained, the encoder is used for effective 3D transfer learning. Our novel self-supervised pretraining for NeRFs, NeRF-MAE, scales remarkably well and improves performance on various challenging 3D tasks. Utilizing unlabeled posed 2D data for pretraining, NeRF-MAE significantly outperforms self-supervised 3D pretraining and NeRF scene understanding baselines on Front3D and ScanNet datasets with an absolute performance improvement of over 20% AP50 and 8% AP25 for 3D object detection.

Faithful evaluation of language model capabilities is crucial for deriving actionable insights that can inform model development. However, rigorous causal evaluations in this domain face significant methodological challenges, including complex confounding effects and prohibitive computational costs associated with extensive retraining. To tackle these challenges, we propose a causal representation learning framework wherein observed benchmark performance is modeled as a linear transformation of a few latent capability factors. Crucially, these latent factors are identified as causally interrelated after appropriately controlling for the base model as a common confounder. Applying this approach to a comprehensive dataset encompassing over 1500 models evaluated across six benchmarks from the Open LLM Leaderboard, we identify a concise three-node linear causal structure that reliably explains the observed performance variations. Further interpretation of this causal structure provides substantial scientific insights beyond simple numerical rankings: specifically, we reveal a clear causal direction starting from general problem-solving capabilities, advancing through instruction-following proficiency, and culminating in mathematical reasoning ability. Our results underscore the essential role of carefully controlling base model variations during evaluation, a step critical to accurately uncovering the underlying causal relationships among latent model capabilities.

Symbolic music generation aims to create musical notes, which can help users compose music, such as generating target instrumental tracks from scratch, or based on user-provided source tracks. Considering the diverse and flexible combination between source and target tracks, a unified model capable of generating any arbitrary tracks is of crucial necessity. Previous works fail to address this need due to inherent constraints in music representations and model architectures. To address this need, we propose a unified representation and diffusion framework named GETMusic (`GET' stands for GEnerate music Tracks), which includes a novel music representation named GETScore, and a diffusion model named GETDiff. GETScore represents notes as tokens and organizes them in a 2D structure, with tracks stacked vertically and progressing horizontally over time. During training, tracks are randomly selected as either the target or source. In the forward process, target tracks are corrupted by masking their tokens, while source tracks remain as ground truth. In the denoising process, GETDiff learns to predict the masked target tokens, conditioning on the source tracks. With separate tracks in GETScore and the non-autoregressive behavior of the model, GETMusic can explicitly control the generation of any target tracks from scratch or conditioning on source tracks. We conduct experiments on music generation involving six instrumental tracks, resulting in a total of 665 combinations. GETMusic provides high-quality results across diverse combinations and surpasses prior works proposed for some specific combinations.

A fundamental question in cognitive neuroscience is what shapes visual perception: the external world's structure or the brain's internal architecture. Although some perceptual variability can be traced to individual differences, brain responses to naturalistic stimuli evoke similar activity patterns across individuals, suggesting a convergent representational principle. Here, we test if this stimulus-driven convergence follows a common trajectory across people and deep neural networks (DNNs) during its transformation from sensory to high-level internal representations. We introduce a unified framework that traces representational flow by combining inter-subject similarity with alignment to model hierarchies. Applying this framework to three independent fMRI datasets of visual scene perception, we reveal a cortex-wide network, conserved across individuals, organized into two pathways: a medial-ventral stream for scene structure and a lateral-dorsal stream tuned for social and biological content. This functional organization is captured by the hierarchies of vision DNNs but not language models, reinforcing the specificity of the visual-to-semantic transformation. These findings show a convergent computational solution for visual encoding in both human and artificial vision, driven by the structure of the external world.

Recent advancements in large language models have significantly improved their context windows, yet challenges in effective long-term memory management remain. We introduce MemTree, an algorithm that leverages a dynamic, tree-structured memory representation to optimize the organization, retrieval, and integration of information, akin to human cognitive schemas. MemTree organizes memory hierarchically, with each node encapsulating aggregated textual content, corresponding semantic embeddings, and varying abstraction levels across the tree's depths. Our algorithm dynamically adapts this memory structure by computing and comparing semantic embeddings of new and existing information to enrich the model's context-awareness. This approach allows MemTree to handle complex reasoning and extended interactions more effectively than traditional memory augmentation methods, which often rely on flat lookup tables. Evaluations on benchmarks for multi-turn dialogue understanding and document question answering show that MemTree significantly enhances performance in scenarios that demand structured memory management.

Joint entity and relation extraction plays a pivotal role in various applications, notably in the construction of knowledge graphs. Despite recent progress, existing approaches often fall short in two key aspects: richness of representation and coherence in output structure. These models often rely on handcrafted heuristics for computing entity and relation representations, potentially leading to loss of crucial information. Furthermore, they disregard task and/or dataset-specific constraints, resulting in output structures that lack coherence. In our work, we introduce EnriCo, which mitigates these shortcomings. Firstly, to foster rich and expressive representation, our model leverage attention mechanisms that allow both entities and relations to dynamically determine the pertinent information required for accurate extraction. Secondly, we introduce a series of decoding algorithms designed to infer the highest scoring solutions while adhering to task and dataset-specific constraints, thus promoting structured and coherent outputs. Our model demonstrates competitive performance compared to baselines when evaluated on Joint IE datasets.

We show that introducing a weighting factor to reduce the influence of identity shortcuts in residual networks significantly enhances semantic feature learning in generative representation learning frameworks, such as masked autoencoders (MAEs) and diffusion models. Our modification notably improves feature quality, raising ImageNet-1K K-Nearest Neighbor accuracy from 27.4% to 63.9% and linear probing accuracy from 67.8% to 72.7% for MAEs with a ViT-B/16 backbone, while also enhancing generation quality in diffusion models. This significant gap suggests that, while residual connection structure serves an essential role in facilitating gradient propagation, it may have a harmful side effect of reducing capacity for abstract learning by virtue of injecting an echo of shallower representations into deeper layers. We ameliorate this downside via a fixed formula for monotonically decreasing the contribution of identity connections as layer depth increases. Our design promotes the gradual development of feature abstractions, without impacting network trainability. Analyzing the representations learned by our modified residual networks, we find correlation between low effective feature rank and downstream task performance.

Unsupervised and self-supervised objectives, such as next token prediction, have enabled pre-training generalist models from large amounts of unlabeled data. In reinforcement learning (RL), however, finding a truly general and scalable unsupervised pre-training objective for generalist policies from offline data remains a major open question. While a number of methods have been proposed to enable generic self-supervised RL, based on principles such as goal-conditioned RL, behavioral cloning, and unsupervised skill learning, such methods remain limited in terms of either the diversity of the discovered behaviors, the need for high-quality demonstration data, or the lack of a clear prompting or adaptation mechanism for downstream tasks. In this work, we propose a novel unsupervised framework to pre-train generalist policies that capture diverse, optimal, long-horizon behaviors from unlabeled offline data such that they can be quickly adapted to any arbitrary new tasks in a zero-shot manner. Our key insight is to learn a structured representation that preserves the temporal structure of the underlying environment, and then to span this learned latent space with directional movements, which enables various zero-shot policy "prompting" schemes for downstream tasks. Through our experiments on simulated robotic locomotion and manipulation benchmarks, we show that our unsupervised policies can solve goal-conditioned and general RL tasks in a zero-shot fashion, even often outperforming prior methods designed specifically for each setting. Our code and videos are available at https://seohong.me/projects/hilp/

To enhance group robustness to spurious correlations, prior work often relies on auxiliary annotations for groups or spurious features and assumes identical sets of groups across source and target domains. These two requirements are both unnatural and impractical in real-world settings. To overcome these limitations, we propose a method that leverages the semantic structure inherent in class labels--specifically, superclass information--to naturally reduce reliance on spurious features. Our model employs gradient-based attention guided by a pre-trained vision-language model to disentangle superclass-relevant and irrelevant features. Then, by promoting the use of all superclass-relevant features for prediction, our approach achieves robustness to more complex spurious correlations without the need to annotate any source samples. Experiments across diverse datasets demonstrate that our method significantly outperforms baselines in domain generalization tasks, with clear improvements in both quantitative metrics and qualitative visualizations.

This paper is dedicated to the design and evaluation of the first AMR parser tailored for clinical notes. Our objective was to facilitate the precise transformation of the clinical notes into structured AMR expressions, thereby enhancing the interpretability and usability of clinical text data at scale. Leveraging the colon cancer dataset from the Temporal Histories of Your Medical Events (THYME) corpus, we adapted a state-of-the-art AMR parser utilizing continuous training. Our approach incorporates data augmentation techniques to enhance the accuracy of AMR structure predictions. Notably, through this learning strategy, our parser achieved an impressive F1 score of 88% on the THYME corpus's colon cancer dataset. Moreover, our research delved into the efficacy of data required for domain adaptation within the realm of clinical notes, presenting domain adaptation data requirements for AMR parsing. This exploration not only underscores the parser's robust performance but also highlights its potential in facilitating a deeper understanding of clinical narratives through structured semantic representations.

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

In recent years, exploiting the domain-specific underlying structure of data and its generative factors for representation learning has shown success in various use-case agnostic applications. However, the diversity and complexity of tabular data have made it challenging to represent these structures in a latent space through multi-dimensional vectors. We design an autoencoder-based framework for building general purpose embeddings, we assess the performance of different autoencoder architectures, and show simpler models outperform complex ones in embedding highly complex tabular data. We apply our framework to produce plug-and-play, rich, and anonymized embeddings representing AWS customers for usage in any model, saving up to 45% of development time, and observe significant improvements in downstream models. Moreover, we propose a significant improvement to the calculation of reconstruction loss for multi-layer contractive autoencoders (CAE) by calculating the Jacobian of the entire encoder leading to a 15% improvement in reconstruction quality when compared to a stacked CAE.

Unsupervised representation learning presents new opportunities for advancing Quantum Architecture Search (QAS) on Noisy Intermediate-Scale Quantum (NISQ) devices. QAS is designed to optimize quantum circuits for Variational Quantum Algorithms (VQAs). Most QAS algorithms tightly couple the search space and search algorithm, typically requiring the evaluation of numerous quantum circuits, resulting in high computational costs and limiting scalability to larger quantum circuits. Predictor-based QAS algorithms mitigate this issue by estimating circuit performance based on structure or embedding. However, these methods often demand time-intensive labeling to optimize gate parameters across many circuits, which is crucial for training accurate predictors. Inspired by the classical neural architecture search algorithm Arch2vec, we investigate the potential of unsupervised representation learning for QAS without relying on predictors. Our framework decouples unsupervised architecture representation learning from the search process, enabling the learned representations to be applied across various downstream tasks. Additionally, it integrates an improved quantum circuit graph encoding scheme, addressing the limitations of existing representations and enhancing search efficiency. This predictor-free approach removes the need for large labeled datasets. During the search, we employ REINFORCE and Bayesian Optimization to explore the latent representation space and compare their performance against baseline methods. Our results demonstrate that the framework efficiently identifies high-performing quantum circuits with fewer search iterations.

Creating controllable, photorealistic, and geometrically detailed digital doubles of real humans solely from video data is a key challenge in Computer Graphics and Vision, especially when real-time performance is required. Recent methods attach a neural radiance field (NeRF) to an articulated structure, e.g., a body model or a skeleton, to map points into a pose canonical space while conditioning the NeRF on the skeletal pose. These approaches typically parameterize the neural field with a multi-layer perceptron (MLP) leading to a slow runtime. To address this drawback, we propose TriHuman a novel human-tailored, deformable, and efficient tri-plane representation, which achieves real-time performance, state-of-the-art pose-controllable geometry synthesis as well as photorealistic rendering quality. At the core, we non-rigidly warp global ray samples into our undeformed tri-plane texture space, which effectively addresses the problem of global points being mapped to the same tri-plane locations. We then show how such a tri-plane feature representation can be conditioned on the skeletal motion to account for dynamic appearance and geometry changes. Our results demonstrate a clear step towards higher quality in terms of geometry and appearance modeling of humans as well as runtime performance.

Comprehensive modeling of the surrounding 3D world is key to the success of autonomous driving. However, existing perception tasks like object detection, road structure segmentation, depth & elevation estimation, and open-set object localization each only focus on a small facet of the holistic 3D scene understanding task. This divide-and-conquer strategy simplifies the algorithm development procedure at the cost of losing an end-to-end unified solution to the problem. In this work, we address this limitation by studying camera-based 3D panoptic segmentation, aiming to achieve a unified occupancy representation for camera-only 3D scene understanding. To achieve this, we introduce a novel method called PanoOcc, which utilizes voxel queries to aggregate spatiotemporal information from multi-frame and multi-view images in a coarse-to-fine scheme, integrating feature learning and scene representation into a unified occupancy representation. We have conducted extensive ablation studies to verify the effectiveness and efficiency of the proposed method. Our approach achieves new state-of-the-art results for camera-based semantic segmentation and panoptic segmentation on the nuScenes dataset. Furthermore, our method can be easily extended to dense occupancy prediction and has shown promising performance on the Occ3D benchmark. The code will be released at https://github.com/Robertwyq/PanoOcc.

