Daily Papers

Dense prediction tasks such as object detection and segmentation require high-quality labels at pixel level, which are costly to obtain. Recent advances in foundation models have enabled the generation of autolabels, which we find to be competitive but not yet sufficient to fully replace human annotations, especially for more complex datasets. Thus, we consider the challenge of selecting a representative subset of images for labeling from a large pool of unlabeled images under a constrained annotation budget. This task is further complicated by imbalanced class distributions, as rare classes are often underrepresented in selected subsets. We propose object-focused data selection (OFDS) which leverages object-level representations to ensure that the selected image subsets semantically cover the target classes, including rare ones. We validate OFDS on PASCAL VOC and Cityscapes for object detection and semantic segmentation tasks. Our experiments demonstrate that prior methods which employ image-level representations fail to consistently outperform random selection. In contrast, OFDS consistently achieves state-of-the-art performance with substantial improvements over all baselines in scenarios with imbalanced class distributions. Moreover, we demonstrate that pre-training with autolabels on the full datasets before fine-tuning on human-labeled subsets selected by OFDS further enhances the final performance.

We propose a game-based formulation for learning dimensionality-reducing representations of feature vectors, when only a prior knowledge on future prediction tasks is available. In this game, the first player chooses a representation, and then the second player adversarially chooses a prediction task from a given class, representing the prior knowledge. The first player aims is to minimize, and the second player to maximize, the regret: The minimal prediction loss using the representation, compared to the same loss using the original features. For the canonical setting in which the representation, the response to predict and the predictors are all linear functions, and under the mean squared error loss function, we derive the theoretically optimal representation in pure strategies, which shows the effectiveness of the prior knowledge, and the optimal regret in mixed strategies, which shows the usefulness of randomizing the representation. For general representations and loss functions, we propose an efficient algorithm to optimize a randomized representation. The algorithm only requires the gradients of the loss function, and is based on incrementally adding a representation rule to a mixture of such rules.

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

In this work, we introduce Multiple Embedding Model for EHR (MEME), an approach that views Electronic Health Records (EHR) as multimodal data. This approach incorporates "pseudo-notes", textual representations of tabular EHR concepts such as diagnoses and medications, and allows us to effectively employ Large Language Models (LLMs) for EHR representation. This framework also adopts a multimodal approach, embedding each EHR modality separately. We demonstrate the effectiveness of MEME by applying it to several tasks within the Emergency Department across multiple hospital systems. Our findings show that MEME surpasses the performance of both single modality embedding methods and traditional machine learning approaches. However, we also observe notable limitations in generalizability across hospital institutions for all tested models.

While neural networks allow highly accurate predictions in many tasks, their lack of robustness towards even slight input perturbations often hampers their deployment. Adversarial attacks such as the seminal projected gradient descent (PGD) offer an effective means to evaluate a model's robustness and dedicated solutions have been proposed for attacks on semantic segmentation or optical flow estimation. While they attempt to increase the attack's efficiency, a further objective is to balance its effect, so that it acts on the entire image domain instead of isolated point-wise predictions. This often comes at the cost of optimization stability and thus efficiency. Here, we propose CosPGD, an attack that encourages more balanced errors over the entire image domain while increasing the attack's overall efficiency. To this end, CosPGD leverages a simple alignment score computed from any pixel-wise prediction and its target to scale the loss in a smooth and fully differentiable way. It leads to efficient evaluations of a model's robustness for semantic segmentation as well as regression models (such as optical flow, disparity estimation, or image restoration), and it allows it to outperform the previous SotA attack on semantic segmentation. We provide code for the CosPGD algorithm and example usage at https://github.com/shashankskagnihotri/cospgd.

Foundation Models (FMs) trained on Electronic Health Records (EHRs) have achieved state-of-the-art results on numerous clinical prediction tasks. However, most existing EHR FMs have context windows of <1k tokens. This prevents them from modeling full patient EHRs which can exceed 10k's of events. Recent advancements in subquadratic long-context architectures (e.g., Mamba) offer a promising solution. However, their application to EHR data has not been well-studied. We address this gap by presenting the first systematic evaluation of the effect of context length on modeling EHR data. We find that longer context models improve predictive performance -- our Mamba-based model surpasses the prior state-of-the-art on 9/14 tasks on the EHRSHOT prediction benchmark. For clinical applications, however, model performance alone is insufficient -- robustness to the unique properties of EHR is crucial. Thus, we also evaluate models across three previously underexplored properties of EHR data: (1) the prevalence of "copy-forwarded" diagnoses which creates artificial repetition of tokens within EHR sequences; (2) the irregular time intervals between EHR events which can lead to a wide range of timespans within a context window; and (3) the natural increase in disease complexity over time which makes later tokens in the EHR harder to predict than earlier ones. Stratifying our EHRSHOT results, we find that higher levels of each property correlate negatively with model performance, but that longer context models are more robust to more extreme levels of these properties. Our work highlights the potential for using long-context architectures to model EHR data, and offers a case study for identifying new challenges in modeling sequential data motivated by domains outside of natural language. We release our models and code at: https://github.com/som-shahlab/long_context_clues

Ribonucleic acid (RNA) plays a variety of crucial roles in fundamental biological processes. Recently, RNA has become an interesting drug target, emphasizing the need to improve our understanding of its structures and functions. Over the years, sequencing technologies have produced an enormous amount of unlabeled RNA data, which hides important knowledge and potential. Motivated by the successes of protein language models, we introduce RiboNucleic Acid Language Model (RiNALMo) to help unveil the hidden code of RNA. RiNALMo is the largest RNA language model to date with 650 million parameters pre-trained on 36 million non-coding RNA sequences from several available databases. RiNALMo is able to extract hidden knowledge and capture the underlying structure information implicitly embedded within the RNA sequences. RiNALMo achieves state-of-the-art results on several downstream tasks. Notably, we show that its generalization capabilities can overcome the inability of other deep learning methods for secondary structure prediction to generalize on unseen RNA families. The code has been made publicly available on https://github.com/lbcb-sci/RiNALMo.

Dense prediction tasks hold significant importance of computer vision, aiming to learn pixel-wise annotated label for an input image. Despite advances in this field, existing methods primarily focus on idealized conditions, with limited generalization to real-world scenarios and facing the challenging scarcity of real-world data. To systematically study this problem, we first introduce DenseWorld, a benchmark spanning a broad set of 25 dense prediction tasks that correspond to urgent real-world applications, featuring unified evaluation across tasks. Then, we propose DenseDiT, which maximally exploits generative models' visual priors to perform diverse real-world dense prediction tasks through a unified strategy. DenseDiT combines a parameter-reuse mechanism and two lightweight branches that adaptively integrate multi-scale context, working with less than 0.1% additional parameters. Evaluations on DenseWorld reveal significant performance drops in existing general and specialized baselines, highlighting their limited real-world generalization. In contrast, DenseDiT achieves superior results using less than 0.01% training data of baselines, underscoring its practical value for real-world deployment. Our data, and checkpoints and codes are available at https://xcltql666.github.io/DenseDiTProj

Dense prediction tasks, such as semantic segmentation, depth estimation, and surface normal prediction, can be easily formulated as per-pixel classification (discrete outputs) or regression (continuous outputs). This per-pixel prediction paradigm has remained popular due to the prevalence of fully convolutional networks. However, on the recent frontier of segmentation task, the community has been witnessing a shift of paradigm from per-pixel prediction to cluster-prediction with the emergence of transformer architectures, particularly the mask transformers, which directly predicts a label for a mask instead of a pixel. Despite this shift, methods based on the per-pixel prediction paradigm still dominate the benchmarks on the other dense prediction tasks that require continuous outputs, such as depth estimation and surface normal prediction. Motivated by the success of DORN and AdaBins in depth estimation, achieved by discretizing the continuous output space, we propose to generalize the cluster-prediction based method to general dense prediction tasks. This allows us to unify dense prediction tasks with the mask transformer framework. Remarkably, the resulting model PolyMaX demonstrates state-of-the-art performance on three benchmarks of NYUD-v2 dataset. We hope our simple yet effective design can inspire more research on exploiting mask transformers for more dense prediction tasks. Code and model will be made available.

Dense image prediction tasks demand features with strong category information and precise spatial boundary details at high resolution. To achieve this, modern hierarchical models often utilize feature fusion, directly adding upsampled coarse features from deep layers and high-resolution features from lower levels. In this paper, we observe rapid variations in fused feature values within objects, resulting in intra-category inconsistency due to disturbed high-frequency features. Additionally, blurred boundaries in fused features lack accurate high frequency, leading to boundary displacement. Building upon these observations, we propose Frequency-Aware Feature Fusion (FreqFusion), integrating an Adaptive Low-Pass Filter (ALPF) generator, an offset generator, and an Adaptive High-Pass Filter (AHPF) generator. The ALPF generator predicts spatially-variant low-pass filters to attenuate high-frequency components within objects, reducing intra-class inconsistency during upsampling. The offset generator refines large inconsistent features and thin boundaries by replacing inconsistent features with more consistent ones through resampling, while the AHPF generator enhances high-frequency detailed boundary information lost during downsampling. Comprehensive visualization and quantitative analysis demonstrate that FreqFusion effectively improves feature consistency and sharpens object boundaries. Extensive experiments across various dense prediction tasks confirm its effectiveness. The code is made publicly available at https://github.com/Linwei-Chen/FreqFusion.

In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) with one model. We first propose Latent Graph Diffusion (LGD), a generative model that can generate node, edge, and graph-level features of all categories simultaneously. We achieve this goal by embedding the graph structures and features into a latent space leveraging a powerful encoder which can also be decoded, then training a diffusion model in the latent space. LGD is also capable of conditional generation through a specifically designed cross-attention mechanism. Then we formulate prediction tasks including regression and classification as (conditional) generation, which enables our LGD to solve tasks of all levels and all types with provable guarantees. We verify the effectiveness of our framework with extensive experiments, where our models achieve state-of-the-art or highly competitive results across generation and regression tasks.

Open-vocabulary dense prediction tasks including object detection and image segmentation have been advanced by the success of Contrastive Language-Image Pre-training (CLIP). CLIP models, particularly those incorporating vision transformers (ViTs), have exhibited remarkable generalization ability in zero-shot image classification. However, when transferring the vision-language alignment of CLIP from global image representation to local region representation for the open-vocabulary dense prediction tasks, CLIP ViTs suffer from the domain shift from full images to local image regions. In this paper, we embark on an in-depth analysis of the region-language alignment in CLIP models, which is essential for downstream open-vocabulary dense prediction tasks. Subsequently, we propose an approach named CLIPSelf, which adapts the image-level recognition ability of CLIP ViT to local image regions without needing any region-text pairs. CLIPSelf empowers ViTs to distill itself by aligning a region representation extracted from its dense feature map with the image-level representation of the corresponding image crop. With the enhanced CLIP ViTs, we achieve new state-of-the-art performance on open-vocabulary object detection, semantic segmentation, and panoptic segmentation across various benchmarks. Models and code will be available at https://github.com/wusize/CLIPSelf.

Learning to predict agent motions with relationship reasoning is important for many applications. In motion prediction tasks, maintaining motion equivariance under Euclidean geometric transformations and invariance of agent interaction is a critical and fundamental principle. However, such equivariance and invariance properties are overlooked by most existing methods. To fill this gap, we propose EqMotion, an efficient equivariant motion prediction model with invariant interaction reasoning. To achieve motion equivariance, we propose an equivariant geometric feature learning module to learn a Euclidean transformable feature through dedicated designs of equivariant operations. To reason agent's interactions, we propose an invariant interaction reasoning module to achieve a more stable interaction modeling. To further promote more comprehensive motion features, we propose an invariant pattern feature learning module to learn an invariant pattern feature, which cooperates with the equivariant geometric feature to enhance network expressiveness. We conduct experiments for the proposed model on four distinct scenarios: particle dynamics, molecule dynamics, human skeleton motion prediction and pedestrian trajectory prediction. Experimental results show that our method is not only generally applicable, but also achieves state-of-the-art prediction performances on all the four tasks, improving by 24.0/30.1/8.6/9.2%. Code is available at https://github.com/MediaBrain-SJTU/EqMotion.

Large Language Models (LLMs) hold great promise to revolutionize current clinical systems for their superior capacities on medical text processing tasks and medical licensing exams. Meanwhile, traditional ML models such as SVM and XGBoost have still been mainly adopted in clinical prediction tasks. An emerging question is Can LLMs beat traditional ML models in clinical prediction? Thus, we build a new benchmark ClinicalBench to comprehensively study the clinical predictive modeling capacities of both general-purpose and medical LLMs, and compare them with traditional ML models. ClinicalBench embraces three common clinical prediction tasks, two databases, 14 general-purpose LLMs, 8 medical LLMs, and 11 traditional ML models. Through extensive empirical investigation, we discover that both general-purpose and medical LLMs, even with different model scales, diverse prompting or fine-tuning strategies, still cannot beat traditional ML models in clinical prediction yet, shedding light on their potential deficiency in clinical reasoning and decision-making. We call for caution when practitioners adopt LLMs in clinical applications. ClinicalBench can be utilized to bridge the gap between LLMs' development for healthcare and real-world clinical practice.