We present a learning-based method, namely GeoUDF,to tackle the long-standing and challenging problem of reconstructing a discrete surface from a sparse point cloud.To be specific, we propose a geometry-guided learning method for UDF and its gradient estimation that explicitly formulates the unsigned distance of a query point as the learnable affine averaging of its distances to the tangent planes of neighboring points on the surface. Besides,we model the local geometric structure of the input point clouds by explicitly learning a quadratic polynomial for each point. This not only facilitates upsampling the input sparse point cloud but also naturally induces unoriented normal, which further augments UDF estimation. Finally, to extract triangle meshes from the predicted UDF we propose a customized edge-based marching cube module. We conduct extensive experiments and ablation studies to demonstrate the significant advantages of our method over state-of-the-art methods in terms of reconstruction accuracy, efficiency, and generality. The source code is publicly available at https://github.com/rsy6318/GeoUDF.

Masked image modelling (e.g., Masked AutoEncoder) and contrastive learning (e.g., Momentum Contrast) have shown impressive performance on unsupervised visual representation learning. This work presents Masked Contrastive Representation Learning (MACRL) for self-supervised visual pre-training. In particular, MACRL leverages the effectiveness of both masked image modelling and contrastive learning. We adopt an asymmetric setting for the siamese network (i.e., encoder-decoder structure in both branches), where one branch with higher mask ratio and stronger data augmentation, while the other adopts weaker data corruptions. We optimize a contrastive learning objective based on the learned features from the encoder in both branches. Furthermore, we minimize the L_1 reconstruction loss according to the decoders' outputs. In our experiments, MACRL presents superior results on various vision benchmarks, including CIFAR-10, CIFAR-100, Tiny-ImageNet, and two other ImageNet subsets. Our framework provides unified insights on self-supervised visual pre-training and future research.

Machine learning frameworks such as graph neural networks typically rely on a given, fixed graph to exploit relational inductive biases and thus effectively learn from network data. However, when said graphs are (partially) unobserved, noisy, or dynamic, the problem of inferring graph structure from data becomes relevant. In this paper, we postulate a graph convolutional relationship between the observed and latent graphs, and formulate the graph learning task as a network inverse (deconvolution) problem. In lieu of eigendecomposition-based spectral methods or iterative optimization solutions, we unroll and truncate proximal gradient iterations to arrive at a parameterized neural network architecture that we call a Graph Deconvolution Network (GDN). GDNs can learn a distribution of graphs in a supervised fashion, perform link prediction or edge-weight regression tasks by adapting the loss function, and they are inherently inductive. We corroborate GDN's superior graph recovery performance and its generalization to larger graphs using synthetic data in supervised settings. Furthermore, we demonstrate the robustness and representation power of GDNs on real world neuroimaging and social network datasets.

Learning causal structure from observational data often assumes that we observe independent and identically distributed (i.\,i.\,d) data. The traditional approach aims to find a graphical representation that encodes the same set of conditional independence relationships as those present in the observed distribution. It is known that under i.\,i.\,d assumption, even with infinite data, there is a limit to how fine-grained a causal structure we can identify. To overcome this limitation, recent work has explored using data originating from different, related environments to learn richer causal structure. These approaches implicitly rely on the independent causal mechanisms (ICM) principle, which postulates that the mechanism giving rise to an effect given its causes and the mechanism which generates the causes do not inform or influence each other. Thus, components of the causal model can independently change from environment to environment. Despite its wide application in machine learning and causal inference, there is a lack of statistical formalization of the ICM principle and how it enables identification of richer causal structures from grouped data. Here we present new causal de Finetti theorems which offer a first statistical formalization of ICM principle and show how causal structure identification is possible from exchangeable data. Our work provides theoretical justification for a broad range of techniques leveraging multi-environment data to learn causal structure.

Motivated by the hypothesis that neural network representations encode abstract, interpretable features as linearly accessible, approximately orthogonal directions, sparse autoencoders (SAEs) have become a popular tool in interpretability. However, recent work has demonstrated phenomenology of model representations that lies outside the scope of this hypothesis, showing signatures of hierarchical, nonlinear, and multi-dimensional features. This raises the question: do SAEs represent features that possess structure at odds with their motivating hypothesis? If not, does avoiding this mismatch help identify said features and gain further insights into neural network representations? To answer these questions, we take a construction-based approach and re-contextualize the popular matching pursuits (MP) algorithm from sparse coding to design MP-SAE -- an SAE that unrolls its encoder into a sequence of residual-guided steps, allowing it to capture hierarchical and nonlinearly accessible features. Comparing this architecture with existing SAEs on a mixture of synthetic and natural data settings, we show: (i) hierarchical concepts induce conditionally orthogonal features, which existing SAEs are unable to faithfully capture, and (ii) the nonlinear encoding step of MP-SAE recovers highly meaningful features, helping us unravel shared structure in the seemingly dichotomous representation spaces of different modalities in a vision-language model, hence demonstrating the assumption that useful features are solely linearly accessible is insufficient. We also show that the sequential encoder principle of MP-SAE affords an additional benefit of adaptive sparsity at inference time, which may be of independent interest. Overall, we argue our results provide credence to the idea that interpretability should begin with the phenomenology of representations, with methods emerging from assumptions that fit it.

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

Learning representations that transfer well to diverse downstream tasks remains a central challenge in representation learning. Existing paradigms -- contrastive learning, self-supervised masking, and denoising auto-encoders -- balance this challenge with different trade-offs. We introduce the {contrastive Mutual Information Machine} (cMIM), a probabilistic framework that extends the Mutual Information Machine (MIM) with a contrastive objective. While MIM maximizes mutual information between inputs and latents and promotes clustering of codes, it falls short on discriminative tasks. cMIM addresses this gap by imposing global discriminative structure while retaining MIM's generative fidelity. Our contributions are threefold. First, we propose cMIM, a contrastive extension of MIM that removes the need for positive data augmentation and is substantially less sensitive to batch size than InfoNCE. Second, we introduce {informative embeddings}, a general technique for extracting enriched features from encoder-decoder models that boosts discriminative performance without additional training and applies broadly beyond MIM. Third, we provide empirical evidence across vision and molecular benchmarks showing that cMIM outperforms MIM and InfoNCE on classification and regression tasks while preserving competitive reconstruction quality. These results position cMIM as a unified framework for representation learning, advancing the goal of models that serve both discriminative and generative applications effectively.

Unsupervised Multiplex Graph Learning (UMGL) aims to learn node representations on various edge types without manual labeling. However, existing research overlooks a key factor: the reliability of the graph structure. Real-world data often exhibit a complex nature and contain abundant task-irrelevant noise, severely compromising UMGL's performance. Moreover, existing methods primarily rely on contrastive learning to maximize mutual information across different graphs, limiting them to multiplex graph redundant scenarios and failing to capture view-unique task-relevant information. In this paper, we focus on a more realistic and challenging task: to unsupervisedly learn a fused graph from multiple graphs that preserve sufficient task-relevant information while removing task-irrelevant noise. Specifically, our proposed Information-aware Unsupervised Multiplex Graph Fusion framework (InfoMGF) uses graph structure refinement to eliminate irrelevant noise and simultaneously maximizes view-shared and view-unique task-relevant information, thereby tackling the frontier of non-redundant multiplex graph. Theoretical analyses further guarantee the effectiveness of InfoMGF. Comprehensive experiments against various baselines on different downstream tasks demonstrate its superior performance and robustness. Surprisingly, our unsupervised method even beats the sophisticated supervised approaches. The source code and datasets are available at https://github.com/zxlearningdeep/InfoMGF.

We identify rare and visually distinctive galaxy populations by searching for structure within the learned representations of pretrained models. We show that these representations arrange galaxies by appearance in patterns beyond those needed to predict the pretraining labels. We design a clustering approach to isolate specific local patterns, revealing groups of galaxies with rare and scientifically-interesting morphologies.

How do humans learn language, and can the first language be learned at all? These fundamental questions are still hotly debated. In contemporary linguistics, there are two major schools of thought that give completely opposite answers. According to Chomsky's theory of universal grammar, language cannot be learned because children are not exposed to sufficient data in their linguistic environment. In contrast, usage-based models of language assume a profound relationship between language structure and language use. In particular, contextual mental processing and mental representations are assumed to have the cognitive capacity to capture the complexity of actual language use at all levels. The prime example is syntax, i.e., the rules by which words are assembled into larger units such as sentences. Typically, syntactic rules are expressed as sequences of word classes. However, it remains unclear whether word classes are innate, as implied by universal grammar, or whether they emerge during language acquisition, as suggested by usage-based approaches. Here, we address this issue from a machine learning and natural language processing perspective. In particular, we trained an artificial deep neural network on predicting the next word, provided sequences of consecutive words as input. Subsequently, we analyzed the emerging activation patterns in the hidden layers of the neural network. Strikingly, we find that the internal representations of nine-word input sequences cluster according to the word class of the tenth word to be predicted as output, even though the neural network did not receive any explicit information about syntactic rules or word classes during training. This surprising result suggests, that also in the human brain, abstract representational categories such as word classes may naturally emerge as a consequence of predictive coding and processing during language acquisition.

Networks have become indispensable and ubiquitous structures in many fields to model the interactions among different entities, such as friendship in social networks or protein interactions in biological graphs. A major challenge is to understand the structure and dynamics of these systems. Although networks evolve through time, most existing graph representation learning methods target only static networks. Whereas approaches have been developed for the modeling of dynamic networks, there is a lack of efficient continuous time dynamic graph representation learning methods that can provide accurate network characterization and visualization in low dimensions while explicitly accounting for prominent network characteristics such as homophily and transitivity. In this paper, we propose the Piecewise-Velocity Model (PiVeM) for the representation of continuous-time dynamic networks. It learns dynamic embeddings in which the temporal evolution of nodes is approximated by piecewise linear interpolations based on a latent distance model with piecewise constant node-specific velocities. The model allows for analytically tractable expressions of the associated Poisson process likelihood with scalable inference invariant to the number of events. We further impose a scalable Kronecker structured Gaussian Process prior to the dynamics accounting for community structure, temporal smoothness, and disentangled (uncorrelated) latent embedding dimensions optimally learned to characterize the network dynamics. We show that PiVeM can successfully represent network structure and dynamics in ultra-low two-dimensional spaces. It outperforms relevant state-of-art methods in downstream tasks such as link prediction. In summary, PiVeM enables easily interpretable dynamic network visualizations and characterizations that can further improve our understanding of the intrinsic dynamics of time-evolving networks.

Quantifying similarity between neural representations -- e.g. hidden layer activation vectors -- is a perennial problem in deep learning and neuroscience research. Existing methods compare deterministic responses (e.g. artificial networks that lack stochastic layers) or averaged responses (e.g., trial-averaged firing rates in biological data). However, these measures of _deterministic_ representational similarity ignore the scale and geometric structure of noise, both of which play important roles in neural computation. To rectify this, we generalize previously proposed shape metrics (Williams et al. 2021) to quantify differences in _stochastic_ representations. These new distances satisfy the triangle inequality, and thus can be used as a rigorous basis for many supervised and unsupervised analyses. Leveraging this novel framework, we find that the stochastic geometries of neurobiological representations of oriented visual gratings and naturalistic scenes respectively resemble untrained and trained deep network representations. Further, we are able to more accurately predict certain network attributes (e.g. training hyperparameters) from its position in stochastic (versus deterministic) shape space.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

Videos inherently represent 2D projections of a dynamic 3D world. However, our analysis suggests that video diffusion models trained solely on raw video data often fail to capture meaningful geometric-aware structure in their learned representations. To bridge this gap between video diffusion models and the underlying 3D nature of the physical world, we propose Geometry Forcing, a simple yet effective method that encourages video diffusion models to internalize latent 3D representations. Our key insight is to guide the model's intermediate representations toward geometry-aware structure by aligning them with features from a pretrained geometric foundation model. To this end, we introduce two complementary alignment objectives: Angular Alignment, which enforces directional consistency via cosine similarity, and Scale Alignment, which preserves scale-related information by regressing unnormalized geometric features from normalized diffusion representation. We evaluate Geometry Forcing on both camera view-conditioned and action-conditioned video generation tasks. Experimental results demonstrate that our method substantially improves visual quality and 3D consistency over the baseline methods. Project page: https://GeometryForcing.github.io.

Self-supervised representation learning is heavily dependent on data augmentations to specify the invariances encoded in representations. Previous work has shown that applying diverse data augmentations is crucial to downstream performance, but augmentation techniques remain under-explored. In this work, we propose a new family of local transformations based on Gaussian random fields to generate image augmentations for self-supervised representation learning. These transformations generalize the well-established affine and color transformations (translation, rotation, color jitter, etc.) and greatly increase the space of augmentations by allowing transformation parameter values to vary from pixel to pixel. The parameters are treated as continuous functions of spatial coordinates, and modeled as independent Gaussian random fields. Empirical results show the effectiveness of the new transformations for self-supervised representation learning. Specifically, we achieve a 1.7% top-1 accuracy improvement over baseline on ImageNet downstream classification, and a 3.6% improvement on out-of-distribution iNaturalist downstream classification. However, due to the flexibility of the new transformations, learned representations are sensitive to hyperparameters. While mild transformations improve representations, we observe that strong transformations can degrade the structure of an image, indicating that balancing the diversity and strength of augmentations is important for improving generalization of learned representations.

Solving image-to-3D from a single view is an ill-posed problem, and current neural reconstruction methods addressing it through diffusion models still rely on scene-specific optimization, constraining their generalization capability. To overcome the limitations of existing approaches regarding generalization and consistency, we introduce a novel neural rendering technique. Our approach employs the signed distance function as the surface representation and incorporates generalizable priors through geometry-encoding volumes and HyperNetworks. Specifically, our method builds neural encoding volumes from generated multi-view inputs. We adjust the weights of the SDF network conditioned on an input image at test-time to allow model adaptation to novel scenes in a feed-forward manner via HyperNetworks. To mitigate artifacts derived from the synthesized views, we propose the use of a volume transformer module to improve the aggregation of image features instead of processing each viewpoint separately. Through our proposed method, dubbed as Hyper-VolTran, we avoid the bottleneck of scene-specific optimization and maintain consistency across the images generated from multiple viewpoints. Our experiments show the advantages of our proposed approach with consistent results and rapid generation.

Reconstructing dynamic 3D scenes from 2D images and generating diverse views over time is challenging due to scene complexity and temporal dynamics. Despite advancements in neural implicit models, limitations persist: (i) Inadequate Scene Structure: Existing methods struggle to reveal the spatial and temporal structure of dynamic scenes from directly learning the complex 6D plenoptic function. (ii) Scaling Deformation Modeling: Explicitly modeling scene element deformation becomes impractical for complex dynamics. To address these issues, we consider the spacetime as an entirety and propose to approximate the underlying spatio-temporal 4D volume of a dynamic scene by optimizing a collection of 4D primitives, with explicit geometry and appearance modeling. Learning to optimize the 4D primitives enables us to synthesize novel views at any desired time with our tailored rendering routine. Our model is conceptually simple, consisting of a 4D Gaussian parameterized by anisotropic ellipses that can rotate arbitrarily in space and time, as well as view-dependent and time-evolved appearance represented by the coefficient of 4D spherindrical harmonics. This approach offers simplicity, flexibility for variable-length video and end-to-end training, and efficient real-time rendering, making it suitable for capturing complex dynamic scene motions. Experiments across various benchmarks, including monocular and multi-view scenarios, demonstrate our 4DGS model's superior visual quality and efficiency.

Self-supervised learning on large-scale multi-modal datasets allows learning semantically meaningful embeddings in a joint multi-modal representation space without relying on human annotations. These joint embeddings enable zero-shot cross-modal tasks like retrieval and classification. However, these methods often struggle to generalize well on out-of-domain data as they ignore the semantic structure present in modality-specific embeddings. In this context, we propose a novel Semantic-Structure-Preserving Consistency approach to improve generalizability by preserving the modality-specific relationships in the joint embedding space. To capture modality-specific semantic relationships between samples, we propose to learn multiple anchors and represent the multifaceted relationship between samples with respect to their relationship with these anchors. To assign multiple anchors to each sample, we propose a novel Multi-Assignment Sinkhorn-Knopp algorithm. Our experimentation demonstrates that our proposed approach learns semantically meaningful anchors in a self-supervised manner. Furthermore, our evaluation on MSR-VTT and YouCook2 datasets demonstrates that our proposed multi-anchor assignment based solution achieves state-of-the-art performance and generalizes to both inand out-of-domain datasets. Code: https://github.com/Swetha5/Multi_Sinkhorn_Knopp

Recent advances in Vision Transformers (ViTs) and State Space Models (SSMs) have challenged the dominance of Convolutional Neural Networks (CNNs) in computer vision. ViTs excel at capturing global context, and SSMs like Mamba offer linear complexity for long sequences, yet they do not capture fine-grained local features as effectively as CNNs. Conversely, CNNs possess strong inductive biases for local features but lack the global reasoning capabilities of transformers and Mamba. To bridge this gap, we introduce VCMamba, a novel vision backbone that integrates the strengths of CNNs and multi-directional Mamba SSMs. VCMamba employs a convolutional stem and a hierarchical structure with convolutional blocks in its early stages to extract rich local features. These convolutional blocks are then processed by later stages incorporating multi-directional Mamba blocks designed to efficiently model long-range dependencies and global context. This hybrid design allows for superior feature representation while maintaining linear complexity with respect to image resolution. We demonstrate VCMamba's effectiveness through extensive experiments on ImageNet-1K classification and ADE20K semantic segmentation. Our VCMamba-B achieves 82.6% top-1 accuracy on ImageNet-1K, surpassing PlainMamba-L3 by 0.3% with 37% fewer parameters, and outperforming Vision GNN-B by 0.3% with 64% fewer parameters. Furthermore, VCMamba-B obtains 47.1 mIoU on ADE20K, exceeding EfficientFormer-L7 by 2.0 mIoU while utilizing 62% fewer parameters. Code is available at https://github.com/Wertyuui345/VCMamba.

What fundamental properties of reward functions enable efficient sparse-reward reinforcement learning? We address this question through the lens of low-rank structure in reward matrices, showing that such structure induces a sharp transition from exponential to polynomial sample complexity, the first result of this kind for sparse-reward RL. We introduce Policy-Aware Matrix Completion (PAMC), which connects matrix completion theory with reinforcement learning via a new analysis of policy-dependent sampling. Our framework provides: (i) impossibility results for general sparse reward observation, (ii) reward-free representation learning from dynamics, (iii) distribution-free confidence sets via conformal prediction, and (iv) robust completion guarantees that degrade gracefully when low-rank structure is only approximate. Empirically, we conduct a pre-registered evaluation across 100 systematically sampled domains, finding exploitable structure in over half. PAMC improves sample efficiency by factors between 1.6 and 2.1 compared to strong exploration, structured, and representation-learning baselines, while adding only about 20 percent computational overhead.These results establish structural reward learning as a promising new paradigm, with immediate implications for robotics, healthcare, and other safety-critical, sample-expensive applications.

Informally, the 'linear representation hypothesis' is the idea that high-level concepts are represented linearly as directions in some representation space. In this paper, we address two closely related questions: What does "linear representation" actually mean? And, how do we make sense of geometric notions (e.g., cosine similarity or projection) in the representation space? To answer these, we use the language of counterfactuals to give two formalizations of "linear representation", one in the output (word) representation space, and one in the input (sentence) space. We then prove these connect to linear probing and model steering, respectively. To make sense of geometric notions, we use the formalization to identify a particular (non-Euclidean) inner product that respects language structure in a sense we make precise. Using this causal inner product, we show how to unify all notions of linear representation. In particular, this allows the construction of probes and steering vectors using counterfactual pairs. Experiments with LLaMA-2 demonstrate the existence of linear representations of concepts, the connection to interpretation and control, and the fundamental role of the choice of inner product.

A well-designed vectorized representation is crucial for the learning systems natively based on 3D Gaussian Splatting. While 3DGS enables efficient and explicit 3D reconstruction, its parameter-based representation remains hard to learn as features, especially for neural-network-based models. Directly feeding raw Gaussian parameters into learning frameworks fails to address the non-unique and heterogeneous nature of the Gaussian parameterization, yielding highly data-dependent models. This challenge motivates us to explore a more principled approach to represent 3D Gaussian Splatting in neural networks that preserves the underlying color and geometric structure while enforcing unique mapping and channel homogeneity. In this paper, we propose an embedding representation of 3DGS based on continuous submanifold fields that encapsulate the intrinsic information of Gaussian primitives, thereby benefiting the learning of 3DGS.

Large Language Models (LLMs) are increasingly applied for Process Modeling (PMo) tasks such as Process Model Generation (PMG). To support these tasks, researchers have introduced a variety of Process Model Representations (PMRs) that serve as model abstractions or generation targets. However, these PMRs differ widely in structure, complexity, and usability, and have never been systematically compared. Moreover, recent PMG approaches rely on distinct evaluation strategies and generation techniques, making comparison difficult. This paper presents the first empirical study that evaluates multiple PMRs in the context of PMo with LLMs. We introduce the PMo Dataset, a new dataset containing 55 process descriptions paired with models in nine different PMRs. We evaluate PMRs along two dimensions: suitability for LLM-based PMo and performance on PMG. Mermaid achieves the highest overall score across six PMo criteria, whereas BPMN text delivers the best PMG results in terms of process element similarity.

Modeling temporal characteristics plays a significant role in the representation learning of audio waveform. We propose Contrastive Long-form Language-Audio Pretraining (CoLLAP) to significantly extend the perception window for both the input audio (up to 5 minutes) and the language descriptions (exceeding 250 words), while enabling contrastive learning across modalities and temporal dynamics. Leveraging recent Music-LLMs to generate long-form music captions for full-length songs, augmented with musical temporal structures, we collect 51.3K audio-text pairs derived from the large-scale AudioSet training dataset, where the average audio length reaches 288 seconds. We propose a novel contrastive learning architecture that fuses language representations with structured audio representations by segmenting each song into clips and extracting their embeddings. With an attention mechanism, we capture multimodal temporal correlations, allowing the model to automatically weigh and enhance the final fusion score for improved contrastive alignment. Finally, we develop two variants of the CoLLAP model with different types of backbone language models. Through comprehensive experiments on multiple long-form music-text retrieval datasets, we demonstrate consistent performance improvement in retrieval accuracy compared with baselines. We also show the pretrained CoLLAP models can be transferred to various music information retrieval tasks, with heterogeneous long-form multimodal contexts.

Understanding biological processes, drug development, and biotechnological advancements requires detailed analysis of protein structures and sequences, a task in protein research that is inherently complex and time-consuming when performed manually. To streamline this process, we introduce ProteinGPT, a state-of-the-art multi-modal protein chat system, that allows users to upload protein sequences and/or structures for comprehensive protein analysis and responsive inquiries. ProteinGPT seamlessly integrates protein sequence and structure encoders with linear projection layers for precise representation adaptation, coupled with a large language model (LLM) to generate accurate and contextually relevant responses. To train ProteinGPT, we construct a large-scale dataset of 132,092 proteins with annotations, and optimize the instruction-tuning process using GPT-4o. This innovative system ensures accurate alignment between the user-uploaded data and prompts, simplifying protein analysis. Experiments show that ProteinGPT can produce promising responses to proteins and their corresponding questions.

Video representation is a long-standing problem that is crucial for various down-stream tasks, such as tracking,depth prediction,segmentation,view synthesis,and editing. However, current methods either struggle to model complex motions due to the absence of 3D structure or rely on implicit 3D representations that are ill-suited for manipulation tasks. To address these challenges, we introduce a novel explicit 3D representation-video Gaussian representation -- that embeds a video into 3D Gaussians. Our proposed representation models video appearance in a 3D canonical space using explicit Gaussians as proxies and associates each Gaussian with 3D motions for video motion. This approach offers a more intrinsic and explicit representation than layered atlas or volumetric pixel matrices. To obtain such a representation, we distill 2D priors, such as optical flow and depth, from foundation models to regularize learning in this ill-posed setting. Extensive applications demonstrate the versatility of our new video representation. It has been proven effective in numerous video processing tasks, including tracking, consistent video depth and feature refinement, motion and appearance editing, and stereoscopic video generation. Project page: https://sunyangtian.github.io/spatter_a_video_web/

Visual Model-Based Reinforcement Learning (MBRL) promises to encapsulate agent's knowledge about the underlying dynamics of the environment, enabling learning a world model as a useful planner. However, top MBRL agents such as Dreamer often struggle with visual pixel-based inputs in the presence of exogenous or irrelevant noise in the observation space, due to failure to capture task-specific features while filtering out irrelevant spatio-temporal details. To tackle this problem, we apply a spatio-temporal masking strategy, a bisimulation principle, combined with latent reconstruction, to capture endogenous task-specific aspects of the environment for world models, effectively eliminating non-essential information. Joint training of representations, dynamics, and policy often leads to instabilities. To further address this issue, we develop a Hybrid Recurrent State-Space Model (HRSSM) structure, enhancing state representation robustness for effective policy learning. Our empirical evaluation demonstrates significant performance improvements over existing methods in a range of visually complex control tasks such as Maniskill gu2023maniskill2 with exogenous distractors from the Matterport environment. Our code is avaliable at https://github.com/bit1029public/HRSSM.

RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA folding model. Understanding the specific local structures (i.e., "motifs") that contribute to undesignability is crucial for refining RNA folding models and determining the limits of RNA designability. Despite its importance, this problem has received very little attention, and previous efforts are neither scalable nor interpretable. We develop a new theoretical framework for motif (un-)designability, and design scalable and interpretable algorithms to identify minimal undesignable motifs within a given RNA secondary structure. Our approach establishes motif undesignability by searching for rival motifs, rather than exhaustively enumerating all (partial) sequences that could potentially fold into the motif. Furthermore, we exploit rotational invariance in RNA structures to detect, group, and reuse equivalent motifs and to construct a database of unique minimal undesignable motifs. To achieve that, we propose a loop-pair graph representation for motifs and a recursive graph isomorphism algorithm for motif equivalence. Our algorithms successfully identify 24 unique minimal undesignable motifs among 18 undesignable puzzles from the Eterna100 benchmark. Surprisingly, we also find over 350 unique minimal undesignable motifs and 663 undesignable native structures in the ArchiveII dataset, drawn from a diverse set of RNA families. Our source code is available at https://github.com/shanry/RNA-Undesign and our web server is available at http://linearfold.org/motifs.

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e.~atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.

Language models pretrained on large collections of tabular data have demonstrated their effectiveness in several downstream tasks. However, many of these models do not take into account the row/column permutation invariances, hierarchical structure, etc. that exist in tabular data. To alleviate these limitations, we propose HYTREL, a tabular language model, that captures the permutation invariances and three more structural properties of tabular data by using hypergraphs - where the table cells make up the nodes and the cells occurring jointly together in each row, column, and the entire table are used to form three different types of hyperedges. We show that HYTREL is maximally invariant under certain conditions for tabular data, i.e., two tables obtain the same representations via HYTREL iff the two tables are identical up to permutations. Our empirical results demonstrate that HYTREL consistently outperforms other competitive baselines on four downstream tasks with minimal pretraining, illustrating the advantages of incorporating the inductive biases associated with tabular data into the representations. Finally, our qualitative analyses showcase that HYTREL can assimilate the table structures to generate robust representations for the cells, rows, columns, and the entire table.