The diverse nature of protein prediction tasks has traditionally necessitated specialized models, hindering the development of broadly applicable and computationally efficient Protein Language Models (PLMs). In this work, we introduce Prot2Token, a unified framework that overcomes these challenges by converting a wide spectrum of protein-related predictions, from sequence-level properties and residue-specific attributes to complex inter-protein interactions, into a standardized next-token prediction format. At its core, Prot2Token employs an autoregressive decoder, conditioned on embeddings from pre-trained protein encoders and guided by learnable task tokens, to perform diverse predictions. This architecture uniquely facilitates multi-task learning, enabling a single model to master numerous tasks with improved efficiency. We present extensive experimental validation across a variety of benchmarks, demonstrating Prot2Tokens strong predictive power in different types of protein-prediction tasks. Key results include significant speedups (e.g., near 1000x over AlphaFold2 with MSA) and performance often matching or exceeding specialized approaches. Beyond that, we introduce an auxiliary self-supervised decoder pre-training approach to improve spatially sensitive task performance. Prot2Token thus offers a significant step towards a versatile, high-throughput paradigm for protein modeling, promising to accelerate biological discovery and the development of novel therapeutics. The code is available at https://github.com/mahdip72/prot2token .

We introduce dense vision transformers, an architecture that leverages vision transformers in place of convolutional networks as a backbone for dense prediction tasks. We assemble tokens from various stages of the vision transformer into image-like representations at various resolutions and progressively combine them into full-resolution predictions using a convolutional decoder. The transformer backbone processes representations at a constant and relatively high resolution and has a global receptive field at every stage. These properties allow the dense vision transformer to provide finer-grained and more globally coherent predictions when compared to fully-convolutional networks. Our experiments show that this architecture yields substantial improvements on dense prediction tasks, especially when a large amount of training data is available. For monocular depth estimation, we observe an improvement of up to 28% in relative performance when compared to a state-of-the-art fully-convolutional network. When applied to semantic segmentation, dense vision transformers set a new state of the art on ADE20K with 49.02% mIoU. We further show that the architecture can be fine-tuned on smaller datasets such as NYUv2, KITTI, and Pascal Context where it also sets the new state of the art. Our models are available at https://github.com/intel-isl/DPT.

Battery degradation remains a critical challenge in the pursuit of green technologies and sustainable energy solutions. Despite significant research efforts, predicting battery capacity loss accurately remains a formidable task due to its complex nature, influenced by both aging and cycling behaviors. To address this challenge, we introduce a novel general-purpose model for battery degradation prediction and synthesis, DiffBatt. Leveraging an innovative combination of conditional and unconditional diffusion models with classifier-free guidance and transformer architecture, DiffBatt achieves high expressivity and scalability. DiffBatt operates as a probabilistic model to capture uncertainty in aging behaviors and a generative model to simulate battery degradation. The performance of the model excels in prediction tasks while also enabling the generation of synthetic degradation curves, facilitating enhanced model training by data augmentation. In the remaining useful life prediction task, DiffBatt provides accurate results with a mean RMSE of 196 cycles across all datasets, outperforming all other models and demonstrating superior generalizability. This work represents an important step towards developing foundational models for battery degradation.

Despite its outstanding performance in various graph tasks, vanilla Message Passing Neural Network (MPNN) usually fails in link prediction tasks, as it only uses representations of two individual target nodes and ignores the pairwise relation between them. To capture the pairwise relations, some models add manual features to the input graph and use the output of MPNN to produce pairwise representations. In contrast, others directly use manual features as pairwise representations. Though this simplification avoids applying a GNN to each link individually and thus improves scalability, these models still have much room for performance improvement due to the hand-crafted and unlearnable pairwise features. To upgrade performance while maintaining scalability, we propose Neural Common Neighbor (NCN), which uses learnable pairwise representations. To further boost NCN, we study the unobserved link problem. The incompleteness of the graph is ubiquitous and leads to distribution shifts between the training and test set, loss of common neighbor information, and performance degradation of models. Therefore, we propose two intervention methods: common neighbor completion and target link removal. Combining the two methods with NCN, we propose Neural Common Neighbor with Completion (NCNC). NCN and NCNC outperform recent strong baselines by large margins. NCNC achieves state-of-the-art performance in link prediction tasks. Our code is available at https://github.com/GraphPKU/NeuralCommonNeighbor.

Accurately predicting the future fluid is important to extensive areas, such as meteorology, oceanology and aerodynamics. However, since the fluid is usually observed from an Eulerian perspective, its active and intricate dynamics are seriously obscured and confounded in static grids, bringing horny challenges to the prediction. This paper introduces a new Lagrangian-guided paradigm to tackle the tanglesome fluid dynamics. Instead of solely predicting the future based on Eulerian observations, we propose the Eulerian-Lagrangian Dual Recurrent Network (EuLagNet), which captures multiscale fluid dynamics by tracking movements of adaptively sampled key particles on multiple scales and integrating dynamics information over time. Concretely, a EuLag Block is presented to communicate the learned Eulerian and Lagrangian features at each moment and scale, where the motion of tracked particles is inferred from Eulerian observations and their accumulated dynamics information is incorporated into Eulerian fields to guide future prediction. Tracking key particles not only provides a clear and interpretable clue for fluid dynamics but also makes our model free from modeling complex correlations among massive grids for better efficiency. Experimentally, EuLagNet excels in three challenging fluid prediction tasks, covering both 2D and 3D, simulated and real-world fluids.

We introduce a novel framework for incorporating human expertise into algorithmic predictions. Our approach leverages human judgment to distinguish inputs which are algorithmically indistinguishable, or "look the same" to predictive algorithms. We argue that this framing clarifies the problem of human-AI collaboration in prediction tasks, as experts often form judgments by drawing on information which is not encoded in an algorithm's training data. Algorithmic indistinguishability yields a natural test for assessing whether experts incorporate this kind of "side information", and further provides a simple but principled method for selectively incorporating human feedback into algorithmic predictions. We show that this method provably improves the performance of any feasible algorithmic predictor and precisely quantify this improvement. We find empirically that although algorithms often outperform their human counterparts on average, human judgment can improve algorithmic predictions on specific instances (which can be identified ex-ante). In an X-ray classification task, we find that this subset constitutes nearly 30% of the patient population. Our approach provides a natural way of uncovering this heterogeneity and thus enabling effective human-AI collaboration.

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in a way such that they can be captured by PLMs. Prior work on structured prediction with PLMs typically flattens the structured output into a sequence, which limits the quality of structural information being learned and leads to inferior performance compared to classic discriminative models. In this work, we describe an approach to model structures as sequences of actions in an autoregressive manner with PLMs, allowing in-structure dependencies to be learned without any loss. Our approach achieves the new state-of-the-art on all the structured prediction tasks we looked at, namely, named entity recognition, end-to-end relation extraction, and coreference resolution.

Vision transformers have recently achieved competitive results across various vision tasks but still suffer from heavy computation costs when processing a large number of tokens. Many advanced approaches have been developed to reduce the total number of tokens in large-scale vision transformers, especially for image classification tasks. Typically, they select a small group of essential tokens according to their relevance with the class token, then fine-tune the weights of the vision transformer. Such fine-tuning is less practical for dense prediction due to the much heavier computation and GPU memory cost than image classification. In this paper, we focus on a more challenging problem, i.e., accelerating large-scale vision transformers for dense prediction without any additional re-training or fine-tuning. In response to the fact that high-resolution representations are necessary for dense prediction, we present two non-parametric operators, a token clustering layer to decrease the number of tokens and a token reconstruction layer to increase the number of tokens. The following steps are performed to achieve this: (i) we use the token clustering layer to cluster the neighboring tokens together, resulting in low-resolution representations that maintain the spatial structures; (ii) we apply the following transformer layers only to these low-resolution representations or clustered tokens; and (iii) we use the token reconstruction layer to re-create the high-resolution representations from the refined low-resolution representations. The results obtained by our method are promising on five dense prediction tasks, including object detection, semantic segmentation, panoptic segmentation, instance segmentation, and depth estimation.

Integrating CNNs and RNNs to capture spatiotemporal dependencies is a prevalent strategy for spatiotemporal prediction tasks. However, the property of CNNs to learn local spatial information decreases their efficiency in capturing spatiotemporal dependencies, thereby limiting their prediction accuracy. In this paper, we propose a new recurrent cell, SwinLSTM, which integrates Swin Transformer blocks and the simplified LSTM, an extension that replaces the convolutional structure in ConvLSTM with the self-attention mechanism. Furthermore, we construct a network with SwinLSTM cell as the core for spatiotemporal prediction. Without using unique tricks, SwinLSTM outperforms state-of-the-art methods on Moving MNIST, Human3.6m, TaxiBJ, and KTH datasets. In particular, it exhibits a significant improvement in prediction accuracy compared to ConvLSTM. Our competitive experimental results demonstrate that learning global spatial dependencies is more advantageous for models to capture spatiotemporal dependencies. We hope that SwinLSTM can serve as a solid baseline to promote the advancement of spatiotemporal prediction accuracy. The codes are publicly available at https://github.com/SongTang-x/SwinLSTM.

Pretrained contextualized embeddings are powerful word representations for structured prediction tasks. Recent work found that better word representations can be obtained by concatenating different types of embeddings. However, the selection of embeddings to form the best concatenated representation usually varies depending on the task and the collection of candidate embeddings, and the ever-increasing number of embedding types makes it a more difficult problem. In this paper, we propose Automated Concatenation of Embeddings (ACE) to automate the process of finding better concatenations of embeddings for structured prediction tasks, based on a formulation inspired by recent progress on neural architecture search. Specifically, a controller alternately samples a concatenation of embeddings, according to its current belief of the effectiveness of individual embedding types in consideration for a task, and updates the belief based on a reward. We follow strategies in reinforcement learning to optimize the parameters of the controller and compute the reward based on the accuracy of a task model, which is fed with the sampled concatenation as input and trained on a task dataset. Empirical results on 6 tasks and 21 datasets show that our approach outperforms strong baselines and achieves state-of-the-art performance with fine-tuned embeddings in all the evaluations.

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

The success of drug discovery and development relies on the precise prediction of molecular activities and properties. While in silico molecular property prediction has shown remarkable potential, its use has been limited so far to assays for which large amounts of data are available. In this study, we use a fine-tuned large language model to integrate biological assays based on their textual information, coupled with Barlow Twins, a Siamese neural network using a novel self-supervised learning approach. This architecture uses both assay information and molecular fingerprints to extract the true molecular information. TwinBooster enables the prediction of properties of unseen bioassays and molecules by providing state-of-the-art zero-shot learning tasks. Remarkably, our artificial intelligence pipeline shows excellent performance on the FS-Mol benchmark. This breakthrough demonstrates the application of deep learning to critical property prediction tasks where data is typically scarce. By accelerating the early identification of active molecules in drug discovery and development, this method has the potential to help streamline the identification of novel therapeutics.

Next-token prediction models have predominantly relied on decoder-only Transformers with causal attention, driven by the common belief that causal attention is essential to prevent "cheating" by masking future tokens. We challenge this widely accepted notion and argue that this design choice is about efficiency rather than necessity. While decoder-only Transformers are still a good choice for practical reasons, they are not the only viable option. In this work, we introduce Encoder-only Next Token Prediction (ENTP). We explore the differences between ENTP and decoder-only Transformers in expressive power and complexity, highlighting potential advantages of ENTP. We introduce the Triplet-Counting task and show, both theoretically and experimentally, that while ENTP can perform this task easily, a decoder-only Transformer cannot. Finally, we empirically demonstrate ENTP's superior performance across various realistic tasks, such as length generalization and in-context learning.

Recently, State Space Models (SSMs) with efficient hardware-aware designs, i.e., Mamba, have demonstrated significant potential in computer vision tasks due to their linear computational complexity with respect to token length and their global receptive field. However, Mamba's performance on dense prediction tasks, including human pose estimation and semantic segmentation, has been constrained by three key challenges: insufficient inductive bias, long-range forgetting, and low-resolution output representation. To address these challenges, we introduce the Dynamic Visual State Space (DVSS) block, which utilizes multi-scale convolutional kernels to extract local features across different scales and enhance inductive bias, and employs deformable convolution to mitigate the long-range forgetting problem while enabling adaptive spatial aggregation based on input and task-specific information. By leveraging the multi-resolution parallel design proposed in HRNet, we introduce High-Resolution Visual State Space Model (HRVMamba) based on the DVSS block, which preserves high-resolution representations throughout the entire process while promoting effective multi-scale feature learning. Extensive experiments highlight HRVMamba's impressive performance on dense prediction tasks, achieving competitive results against existing benchmark models without bells and whistles. Code is available at https://github.com/zhanghao5201/HRVMamba.

Disease risk prediction has attracted increasing attention in the field of modern healthcare, especially with the latest advances in artificial intelligence (AI). Electronic health records (EHRs), which contain heterogeneous patient information, are widely used in disease risk prediction tasks. One challenge of applying AI models for risk prediction lies in generating interpretable evidence to support the prediction results while retaining the prediction ability. In order to address this problem, we propose the method of jointly embedding words and labels whereby attention modules learn the weights of words from medical notes according to their relevance to the names of risk prediction labels. This approach boosts interpretability by employing an attention mechanism and including the names of prediction tasks in the model. However, its application is only limited to the handling of textual inputs such as medical notes. In this paper, we propose a label dependent attention model LDAM to 1) improve the interpretability by exploiting Clinical-BERT (a biomedical language model pre-trained on a large clinical corpus) to encode biomedically meaningful features and labels jointly; 2) extend the idea of joint embedding to the processing of time-series data, and develop a multi-modal learning framework for integrating heterogeneous information from medical notes and time-series health status indicators. To demonstrate our method, we apply LDAM to the MIMIC-III dataset to predict different disease risks. We evaluate our method both quantitatively and qualitatively. Specifically, the predictive power of LDAM will be shown, and case studies will be carried out to illustrate its interpretability.

This large scale study focuses on quantifying what X-rays diagnostic prediction tasks generalize well across multiple different datasets. We present evidence that the issue of generalization is not due to a shift in the images but instead a shift in the labels. We study the cross-domain performance, agreement between models, and model representations. We find interesting discrepancies between performance and agreement where models which both achieve good performance disagree in their predictions as well as models which agree yet achieve poor performance. We also test for concept similarity by regularizing a network to group tasks across multiple datasets together and observe variation across the tasks. All code is made available online and data is publicly available: https://github.com/mlmed/torchxrayvision

We propose split-brain autoencoders, a straightforward modification of the traditional autoencoder architecture, for unsupervised representation learning. The method adds a split to the network, resulting in two disjoint sub-networks. Each sub-network is trained to perform a difficult task -- predicting one subset of the data channels from another. Together, the sub-networks extract features from the entire input signal. By forcing the network to solve cross-channel prediction tasks, we induce a representation within the network which transfers well to other, unseen tasks. This method achieves state-of-the-art performance on several large-scale transfer learning benchmarks.

Model evolution and constant availability of data are two common phenomena in large-scale real-world machine learning applications, e.g. ads and recommendation systems. To adapt, the real-world system typically retrain with all available data and online learn with recently available data to update the models periodically with the goal of better serving performance. In this paper, we propose a novel framework, named Confidence Ranking, which designs the optimization objective as a ranking function with two different models. Our confidence ranking loss allows direct optimization of the logits output for different convex surrogate functions of metrics, e.g. AUC and Accuracy depending on the target task and dataset. Armed with our proposed methods, our experiments show that the introduction of confidence ranking loss can outperform all baselines on the CTR prediction tasks of public and industrial datasets. This framework has been deployed in the advertisement system of JD.com to serve the main traffic in the fine-rank stage.

Machine learning models are often personalized with categorical attributes that are protected, sensitive, self-reported, or costly to acquire. In this work, we show models that are personalized with group attributes can reduce performance at a group level. We propose formal conditions to ensure the "fair use" of group attributes in prediction tasks by training one additional model -- i.e., collective preference guarantees to ensure that each group who provides personal data will receive a tailored gain in performance in return. We present sufficient conditions to ensure fair use in empirical risk minimization and characterize failure modes that lead to fair use violations due to standard practices in model development and deployment. We present a comprehensive empirical study of fair use in clinical prediction tasks. Our results demonstrate the prevalence of fair use violations in practice and illustrate simple interventions to mitigate their harm.

Activity and property prediction models are the central workhorses in drug discovery and materials sciences, but currently they have to be trained or fine-tuned for new tasks. Without training or fine-tuning, scientific language models could be used for such low-data tasks through their announced zero- and few-shot capabilities. However, their predictive quality at activity prediction is lacking. In this work, we envision a novel type of activity prediction model that is able to adapt to new prediction tasks at inference time, via understanding textual information describing the task. To this end, we propose a new architecture with separate modules for chemical and natural language inputs, and a contrastive pre-training objective on data from large biochemical databases. In extensive experiments, we show that our method CLAMP yields improved predictive performance on few-shot learning benchmarks and zero-shot problems in drug discovery. We attribute the advances of our method to the modularized architecture and to our pre-training objective.

In the present research, we delve into the intricate realm of electroencephalogram (EEG) data analysis, focusing on sequence-to-sequence prediction of data across 32 EEG channels. The study harmoniously fuses the principles of applied chaos theory and dynamical systems theory to engender a novel feature set, enriching the representational capacity of our deep learning model. The endeavour's cornerstone is a transformer-based sequence-to-sequence architecture, calibrated meticulously to capture the non-linear and high-dimensional temporal dependencies inherent in EEG sequences. Through judicious architecture design, parameter initialisation strategies, and optimisation techniques, we have navigated the intricate balance between computational expediency and predictive performance. Our model stands as a vanguard in EEG data sequence prediction, demonstrating remarkable generalisability and robustness. The findings not only extend our understanding of EEG data dynamics but also unveil a potent analytical framework that can be adapted to diverse temporal sequence prediction tasks in neuroscience and beyond.

Large language models have evolved data-efficient generalists, benefiting from the universal language interface and large-scale pre-training. However, constructing a data-efficient generalist for dense visual prediction presents a distinct challenge due to the variation in label structures across different tasks. Consequently, generalization to unseen dense prediction tasks in the low-data regime is not straightforward and has received less attention from previous vision generalists. In this study, we explore a universal model that can flexibly adapt to unseen dense label structures with a few examples, enabling it to serve as a data-efficient vision generalist in diverse real-world scenarios. To this end, we base our method on a powerful meta-learning framework and explore several axes to improve its performance and versatility for real-world problems, such as flexible adaptation mechanisms and scalability. We evaluate our model across a spectrum of unseen real-world scenarios where low-shot learning is desirable, including video, 3D, medical, biological, and user-interactive tasks. Equipped with a generic architecture and an effective adaptation mechanism, our model flexibly adapts to all of these tasks with at most 50 labeled images, showcasing a significant advancement over existing data-efficient generalist approaches. Codes are available at https://github.com/GitGyun/chameleon.

We propose a simple, efficient, yet powerful framework for dense visual predictions based on the conditional diffusion pipeline. Our approach follows a "noise-to-map" generative paradigm for prediction by progressively removing noise from a random Gaussian distribution, guided by the image. The method, called DDP, efficiently extends the denoising diffusion process into the modern perception pipeline. Without task-specific design and architecture customization, DDP is easy to generalize to most dense prediction tasks, e.g., semantic segmentation and depth estimation. In addition, DDP shows attractive properties such as dynamic inference and uncertainty awareness, in contrast to previous single-step discriminative methods. We show top results on three representative tasks with six diverse benchmarks, without tricks, DDP achieves state-of-the-art or competitive performance on each task compared to the specialist counterparts. For example, semantic segmentation (83.9 mIoU on Cityscapes), BEV map segmentation (70.6 mIoU on nuScenes), and depth estimation (0.05 REL on KITTI). We hope that our approach will serve as a solid baseline and facilitate future research

Accurate uncertainty measurement is a key step to building robust and reliable machine learning systems. Conformal prediction is a distribution-free uncertainty quantification algorithm popular for its ease of implementation, statistical coverage guarantees, and versatility for underlying forecasters. However, existing conformal prediction algorithms for time series are limited to single-step prediction without considering the temporal dependency. In this paper, we propose a Copula Conformal Prediction algorithm for multivariate, multi-step Time Series forecasting, CopulaCPTS. We prove that CopulaCPTS has finite sample validity guarantee. On several synthetic and real-world multivariate time series datasets, we show that CopulaCPTS produces more calibrated and sharp confidence intervals for multi-step prediction tasks than existing techniques.

Recent progress has shown that large-scale pre-training using contrastive image-text pairs can be a promising alternative for high-quality visual representation learning from natural language supervision. Benefiting from a broader source of supervision, this new paradigm exhibits impressive transferability to downstream classification tasks and datasets. However, the problem of transferring the knowledge learned from image-text pairs to more complex dense prediction tasks has barely been visited. In this work, we present a new framework for dense prediction by implicitly and explicitly leveraging the pre-trained knowledge from CLIP. Specifically, we convert the original image-text matching problem in CLIP to a pixel-text matching problem and use the pixel-text score maps to guide the learning of dense prediction models. By further using the contextual information from the image to prompt the language model, we are able to facilitate our model to better exploit the pre-trained knowledge. Our method is model-agnostic, which can be applied to arbitrary dense prediction systems and various pre-trained visual backbones including both CLIP models and ImageNet pre-trained models. Extensive experiments demonstrate the superior performance of our methods on semantic segmentation, object detection, and instance segmentation tasks. Code is available at https://github.com/raoyongming/DenseCLIP

Although using convolutional neural networks (CNNs) as backbones achieves great successes in computer vision, this work investigates a simple backbone network useful for many dense prediction tasks without convolutions. Unlike the recently-proposed Transformer model (e.g., ViT) that is specially designed for image classification, we propose Pyramid Vision Transformer~(PVT), which overcomes the difficulties of porting Transformer to various dense prediction tasks. PVT has several merits compared to prior arts. (1) Different from ViT that typically has low-resolution outputs and high computational and memory cost, PVT can be not only trained on dense partitions of the image to achieve high output resolution, which is important for dense predictions but also using a progressive shrinking pyramid to reduce computations of large feature maps. (2) PVT inherits the advantages from both CNN and Transformer, making it a unified backbone in various vision tasks without convolutions by simply replacing CNN backbones. (3) We validate PVT by conducting extensive experiments, showing that it boosts the performance of many downstream tasks, e.g., object detection, semantic, and instance segmentation. For example, with a comparable number of parameters, RetinaNet+PVT achieves 40.4 AP on the COCO dataset, surpassing RetinNet+ResNet50 (36.3 AP) by 4.1 absolute AP. We hope PVT could serve as an alternative and useful backbone for pixel-level predictions and facilitate future researches. Code is available at https://github.com/whai362/PVT.

Machine learning models in health care are often deployed in settings where it is important to protect patient privacy. In such settings, methods for differentially private (DP) learning provide a general-purpose approach to learn models with privacy guarantees. Modern methods for DP learning ensure privacy through mechanisms that censor information judged as too unique. The resulting privacy-preserving models, therefore, neglect information from the tails of a data distribution, resulting in a loss of accuracy that can disproportionately affect small groups. In this paper, we study the effects of DP learning in health care. We use state-of-the-art methods for DP learning to train privacy-preserving models in clinical prediction tasks, including x-ray classification of images and mortality prediction in time series data. We use these models to perform a comprehensive empirical investigation of the tradeoffs between privacy, utility, robustness to dataset shift, and fairness. Our results highlight lesser-known limitations of methods for DP learning in health care, models that exhibit steep tradeoffs between privacy and utility, and models whose predictions are disproportionately influenced by large demographic groups in the training data. We discuss the costs and benefits of differentially private learning in health care.

The recent DeepSeek-R1 has showcased the emergence of reasoning capabilities in LLMs through reinforcement learning (RL) with rule-based rewards. Building on this idea, we are the first to explore how rule-based RL can enhance the reasoning capabilities of multimodal large language models (MLLMs) for graphic user interface (GUI) action prediction tasks. To this end, we curate a small yet high-quality dataset of 136 challenging tasks, encompassing five common action types on mobile devices. We also introduce a unified rule-based action reward, enabling model optimization via policy-based algorithms such as Group Relative Policy Optimization (GRPO). Experimental results demonstrate that our proposed data-efficient model, UI-R1-3B, achieves substantial improvements on both in-domain (ID) and out-of-domain (OOD) tasks. Specifically, on the ID benchmark AndroidControl, the action type accuracy improves by 15%, while grounding accuracy increases by 10.3%, compared with the base model (i.e. Qwen2.5-VL-3B). On the OOD GUI grounding benchmark ScreenSpot-Pro, our model surpasses the base model by 6.0% and achieves competitive performance with larger models (e.g., OS-Atlas-7B), which are trained via supervised fine-tuning (SFT) on 76K data. These results underscore the potential of rule-based reinforcement learning to advance GUI understanding and control, paving the way for future research in this domain.

Central to our understanding of chemical reactivity is the principle of mass conservation, which is fundamental for ensuring physical consistency, balancing equations, and guiding reaction design. However, data-driven computational models for tasks such as reaction product prediction rarely abide by this most basic constraint. In this work, we recast the problem of reaction prediction as a problem of electron redistribution using the modern deep generative framework of flow matching. Our model, FlowER, overcomes limitations inherent in previous approaches by enforcing exact mass conservation, thereby resolving hallucinatory failure modes, recovering mechanistic reaction sequences for unseen substrate scaffolds, and generalizing effectively to out-of-domain reaction classes with extremely data-efficient fine-tuning. FlowER additionally enables estimation of thermodynamic or kinetic feasibility and manifests a degree of chemical intuition in reaction prediction tasks. This inherently interpretable framework represents a significant step in bridging the gap between predictive accuracy and mechanistic understanding in data-driven reaction outcome prediction.

Learning about the three-dimensional world from two-dimensional images is a fundamental problem in computer vision. An ideal neural network architecture for such tasks would leverage the fact that objects can be rotated and translated in three dimensions to make predictions about novel images. However, imposing SO(3)-equivariance on two-dimensional inputs is difficult because the group of three-dimensional rotations does not have a natural action on the two-dimensional plane. Specifically, it is possible that an element of SO(3) will rotate an image out of plane. We show that an algorithm that learns a three-dimensional representation of the world from two dimensional images must satisfy certain geometric consistency properties which we formulate as SO(2)-equivariance constraints. We use the induced and restricted representations of SO(2) on SO(3) to construct and classify architectures which satisfy these geometric consistency constraints. We prove that any architecture which respects said consistency constraints can be realized as an instance of our construction. We show that three previously proposed neural architectures for 3D pose prediction are special cases of our construction. We propose a new algorithm that is a learnable generalization of previously considered methods. We test our architecture on three pose predictions task and achieve SOTA results on both the PASCAL3D+ and SYMSOL pose estimation tasks.

In this paper, we study the problem of inference in high-order structured prediction tasks. In the context of Markov random fields, the goal of a high-order inference task is to maximize a score function on the space of labels, and the score function can be decomposed into sum of unary and high-order potentials. We apply a generative model approach to study the problem of high-order inference, and provide a two-stage convex optimization algorithm for exact label recovery. We also provide a new class of hypergraph structural properties related to hyperedge expansion that drives the success in general high-order inference problems. Finally, we connect the performance of our algorithm and the hyperedge expansion property using a novel hypergraph Cheeger-type inequality.