Symmetry learning has proven to be an effective approach for extracting the hidden structure of data, with the concept of equivariance relation playing the central role. However, most of the current studies are built on architectural theory and corresponding assumptions on the form of data. We propose Neural Fourier Transform (NFT), a general framework of learning the latent linear action of the group without assuming explicit knowledge of how the group acts on data. We present the theoretical foundations of NFT and show that the existence of a linear equivariant feature, which has been assumed ubiquitously in equivariance learning, is equivalent to the existence of a group invariant kernel on the dataspace. We also provide experimental results to demonstrate the application of NFT in typical scenarios with varying levels of knowledge about the acting group.

Understanding and mapping a new environment are core abilities of any autonomously navigating agent. While classical robotics usually estimates maps in a stand-alone manner with SLAM variants, which maintain a topological or metric representation, end-to-end learning of navigation keeps some form of memory in a neural network. Networks are typically imbued with inductive biases, which can range from vectorial representations to birds-eye metric tensors or topological structures. In this work, we propose to structure neural networks with two neural implicit representations, which are learned dynamically during each episode and map the content of the scene: (i) the Semantic Finder predicts the position of a previously seen queried object; (ii) the Occupancy and Exploration Implicit Representation encapsulates information about explored area and obstacles, and is queried with a novel global read mechanism which directly maps from function space to a usable embedding space. Both representations are leveraged by an agent trained with Reinforcement Learning (RL) and learned online during each episode. We evaluate the agent on Multi-Object Navigation and show the high impact of using neural implicit representations as a memory source.

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.

Recent research demonstrates the effectiveness of using pretrained language models (PLM) to improve dense retrieval and multilingual dense retrieval. In this work, we present a simple but effective monolingual pretraining task called contrastive context prediction~(CCP) to learn sentence representation by modeling sentence level contextual relation. By pushing the embedding of sentences in a local context closer and pushing random negative samples away, different languages could form isomorphic structure, then sentence pairs in two different languages will be automatically aligned. Our experiments show that model collapse and information leakage are very easy to happen during contrastive training of language model, but language-specific memory bank and asymmetric batch normalization operation play an essential role in preventing collapsing and information leakage, respectively. Besides, a post-processing for sentence embedding is also very effective to achieve better retrieval performance. On the multilingual sentence retrieval task Tatoeba, our model achieves new SOTA results among methods without using bilingual data. Our model also shows larger gain on Tatoeba when transferring between non-English pairs. On two multi-lingual query-passage retrieval tasks, XOR Retrieve and Mr.TYDI, our model even achieves two SOTA results in both zero-shot and supervised setting among all pretraining models using bilingual data.

Time-series representation learning is a fundamental task for time-series analysis. While significant progress has been made to achieve accurate representations for downstream applications, the learned representations often lack interpretability and do not expose semantic meanings. Different from previous efforts on the entangled feature space, we aim to extract the semantic-rich temporal correlations in the latent interpretable factorized representation of the data. Motivated by the success of disentangled representation learning in computer vision, we study the possibility of learning semantic-rich time-series representations, which remains unexplored due to three main challenges: 1) sequential data structure introduces complex temporal correlations and makes the latent representations hard to interpret, 2) sequential models suffer from KL vanishing problem, and 3) interpretable semantic concepts for time-series often rely on multiple factors instead of individuals. To bridge the gap, we propose Disentangle Time Series (DTS), a novel disentanglement enhancement framework for sequential data. Specifically, to generate hierarchical semantic concepts as the interpretable and disentangled representation of time-series, DTS introduces multi-level disentanglement strategies by covering both individual latent factors and group semantic segments. We further theoretically show how to alleviate the KL vanishing problem: DTS introduces a mutual information maximization term, while preserving a heavier penalty on the total correlation and the dimension-wise KL to keep the disentanglement property. Experimental results on various real-world benchmark datasets demonstrate that the representations learned by DTS achieve superior performance in downstream applications, with high interpretability of semantic concepts.

While understanding the knowledge boundaries of LLMs is crucial to prevent hallucination, research on knowledge boundaries of LLMs has predominantly focused on English. In this work, we present the first study to analyze how LLMs recognize knowledge boundaries across different languages by probing their internal representations when processing known and unknown questions in multiple languages. Our empirical studies reveal three key findings: 1) LLMs' perceptions of knowledge boundaries are encoded in the middle to middle-upper layers across different languages. 2) Language differences in knowledge boundary perception follow a linear structure, which motivates our proposal of a training-free alignment method that effectively transfers knowledge boundary perception ability across languages, thereby helping reduce hallucination risk in low-resource languages; 3) Fine-tuning on bilingual question pair translation further enhances LLMs' recognition of knowledge boundaries across languages. Given the absence of standard testbeds for cross-lingual knowledge boundary analysis, we construct a multilingual evaluation suite comprising three representative types of knowledge boundary data. Our code and datasets are publicly available at https://github.com/DAMO-NLP-SG/LLM-Multilingual-Knowledge-Boundaries.

Current visual foundation models are trained purely on unstructured 2D data, limiting their understanding of 3D structure of objects and scenes. In this work, we show that fine-tuning on 3D-aware data improves the quality of emerging semantic features. We design a method to lift semantic 2D features into an efficient 3D Gaussian representation, which allows us to re-render them for arbitrary views. Using the rendered 3D-aware features, we design a fine-tuning strategy to transfer such 3D awareness into a 2D foundation model. We demonstrate that models fine-tuned in that way produce features that readily improve downstream task performance in semantic segmentation and depth estimation through simple linear probing. Notably, though fined-tuned on a single indoor dataset, the improvement is transferable to a variety of indoor datasets and out-of-domain datasets. We hope our study encourages the community to consider injecting 3D awareness when training 2D foundation models. Project page: https://ywyue.github.io/FiT3D.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

Precise recognition, editing, and generation of molecules are essential prerequisites for both chemists and AI systems tackling various chemical tasks. We present MolLangBench, a comprehensive benchmark designed to evaluate fundamental molecule-language interface tasks: language-prompted molecular structure recognition, editing, and generation. To ensure high-quality, unambiguous, and deterministic outputs, we construct the recognition tasks using automated cheminformatics tools, and curate editing and generation tasks through rigorous expert annotation and validation. MolLangBench supports the evaluation of models that interface language with different molecular representations, including linear strings, molecular images, and molecular graphs. Evaluations of state-of-the-art models reveal significant limitations: the strongest model (o3) achieves 79.2% and 78.5% accuracy on recognition and editing tasks, which are intuitively simple for humans, and performs even worse on the generation task, reaching only 29.0% accuracy. These results highlight the shortcomings of current AI systems in handling even preliminary molecular recognition and manipulation tasks. We hope MolLangBench will catalyze further research toward more effective and reliable AI systems for chemical applications.

Understanding how humans conceptualize and categorize natural objects offers critical insights into perception and cognition. With the advent of Large Language Models (LLMs), a key question arises: can these models develop human-like object representations from linguistic and multimodal data? In this study, we combined behavioral and neuroimaging analyses to explore the relationship between object concept representations in LLMs and human cognition. We collected 4.7 million triplet judgments from LLMs and Multimodal LLMs (MLLMs) to derive low-dimensional embeddings that capture the similarity structure of 1,854 natural objects. The resulting 66-dimensional embeddings were stable, predictive, and exhibited semantic clustering similar to human mental representations. Remarkably, the dimensions underlying these embeddings were interpretable, suggesting that LLMs and MLLMs develop human-like conceptual representations of objects. Further analysis showed strong alignment between model embeddings and neural activity patterns in brain regions such as EBA, PPA, RSC, and FFA. This provides compelling evidence that the object representations in LLMs, while not identical to human ones, share fundamental similarities that reflect key aspects of human conceptual knowledge. Our findings advance the understanding of machine intelligence and inform the development of more human-like artificial cognitive systems.

Causal abstraction is a promising theoretical framework for explainable artificial intelligence that defines when an interpretable high-level causal model is a faithful simplification of a low-level deep learning system. However, existing causal abstraction methods have two major limitations: they require a brute-force search over alignments between the high-level model and the low-level one, and they presuppose that variables in the high-level model will align with disjoint sets of neurons in the low-level one. In this paper, we present distributed alignment search (DAS), which overcomes these limitations. In DAS, we find the alignment between high-level and low-level models using gradient descent rather than conducting a brute-force search, and we allow individual neurons to play multiple distinct roles by analyzing representations in non-standard bases-distributed representations. Our experiments show that DAS can discover internal structure that prior approaches miss. Overall, DAS removes previous obstacles to conducting causal abstraction analyses and allows us to find conceptual structure in trained neural nets.

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

Representation learning has become an invaluable approach for learning from symbolic data such as text and graphs. However, while complex symbolic datasets often exhibit a latent hierarchical structure, state-of-the-art methods typically learn embeddings in Euclidean vector spaces, which do not account for this property. For this purpose, we introduce a new approach for learning hierarchical representations of symbolic data by embedding them into hyperbolic space -- or more precisely into an n-dimensional Poincar\'e ball. Due to the underlying hyperbolic geometry, this allows us to learn parsimonious representations of symbolic data by simultaneously capturing hierarchy and similarity. We introduce an efficient algorithm to learn the embeddings based on Riemannian optimization and show experimentally that Poincar\'e embeddings outperform Euclidean embeddings significantly on data with latent hierarchies, both in terms of representation capacity and in terms of generalization ability.

Sparse Autoencoders (SAEs) have emerged as a popular tool for interpreting the hidden states of large language models (LLMs). By learning to reconstruct activations from a sparse bottleneck layer, SAEs discover interpretable features from the high-dimensional internal representations of LLMs. Despite their popularity with language models, SAEs remain understudied in the visual domain. In this work, we provide an extensive evaluation the representational power of SAEs for vision models using a broad range of image-based tasks. Our experimental results demonstrate that SAE features are semantically meaningful, improve out-of-distribution generalization, and enable controllable generation across three vision model architectures: vision embedding models, multi-modal LMMs and diffusion models. In vision embedding models, we find that learned SAE features can be used for OOD detection and provide evidence that they recover the ontological structure of the underlying model. For diffusion models, we demonstrate that SAEs enable semantic steering through text encoder manipulation and develop an automated pipeline for discovering human-interpretable attributes. Finally, we conduct exploratory experiments on multi-modal LLMs, finding evidence that SAE features reveal shared representations across vision and language modalities. Our study provides a foundation for SAE evaluation in vision models, highlighting their strong potential improving interpretability, generalization, and steerability in the visual domain.

Implicit Neural Representations (INRs) have recently shown impressive results, but their fundamental capacity, implicit biases, and scaling behavior remain poorly understood. We investigate the performance of diverse INRs across a suite of 2D and 3D real and synthetic signals with varying effective bandwidth, as well as both overfitting and generalization tasks including tomography, super-resolution, and denoising. By stratifying performance according to model size as well as signal type and bandwidth, our results shed light on how different INR and grid representations allocate their capacity. We find that, for most tasks and signals, a simple regularized grid with interpolation trains faster and to higher quality than any INR with the same number of parameters. We also find limited settings where INRs outperform grids -- namely fitting signals with underlying lower-dimensional structure such as shape contours -- to guide future use of INRs towards the most advantageous applications. Code and synthetic signals used in our analysis are available at https://github.com/voilalab/INR-benchmark.

Protein language models (PLMs) have emerged as powerful tools to detect complex patterns of protein sequences. However, the capability of PLMs to fully capture information on protein sequences might be limited by focusing on single pre-training tasks. Although adding data modalities or supervised objectives can improve the performance of PLMs, pre-training often remains focused on denoising corrupted sequences. To push the boundaries of PLMs, our research investigated a multi-task pre-training strategy. We developed Ankh3, a model jointly optimized on two objectives: masked language modeling with multiple masking probabilities and protein sequence completion relying only on protein sequences as input. This multi-task pre-training demonstrated that PLMs can learn richer and more generalizable representations solely from protein sequences. The results demonstrated improved performance in downstream tasks, such as secondary structure prediction, fluorescence, GB1 fitness, and contact prediction. The integration of multiple tasks gave the model a more comprehensive understanding of protein properties, leading to more robust and accurate predictions.

Multi-vector models, such as ColBERT, are a significant advancement in neural information retrieval (IR), delivering state-of-the-art performance by representing queries and documents by multiple contextualized token-level embeddings. However, this increased representation size introduces considerable storage and computational overheads which have hindered widespread adoption in practice. A common approach to mitigate this overhead is to cluster the model's frozen vectors, but this strategy's effectiveness is fundamentally limited by the intrinsic clusterability of these embeddings. In this work, we introduce CRISP (Clustered Representations with Intrinsic Structure Pruning), a novel multi-vector training method which learns inherently clusterable representations directly within the end-to-end training process. By integrating clustering into the training phase rather than imposing it post-hoc, CRISP significantly outperforms post-hoc clustering at all representation sizes, as well as other token pruning methods. On the BEIR retrieval benchmarks, CRISP achieves a significant rate of ~3x reduction in the number of vectors while outperforming the original unpruned model. This indicates that learned clustering effectively denoises the model by filtering irrelevant information, thereby generating more robust multi-vector representations. With more aggressive clustering, CRISP achieves an 11x reduction in the number of vectors with only a 3.6% quality loss.