This paper describes the performance of the team cs60075_team2 at SemEval 2021 Task 1 - Lexical Complexity Prediction. The main contribution of this paper is to fine-tune transformer-based language models pre-trained on several text corpora, some being general (E.g., Wikipedia, BooksCorpus), some being the corpora from which the CompLex Dataset was extracted, and others being from other specific domains such as Finance, Law, etc. We perform ablation studies on selecting the transformer models and how their individual complexity scores are aggregated to get the resulting complexity scores. Our method achieves a best Pearson Correlation of 0.784 in sub-task 1 (single word) and 0.836 in sub-task 2 (multiple word expressions).

Legal judgment prediction is the task of automatically predicting the outcome of a court case, given a text describing the case's facts. Previous work on using neural models for this task has focused on Chinese; only feature-based models (e.g., using bags of words and topics) have been considered in English. We release a new English legal judgment prediction dataset, containing cases from the European Court of Human Rights. We evaluate a broad variety of neural models on the new dataset, establishing strong baselines that surpass previous feature-based models in three tasks: (1) binary violation classification; (2) multi-label classification; (3) case importance prediction. We also explore if models are biased towards demographic information via data anonymization. As a side-product, we propose a hierarchical version of BERT, which bypasses BERT's length limitation.

CLIP models perform remarkably well on zero-shot classification and retrieval tasks. But recent studies have shown that learnt representations in CLIP are not well suited for dense prediction tasks like object detection, semantic segmentation or depth estimation. More recently, multi-stage training methods for CLIP models was introduced to mitigate the weak performance of CLIP on downstream tasks. In this work, we find that simply improving the quality of captions in image-text datasets improves the quality of CLIP's visual representations, resulting in significant improvement on downstream dense prediction vision tasks. In fact, we find that CLIP pretraining with good quality captions can surpass recent supervised, self-supervised and weakly supervised pretraining methods. We show that when CLIP model with ViT-B/16 as image encoder is trained on well aligned image-text pairs it obtains 12.1% higher mIoU and 11.5% lower RMSE on semantic segmentation and depth estimation tasks over recent state-of-the-art Masked Image Modeling (MIM) pretraining methods like Masked Autoencoder (MAE). We find that mobile architectures also benefit significantly from CLIP pretraining. A recent mobile vision architecture, MCi2, with CLIP pretraining obtains similar performance as Swin-L, pretrained on ImageNet-22k for semantic segmentation task while being 6.1times smaller. Moreover, we show that improving caption quality results in 10times data efficiency when finetuning for dense prediction tasks.

Accurate Urban SpatioTemporal Prediction (USTP) is of great importance to the development and operation of the smart city. As an emerging building block, multi-sourced urban data are usually integrated as urban knowledge graphs (UrbanKGs) to provide critical knowledge for urban spatiotemporal prediction models. However, existing UrbanKGs are often tailored for specific downstream prediction tasks and are not publicly available, which limits the potential advancement. This paper presents UUKG, the unified urban knowledge graph dataset for knowledge-enhanced urban spatiotemporal predictions. Specifically, we first construct UrbanKGs consisting of millions of triplets for two metropolises by connecting heterogeneous urban entities such as administrative boroughs, POIs, and road segments. Moreover, we conduct qualitative and quantitative analysis on constructed UrbanKGs and uncover diverse high-order structural patterns, such as hierarchies and cycles, that can be leveraged to benefit downstream USTP tasks. To validate and facilitate the use of UrbanKGs, we implement and evaluate 15 KG embedding methods on the KG completion task and integrate the learned KG embeddings into 9 spatiotemporal models for five different USTP tasks. The extensive experimental results not only provide benchmarks of knowledge-enhanced USTP models under different task settings but also highlight the potential of state-of-the-art high-order structure-aware UrbanKG embedding methods. We hope the proposed UUKG fosters research on urban knowledge graphs and broad smart city applications. The dataset and source code are available at https://github.com/usail-hkust/UUKG/.

Data organized in tabular format is ubiquitous in real-world applications, and users often craft tables with biased feature definitions and flexibly set prediction targets of their interests. Thus, a rapid development of a robust, effective, dataset-versatile, user-friendly tabular prediction approach is highly desired. While Gradient Boosting Decision Trees (GBDTs) and existing deep neural networks (DNNs) have been extensively utilized by professional users, they present several challenges for casual users, particularly: (i) the dilemma of model selection due to their different dataset preferences, and (ii) the need for heavy hyperparameter searching, failing which their performances are deemed inadequate. In this paper, we delve into this question: Can we develop a deep learning model that serves as a "sure bet" solution for a wide range of tabular prediction tasks, while also being user-friendly for casual users? We delve into three key drawbacks of deep tabular models, encompassing: (P1) lack of rotational variance property, (P2) large data demand, and (P3) over-smooth solution. We propose ExcelFormer, addressing these challenges through a semi-permeable attention module that effectively constrains the influence of less informative features to break the DNNs' rotational invariance property (for P1), data augmentation approaches tailored for tabular data (for P2), and attentive feedforward network to boost the model fitting capability (for P3). These designs collectively make ExcelFormer a "sure bet" solution for diverse tabular datasets. Extensive and stratified experiments conducted on real-world datasets demonstrate that our model outperforms previous approaches across diverse tabular data prediction tasks, and this framework can be friendly to casual users, offering ease of use without the heavy hyperparameter tuning.

Machine learning interatomic potentials (MLIPs) have become increasingly effective at approximating quantum mechanical calculations at a fraction of the computational cost. However, lower errors on held out test sets do not always translate to improved results on downstream physical property prediction tasks. In this paper, we propose testing MLIPs on their practical ability to conserve energy during molecular dynamic simulations. If passed, improved correlations are found between test errors and their performance on physical property prediction tasks. We identify choices which may lead to models failing this test, and use these observations to improve upon highly-expressive models. The resulting model, eSEN, provides state-of-the-art results on a range of physical property prediction tasks, including materials stability prediction, thermal conductivity prediction, and phonon calculations.

The integration of artificial intelligence (AI) in legal judgment prediction (LJP) has the potential to transform the legal landscape, particularly in jurisdictions like India, where a significant backlog of cases burdens the legal system. This paper introduces NyayaAnumana, the largest and most diverse corpus of Indian legal cases compiled for LJP, encompassing a total of 7,02,945 preprocessed cases. NyayaAnumana, which combines the words "Nyay" (judgment) and "Anuman" (prediction or inference) respectively for most major Indian languages, includes a wide range of cases from the Supreme Court, High Courts, Tribunal Courts, District Courts, and Daily Orders and, thus, provides unparalleled diversity and coverage. Our dataset surpasses existing datasets like PredEx and ILDC, offering a comprehensive foundation for advanced AI research in the legal domain. In addition to the dataset, we present INLegalLlama, a domain-specific generative large language model (LLM) tailored to the intricacies of the Indian legal system. It is developed through a two-phase training approach over a base LLaMa model. First, Indian legal documents are injected using continual pretraining. Second, task-specific supervised finetuning is done. This method allows the model to achieve a deeper understanding of legal contexts. Our experiments demonstrate that incorporating diverse court data significantly boosts model accuracy, achieving approximately 90% F1-score in prediction tasks. INLegalLlama not only improves prediction accuracy but also offers comprehensible explanations, addressing the need for explainability in AI-assisted legal decisions.

Graph neural networks (GNNs) have shown promising performance for knowledge graph reasoning. A recent variant of GNN called progressive relational graph neural network (PRGNN), utilizes relational rules to infer missing knowledge in relational digraphs and achieves notable results. However, during reasoning with PRGNN, two important properties are often overlooked: (1) the sequentiality of relation composition, where the order of combining different relations affects the semantics of the relational rules, and (2) the lagged entity information propagation, where the transmission speed of required information lags behind the appearance speed of new entities. Ignoring these properties leads to incorrect relational rule learning and decreased reasoning accuracy. To address these issues, we propose a novel knowledge graph reasoning approach, the Relational rUle eNhanced Graph Neural Network (RUN-GNN). Specifically, RUN-GNN employs a query related fusion gate unit to model the sequentiality of relation composition and utilizes a buffering update mechanism to alleviate the negative effect of lagged entity information propagation, resulting in higher-quality relational rule learning. Experimental results on multiple datasets demonstrate the superiority of RUN-GNN is superior on both transductive and inductive link prediction tasks.

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at https://github.com/ChnQ/LLM4Mol.

Leveraging the visual priors of pre-trained text-to-image diffusion models offers a promising solution to enhance zero-shot generalization in dense prediction tasks. However, existing methods often uncritically use the original diffusion formulation, which may not be optimal due to the fundamental differences between dense prediction and image generation. In this paper, we provide a systemic analysis of the diffusion formulation for the dense prediction, focusing on both quality and efficiency. And we find that the original parameterization type for image generation, which learns to predict noise, is harmful for dense prediction; the multi-step noising/denoising diffusion process is also unnecessary and challenging to optimize. Based on these insights, we introduce Lotus, a diffusion-based visual foundation model with a simple yet effective adaptation protocol for dense prediction. Specifically, Lotus is trained to directly predict annotations instead of noise, thereby avoiding harmful variance. We also reformulate the diffusion process into a single-step procedure, simplifying optimization and significantly boosting inference speed. Additionally, we introduce a novel tuning strategy called detail preserver, which achieves more accurate and fine-grained predictions. Without scaling up the training data or model capacity, Lotus achieves SoTA performance in zero-shot depth and normal estimation across various datasets. It also significantly enhances efficiency, being hundreds of times faster than most existing diffusion-based methods.

Advances in large language models (LLMs) have empowered a variety of applications. However, there is still a significant gap in research when it comes to understanding and enhancing the capabilities of LLMs in the field of mental health. In this work, we present the first comprehensive evaluation of multiple LLMs, including Alpaca, Alpaca-LoRA, FLAN-T5, GPT-3.5, and GPT-4, on various mental health prediction tasks via online text data. We conduct a broad range of experiments, covering zero-shot prompting, few-shot prompting, and instruction fine-tuning. The results indicate a promising yet limited performance of LLMs with zero-shot and few-shot prompt designs for the mental health tasks. More importantly, our experiments show that instruction finetuning can significantly boost the performance of LLMs for all tasks simultaneously. Our best-finetuned models, Mental-Alpaca and Mental-FLAN-T5, outperform the best prompt design of GPT-3.5 (25 and 15 times bigger) by 10.9% on balanced accuracy and the best of GPT-4 (250 and 150 times bigger) by 4.8%. They further perform on par with the state-of-the-art task-specific language model. We also conduct an exploratory case study on LLMs' capability on the mental health reasoning tasks, illustrating the promising capability of certain models such as GPT-4. We summarize our findings into a set of action guidelines for potential methods to enhance LLMs' capability for mental health tasks. Meanwhile, we also emphasize the important limitations before achieving deployability in real-world mental health settings, such as known racial and gender bias. We highlight the important ethical risks accompanying this line of research.

The task of predicting time and location from images is challenging and requires complex human-like puzzle-solving ability over different clues. In this work, we formalize this ability into core skills and implement them using different modules in an expert pipeline called PuzzleGPT. PuzzleGPT consists of a perceiver to identify visual clues, a reasoner to deduce prediction candidates, a combiner to combinatorially combine information from different clues, a web retriever to get external knowledge if the task can't be solved locally, and a noise filter for robustness. This results in a zero-shot, interpretable, and robust approach that records state-of-the-art performance on two datasets -- TARA and WikiTilo. PuzzleGPT outperforms large VLMs such as BLIP-2, InstructBLIP, LLaVA, and even GPT-4V, as well as automatically generated reasoning pipelines like VisProg, by at least 32% and 38%, respectively. It even rivals or surpasses finetuned models.

Pre-trained vision-language models (VLMs), such as CLIP, have demonstrated impressive zero-shot recognition capability, but still underperform in dense prediction tasks. Self-distillation recently is emerging as a promising approach for fine-tuning VLMs to better adapt to local regions without requiring extensive annotations. However, previous state-of-the-art approaches often suffer from significant `foreground bias', where models tend to wrongly identify background regions as foreground objects. To alleviate this issue, we propose DenseVLM, a framework designed to learn unbiased region-language alignment from powerful pre-trained VLM representations. To alleviate this issue, we propose DenseVLM, a framework designed to learn unbiased region-language alignment from powerful pre-trained VLM representations. DenseVLM leverages the pre-trained VLM to retrieve categories for unlabeled regions and then decouples the interference between foreground and background features. We show that DenseVLM can directly replace the original VLM in open-vocabulary object detection and image segmentation methods, leading to notable performance improvements. Furthermore, it exhibits promising zero-shot scalability when training on more extensive and diverse datasets. Our code is available at https://github.com/HVision-NKU/DenseVLM.

The transferability of deep neural networks (DNNs) has made significant progress in image and language processing. However, due to the heterogeneity among tables, such DNN bonus is still far from being well exploited on tabular data prediction (e.g., regression or classification tasks). Condensing knowledge from diverse domains, language models (LMs) possess the capability to comprehend feature names from various tables, potentially serving as versatile learners in transferring knowledge across distinct tables and diverse prediction tasks, but their discrete text representation space is inherently incompatible with numerical feature values in tables. In this paper, we present TP-BERTa, a specifically pre-trained LM for tabular data prediction. Concretely, a novel relative magnitude tokenization converts scalar numerical feature values to finely discrete, high-dimensional tokens, and an intra-feature attention approach integrates feature values with the corresponding feature names. Comprehensive experiments demonstrate that our pre-trained TP-BERTa leads the performance among tabular DNNs and is competitive with Gradient Boosted Decision Tree models in typical tabular data regime.

Automatically generating scripts (i.e. sequences of key steps described in text) from video demonstrations and reasoning about the subsequent steps are crucial to the modern AI virtual assistants to guide humans to complete everyday tasks, especially unfamiliar ones. However, current methods for generative script learning rely heavily on well-structured preceding steps described in text and/or images or are limited to a certain domain, resulting in a disparity with real-world user scenarios. To address these limitations, we present a new benchmark challenge -- MultiScript, with two new tasks on task-oriented multimodal script learning: (1) multimodal script generation, and (2) subsequent step prediction. For both tasks, the input consists of a target task name and a video illustrating what has been done to complete the target task, and the expected output is (1) a sequence of structured step descriptions in text based on the demonstration video, and (2) a single text description for the subsequent step, respectively. Built from WikiHow, MultiScript covers multimodal scripts in videos and text descriptions for over 6,655 human everyday tasks across 19 diverse domains. To establish baseline performance on MultiScript, we propose two knowledge-guided multimodal generative frameworks that incorporate the task-related knowledge prompted from large language models such as Vicuna. Experimental results show that our proposed approaches significantly improve over the competitive baselines.

Knowledge Graphs (KGs) are symbolically structured storages of facts. The KG embedding contains concise data used in NLP tasks requiring implicit information about the real world. Furthermore, the size of KGs that may be useful in actual NLP assignments is enormous, and creating embedding over it has memory cost issues. We represent KG as a 3rd-order binary tensor and move beyond the standard CP decomposition by using a data-specific generalized version of it. The generalization of the standard CP-ALS algorithm allows obtaining optimization gradients without a backpropagation mechanism. It reduces the memory needed in training while providing computational benefits. We propose a MEKER, a memory-efficient KG embedding model, which yields SOTA-comparable performance on link prediction tasks and KG-based Question Answering.

GNNs and chemical fingerprints are the predominant approaches to representing molecules for property prediction. However, in NLP, transformers have become the de-facto standard for representation learning thanks to their strong downstream task transfer. In parallel, the software ecosystem around transformers is maturing rapidly, with libraries like HuggingFace and BertViz enabling streamlined training and introspection. In this work, we make one of the first attempts to systematically evaluate transformers on molecular property prediction tasks via our ChemBERTa model. ChemBERTa scales well with pretraining dataset size, offering competitive downstream performance on MoleculeNet and useful attention-based visualization modalities. Our results suggest that transformers offer a promising avenue of future work for molecular representation learning and property prediction. To facilitate these efforts, we release a curated dataset of 77M SMILES from PubChem suitable for large-scale self-supervised pretraining.

Vehicle-to-everything (V2X) technologies offer a promising paradigm to mitigate the limitations of constrained observability in single-vehicle systems. Prior work primarily focuses on single-frame cooperative perception, which fuses agents' information across different spatial locations but ignores temporal cues and temporal tasks (e.g., temporal perception and prediction). In this paper, we focus on the spatio-temporal fusion in V2X scenarios and design one-step and multi-step communication strategies (when to transmit) as well as examine their integration with three fusion strategies - early, late, and intermediate (what to transmit), providing comprehensive benchmarks with 11 fusion models (how to fuse). Furthermore, we propose V2XPnP, a novel intermediate fusion framework within one-step communication for end-to-end perception and prediction. Our framework employs a unified Transformer-based architecture to effectively model complex spatio-temporal relationships across multiple agents, frames, and high-definition map. Moreover, we introduce the V2XPnP Sequential Dataset that supports all V2X collaboration modes and addresses the limitations of existing real-world datasets, which are restricted to single-frame or single-mode cooperation. Extensive experiments demonstrate our framework outperforms state-of-the-art methods in both perception and prediction tasks. The codebase and dataset will be released to facilitate future V2X research.

In biological research, fluorescence staining is a key technique to reveal the locations and morphology of subcellular structures. However, it is slow, expensive, and harmful to cells. In this paper, we model it as a deep learning task termed subcellular structure prediction (SSP), aiming to predict the 3D fluorescent images of multiple subcellular structures from a 3D transmitted-light image. Unfortunately, due to the limitations of current biotechnology, each image is partially labeled in SSP. Besides, naturally, subcellular structures vary considerably in size, which causes the multi-scale issue of SSP. To overcome these challenges, we propose Re-parameterizing Mixture-of-Diverse-Experts (RepMode), a network that dynamically organizes its parameters with task-aware priors to handle specified single-label prediction tasks. In RepMode, the Mixture-of-Diverse-Experts (MoDE) block is designed to learn the generalized parameters for all tasks, and gating re-parameterization (GatRep) is performed to generate the specialized parameters for each task, by which RepMode can maintain a compact practical topology exactly like a plain network, and meanwhile achieves a powerful theoretical topology. Comprehensive experiments show that RepMode can achieve state-of-the-art overall performance in SSP.

The mainstream of the existing approaches for video prediction builds up their models based on a Single-In-Single-Out (SISO) architecture, which takes the current frame as input to predict the next frame in a recursive manner. This way often leads to severe performance degradation when they try to extrapolate a longer period of future, thus limiting the practical use of the prediction model. Alternatively, a Multi-In-Multi-Out (MIMO) architecture that outputs all the future frames at one shot naturally breaks the recursive manner and therefore prevents error accumulation. However, only a few MIMO models for video prediction are proposed and they only achieve inferior performance due to the date. The real strength of the MIMO model in this area is not well noticed and is largely under-explored. Motivated by that, we conduct a comprehensive investigation in this paper to thoroughly exploit how far a simple MIMO architecture can go. Surprisingly, our empirical studies reveal that a simple MIMO model can outperform the state-of-the-art work with a large margin much more than expected, especially in dealing with longterm error accumulation. After exploring a number of ways and designs, we propose a new MIMO architecture based on extending the pure Transformer with local spatio-temporal blocks and a new multi-output decoder, namely MIMO-VP, to establish a new standard in video prediction. We evaluate our model in four highly competitive benchmarks (Moving MNIST, Human3.6M, Weather, KITTI). Extensive experiments show that our model wins 1st place on all the benchmarks with remarkable performance gains and surpasses the best SISO model in all aspects including efficiency, quantity, and quality. We believe our model can serve as a new baseline to facilitate the future research of video prediction tasks. The code will be released.

The irregularity and permutation invariance of point cloud data pose challenges for effective learning. Conventional methods for addressing this issue involve converting raw point clouds to intermediate representations such as 3D voxel grids or range images. While such intermediate representations solve the problem of permutation invariance, they can result in significant loss of information. Approaches that do learn on raw point clouds either have trouble in resolving neighborhood relationships between points or are too complicated in their formulation. In this paper, we propose a novel approach to representing point clouds as a locality preserving 1D ordering induced by the Hilbert space-filling curve. We also introduce Point2Point, a neural architecture that can effectively learn on Hilbert-sorted point clouds. We show that Point2Point shows competitive performance on point cloud segmentation and generation tasks. Finally, we show the performance of Point2Point on Spatio-temporal Occupancy prediction from Point clouds.

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks.

Dense visual prediction tasks have been constrained by their reliance on predefined categories, limiting their applicability in real-world scenarios where visual concepts are unbounded. While Vision-Language Models (VLMs) like CLIP have shown promise in open-vocabulary tasks, their direct application to dense prediction often leads to suboptimal performance due to limitations in local feature representation. In this work, we present our observation that CLIP's image tokens struggle to effectively aggregate information from spatially or semantically related regions, resulting in features that lack local discriminability and spatial consistency. To address this issue, we propose DeCLIP, a novel framework that enhances CLIP by decoupling the self-attention module to obtain ``content'' and ``context'' features respectively. The ``content'' features are aligned with image crop representations to improve local discriminability, while ``context'' features learn to retain the spatial correlations under the guidance of vision foundation models, such as DINO. Extensive experiments demonstrate that DeCLIP significantly outperforms existing methods across multiple open-vocabulary dense prediction tasks, including object detection and semantic segmentation. Code is available at magenta{https://github.com/xiaomoguhz/DeCLIP}.

Many pixelwise dense prediction tasks-depth estimation and semantic segmentation in computer vision today rely on pretrained image representations. Therefore, curating effective pretraining datasets is vital. Unfortunately, the effective pretraining datasets are those with multi-view scenes and have only been curated using annotated 3D meshes, point clouds, and camera parameters from simulated environments. We propose a dataset-curation mechanism that does not require any annotations. We mine two datasets: MIMIC-1M with 1.3M and MIMIC-3M with 3.1M multi-view image pairs from open-sourced video datasets and from synthetic 3D environments. We train multiple self-supervised models with different masked image modeling objectives to showcase the following findings: Representations trained on MIMIC-3M outperform those mined using annotations on multiple downstream tasks, including depth estimation, semantic segmentation, surface normals, and pose estimation. They also outperform representations that are frozen and when downstream training data is limited to few-shot. Larger dataset (MIMIC-3M) significantly improves performance, which is promising since our curation method can arbitrarily scale to produce even larger datasets. MIMIC code, dataset, and pretrained models are open-sourced at https://github.com/RAIVNLab/MIMIC.

We investigate the capabilities of transformer large language models (LLMs) on relational reasoning tasks involving abstract symbols. Such tasks have long been studied in the neuroscience literature as fundamental building blocks for more complex abilities in programming, mathematics, and verbal reasoning. For (i) regression tasks, we prove that transformers generalize when trained, but require astonishingly large quantities of training data. For (ii) next-token-prediction tasks with symbolic labels, we show an "inverse scaling law": transformers fail to generalize as their embedding dimension increases. For both settings (i) and (ii), we propose subtle transformer modifications which can reduce the amount of data needed by adding two trainable parameters per head.

Transformers have revolutionized computer vision and natural language processing, but their high computational complexity limits their application in high-resolution image processing and long-context analysis. This paper introduces Vision-RWKV (VRWKV), a model adapted from the RWKV model used in the NLP field with necessary modifications for vision tasks. Similar to the Vision Transformer (ViT), our model is designed to efficiently handle sparse inputs and demonstrate robust global processing capabilities, while also scaling up effectively, accommodating both large-scale parameters and extensive datasets. Its distinctive advantage lies in its reduced spatial aggregation complexity, which renders it exceptionally adept at processing high-resolution images seamlessly, eliminating the necessity for windowing operations. Our evaluations demonstrate that VRWKV surpasses ViT's performance in image classification and has significantly faster speeds and lower memory usage processing high-resolution inputs. In dense prediction tasks, it outperforms window-based models, maintaining comparable speeds. These results highlight VRWKV's potential as a more efficient alternative for visual perception tasks. Code is released at https://github.com/OpenGVLab/Vision-RWKV.

Dense visual prediction tasks, such as detection and segmentation, are crucial for time-critical applications (e.g., autonomous driving and video surveillance). While deep models achieve strong performance, their efficiency remains a challenge. Knowledge distillation (KD) is an effective model compression technique, but existing feature-based KD methods rely on static, teacher-driven feature selection, failing to adapt to the student's evolving learning state or leverage dynamic student-teacher interactions. To address these limitations, we propose Adaptive student-teacher Cooperative Attention Masking for Knowledge Distillation (ACAM-KD), which introduces two key components: (1) Student-Teacher Cross-Attention Feature Fusion (STCA-FF), which adaptively integrates features from both models for a more interactive distillation process, and (2) Adaptive Spatial-Channel Masking (ASCM), which dynamically generates importance masks to enhance both spatial and channel-wise feature selection. Unlike conventional KD methods, ACAM-KD adapts to the student's evolving needs throughout the entire distillation process. Extensive experiments on multiple benchmarks validate its effectiveness. For instance, on COCO2017, ACAM-KD improves object detection performance by up to 1.4 mAP over the state-of-the-art when distilling a ResNet-50 student from a ResNet-101 teacher. For semantic segmentation on Cityscapes, it boosts mIoU by 3.09 over the baseline with DeepLabV3-MobileNetV2 as the student model.

The success of self-supervised learning in computer vision and natural language processing has motivated pretraining methods on tabular data. However, most existing tabular self-supervised learning models fail to leverage information across multiple data tables and cannot generalize to new tables. In this work, we introduce XTab, a framework for cross-table pretraining of tabular transformers on datasets from various domains. We address the challenge of inconsistent column types and quantities among tables by utilizing independent featurizers and using federated learning to pretrain the shared component. Tested on 84 tabular prediction tasks from the OpenML-AutoML Benchmark (AMLB), we show that (1) XTab consistently boosts the generalizability, learning speed, and performance of multiple tabular transformers, (2) by pretraining FT-Transformer via XTab, we achieve superior performance than other state-of-the-art tabular deep learning models on various tasks such as regression, binary, and multiclass classification.

Can we teach natural language understanding models to track their beliefs through intermediate points in text? We propose a representation learning framework called breakpoint modeling that allows for learning of this type. Given any text encoder and data marked with intermediate states (breakpoints) along with corresponding textual queries viewed as true/false propositions (i.e., the candidate beliefs of a model, consisting of information changing through time) our approach trains models in an efficient and end-to-end fashion to build intermediate representations that facilitate teaching and direct querying of beliefs at arbitrary points alongside solving other end tasks. To show the benefit of our approach, we experiment with a diverse set of NLU tasks including relational reasoning on CLUTRR and narrative understanding on bAbI. Using novel belief prediction tasks for both tasks, we show the benefit of our main breakpoint transformer, based on T5, over conventional representation learning approaches in terms of processing efficiency, prediction accuracy and prediction consistency, all with minimal to no effect on corresponding QA end tasks. To show the feasibility of incorporating our belief tracker into more complex reasoning pipelines, we also obtain SOTA performance on the three-tiered reasoning challenge for the TRIP benchmark (around 23-32% absolute improvement on Tasks 2-3).