Table Structure Recognition (TSR) is vital for various downstream tasks like information retrieval, table reconstruction, and document understanding. While most state-of-the-art (SOTA) research predominantly focuses on TSR in English documents, the need for similar capabilities in other languages is evident, considering the global diversity of data. Moreover, creating substantial labeled data in non-English languages and training these SOTA models from scratch is costly and time-consuming. We propose TSR as a language-agnostic cell arrangement prediction and introduce SPRINT, Script-agnostic Structure Recognition in Tables. SPRINT uses recently introduced Optimized Table Structure Language (OTSL) sequences to predict table structures. We show that when coupled with a pre-trained table grid estimator, SPRINT can improve the overall tree edit distance-based similarity structure scores of tables even for non-English documents. We experimentally evaluate our performance across benchmark TSR datasets including PubTabNet, FinTabNet, and PubTables-1M. Our findings reveal that SPRINT not only matches SOTA models in performance on standard datasets but also demonstrates lower latency. Additionally, SPRINT excels in accurately identifying table structures in non-English documents, surpassing current leading models by showing an absolute average increase of 11.12%. We also present an algorithm for converting valid OTSL predictions into a widely used HTML-based table representation. To encourage further research, we release our code and Multilingual Scanned and Scene Table Structure Recognition Dataset, MUSTARD labeled with OTSL sequences for 1428 tables in thirteen languages encompassing several scripts at https://github.com/IITB-LEAP-OCR/SPRINT

Transformer models underpin many recent advances in practical machine learning applications, yet understanding their internal behavior continues to elude researchers. Given the size and complexity of these models, forming a comprehensive picture of their inner workings remains a significant challenge. To this end, we set out to understand small transformer models in a more tractable setting: that of solving mazes. In this work, we focus on the abstractions formed by these models and find evidence for the consistent emergence of structured internal representations of maze topology and valid paths. We demonstrate this by showing that the residual stream of only a single token can be linearly decoded to faithfully reconstruct the entire maze. We also find that the learned embeddings of individual tokens have spatial structure. Furthermore, we take steps towards deciphering the circuity of path-following by identifying attention heads (dubbed adjacency heads), which are implicated in finding valid subsequent tokens.

Graph representation learning is fundamental for analyzing graph-structured data. Exploring invariant graph representations remains a challenge for most existing graph representation learning methods. In this paper, we propose a cross-view graph consistency learning (CGCL) method that learns invariant graph representations for link prediction. First, two complementary augmented views are derived from an incomplete graph structure through a bidirectional graph structure augmentation scheme. This augmentation scheme mitigates the potential information loss that is commonly associated with various data augmentation techniques involving raw graph data, such as edge perturbation, node removal, and attribute masking. Second, we propose a CGCL model that can learn invariant graph representations. A cross-view training scheme is proposed to train the proposed CGCL model. This scheme attempts to maximize the consistency information between one augmented view and the graph structure reconstructed from the other augmented view. Furthermore, we offer a comprehensive theoretical CGCL analysis. This paper empirically and experimentally demonstrates the effectiveness of the proposed CGCL method, achieving competitive results on graph datasets in comparisons with several state-of-the-art algorithms.

The goal of knowledge graph completion (KGC) is to predict missing links in a KG using trained facts that are already known. In recent, pre-trained language model (PLM) based methods that utilize both textual and structural information are emerging, but their performances lag behind state-of-the-art (SOTA) structure-based methods or some methods lose their inductive inference capabilities in the process of fusing structure embedding to text encoder. In this paper, we propose a novel method to effectively unify structure information and language semantics without losing the power of inductive reasoning. We adopt entity anchors and these anchors and textual description of KG elements are fed together into the PLM-based encoder to learn unified representations. In addition, the proposed method utilizes additional random negative samples which can be reused in the each mini-batch during contrastive learning to learn a generalized entity representations. We verify the effectiveness of the our proposed method through various experiments and analysis. The experimental results on standard benchmark widely used in link prediction task show that the proposed model outperforms existing the SOTA KGC models. Especially, our method show the largest performance improvement on FB15K-237, which is competitive to the SOTA of structure-based KGC methods.

We present ReCAT, a recursive composition augmented Transformer that is able to explicitly model hierarchical syntactic structures of raw texts without relying on gold trees during both learning and inference. Existing research along this line restricts data to follow a hierarchical tree structure and thus lacks inter-span communications. To overcome the problem, we propose a novel contextual inside-outside (CIO) layer that learns contextualized representations of spans through bottom-up and top-down passes, where a bottom-up pass forms representations of high-level spans by composing low-level spans, while a top-down pass combines information inside and outside a span. By stacking several CIO layers between the embedding layer and the attention layers in Transformer, the ReCAT model can perform both deep intra-span and deep inter-span interactions, and thus generate multi-grained representations fully contextualized with other spans. Moreover, the CIO layers can be jointly pre-trained with Transformers, making ReCAT enjoy scaling ability, strong performance, and interpretability at the same time. We conduct experiments on various sentence-level and span-level tasks. Evaluation results indicate that ReCAT can significantly outperform vanilla Transformer models on all span-level tasks and baselines that combine recursive networks with Transformers on natural language inference tasks. More interestingly, the hierarchical structures induced by ReCAT exhibit strong consistency with human-annotated syntactic trees, indicating good interpretability brought by the CIO layers.

Estimating a dense depth map from a single view is geometrically ill-posed, and state-of-the-art methods rely on learning depth's relation with visual appearance using deep neural networks. On the other hand, Structure from Motion (SfM) leverages multi-view constraints to produce very accurate but sparse maps, as matching across images is typically limited by locally discriminative texture. In this work, we combine the strengths of both approaches by proposing a novel test-time refinement (TTR) method, denoted as SfM-TTR, that boosts the performance of single-view depth networks at test time using SfM multi-view cues. Specifically, and differently from the state of the art, we use sparse SfM point clouds as test-time self-supervisory signal, fine-tuning the network encoder to learn a better representation of the test scene. Our results show how the addition of SfM-TTR to several state-of-the-art self-supervised and supervised networks improves significantly their performance, outperforming previous TTR baselines mainly based on photometric multi-view consistency. The code is available at https://github.com/serizba/SfM-TTR.

Graph structure learning aims to learn connectivity in a graph from data. It is particularly important for many computer vision related tasks since no explicit graph structure is available for images for most cases. A natural way to construct a graph among images is to treat each image as a node and assign pairwise image similarities as weights to corresponding edges. It is well known that pairwise similarities between images are sensitive to the noise in feature representations, leading to unreliable graph structures. We address this problem from the viewpoint of statistical tests. By viewing the feature vector of each node as an independent sample, the decision of whether creating an edge between two nodes based on their similarity in feature representation can be thought as a {it single} statistical test. To improve the robustness in the decision of creating an edge, multiple samples are drawn and integrated by {it multiple} statistical tests to generate a more reliable similarity measure, consequentially more reliable graph structure. The corresponding elegant matrix form named B-Attention is designed for efficiency. The effectiveness of multiple tests for graph structure learning is verified both theoretically and empirically on multiple clustering and ReID benchmark datasets. Source codes are available at https://github.com/Thomas-wyh/B-Attention.

Devising augmentations for graph contrastive learning is challenging due to their irregular structure, drastic distribution shifts, and nonequivalent feature spaces across datasets. We introduce LG2AR, Learning Graph Augmentations to Learn Graph Representations, which is an end-to-end automatic graph augmentation framework that helps encoders learn generalizable representations on both node and graph levels. LG2AR consists of a probabilistic policy that learns a distribution over augmentations and a set of probabilistic augmentation heads that learn distributions over augmentation parameters. We show that LG2AR achieves state-of-the-art results on 18 out of 20 graph-level and node-level benchmarks compared to previous unsupervised models under both linear and semi-supervised evaluation protocols. The source code will be released here: https://github.com/kavehhassani/lg2ar

Recent advancements in video autoencoders (Video AEs) have significantly improved the quality and efficiency of video generation. In this paper, we propose a novel and compact video autoencoder, VidTwin, that decouples video into two distinct latent spaces: Structure latent vectors, which capture overall content and global movement, and Dynamics latent vectors, which represent fine-grained details and rapid movements. Specifically, our approach leverages an Encoder-Decoder backbone, augmented with two submodules for extracting these latent spaces, respectively. The first submodule employs a Q-Former to extract low-frequency motion trends, followed by downsampling blocks to remove redundant content details. The second averages the latent vectors along the spatial dimension to capture rapid motion. Extensive experiments show that VidTwin achieves a high compression rate of 0.20% with high reconstruction quality (PSNR of 28.14 on the MCL-JCV dataset), and performs efficiently and effectively in downstream generative tasks. Moreover, our model demonstrates explainability and scalability, paving the way for future research in video latent representation and generation. Our code has been released at https://github.com/microsoft/VidTok/tree/main/vidtwin.

Contrastive Language Image Pre-training (CLIP) has recently demonstrated success across various tasks due to superior feature representation empowered by image-text contrastive learning. However, the instance discrimination method used by CLIP can hardly encode the semantic structure of training data. To handle this limitation, cluster discrimination has been proposed through iterative cluster assignment and classification. Nevertheless, most cluster discrimination approaches only define a single pseudo-label for each image, neglecting multi-label signals in the image. In this paper, we propose a novel Multi-Label Cluster Discrimination method named MLCD to enhance representation learning. In the clustering step, we first cluster the large-scale LAION-400M dataset into one million centers based on off-the-shelf embedding features. Considering that natural images frequently contain multiple visual objects or attributes, we select the multiple closest centers as auxiliary class labels. In the discrimination step, we design a novel multi-label classification loss, which elegantly separates losses from positive classes and negative classes, and alleviates ambiguity on decision boundary. We validate the proposed multi-label cluster discrimination method with experiments on different scales of models and pre-training datasets. Experimental results show that our method achieves state-of-the-art performance on multiple downstream tasks including linear probe, zero-shot classification, and image-text retrieval.

Effective and efficient tokenization plays an important role in image representation and generation. Conventional methods, constrained by uniform 2D/1D grid tokenization, are inflexible to represent regions with varying shapes and textures and at different locations, limiting their efficacy of feature representation. In this work, we propose GPSToken, a novel Gaussian Parameterized Spatially-adaptive Tokenization framework, to achieve non-uniform image tokenization by leveraging parametric 2D Gaussians to dynamically model the shape, position, and textures of different image regions. We first employ an entropy-driven algorithm to partition the image into texture-homogeneous regions of variable sizes. Then, we parameterize each region as a 2D Gaussian (mean for position, covariance for shape) coupled with texture features. A specialized transformer is trained to optimize the Gaussian parameters, enabling continuous adaptation of position/shape and content-aware feature extraction. During decoding, Gaussian parameterized tokens are reconstructed into 2D feature maps through a differentiable splatting-based renderer, bridging our adaptive tokenization with standard decoders for end-to-end training. GPSToken disentangles spatial layout (Gaussian parameters) from texture features to enable efficient two-stage generation: structural layout synthesis using lightweight networks, followed by structure-conditioned texture generation. Experiments demonstrate the state-of-the-art performance of GPSToken, which achieves rFID and FID scores of 0.65 and 1.50 on image reconstruction and generation tasks using 128 tokens, respectively. Codes and models of GPSToken can be found at https://github.com/xtudbxk/GPSToken{https://github.com/xtudbxk/GPSToken}.

Mean Opinion Score (MOS) prediction for text to music systems requires evaluating both overall musical quality and text prompt alignment. This paper introduces WhisQ, a multimodal architecture that addresses this dual-assessment challenge through sequence level co-attention and optimal transport regularization. WhisQ employs the Whisper Base pretrained model for temporal audio encoding and Qwen 3, a 0.6B Small Language Model (SLM), for text encoding, with both maintaining sequence structure for fine grained cross-modal modeling. The architecture features specialized prediction pathways: OMQ is predicted from pooled audio embeddings, while TA leverages bidirectional sequence co-attention between audio and text. Sinkhorn optimal transport loss further enforce semantic alignment in the shared embedding space. On the MusicEval Track-1 dataset, WhisQ achieves substantial improvements over the baseline: 7% improvement in Spearman correlation for OMQ and 14% for TA. Ablation studies reveal that optimal transport regularization provides the largest performance gain (10% SRCC improvement), demonstrating the importance of explicit cross-modal alignment for text-to-music evaluation.

This paper presents MetricGrids, a novel grid-based neural representation that combines elementary metric grids in various metric spaces to approximate complex nonlinear signals. While grid-based representations are widely adopted for their efficiency and scalability, the existing feature grids with linear indexing for continuous-space points can only provide degenerate linear latent space representations, and such representations cannot be adequately compensated to represent complex nonlinear signals by the following compact decoder. To address this problem while keeping the simplicity of a regular grid structure, our approach builds upon the standard grid-based paradigm by constructing multiple elementary metric grids as high-order terms to approximate complex nonlinearities, following the Taylor expansion principle. Furthermore, we enhance model compactness with hash encoding based on different sparsities of the grids to prevent detrimental hash collisions, and a high-order extrapolation decoder to reduce explicit grid storage requirements. experimental results on both 2D and 3D reconstructions demonstrate the superior fitting and rendering accuracy of the proposed method across diverse signal types, validating its robustness and generalizability. Code is available at https://github.com/wangshu31/MetricGrids}{https://github.com/wangshu31/MetricGrids.