Change detection is an important tool for long-term earth observation missions. It takes bi-temporal images as input and predicts "where" the change has occurred. Different from other dense prediction tasks, a meaningful consideration for change detection is the interaction between bi-temporal features. With this motivation, in this paper we propose a novel general change detection architecture, MetaChanger, which includes a series of alternative interaction layers in the feature extractor. To verify the effectiveness of MetaChanger, we propose two derived models, ChangerAD and ChangerEx with simple interaction strategies: Aggregation-Distribution (AD) and "exchange". AD is abstracted from some complex interaction methods, and "exchange" is a completely parameter\&computation-free operation by exchanging bi-temporal features. In addition, for better alignment of bi-temporal features, we propose a flow dual-alignment fusion (FDAF) module which allows interactive alignment and feature fusion. Crucially, we observe Changer series models achieve competitive performance on different scale change detection datasets. Further, our proposed ChangerAD and ChangerEx could serve as a starting baseline for future MetaChanger design.

Although the fairness community has recognized the importance of data, researchers in the area primarily rely on UCI Adult when it comes to tabular data. Derived from a 1994 US Census survey, this dataset has appeared in hundreds of research papers where it served as the basis for the development and comparison of many algorithmic fairness interventions. We reconstruct a superset of the UCI Adult data from available US Census sources and reveal idiosyncrasies of the UCI Adult dataset that limit its external validity. Our primary contribution is a suite of new datasets derived from US Census surveys that extend the existing data ecosystem for research on fair machine learning. We create prediction tasks relating to income, employment, health, transportation, and housing. The data span multiple years and all states of the United States, allowing researchers to study temporal shift and geographic variation. We highlight a broad initial sweep of new empirical insights relating to trade-offs between fairness criteria, performance of algorithmic interventions, and the role of distribution shift based on our new datasets. Our findings inform ongoing debates, challenge some existing narratives, and point to future research directions. Our datasets are available at https://github.com/zykls/folktables.

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

There are five types of trajectory prediction tasks: deterministic, stochastic, domain adaptation, momentary observation, and few-shot. These associated tasks are defined by various factors, such as the length of input paths, data split and pre-processing methods. Interestingly, even though they commonly take sequential coordinates of observations as input and infer future paths in the same coordinates as output, designing specialized architectures for each task is still necessary. For the other task, generality issues can lead to sub-optimal performances. In this paper, we propose SingularTrajectory, a diffusion-based universal trajectory prediction framework to reduce the performance gap across the five tasks. The core of SingularTrajectory is to unify a variety of human dynamics representations on the associated tasks. To do this, we first build a Singular space to project all types of motion patterns from each task into one embedding space. We next propose an adaptive anchor working in the Singular space. Unlike traditional fixed anchor methods that sometimes yield unacceptable paths, our adaptive anchor enables correct anchors, which are put into a wrong location, based on a traversability map. Finally, we adopt a diffusion-based predictor to further enhance the prototype paths using a cascaded denoising process. Our unified framework ensures the generality across various benchmark settings such as input modality, and trajectory lengths. Extensive experiments on five public benchmarks demonstrate that SingularTrajectory substantially outperforms existing models, highlighting its effectiveness in estimating general dynamics of human movements. Code is publicly available at https://github.com/inhwanbae/SingularTrajectory .

Vision transformers have achieved leading performance on various visual tasks yet still suffer from high computational complexity. The situation deteriorates in dense prediction tasks like semantic segmentation, as high-resolution inputs and outputs usually imply more tokens involved in computations. Directly removing the less attentive tokens has been discussed for the image classification task but can not be extended to semantic segmentation since a dense prediction is required for every patch. To this end, this work introduces a Dynamic Token Pruning (DToP) method based on the early exit of tokens for semantic segmentation. Motivated by the coarse-to-fine segmentation process by humans, we naturally split the widely adopted auxiliary-loss-based network architecture into several stages, where each auxiliary block grades every token's difficulty level. We can finalize the prediction of easy tokens in advance without completing the entire forward pass. Moreover, we keep k highest confidence tokens for each semantic category to uphold the representative context information. Thus, computational complexity will change with the difficulty of the input, akin to the way humans do segmentation. Experiments suggest that the proposed DToP architecture reduces on average 20% - 35% of computational cost for current semantic segmentation methods based on plain vision transformers without accuracy degradation.

Expressing confidence is challenging for embodied agents navigating dynamic multimodal environments, where uncertainty arises from both perception and decision-making processes. We present the first work investigating embodied confidence elicitation in open-ended multimodal environments. We introduce Elicitation Policies, which structure confidence assessment across inductive, deductive, and abductive reasoning, along with Execution Policies, which enhance confidence calibration through scenario reinterpretation, action sampling, and hypothetical reasoning. Evaluating agents in calibration and failure prediction tasks within the Minecraft environment, we show that structured reasoning approaches, such as Chain-of-Thoughts, improve confidence calibration. However, our findings also reveal persistent challenges in distinguishing uncertainty, particularly under abductive settings, underscoring the need for more sophisticated embodied confidence elicitation methods.

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

Predictive Coding (PC) is a theoretical framework in cognitive science suggesting that the human brain processes cognition through spatiotemporal prediction of the visual world. Existing studies have developed spatiotemporal prediction neural networks based on the PC theory, emulating its two core mechanisms: Correcting predictions from residuals and hierarchical learning. However, these models do not show the enhancement of prediction skills on real-world forecasting tasks and ignore the Precision Weighting mechanism of PC theory. The precision weighting mechanism posits that the brain allocates more attention to signals with lower precision, contributing to the cognitive ability of human brains. This work introduces the Cognitive Diffusion Probabilistic Models (CogDPM), which demonstrate the connection between diffusion probabilistic models and PC theory. CogDPM features a precision estimation method based on the hierarchical sampling capabilities of diffusion models and weight the guidance with precision weights estimated by the inherent property of diffusion models. We experimentally show that the precision weights effectively estimate the data predictability. We apply CogDPM to real-world prediction tasks using the United Kindom precipitation and ERA surface wind datasets. Our results demonstrate that CogDPM outperforms both existing domain-specific operational models and general deep prediction models by providing more proficient forecasting.

This paper studies sequence modeling for prediction tasks with long range dependencies. We propose a new formulation for state space models (SSMs) based on learning linear dynamical systems with the spectral filtering algorithm (Hazan et al. (2017)). This gives rise to a novel sequence prediction architecture we call a spectral state space model. Spectral state space models have two primary advantages. First, they have provable robustness properties as their performance depends on neither the spectrum of the underlying dynamics nor the dimensionality of the problem. Second, these models are constructed with fixed convolutional filters that do not require learning while still outperforming SSMs in both theory and practice. The resulting models are evaluated on synthetic dynamical systems and long-range prediction tasks of various modalities. These evaluations support the theoretical benefits of spectral filtering for tasks requiring very long range memory.

Property prediction plays an important role in material discovery. As an initial step to eventually develop a foundation model for material science, we introduce a new autoencoder called the MHG-GNN, which combines graph neural network (GNN) with Molecular Hypergraph Grammar (MHG). Results on a variety of property prediction tasks with diverse materials show that MHG-GNN is promising.

Medical applications of machine learning (ML) have experienced a surge in popularity in recent years. The intensive care unit (ICU) is a natural habitat for ML given the abundance of available data from electronic health records. Models have been proposed to address numerous ICU prediction tasks like the early detection of complications. While authors frequently report state-of-the-art performance, it is challenging to verify claims of superiority. Datasets and code are not always published, and cohort definitions, preprocessing pipelines, and training setups are difficult to reproduce. This work introduces Yet Another ICU Benchmark (YAIB), a modular framework that allows researchers to define reproducible and comparable clinical ML experiments; we offer an end-to-end solution from cohort definition to model evaluation. The framework natively supports most open-access ICU datasets (MIMIC III/IV, eICU, HiRID, AUMCdb) and is easily adaptable to future ICU datasets. Combined with a transparent preprocessing pipeline and extensible training code for multiple ML and deep learning models, YAIB enables unified model development. Our benchmark comes with five predefined established prediction tasks (mortality, acute kidney injury, sepsis, kidney function, and length of stay) developed in collaboration with clinicians. Adding further tasks is straightforward by design. Using YAIB, we demonstrate that the choice of dataset, cohort definition, and preprocessing have a major impact on the prediction performance - often more so than model class - indicating an urgent need for YAIB as a holistic benchmarking tool. We provide our work to the clinical ML community to accelerate method development and enable real-world clinical implementations. Software Repository: https://github.com/rvandewater/YAIB.

Health conditions among patients in intensive care units (ICUs) are monitored via electronic health records (EHRs), composed of numerical time series and lengthy clinical note sequences, both taken at irregular time intervals. Dealing with such irregularity in every modality, and integrating irregularity into multimodal representations to improve medical predictions, is a challenging problem. Our method first addresses irregularity in each single modality by (1) modeling irregular time series by dynamically incorporating hand-crafted imputation embeddings into learned interpolation embeddings via a gating mechanism, and (2) casting a series of clinical note representations as multivariate irregular time series and tackling irregularity via a time attention mechanism. We further integrate irregularity in multimodal fusion with an interleaved attention mechanism across temporal steps. To the best of our knowledge, this is the first work to thoroughly model irregularity in multimodalities for improving medical predictions. Our proposed methods for two medical prediction tasks consistently outperforms state-of-the-art (SOTA) baselines in each single modality and multimodal fusion scenarios. Specifically, we observe relative improvements of 6.5\%, 3.6\%, and 4.3\% in F1 for time series, clinical notes, and multimodal fusion, respectively. These results demonstrate the effectiveness of our methods and the importance of considering irregularity in multimodal EHRs.

The COVID-19 pandemic has posed a heavy burden to the healthcare system worldwide and caused huge social disruption and economic loss. Many deep learning models have been proposed to conduct clinical predictive tasks such as mortality prediction for COVID-19 patients in intensive care units using Electronic Health Record (EHR) data. Despite their initial success in certain clinical applications, there is currently a lack of benchmarking results to achieve a fair comparison so that we can select the optimal model for clinical use. Furthermore, there is a discrepancy between the formulation of traditional prediction tasks and real-world clinical practice in intensive care. To fill these gaps, we propose two clinical prediction tasks, Outcome-specific length-of-stay prediction and Early mortality prediction for COVID-19 patients in intensive care units. The two tasks are adapted from the naive length-of-stay and mortality prediction tasks to accommodate the clinical practice for COVID-19 patients. We propose fair, detailed, open-source data-preprocessing pipelines and evaluate 17 state-of-the-art predictive models on two tasks, including 5 machine learning models, 6 basic deep learning models and 6 deep learning predictive models specifically designed for EHR data. We provide benchmarking results using data from two real-world COVID-19 EHR datasets. One dataset is publicly available without needing any inquiry and another dataset can be accessed on request. We provide fair, reproducible benchmarking results for two tasks. We deploy all experiment results and models on an online platform. We also allow clinicians and researchers to upload their data to the platform and get quick prediction results using our trained models. We hope our efforts can further facilitate deep learning and machine learning research for COVID-19 predictive modeling.

This paper surveys and organizes research works in a new paradigm in natural language processing, which we dub "prompt-based learning". Unlike traditional supervised learning, which trains a model to take in an input x and predict an output y as P(y|x), prompt-based learning is based on language models that model the probability of text directly. To use these models to perform prediction tasks, the original input x is modified using a template into a textual string prompt x' that has some unfilled slots, and then the language model is used to probabilistically fill the unfilled information to obtain a final string x, from which the final output y can be derived. This framework is powerful and attractive for a number of reasons: it allows the language model to be pre-trained on massive amounts of raw text, and by defining a new prompting function the model is able to perform few-shot or even zero-shot learning, adapting to new scenarios with few or no labeled data. In this paper we introduce the basics of this promising paradigm, describe a unified set of mathematical notations that can cover a wide variety of existing work, and organize existing work along several dimensions, e.g.the choice of pre-trained models, prompts, and tuning strategies. To make the field more accessible to interested beginners, we not only make a systematic review of existing works and a highly structured typology of prompt-based concepts, but also release other resources, e.g., a website http://pretrain.nlpedia.ai/ including constantly-updated survey, and paperlist.

To date, most existing self-supervised learning methods are designed and optimized for image classification. These pre-trained models can be sub-optimal for dense prediction tasks due to the discrepancy between image-level prediction and pixel-level prediction. To fill this gap, we aim to design an effective, dense self-supervised learning method that directly works at the level of pixels (or local features) by taking into account the correspondence between local features. We present dense contrastive learning, which implements self-supervised learning by optimizing a pairwise contrastive (dis)similarity loss at the pixel level between two views of input images. Compared to the baseline method MoCo-v2, our method introduces negligible computation overhead (only <1% slower), but demonstrates consistently superior performance when transferring to downstream dense prediction tasks including object detection, semantic segmentation and instance segmentation; and outperforms the state-of-the-art methods by a large margin. Specifically, over the strong MoCo-v2 baseline, our method achieves significant improvements of 2.0% AP on PASCAL VOC object detection, 1.1% AP on COCO object detection, 0.9% AP on COCO instance segmentation, 3.0% mIoU on PASCAL VOC semantic segmentation and 1.8% mIoU on Cityscapes semantic segmentation. Code is available at: https://git.io/AdelaiDet

A model involving Gaussian processes (GPs) is introduced to simultaneously handle multi-task learning, clustering, and prediction for multiple functional data. This procedure acts as a model-based clustering method for functional data as well as a learning step for subsequent predictions for new tasks. The model is instantiated as a mixture of multi-task GPs with common mean processes. A variational EM algorithm is derived for dealing with the optimisation of the hyper-parameters along with the hyper-posteriors' estimation of latent variables and processes. We establish explicit formulas for integrating the mean processes and the latent clustering variables within a predictive distribution, accounting for uncertainty on both aspects. This distribution is defined as a mixture of cluster-specific GP predictions, which enhances the performances when dealing with group-structured data. The model handles irregular grid of observations and offers different hypotheses on the covariance structure for sharing additional information across tasks. The performances on both clustering and prediction tasks are assessed through various simulated scenarios and real datasets. The overall algorithm, called MagmaClust, is publicly available as an R package.