Multimodal LLMs have reached remarkable levels of proficiency in understanding multimodal inputs, driving extensive research to develop increasingly powerful models. However, much less attention has been paid to understanding and explaining the underlying mechanisms of these models. Most existing explainability research examines these models only in their final states, overlooking the dynamic representational shifts that occur during training. In this work, we systematically analyze the evolution of hidden state representations to reveal how fine-tuning alters the internal structure of a model to specialize in new multimodal tasks. Using a concept-based approach, we map hidden states to interpretable visual and textual concepts, enabling us to trace changes in encoded concepts across modalities as training progresses. We also demonstrate the use of shift vectors to capture these concepts changes. These shift vectors allow us to recover fine-tuned concepts by shifting those in the original model. Finally, we explore the practical impact of our findings on model steering, showing that we can adjust multimodal LLMs behaviors without any training, such as modifying answer types, captions style, or biasing the model toward specific responses. Our work sheds light on how multimodal representations evolve through fine-tuning and offers a new perspective for interpreting model adaptation in multimodal tasks. The code for this project is publicly available at https://github.com/mshukor/xl-vlms.

The integration of Large Language Models (LLM) with Knowledge Representation Learning (KRL) signifies a significant advancement in the field of artificial intelligence (AI), enhancing the ability to capture and utilize both structure and textual information. Despite the increasing research on enhancing KRL with LLMs, a thorough survey that analyse processes of these enhanced models is conspicuously absent. Our survey addresses this by categorizing these models based on three distinct Transformer architectures, and by analyzing experimental data from various KRL downstream tasks to evaluate the strengths and weaknesses of each approach. Finally, we identify and explore potential future research directions in this emerging yet underexplored domain.

Graph Transformers have recently been successful in various graph representation learning tasks, providing a number of advantages over message-passing Graph Neural Networks. Utilizing Graph Transformers for learning the representation of the brain functional connectivity network is also gaining interest. However, studies to date have underlooked the temporal dynamics of functional connectivity, which fluctuates over time. Here, we propose a method for learning the representation of dynamic functional connectivity with Graph Transformers. Specifically, we define the connectome embedding, which holds the position, structure, and time information of the functional connectivity graph, and use Transformers to learn its representation across time. We perform experiments with over 50,000 resting-state fMRI samples obtained from three datasets, which is the largest number of fMRI data used in studies by far. The experimental results show that our proposed method outperforms other competitive baselines in gender classification and age regression tasks based on the functional connectivity extracted from the fMRI data.

Motion prediction is crucial for autonomous vehicles to operate safely in complex traffic environments. Extracting effective spatiotemporal relationships among traffic elements is key to accurate forecasting. Inspired by the successful practice of pretrained large language models, this paper presents SEPT, a modeling framework that leverages self-supervised learning to develop powerful spatiotemporal understanding for complex traffic scenes. Specifically, our approach involves three masking-reconstruction modeling tasks on scene inputs including agents' trajectories and road network, pretraining the scene encoder to capture kinematics within trajectory, spatial structure of road network, and interactions among roads and agents. The pretrained encoder is then finetuned on the downstream forecasting task. Extensive experiments demonstrate that SEPT, without elaborate architectural design or manual feature engineering, achieves state-of-the-art performance on the Argoverse 1 and Argoverse 2 motion forecasting benchmarks, outperforming previous methods on all main metrics by a large margin.

Talking head video generation aims to animate a human face in a still image with dynamic poses and expressions using motion information derived from a target-driving video, while maintaining the person's identity in the source image. However, dramatic and complex motions in the driving video cause ambiguous generation, because the still source image cannot provide sufficient appearance information for occluded regions or delicate expression variations, which produces severe artifacts and significantly degrades the generation quality. To tackle this problem, we propose to learn a global facial representation space, and design a novel implicit identity representation conditioned memory compensation network, coined as MCNet, for high-fidelity talking head generation.~Specifically, we devise a network module to learn a unified spatial facial meta-memory bank from all training samples, which can provide rich facial structure and appearance priors to compensate warped source facial features for the generation. Furthermore, we propose an effective query mechanism based on implicit identity representations learned from the discrete keypoints of the source image. It can greatly facilitate the retrieval of more correlated information from the memory bank for the compensation. Extensive experiments demonstrate that MCNet can learn representative and complementary facial memory, and can clearly outperform previous state-of-the-art talking head generation methods on VoxCeleb1 and CelebV datasets. Please check our https://github.com/harlanhong/ICCV2023-MCNET{Project}.

Autonomous driving requires a comprehensive understanding of the surrounding environment for reliable trajectory planning. Previous works rely on dense rasterized scene representation (e.g., agent occupancy and semantic map) to perform planning, which is computationally intensive and misses the instance-level structure information. In this paper, we propose VAD, an end-to-end vectorized paradigm for autonomous driving, which models the driving scene as a fully vectorized representation. The proposed vectorized paradigm has two significant advantages. On one hand, VAD exploits the vectorized agent motion and map elements as explicit instance-level planning constraints which effectively improves planning safety. On the other hand, VAD runs much faster than previous end-to-end planning methods by getting rid of computation-intensive rasterized representation and hand-designed post-processing steps. VAD achieves state-of-the-art end-to-end planning performance on the nuScenes dataset, outperforming the previous best method by a large margin. Our base model, VAD-Base, greatly reduces the average collision rate by 29.0% and runs 2.5x faster. Besides, a lightweight variant, VAD-Tiny, greatly improves the inference speed (up to 9.3x) while achieving comparable planning performance. We believe the excellent performance and the high efficiency of VAD are critical for the real-world deployment of an autonomous driving system. Code and models are available at https://github.com/hustvl/VAD for facilitating future research.

Medical imaging analysis plays a critical role in the diagnosis and treatment of various medical conditions. This paper focuses on chest X-ray images and their corresponding radiological reports. It presents a new model that learns a joint X-ray image & report representation. The model is based on a novel alignment scheme between the visual data and the text, which takes into account both local and global information. Furthermore, the model integrates domain-specific information of two types -- lateral images and the consistent visual structure of chest images. Our representation is shown to benefit three types of retrieval tasks: text-image retrieval, class-based retrieval, and phrase-grounding.

We propose a framework to learn to schedule a job-shop problem (JSSP) using a graph neural network (GNN) and reinforcement learning (RL). We formulate the scheduling process of JSSP as a sequential decision-making problem with graph representation of the state to consider the structure of JSSP. In solving the formulated problem, the proposed framework employs a GNN to learn that node features that embed the spatial structure of the JSSP represented as a graph (representation learning) and derive the optimum scheduling policy that maps the embedded node features to the best scheduling action (policy learning). We employ Proximal Policy Optimization (PPO) based RL strategy to train these two modules in an end-to-end fashion. We empirically demonstrate that the GNN scheduler, due to its superb generalization capability, outperforms practically favored dispatching rules and RL-based schedulers on various benchmark JSSP. We also confirmed that the proposed framework learns a transferable scheduling policy that can be employed to schedule a completely new JSSP (in terms of size and parameters) without further training.

Graph representation learning nowadays becomes fundamental in analyzing graph-structured data. Inspired by recent success of contrastive methods, in this paper, we propose a novel framework for unsupervised graph representation learning by leveraging a contrastive objective at the node level. Specifically, we generate two graph views by corruption and learn node representations by maximizing the agreement of node representations in these two views. To provide diverse node contexts for the contrastive objective, we propose a hybrid scheme for generating graph views on both structure and attribute levels. Besides, we provide theoretical justification behind our motivation from two perspectives, mutual information and the classical triplet loss. We perform empirical experiments on both transductive and inductive learning tasks using a variety of real-world datasets. Experimental experiments demonstrate that despite its simplicity, our proposed method consistently outperforms existing state-of-the-art methods by large margins. Moreover, our unsupervised method even surpasses its supervised counterparts on transductive tasks, demonstrating its great potential in real-world applications.

Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when only a subset of these variables is documented by the clinician. A feasible approach to improving the representation learning of EHR data is to associate relevant medical concepts and utilize these connections. Existing medical ontologies can be the reference for EHR structures, but they place numerous constraints on the data source. Recent progress on graph neural networks (GNN) enables end-to-end learning of topological structures for non-grid or non-sequential data. However, there are problems to be addressed on how to learn the medical graph adaptively and how to understand the effect of the medical graph on representation learning. In this paper, we propose a variationally regularized encoder-decoder graph network that achieves more robustness in graph structure learning by regularizing node representations. Our model outperforms the existing graph and non-graph based methods in various EHR predictive tasks based on both public data and real-world clinical data. Besides the improvements in empirical experiment performances, we provide an interpretation of the effect of variational regularization compared to standard graph neural network, using singular value analysis.

Research on parsing language to SQL has largely ignored the structure of the database (DB) schema, either because the DB was very simple, or because it was observed at both training and test time. In Spider, a recently-released text-to-SQL dataset, new and complex DBs are given at test time, and so the structure of the DB schema can inform the predicted SQL query. In this paper, we present an encoder-decoder semantic parser, where the structure of the DB schema is encoded with a graph neural network, and this representation is later used at both encoding and decoding time. Evaluation shows that encoding the schema structure improves our parser accuracy from 33.8% to 39.4%, dramatically above the current state of the art, which is at 19.7%.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

Vision-Language Models (VLMs) can process visual and textual information in multiple formats: texts, images, interleaved texts and images, or even hour-long videos. In this work, we conduct fine-grained quantitative and qualitative analyses of automatic summarization of multimodal presentations using VLMs with various representations as input. From these experiments, we suggest cost-effective strategies for generating summaries from text-heavy multimodal documents under different input-length budgets using VLMs. We show that slides extracted from the video stream can be beneficially used as input against the raw video, and that a structured representation from interleaved slides and transcript provides the best performance. Finally, we reflect and comment on the nature of cross-modal interactions in multimodal presentations and share suggestions to improve the capabilities of VLMs to understand documents of this nature.

Audio-visual large language models (LLM) have drawn significant attention, yet the fine-grained combination of both input streams is rather under-explored, which is challenging but necessary for LLMs to understand general video inputs. To this end, a fine-grained audio-visual joint representation (FAVOR) learning framework for multimodal LLMs is proposed in this paper, which extends a text-based LLM to simultaneously perceive speech and audio events in the audio input stream and images or videos in the visual input stream, at the frame level. To fuse the audio and visual feature streams into joint representations and to align the joint space with the LLM input embedding space, we propose a causal Q-Former structure with a causal attention module to enhance the capture of causal relations of the audio-visual frames across time. An audio-visual evaluation benchmark (AVEB) is also proposed which comprises six representative single-modal tasks with five cross-modal tasks reflecting audio-visual co-reasoning abilities. While achieving competitive single-modal performance on audio, speech and image tasks in AVEB, FAVOR achieved over 20% accuracy improvements on the video question-answering task when fine-grained information or temporal causal reasoning is required. FAVOR, in addition, demonstrated remarkable video comprehension and reasoning abilities on tasks that are unprecedented by other multimodal LLMs. An interactive demo of FAVOR is available at https://github.com/BriansIDP/AudioVisualLLM.git, and the training code and model checkpoints will be released soon.

Self-supervised learning in vision-language processing exploits semantic alignment between imaging and text modalities. Prior work in biomedical VLP has mostly relied on the alignment of single image and report pairs even though clinical notes commonly refer to prior images. This does not only introduce poor alignment between the modalities but also a missed opportunity to exploit rich self-supervision through existing temporal content in the data. In this work, we explicitly account for prior images and reports when available during both training and fine-tuning. Our approach, named BioViL-T, uses a CNN-Transformer hybrid multi-image encoder trained jointly with a text model. It is designed to be versatile to arising challenges such as pose variations and missing input images across time. The resulting model excels on downstream tasks both in single- and multi-image setups, achieving state-of-the-art performance on (I) progression classification, (II) phrase grounding, and (III) report generation, whilst offering consistent improvements on disease classification and sentence-similarity tasks. We release a novel multi-modal temporal benchmark dataset, MS-CXR-T, to quantify the quality of vision-language representations in terms of temporal semantics. Our experimental results show the advantages of incorporating prior images and reports to make most use of the data.

Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target protein, e.g. SARS-CoV-2 Spike protein, obtained from computationally expensive molecular simulations. Model tasks involve characterizing the distinct structural fluctuations of the protein bound to various drug molecules, as well as efficient generation of protein conformations that can serve as an complement of a molecular simulation engine. Specifically, we present a geometric autoencoder framework to learn separate latent space encodings of the intrinsic and extrinsic geometries of the protein structure. For this purpose, the proposed Protein Geometric AutoEncoder (ProGAE) model is trained on the protein contact map and the orientation of the backbone bonds of the protein. Using ProGAE latent embeddings, we reconstruct and generate the conformational ensemble of a protein at or near the experimental resolution, while gaining better interpretability and controllability in term of protein structure generation from the learned latent space. Additionally, ProGAE models are transferable to a different state of the same protein or to a new protein of different size, where only the dense layer decoding from the latent representation needs to be retrained. Results show that our geometric learning-based method enjoys both accuracy and efficiency for generating complex structural variations, charting the path toward scalable and improved approaches for analyzing and enhancing high-cost simulations of drug-target proteins.