Learning to capture text-table alignment is essential for tasks like text-to-SQL. A model needs to correctly recognize natural language references to columns and values and to ground them in the given database schema. In this paper, we present a novel weakly supervised Structure-Grounded pretraining framework (StruG) for text-to-SQL that can effectively learn to capture text-table alignment based on a parallel text-table corpus. We identify a set of novel prediction tasks: column grounding, value grounding and column-value mapping, and leverage them to pretrain a text-table encoder. Additionally, to evaluate different methods under more realistic text-table alignment settings, we create a new evaluation set Spider-Realistic based on Spider dev set with explicit mentions of column names removed, and adopt eight existing text-to-SQL datasets for cross-database evaluation. STRUG brings significant improvement over BERT-LARGE in all settings. Compared with existing pretraining methods such as GRAPPA, STRUG achieves similar performance on Spider, and outperforms all baselines on more realistic sets. The Spider-Realistic dataset is available at https://doi.org/10.5281/zenodo.5205322.

The multi-modal nature of many vision problems calls for neural network architectures that can perform multiple tasks concurrently. Typically, such architectures have been handcrafted in the literature. However, given the size and complexity of the problem, this manual architecture exploration likely exceeds human design abilities. In this paper, we propose a principled approach, rooted in differentiable neural architecture search, to automatically define branching (tree-like) structures in the encoding stage of a multi-task neural network. To allow flexibility within resource-constrained environments, we introduce a proxyless, resource-aware loss that dynamically controls the model size. Evaluations across a variety of dense prediction tasks show that our approach consistently finds high-performing branching structures within limited resource budgets.

Self-supervised representation learning solves auxiliary prediction tasks (known as pretext tasks) without requiring labeled data to learn useful semantic representations. These pretext tasks are created solely using the input features, such as predicting a missing image patch, recovering the color channels of an image from context, or predicting missing words in text; yet predicting this known information helps in learning representations effective for downstream prediction tasks. We posit a mechanism exploiting the statistical connections between certain {\em reconstruction-based} pretext tasks that guarantee to learn a good representation. Formally, we quantify how the approximate independence between the components of the pretext task (conditional on the label and latent variables) allows us to learn representations that can solve the downstream task by just training a linear layer on top of the learned representation. We prove the linear layer yields small approximation error even for complex ground truth function class and will drastically reduce labeled sample complexity. Next, we show a simple modification of our method leads to nonlinear CCA, analogous to the popular SimSiam algorithm, and show similar guarantees for nonlinear CCA.

Multi-hop query answering over a Knowledge Graph (KG) involves traversing one or more hops from the start node to answer a query. Path-based and logic-based methods are state-of-the-art for multi-hop question answering. The former is used in link prediction tasks. The latter is for answering complex logical queries. The logical multi-hop querying technique embeds the KG and queries in the same embedding space. The existing work incorporates First Order Logic (FOL) operators, such as conjunction (wedge), disjunction (vee), and negation (neg), in queries. Though current models have most of the building blocks to execute the FOL queries, they cannot use the dense information of multi-modal entities in the case of Multi-Modal Knowledge Graphs (MMKGs). We propose RConE, an embedding method to capture the multi-modal information needed to answer a query. The model first shortlists candidate (multi-modal) entities containing the answer. It then finds the solution (sub-entities) within those entities. Several existing works tackle path-based question-answering in MMKGs. However, to our knowledge, we are the first to introduce logical constructs in querying MMKGs and to answer queries that involve sub-entities of multi-modal entities as the answer. Extensive evaluation of four publicly available MMKGs indicates that RConE outperforms the current state-of-the-art.

We introduce SynCLR, a novel approach for learning visual representations exclusively from synthetic images and synthetic captions, without any real data. We synthesize a large dataset of image captions using LLMs, then use an off-the-shelf text-to-image model to generate multiple images corresponding to each synthetic caption. We perform visual representation learning on these synthetic images via contrastive learning, treating images sharing the same caption as positive pairs. The resulting representations transfer well to many downstream tasks, competing favorably with other general-purpose visual representation learners such as CLIP and DINO v2 in image classification tasks. Furthermore, in dense prediction tasks such as semantic segmentation, SynCLR outperforms previous self-supervised methods by a significant margin, e.g., improving over MAE and iBOT by 6.2 and 4.3 mIoU on ADE20k for ViT-B/16.

Image-Text pretraining on web-scale image caption dataset has become the default recipe for open vocabulary classification and retrieval models thanks to the success of CLIP and its variants. Several works have also used CLIP features for dense prediction tasks and have shown the emergence of open-set abilities. However, the contrastive objective only focuses on image-text alignment and does not incentivise image feature learning for dense prediction tasks. In this work, we propose the simple addition of local-to-global correspondence learning by self-distillation as an additional objective for contrastive pre-training to propose SILC. We show that distilling local image features from an exponential moving average (EMA) teacher model significantly improves model performance on several computer vision tasks including classification, retrieval, and especially segmentation. We further show that SILC scales better with the same training duration compared to the baselines. Our model SILC sets a new state of the art for zero-shot classification, few shot classification, image and text retrieval, zero-shot segmentation, and open vocabulary segmentation.

Multimodal Large Language Models (MLLMs) demonstrate robust zero-shot capabilities across diverse vision-language tasks after training on mega-scale datasets. However, dense prediction tasks, such as semantic segmentation and keypoint detection, pose significant challenges for MLLMs when represented solely as text outputs. Simultaneously, current MLLMs utilizing latent embeddings for visual task decoding generally demonstrate limited adaptability to both multi-task learning and multi-granularity scenarios. In this work, we present REF-VLM, an end-to-end framework for unified training of various visual decoding tasks. To address complex visual decoding scenarios, we introduce the Triplet-Based Referring Paradigm (TRP), which explicitly decouples three critical dimensions in visual decoding tasks through a triplet structure: concepts, decoding types, and targets. TRP employs symbolic delimiters to enforce structured representation learning, enhancing the parsability and interpretability of model outputs. Additionally, we construct Visual-Task Instruction Following Dataset (VTInstruct), a large-scale multi-task dataset containing over 100 million multimodal dialogue samples across 25 task types. Beyond text inputs and outputs, VT-Instruct incorporates various visual prompts such as point, box, scribble, and mask, and generates outputs composed of text and visual units like box, keypoint, depth and mask. The combination of different visual prompts and visual units generates a wide variety of task types, expanding the applicability of REF-VLM significantly. Both qualitative and quantitative experiments demonstrate that our REF-VLM outperforms other MLLMs across a variety of standard benchmarks. The code, dataset, and demo available at https://github.com/MacavityT/REF-VLM.

Despite the outstanding performance of deep learning models in clinical prediction tasks, explainability remains a significant challenge. Inspired by transformer architectures, we introduce the Temporal-Feature Cross Attention Mechanism (TFCAM), a novel deep learning framework designed to capture dynamic interactions among clinical features across time, enhancing both predictive accuracy and interpretability. In an experiment with 1,422 patients with Chronic Kidney Disease, predicting progression to End-Stage Renal Disease, TFCAM outperformed LSTM and RETAIN baselines, achieving an AUROC of 0.95 and an F1-score of 0.69. Beyond performance gains, TFCAM provides multi-level explainability by identifying critical temporal periods, ranking feature importance, and quantifying how features influence each other across time before affecting predictions. Our approach addresses the "black box" limitations of deep learning in healthcare, offering clinicians transparent insights into disease progression mechanisms while maintaining state-of-the-art predictive performance.

Recently, binary representation has been proposed as a novel representation that lies between continuous and discrete representations. It exhibits considerable information-preserving capability when being used to replace continuous input vectors. In this paper, we investigate the feasibility of further introducing it to the output side, aiming to allow models to output binary labels instead. To preserve the structural information on the output side along with label information, we extend the previous contrastive hashing method as structured contrastive hashing. More specifically, we upgrade CKY from label-level to bit-level, define a new similarity function with span marginal probabilities, and introduce a novel contrastive loss function with a carefully designed instance selection strategy. Our model achieves competitive performance on various structured prediction tasks, and demonstrates that binary representation can be considered a novel representation that further bridges the gap between the continuous nature of deep learning and the discrete intrinsic property of natural languages.

Although Vision Transformer (ViT) has achieved significant success in computer vision, it does not perform well in dense prediction tasks due to the lack of inner-patch information interaction and the limited diversity of feature scale. Most existing studies are devoted to designing vision-specific transformers to solve the above problems, which introduce additional pre-training costs. Therefore, we present a plain, pre-training-free, and feature-enhanced ViT backbone with Convolutional Multi-scale feature interaction, named ViT-CoMer, which facilitates bidirectional interaction between CNN and transformer. Compared to the state-of-the-art, ViT-CoMer has the following advantages: (1) We inject spatial pyramid multi-receptive field convolutional features into the ViT architecture, which effectively alleviates the problems of limited local information interaction and single-feature representation in ViT. (2) We propose a simple and efficient CNN-Transformer bidirectional fusion interaction module that performs multi-scale fusion across hierarchical features, which is beneficial for handling dense prediction tasks. (3) We evaluate the performance of ViT-CoMer across various dense prediction tasks, different frameworks, and multiple advanced pre-training. Notably, our ViT-CoMer-L achieves 64.3% AP on COCO val2017 without extra training data, and 62.1% mIoU on ADE20K val, both of which are comparable to state-of-the-art methods. We hope ViT-CoMer can serve as a new backbone for dense prediction tasks to facilitate future research. The code will be released at https://github.com/Traffic-X/ViT-CoMer.

Large language models (LLMs) effectively generate fluent text when the target output follows natural language patterns. However, structured prediction tasks confine the output format to a limited ontology, causing even very large models to struggle since they were never trained with such restrictions in mind. The difficulty of using LLMs for direct prediction is exacerbated in few-shot learning scenarios, which commonly arise due to domain shift and resource limitations. We flip the problem on its head by leveraging the LLM as a tool for data augmentation rather than direct prediction. Our proposed Mixture of Soft Prompts (MSP) serves as a parameter-efficient procedure for generating data in a controlled manner. Denoising mechanisms are further applied to improve the quality of synthesized data. Automatic metrics show our method is capable of producing diverse and natural text, while preserving label semantics. Moreover, MSP achieves state-of-the-art results on three benchmarks when compared against strong baselines. Our method offers an alternate data-centric approach for applying LLMs to complex prediction tasks.

This paper presents SimCLR: a simple framework for contrastive learning of visual representations. We simplify recently proposed contrastive self-supervised learning algorithms without requiring specialized architectures or a memory bank. In order to understand what enables the contrastive prediction tasks to learn useful representations, we systematically study the major components of our framework. We show that (1) composition of data augmentations plays a critical role in defining effective predictive tasks, (2) introducing a learnable nonlinear transformation between the representation and the contrastive loss substantially improves the quality of the learned representations, and (3) contrastive learning benefits from larger batch sizes and more training steps compared to supervised learning. By combining these findings, we are able to considerably outperform previous methods for self-supervised and semi-supervised learning on ImageNet. A linear classifier trained on self-supervised representations learned by SimCLR achieves 76.5% top-1 accuracy, which is a 7% relative improvement over previous state-of-the-art, matching the performance of a supervised ResNet-50. When fine-tuned on only 1% of the labels, we achieve 85.8% top-5 accuracy, outperforming AlexNet with 100X fewer labels.

Recent advances in neural surrogate modeling offer the potential for transformative innovations in applications such as automotive aerodynamics. Yet, industrial-scale problems often involve volumetric meshes with cell counts reaching the 100 millions, presenting major scalability challenges. Complex geometries further complicate modeling through intricate surface-volume interactions, while quantities such as vorticity are highly nonlinear and must satisfy strict divergence-free constraints. To address these requirements, we introduce AB-UPT as a novel modeling scheme for building neural surrogates for CFD simulations. AB-UPT is designed to: (i) decouple geometry encoding and prediction tasks via multi-branch operators; (ii) enable scalability to high-resolution outputs via neural simulation in a low-dimensional latent space, coupled with anchored neural field decoders to predict high-fidelity outputs; (iii) enforce physics consistency by a novel divergence-free formulation. We show that AB-UPT yields state-of-the-art predictive accuracy of surface and volume fields on automotive CFD simulations ranging from 33 thousand up to 150 million mesh cells. Furthermore, our anchored neural field architecture enables the enforcement of hard physical constraints on the physics predictions without degradation in performance, exemplified by modeling divergence-free vorticity fields. Notably, the proposed models can be trained on a single GPU in less than a day and predict industry-standard surface and volume fields within seconds. Additionally, we show that the flexible design of our method enables neural simulation from a CAD geometry alone, omitting the need for costly CFD meshing procedures.