This paper presents a domain-specific implementation of Retrieval-Augmented Generation (RAG) tailored to the Fair Use Doctrine in U.S. copyright law. Motivated by the increasing prevalence of DMCA takedowns and the lack of accessible legal support for content creators, we propose a structured approach that combines semantic search with legal knowledge graphs and court citation networks to improve retrieval quality and reasoning reliability. Our prototype models legal precedents at the statutory factor level (e.g., purpose, nature, amount, market effect) and incorporates citation-weighted graph representations to prioritize doctrinally authoritative sources. We use Chain-of-Thought reasoning and interleaved retrieval steps to better emulate legal reasoning. Preliminary testing suggests this method improves doctrinal relevance in the retrieval process, laying groundwork for future evaluation and deployment of LLM-based legal assistance tools.

Accurate ocean modeling and coastal hazard prediction depend on high-resolution bathymetric data; yet, current worldwide datasets are too coarse for exact numerical simulations. While recent deep learning advances have improved earth observation data resolution, existing methods struggle with the unique challenges of producing detailed ocean floor maps, especially in maintaining physical structure consistency and quantifying uncertainties. This work presents a novel uncertainty-aware mechanism using spatial blocks to efficiently capture local bathymetric complexity based on block-based conformal prediction. Using the Vector Quantized Variational Autoencoder (VQ-VAE) architecture, the integration of this uncertainty quantification framework yields spatially adaptive confidence estimates while preserving topographical features via discrete latent representations. With smaller uncertainty widths in well-characterized areas and appropriately larger bounds in areas of complex seafloor structures, the block-based design adapts uncertainty estimates to local bathymetric complexity. Compared to conventional techniques, experimental results over several ocean regions show notable increases in both reconstruction quality and uncertainty estimation reliability. This framework increases the reliability of bathymetric reconstructions by preserving structural integrity while offering spatially adaptive uncertainty estimates, so opening the path for more solid climate modeling and coastal hazard assessment.

Recent work has demonstrated that semantics specified by pretraining data influence how representations of different concepts are organized in a large language model (LLM). However, given the open-ended nature of LLMs, e.g., their ability to in-context learn, we can ask whether models alter these pretraining semantics to adopt alternative, context-specified ones. Specifically, if we provide in-context exemplars wherein a concept plays a different role than what the pretraining data suggests, do models reorganize their representations in accordance with these novel semantics? To answer this question, we take inspiration from the theory of conceptual role semantics and define a toy "graph tracing" task wherein the nodes of the graph are referenced via concepts seen during training (e.g., apple, bird, etc.) and the connectivity of the graph is defined via some predefined structure (e.g., a square grid). Given exemplars that indicate traces of random walks on the graph, we analyze intermediate representations of the model and find that as the amount of context is scaled, there is a sudden re-organization from pretrained semantic representations to in-context representations aligned with the graph structure. Further, we find that when reference concepts have correlations in their semantics (e.g., Monday, Tuesday, etc.), the context-specified graph structure is still present in the representations, but is unable to dominate the pretrained structure. To explain these results, we analogize our task to energy minimization for a predefined graph topology, providing evidence towards an implicit optimization process to infer context-specified semantics. Overall, our findings indicate scaling context-size can flexibly re-organize model representations, possibly unlocking novel capabilities.

Recent works have argued that high-level semantic concepts are encoded "linearly" in the representation space of large language models. In this work, we study the origins of such linear representations. To that end, we introduce a simple latent variable model to abstract and formalize the concept dynamics of the next token prediction. We use this formalism to show that the next token prediction objective (softmax with cross-entropy) and the implicit bias of gradient descent together promote the linear representation of concepts. Experiments show that linear representations emerge when learning from data matching the latent variable model, confirming that this simple structure already suffices to yield linear representations. We additionally confirm some predictions of the theory using the LLaMA-2 large language model, giving evidence that the simplified model yields generalizable insights.

High-throughput drug screening -- using cell imaging or gene expression measurements as readouts of drug effect -- is a critical tool in biotechnology to assess and understand the relationship between the chemical structure and biological activity of a drug. Since large-scale screens have to be divided into multiple experiments, a key difficulty is dealing with batch effects, which can introduce systematic errors and non-biological associations in the data. We propose InfoCORE, an Information maximization approach for COnfounder REmoval, to effectively deal with batch effects and obtain refined molecular representations. InfoCORE establishes a variational lower bound on the conditional mutual information of the latent representations given a batch identifier. It adaptively reweighs samples to equalize their implied batch distribution. Extensive experiments on drug screening data reveal InfoCORE's superior performance in a multitude of tasks including molecular property prediction and molecule-phenotype retrieval. Additionally, we show results for how InfoCORE offers a versatile framework and resolves general distribution shifts and issues of data fairness by minimizing correlation with spurious features or removing sensitive attributes. The code is available at https://github.com/uhlerlab/InfoCORE.

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

Self-supervised learning methods overcome the key bottleneck for building more capable AI: limited availability of labeled data. However, one of the drawbacks of self-supervised architectures is that the representations that they learn are implicit and it is hard to extract meaningful information about the encoded world states, such as 3D structure of the visual scene encoded in a depth map. Moreover, in the visual domain such representations only rarely undergo evaluations that may be critical for downstream tasks, such as vision for autonomous cars. Herein, we propose a framework for evaluating visual representations for illumination invariance in the context of depth perception. We develop a new predictive coding-based architecture and a hybrid fully-supervised/self-supervised learning method. We propose a novel architecture that extends the predictive coding approach: PRedictive Lateral bottom-Up and top-Down Encoder-decoder Network (PreludeNet), which explicitly learns to infer and predict depth from video frames. In PreludeNet, the encoder's stack of predictive coding layers is trained in a self-supervised manner, while the predictive decoder is trained in a supervised manner to infer or predict the depth. We evaluate the robustness of our model on a new synthetic dataset, in which lighting conditions (such as overall illumination, and effect of shadows) can be be parametrically adjusted while keeping all other aspects of the world constant. PreludeNet achieves both competitive depth inference performance and next frame prediction accuracy. We also show how this new network architecture, coupled with the hybrid fully-supervised/self-supervised learning method, achieves balance between the said performance and invariance to changes in lighting. The proposed framework for evaluating visual representations can be extended to diverse task domains and invariance tests.

The objective of pre-trained language models is to learn contextual representations of textual data. Pre-trained language models have become mainstream in natural language processing and code modeling. Using probes, a technique to study the linguistic properties of hidden vector spaces, previous works have shown that these pre-trained language models encode simple linguistic properties in their hidden representations. However, none of the previous work assessed whether these models encode the whole grammatical structure of a programming language. In this paper, we prove the existence of a syntactic subspace, lying in the hidden representations of pre-trained language models, which contain the syntactic information of the programming language. We show that this subspace can be extracted from the models' representations and define a novel probing method, the AST-Probe, that enables recovering the whole abstract syntax tree (AST) of an input code snippet. In our experimentations, we show that this syntactic subspace exists in five state-of-the-art pre-trained language models. In addition, we highlight that the middle layers of the models are the ones that encode most of the AST information. Finally, we estimate the optimal size of this syntactic subspace and show that its dimension is substantially lower than those of the models' representation spaces. This suggests that pre-trained language models use a small part of their representation spaces to encode syntactic information of the programming languages.

While deep reinforcement learning excels at solving tasks where large amounts of data can be collected through virtually unlimited interaction with the environment, learning from limited interaction remains a key challenge. We posit that an agent can learn more efficiently if we augment reward maximization with self-supervised objectives based on structure in its visual input and sequential interaction with the environment. Our method, Self-Predictive Representations(SPR), trains an agent to predict its own latent state representations multiple steps into the future. We compute target representations for future states using an encoder which is an exponential moving average of the agent's parameters and we make predictions using a learned transition model. On its own, this future prediction objective outperforms prior methods for sample-efficient deep RL from pixels. We further improve performance by adding data augmentation to the future prediction loss, which forces the agent's representations to be consistent across multiple views of an observation. Our full self-supervised objective, which combines future prediction and data augmentation, achieves a median human-normalized score of 0.415 on Atari in a setting limited to 100k steps of environment interaction, which represents a 55% relative improvement over the previous state-of-the-art. Notably, even in this limited data regime, SPR exceeds expert human scores on 7 out of 26 games. The code associated with this work is available at https://github.com/mila-iqia/spr

The visual world is vast and varied, but its variations divide into structured and unstructured factors. We compose free-form filters and structured Gaussian filters, optimized end-to-end, to factorize deep representations and learn both local features and their degree of locality. Our semi-structured composition is strictly more expressive than free-form filtering, and changes in its structured parameters would require changes in free-form architecture. In effect this optimizes over receptive field size and shape, tuning locality to the data and task. Dynamic inference, in which the Gaussian structure varies with the input, adapts receptive field size to compensate for local scale variation. Optimizing receptive field size improves semantic segmentation accuracy on Cityscapes by 1-2 points for strong dilated and skip architectures and by up to 10 points for suboptimal designs. Adapting receptive fields by dynamic Gaussian structure further improves results, equaling the accuracy of free-form deformation while improving efficiency.

Bias in Large Language Models (LLMs) significantly undermines their reliability and fairness. We focus on a common form of bias: when two reference concepts in the model's concept space, such as sentiment polarities (e.g., "positive" and "negative"), are asymmetrically correlated with a third, target concept, such as a reviewing aspect, the model exhibits unintended bias. For instance, the understanding of "food" should not skew toward any particular sentiment. Existing bias evaluation methods assess behavioral differences of LLMs by constructing labeled data for different social groups and measuring model responses across them, a process that requires substantial human effort and captures only a limited set of social concepts. To overcome these limitations, we propose BiasLens, a test-set-free bias analysis framework based on the structure of the model's vector space. BiasLens combines Concept Activation Vectors (CAVs) with Sparse Autoencoders (SAEs) to extract interpretable concept representations, and quantifies bias by measuring the variation in representational similarity between the target concept and each of the reference concepts. Even without labeled data, BiasLens shows strong agreement with traditional bias evaluation metrics (Spearman correlation r > 0.85). Moreover, BiasLens reveals forms of bias that are difficult to detect using existing methods. For example, in simulated clinical scenarios, a patient's insurance status can cause the LLM to produce biased diagnostic assessments. Overall, BiasLens offers a scalable, interpretable, and efficient paradigm for bias discovery, paving the way for improving fairness and transparency in LLMs.

While large language models based on the transformer architecture have demonstrated remarkable in-context learning (ICL) capabilities, understandings of such capabilities are still in an early stage, where existing theory and mechanistic understanding focus mostly on simple scenarios such as learning simple function classes. This paper takes initial steps on understanding ICL in more complex scenarios, by studying learning with representations. Concretely, we construct synthetic in-context learning problems with a compositional structure, where the label depends on the input through a possibly complex but fixed representation function, composed with a linear function that differs in each instance. By construction, the optimal ICL algorithm first transforms the inputs by the representation function, and then performs linear ICL on top of the transformed dataset. We show theoretically the existence of transformers that approximately implement such algorithms with mild depth and size. Empirically, we find trained transformers consistently achieve near-optimal ICL performance in this setting, and exhibit the desired dissection where lower layers transforms the dataset and upper layers perform linear ICL. Through extensive probing and a new pasting experiment, we further reveal several mechanisms within the trained transformers, such as concrete copying behaviors on both the inputs and the representations, linear ICL capability of the upper layers alone, and a post-ICL representation selection mechanism in a harder mixture setting. These observed mechanisms align well with our theory and may shed light on how transformers perform ICL in more realistic scenarios.

Recent AI-based scoliosis screening methods primarily rely on large-scale silhouette datasets, often neglecting clinically relevant postural asymmetries-key indicators in traditional screening. In contrast, pose data provide an intuitive skeletal representation, enhancing clinical interpretability across various medical applications. However, pose-based scoliosis screening remains underexplored due to two main challenges: (1) the scarcity of large-scale, annotated pose datasets; and (2) the discrete and noise-sensitive nature of raw pose coordinates, which hinders the modeling of subtle asymmetries. To address these limitations, we introduce Scoliosis1K-Pose, a 2D human pose annotation set that extends the original Scoliosis1K dataset, comprising 447,900 frames of 2D keypoints from 1,050 adolescents. Building on this dataset, we introduce the Dual Representation Framework (DRF), which integrates a continuous skeleton map to preserve spatial structure with a discrete Postural Asymmetry Vector (PAV) that encodes clinically relevant asymmetry descriptors. A novel PAV-Guided Attention (PGA) module further uses the PAV as clinical prior to direct feature extraction from the skeleton map, focusing on clinically meaningful asymmetries. Extensive experiments demonstrate that DRF achieves state-of-the-art performance. Visualizations further confirm that the model leverages clinical asymmetry cues to guide feature extraction and promote synergy between its dual representations. The dataset and code are publicly available at https://zhouzi180.github.io/Scoliosis1K/.

Finding meaningful representations and distances of hierarchical data is important in many fields. This paper presents a new method for hierarchical data embedding and distance. Our method relies on combining diffusion geometry, a central approach to manifold learning, and hyperbolic geometry. Specifically, using diffusion geometry, we build multi-scale densities on the data, aimed to reveal their hierarchical structure, and then embed them into a product of hyperbolic spaces. We show theoretically that our embedding and distance recover the underlying hierarchical structure. In addition, we demonstrate the efficacy of the proposed method and its advantages compared to existing methods on graph embedding benchmarks and hierarchical datasets.

Pre-trained models for programming languages have recently demonstrated great success on code intelligence. To support both code-related understanding and generation tasks, recent works attempt to pre-train unified encoder-decoder models. However, such encoder-decoder framework is sub-optimal for auto-regressive tasks, especially code completion that requires a decoder-only manner for efficient inference. In this paper, we present UniXcoder, a unified cross-modal pre-trained model for programming language. The model utilizes mask attention matrices with prefix adapters to control the behavior of the model and leverages cross-modal contents like AST and code comment to enhance code representation. To encode AST that is represented as a tree in parallel, we propose a one-to-one mapping method to transform AST in a sequence structure that retains all structural information from the tree. Furthermore, we propose to utilize multi-modal contents to learn representation of code fragment with contrastive learning, and then align representations among programming languages using a cross-modal generation task. We evaluate UniXcoder on five code-related tasks over nine datasets. To further evaluate the performance of code fragment representation, we also construct a dataset for a new task, called zero-shot code-to-code search. Results show that our model achieves state-of-the-art performance on most tasks and analysis reveals that comment and AST can both enhance UniXcoder.

Despite the success of deep neural networks, there are still many challenges in deep representation learning due to the data scarcity issues such as data imbalance, unseen distribution, and domain shift. To address the above-mentioned issues, a variety of methods have been devised to explore the sample relationships in a vanilla way (i.e., from the perspectives of either the input or the loss function), failing to explore the internal structure of deep neural networks for learning with sample relationships. Inspired by this, we propose to enable deep neural networks themselves with the ability to learn the sample relationships from each mini-batch. Specifically, we introduce a batch transformer module or BatchFormer, which is then applied into the batch dimension of each mini-batch to implicitly explore sample relationships during training. By doing this, the proposed method enables the collaboration of different samples, e.g., the head-class samples can also contribute to the learning of the tail classes for long-tailed recognition. Furthermore, to mitigate the gap between training and testing, we share the classifier between with or without the BatchFormer during training, which can thus be removed during testing. We perform extensive experiments on over ten datasets and the proposed method achieves significant improvements on different data scarcity applications without any bells and whistles, including the tasks of long-tailed recognition, compositional zero-shot learning, domain generalization, and contrastive learning. Code will be made publicly available at https://github.com/zhihou7/BatchFormer.

Face clustering has attracted rising research interest recently to take advantage of massive amounts of face images on the web. State-of-the-art performance has been achieved by Graph Convolutional Networks (GCN) due to their powerful representation capacity. However, existing GCN-based methods build face graphs mainly according to kNN relations in the feature space, which may lead to a lot of noise edges connecting two faces of different classes. The face features will be polluted when messages pass along these noise edges, thus degrading the performance of GCNs. In this paper, a novel algorithm named Ada-NETS is proposed to cluster faces by constructing clean graphs for GCNs. In Ada-NETS, each face is transformed to a new structure space, obtaining robust features by considering face features of the neighbour images. Then, an adaptive neighbour discovery strategy is proposed to determine a proper number of edges connecting to each face image. It significantly reduces the noise edges while maintaining the good ones to build a graph with clean yet rich edges for GCNs to cluster faces. Experiments on multiple public clustering datasets show that Ada-NETS significantly outperforms current state-of-the-art methods, proving its superiority and generalization. Code is available at https://github.com/damo-cv/Ada-NETS.

Position encoding (PE), an essential part of self-attention networks (SANs), is used to preserve the word order information for natural language processing tasks, generating fixed position indices for input sequences. However, in cross-lingual scenarios, e.g. machine translation, the PEs of source and target sentences are modeled independently. Due to word order divergences in different languages, modeling the cross-lingual positional relationships might help SANs tackle this problem. In this paper, we augment SANs with cross-lingual position representations to model the bilingually aware latent structure for the input sentence. Specifically, we utilize bracketing transduction grammar (BTG)-based reordering information to encourage SANs to learn bilingual diagonal alignments. Experimental results on WMT'14 EnglishRightarrowGerman, WAT'17 JapaneseRightarrowEnglish, and WMT'17 ChineseLeftrightarrowEnglish translation tasks demonstrate that our approach significantly and consistently improves translation quality over strong baselines. Extensive analyses confirm that the performance gains come from the cross-lingual information.

The abilities to perceive, learn, and use generalities, similarities, classes, i.e., semantic memory (SM), is central to cognition. Machine learning (ML), neural network, and AI research has been primarily driven by tasks requiring such abilities. However, another central facet of cognition, single-trial formation of permanent memories of experiences, i.e., episodic memory (EM), has had relatively little focus. Only recently has EM-like functionality been added to Deep Learning (DL) models, e.g., Neural Turing Machine, Memory Networks. However, in these cases: a) EM is implemented as a separate module, which entails substantial data movement (and so, time and power) between the DL net itself and EM; and b) individual items are stored localistically within the EM, precluding realizing the exponential representational efficiency of distributed over localist coding. We describe Sparsey, an unsupervised, hierarchical, spatial/spatiotemporal associative memory model differing fundamentally from mainstream ML models, most crucially, in its use of sparse distributed representations (SDRs), or, cell assemblies, which admits an extremely efficient, single-trial learning algorithm that maps input similarity into code space similarity (measured as intersection). SDRs of individual inputs are stored in superposition and because similarity is preserved, the patterns of intersections over the assigned codes reflect the similarity, i.e., statistical, structure, of all orders, not simply pairwise, over the inputs. Thus, SM, i.e., a generative model, is built as a computationally free side effect of the act of storing episodic memory traces of individual inputs, either spatial patterns or sequences. We report initial results on MNIST and on the Weizmann video event recognition benchmarks. While we have not yet attained SOTA class accuracy, learning takes only minutes on a single CPU.

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

Learning implicit representations has been a widely used solution for surface reconstruction from 3D point clouds. The latest methods infer a distance or occupancy field by overfitting a neural network on a single point cloud. However, these methods suffer from a slow inference due to the slow convergence of neural networks and the extensive calculation of distances to surface points, which limits them to small scale points. To resolve the scalability issue in surface reconstruction, we propose GridPull to improve the efficiency of learning implicit representations from large scale point clouds. Our novelty lies in the fast inference of a discrete distance field defined on grids without using any neural components. To remedy the lack of continuousness brought by neural networks, we introduce a loss function to encourage continuous distances and consistent gradients in the field during pulling queries onto the surface in grids near to the surface. We use uniform grids for a fast grid search to localize sampled queries, and organize surface points in a tree structure to speed up the calculation of distances to the surface. We do not rely on learning priors or normal supervision during optimization, and achieve superiority over the latest methods in terms of complexity and accuracy. We evaluate our method on shape and scene benchmarks, and report numerical and visual comparisons with the latest methods to justify our effectiveness and superiority. The code is available at https://github.com/chenchao15/GridPull.

Despite the significant advancements in pre-training methods for point cloud understanding, directly capturing intricate shape information from irregular point clouds without reliance on external data remains a formidable challenge. To address this problem, we propose GPSFormer, an innovative Global Perception and Local Structure Fitting-based Transformer, which learns detailed shape information from point clouds with remarkable precision. The core of GPSFormer is the Global Perception Module (GPM) and the Local Structure Fitting Convolution (LSFConv). Specifically, GPM utilizes Adaptive Deformable Graph Convolution (ADGConv) to identify short-range dependencies among similar features in the feature space and employs Multi-Head Attention (MHA) to learn long-range dependencies across all positions within the feature space, ultimately enabling flexible learning of contextual representations. Inspired by Taylor series, we design LSFConv, which learns both low-order fundamental and high-order refinement information from explicitly encoded local geometric structures. Integrating the GPM and LSFConv as fundamental components, we construct GPSFormer, a cutting-edge Transformer that effectively captures global and local structures of point clouds. Extensive experiments validate GPSFormer's effectiveness in three point cloud tasks: shape classification, part segmentation, and few-shot learning. The code of GPSFormer is available at https://github.com/changshuowang/GPSFormer.

Learning effective representations of source code is critical for any Machine Learning for Software Engineering (ML4SE) system. Inspired by natural language processing, large language models (LLMs) like Codex and CodeGen treat code as generic sequences of text and are trained on huge corpora of code data, achieving state of the art performance on several software engineering (SE) tasks. However, valid source code, unlike natural language, follows a strict structure and pattern governed by the underlying grammar of the programming language. Current LLMs do not exploit this property of the source code as they treat code like a sequence of tokens and overlook key structural and semantic properties of code that can be extracted from code-views like the Control Flow Graph (CFG), Data Flow Graph (DFG), Abstract Syntax Tree (AST), etc. Unfortunately, the process of generating and integrating code-views for every programming language is cumbersome and time consuming. To overcome this barrier, we propose our tool COMEX - a framework that allows researchers and developers to create and combine multiple code-views which can be used by machine learning (ML) models for various SE tasks. Some salient features of our tool are: (i) it works directly on source code (which need not be compilable), (ii) it currently supports Java and C#, (iii) it can analyze both method-level snippets and program-level snippets by using both intra-procedural and inter-procedural analysis, and (iv) it is easily extendable to other languages as it is built on tree-sitter - a widely used incremental parser that supports over 40 languages. We believe this easy-to-use code-view generation and customization tool will give impetus to research in source code representation learning methods and ML4SE. Tool: https://pypi.org/project/comex - GitHub: https://github.com/IBM/tree-sitter-codeviews - Demo: https://youtu.be/GER6U87FVbU

The general sequential decision-making problem, which includes Markov decision processes (MDPs) and partially observable MDPs (POMDPs) as special cases, aims at maximizing a cumulative reward by making a sequence of decisions based on a history of observations and actions over time. Recent studies have shown that the sequential decision-making problem is statistically learnable if it admits a low-rank structure modeled by predictive state representations (PSRs). Despite these advancements, existing approaches typically involve oracles or steps that are computationally intractable. On the other hand, the upper confidence bound (UCB) based approaches, which have served successfully as computationally efficient methods in bandits and MDPs, have not been investigated for more general PSRs, due to the difficulty of optimistic bonus design in these more challenging settings. This paper proposes the first known UCB-type approach for PSRs, featuring a novel bonus term that upper bounds the total variation distance between the estimated and true models. We further characterize the sample complexity bounds for our designed UCB-type algorithms for both online and offline PSRs. In contrast to existing approaches for PSRs, our UCB-type algorithms enjoy computational tractability, last-iterate guaranteed near-optimal policy, and guaranteed model accuracy.

Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery. However, it remains a challenging computational task due to the large modeling space of protein structures. In this study, we propose a latent diffusion model that can reduce the complexity of protein modeling while flexibly capturing the distribution of natural protein structures in a condensed latent space. Specifically, we propose an equivariant protein autoencoder that embeds proteins into a latent space and then uses an equivariant diffusion model to learn the distribution of the latent protein representations. Experimental results demonstrate that our method can effectively generate novel protein backbone structures with high designability and efficiency.

Many tasks in natural language processing require the extraction of relationship information for a given condition, such as event argument extraction, relation extraction, and task-oriented semantic parsing. Recent works usually propose sophisticated models for each task independently and pay less attention to the commonality of these tasks and to have a unified framework for all the tasks. In this work, we propose to take a unified view of all these tasks and introduce TAGPRIME to address relational structure extraction problems. TAGPRIME is a sequence tagging model that appends priming words about the information of the given condition (such as an event trigger) to the input text. With the self-attention mechanism in pre-trained language models, the priming words make the output contextualized representations contain more information about the given condition, and hence become more suitable for extracting specific relationships for the condition. Extensive experiments and analyses on three different tasks that cover ten datasets across five different languages demonstrate the generality and effectiveness of TAGPRIME.

Multi-layer perceptrons (MLP) have proven to be effective scene encoders when combined with higher-dimensional projections of the input, commonly referred to as positional encoding. However, scenes with a wide frequency spectrum remain a challenge: choosing high frequencies for positional encoding introduces noise in low structure areas, while low frequencies result in poor fitting of detailed regions. To address this, we propose a progressive positional encoding, exposing a hierarchical MLP structure to incremental sets of frequency encodings. Our model accurately reconstructs scenes with wide frequency bands and learns a scene representation at progressive level of detail without explicit per-level supervision. The architecture is modular: each level encodes a continuous implicit representation that can be leveraged separately for its respective resolution, meaning a smaller network for coarser reconstructions. Experiments on several 2D and 3D datasets show improvements in reconstruction accuracy, representational capacity and training speed compared to baselines.

Text representations using neural word embeddings have proven effective in many NLP applications. Recent researches adapt the traditional word embedding models to learn vectors of multiword expressions (concepts/entities). However, these methods are limited to textual knowledge bases (e.g., Wikipedia). In this paper, we propose a novel and simple technique for integrating the knowledge about concepts from two large scale knowledge bases of different structure (Wikipedia and Probase) in order to learn concept representations. We adapt the efficient skip-gram model to seamlessly learn from the knowledge in Wikipedia text and Probase concept graph. We evaluate our concept embedding models on two tasks: (1) analogical reasoning, where we achieve a state-of-the-art performance of 91% on semantic analogies, (2) concept categorization, where we achieve a state-of-the-art performance on two benchmark datasets achieving categorization accuracy of 100% on one and 98% on the other. Additionally, we present a case study to evaluate our model on unsupervised argument type identification for neural semantic parsing. We demonstrate the competitive accuracy of our unsupervised method and its ability to better generalize to out of vocabulary entity mentions compared to the tedious and error prone methods which depend on gazetteers and regular expressions.