Generative modeling of crystal data distribution is an important yet challenging task due to the unique periodic physical symmetry of crystals. Diffusion-based methods have shown early promise in modeling crystal distribution. More recently, Bayesian Flow Networks were introduced to aggregate noisy latent variables, resulting in a variance-reduced parameter space that has been shown to be advantageous for modeling Euclidean data distributions with structural constraints (Song et al., 2023). Inspired by this, we seek to unlock its potential for modeling variables located in non-Euclidean manifolds e.g. those within crystal structures, by overcoming challenging theoretical issues. We introduce CrysBFN, a novel crystal generation method by proposing a periodic Bayesian flow, which essentially differs from the original Gaussian-based BFN by exhibiting non-monotonic entropy dynamics. To successfully realize the concept of periodic Bayesian flow, CrysBFN integrates a new entropy conditioning mechanism and empirically demonstrates its significance compared to time-conditioning. Extensive experiments over both crystal ab initio generation and crystal structure prediction tasks demonstrate the superiority of CrysBFN, which consistently achieves new state-of-the-art on all benchmarks. Surprisingly, we found that CrysBFN enjoys a significant improvement in sampling efficiency, e.g., ~100x speedup 10 v.s. 2000 steps network forwards) compared with previous diffusion-based methods on MP-20 dataset. Code is available at https://github.com/wu-han-lin/CrysBFN.

Sparse Multi-view Images can be Learned to predict explicit radiance fields via Generalizable Gaussian Splatting approaches, which can achieve wider application prospects in real-life when ground-truth camera parameters are not required as inputs. In this paper, a novel generalizable Gaussian Splatting method, SmileSplat, is proposed to reconstruct pixel-aligned Gaussian surfels for diverse scenarios only requiring unconstrained sparse multi-view images. First, Gaussian surfels are predicted based on the multi-head Gaussian regression decoder, which can are represented with less degree-of-freedom but have better multi-view consistency. Furthermore, the normal vectors of Gaussian surfel are enhanced based on high-quality of normal priors. Second, the Gaussians and camera parameters (both extrinsic and intrinsic) are optimized to obtain high-quality Gaussian radiance fields for novel view synthesis tasks based on the proposed Bundle-Adjusting Gaussian Splatting module. Extensive experiments on novel view rendering and depth map prediction tasks are conducted on public datasets, demonstrating that the proposed method achieves state-of-the-art performance in various 3D vision tasks. More information can be found on our project page (https://yanyan-li.github.io/project/gs/smilesplat)

The hybrid deep models of Vision Transformer (ViT) and Convolution Neural Network (CNN) have emerged as a powerful class of backbones for vision tasks. Scaling up the input resolution of such hybrid backbones naturally strengthes model capacity, but inevitably suffers from heavy computational cost that scales quadratically. Instead, we present a new hybrid backbone with HIgh-Resolution Inputs (namely HIRI-ViT), that upgrades prevalent four-stage ViT to five-stage ViT tailored for high-resolution inputs. HIRI-ViT is built upon the seminal idea of decomposing the typical CNN operations into two parallel CNN branches in a cost-efficient manner. One high-resolution branch directly takes primary high-resolution features as inputs, but uses less convolution operations. The other low-resolution branch first performs down-sampling and then utilizes more convolution operations over such low-resolution features. Experiments on both recognition task (ImageNet-1K dataset) and dense prediction tasks (COCO and ADE20K datasets) demonstrate the superiority of HIRI-ViT. More remarkably, under comparable computational cost (sim5.0 GFLOPs), HIRI-ViT achieves to-date the best published Top-1 accuracy of 84.3% on ImageNet with 448times448 inputs, which absolutely improves 83.4% of iFormer-S by 0.9% with 224times224 inputs.

Transformer-based deep neural networks have revolutionized the field of molecular-related prediction tasks by treating molecules as symbolic sequences. These models have been successfully applied in various organic chemical applications by pretraining them with extensive compound libraries and subsequently fine-tuning them with smaller in-house datasets for specific tasks. However, many conventional methods primarily focus on single molecules, with limited exploration of pretraining for reactions involving multiple molecules. In this paper, we propose ReactionT5, a novel model that leverages pretraining on the Open Reaction Database (ORD), a publicly available large-scale resource. We further fine-tune this model for yield prediction and product prediction tasks, demonstrating its impressive performance even with limited fine-tuning data compared to traditional models. The pre-trained ReactionT5 model is publicly accessible on the Hugging Face platform.

Clinical predictive models often rely on patients' electronic health records (EHR), but integrating medical knowledge to enhance predictions and decision-making is challenging. This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data. To address this, we propose GraphCare, an open-world framework that uses external KGs to improve EHR-based predictions. Our method extracts knowledge from large language models (LLMs) and external biomedical KGs to build patient-specific KGs, which are then used to train our proposed Bi-attention AugmenTed (BAT) graph neural network (GNN) for healthcare predictions. On two public datasets, MIMIC-III and MIMIC-IV, GraphCare surpasses baselines in four vital healthcare prediction tasks: mortality, readmission, length of stay (LOS), and drug recommendation. On MIMIC-III, it boosts AUROC by 17.6\% and 6.6\% for mortality and readmission, and F1-score by 7.9\% and 10.8\% for LOS and drug recommendation, respectively. Notably, GraphCare demonstrates a substantial edge in scenarios with limited data availability. Our findings highlight the potential of using external KGs in healthcare prediction tasks and demonstrate the promise of GraphCare in generating personalized KGs for promoting personalized medicine.

The approximation capability of ANNs and their RNN instantiations, is strongly correlated with the number of parameters packed into these networks. However, the complexity barrier for human understanding, is arguably related to the number of neurons and synapses in the networks, and to the associated nonlinear transformations. In this paper we show that the use of biophysical synapses, as found in LTCs, have two main benefits. First, they allow to pack more parameters for a given number of neurons and synapses. Second, they allow to formulate the nonlinear-network transformation, as a linear system with state-dependent coefficients. Both increase interpretability, as for a given task, they allow to learn a system linear in its input features, that is smaller in size compared to the state of the art. We substantiate the above claims on various time-series prediction tasks, but we believe that our results are applicable to any feedforward or recurrent ANN.

Machine learning models are often personalized with information that is protected, sensitive, self-reported, or costly to acquire. These models use information about people but do not facilitate nor inform their consent. Individuals cannot opt out of reporting personal information to a model, nor tell if they benefit from personalization in the first place. We introduce a family of classification models, called participatory systems, that let individuals opt into personalization at prediction time. We present a model-agnostic algorithm to learn participatory systems for personalization with categorical group attributes. We conduct a comprehensive empirical study of participatory systems in clinical prediction tasks, benchmarking them with common approaches for personalization and imputation. Our results demonstrate that participatory systems can facilitate and inform consent while improving performance and data use across all groups who report personal data.

Tabular data is a common form of organizing data. Multiple models are available to generate synthetic tabular datasets where observations are independent, but few have the ability to produce relational datasets. Modeling relational data is challenging as it requires modeling both a "parent" table and its relationships across tables. We introduce REaLTabFormer (Realistic Relational and Tabular Transformer), a tabular and relational synthetic data generation model. It first creates a parent table using an autoregressive GPT-2 model, then generates the relational dataset conditioned on the parent table using a sequence-to-sequence (Seq2Seq) model. We implement target masking to prevent data copying and propose the Q_{delta} statistic and statistical bootstrapping to detect overfitting. Experiments using real-world datasets show that REaLTabFormer captures the relational structure better than a baseline model. REaLTabFormer also achieves state-of-the-art results on prediction tasks, "out-of-the-box", for large non-relational datasets without needing fine-tuning.

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially reshape structural biology. However, the utility of the PLM module in AlphaFold, Evoformer, has not been explored beyond structure prediction. In this paper, we investigate the representation ability of three popular PLMs: ESM-1b (single sequence), MSA-Transformer (multiple sequence alignment) and Evoformer (structural), with a special focus on Evoformer. Specifically, we aim to answer the following key questions: (i) Does the Evoformer trained as part of AlphaFold produce representations amenable to predicting protein function? (ii) If yes, can Evoformer replace ESM-1b and MSA-Transformer? (ii) How much do these PLMs rely on evolution-related protein data? In this regard, are they complementary to each other? We compare these models by empirical study along with new insights and conclusions. All code and datasets for reproducibility are available at https://github.com/elttaes/Revisiting-PLMs.

There have been many successful applications of sentence embedding methods. However, it has not been well understood what properties are captured in the resulting sentence embeddings depending on the supervision signals. In this paper, we focus on two types of sentence embedding methods with similar architectures and tasks: one fine-tunes pre-trained language models on the natural language inference task, and the other fine-tunes pre-trained language models on word prediction task from its definition sentence, and investigate their properties. Specifically, we compare their performances on semantic textual similarity (STS) tasks using STS datasets partitioned from two perspectives: 1) sentence source and 2) superficial similarity of the sentence pairs, and compare their performances on the downstream and probing tasks. Furthermore, we attempt to combine the two methods and demonstrate that combining the two methods yields substantially better performance than the respective methods on unsupervised STS tasks and downstream tasks.

This work presents a simple vision transformer design as a strong baseline for object localization and instance segmentation tasks. Transformers recently demonstrate competitive performance in image classification tasks. To adopt ViT to object detection and dense prediction tasks, many works inherit the multistage design from convolutional networks and highly customized ViT architectures. Behind this design, the goal is to pursue a better trade-off between computational cost and effective aggregation of multiscale global contexts. However, existing works adopt the multistage architectural design as a black-box solution without a clear understanding of its true benefits. In this paper, we comprehensively study three architecture design choices on ViT -- spatial reduction, doubled channels, and multiscale features -- and demonstrate that a vanilla ViT architecture can fulfill this goal without handcrafting multiscale features, maintaining the original ViT design philosophy. We further complete a scaling rule to optimize our model's trade-off on accuracy and computation cost / model size. By leveraging a constant feature resolution and hidden size throughout the encoder blocks, we propose a simple and compact ViT architecture called Universal Vision Transformer (UViT) that achieves strong performance on COCO object detection and instance segmentation tasks.

Contrastive learning methods for unsupervised visual representation learning have reached remarkable levels of transfer performance. We argue that the power of contrastive learning has yet to be fully unleashed, as current methods are trained only on instance-level pretext tasks, leading to representations that may be sub-optimal for downstream tasks requiring dense pixel predictions. In this paper, we introduce pixel-level pretext tasks for learning dense feature representations. The first task directly applies contrastive learning at the pixel level. We additionally propose a pixel-to-propagation consistency task that produces better results, even surpassing the state-of-the-art approaches by a large margin. Specifically, it achieves 60.2 AP, 41.4 / 40.5 mAP and 77.2 mIoU when transferred to Pascal VOC object detection (C4), COCO object detection (FPN / C4) and Cityscapes semantic segmentation using a ResNet-50 backbone network, which are 2.6 AP, 0.8 / 1.0 mAP and 1.0 mIoU better than the previous best methods built on instance-level contrastive learning. Moreover, the pixel-level pretext tasks are found to be effective for pre-training not only regular backbone networks but also head networks used for dense downstream tasks, and are complementary to instance-level contrastive methods. These results demonstrate the strong potential of defining pretext tasks at the pixel level, and suggest a new path forward in unsupervised visual representation learning. Code is available at https://github.com/zdaxie/PixPro.

We propose a knowledge-enhanced approach, ERNIE-ViL, which incorporates structured knowledge obtained from scene graphs to learn joint representations of vision-language. ERNIE-ViL tries to build the detailed semantic connections (objects, attributes of objects and relationships between objects) across vision and language, which are essential to vision-language cross-modal tasks. Utilizing scene graphs of visual scenes, ERNIE-ViL constructs Scene Graph Prediction tasks, i.e., Object Prediction, Attribute Prediction and Relationship Prediction tasks in the pre-training phase. Specifically, these prediction tasks are implemented by predicting nodes of different types in the scene graph parsed from the sentence. Thus, ERNIE-ViL can learn the joint representations characterizing the alignments of the detailed semantics across vision and language. After pre-training on large scale image-text aligned datasets, we validate the effectiveness of ERNIE-ViL on 5 cross-modal downstream tasks. ERNIE-ViL achieves state-of-the-art performances on all these tasks and ranks the first place on the VCR leaderboard with an absolute improvement of 3.7%.

Mutual information maximization has emerged as a powerful learning objective for unsupervised representation learning obtaining state-of-the-art performance in applications such as object recognition, speech recognition, and reinforcement learning. However, such approaches are fundamentally limited since a tight lower bound of mutual information requires sample size exponential in the mutual information. This limits the applicability of these approaches for prediction tasks with high mutual information, such as in video understanding or reinforcement learning. In these settings, such techniques are prone to overfit, both in theory and in practice, and capture only a few of the relevant factors of variation. This leads to incomplete representations that are not optimal for downstream tasks. In this work, we empirically demonstrate that mutual information-based representation learning approaches do fail to learn complete representations on a number of designed and real-world tasks. To mitigate these problems we introduce the Wasserstein dependency measure, which learns more complete representations by using the Wasserstein distance instead of the KL divergence in the mutual information estimator. We show that a practical approximation to this theoretically motivated solution, constructed using Lipschitz constraint techniques from the GAN literature, achieves substantially improved results on tasks where incomplete representations are a major challenge.

Current question-answering benchmarks predominantly focus on accuracy in realizable prediction tasks. Conditioned on a question and answer-key, does the most likely token match the ground truth? Such benchmarks necessarily fail to evaluate LLMs' ability to quantify ground-truth outcome uncertainty. In this work, we focus on the use of LLMs as risk scores for unrealizable prediction tasks. We introduce folktexts, a software package to systematically generate risk scores using LLMs, and evaluate them against US Census data products. A flexible API enables the use of different prompting schemes, local or web-hosted models, and diverse census columns that can be used to compose custom prediction tasks. We evaluate 17 recent LLMs across five proposed benchmark tasks. We find that zero-shot risk scores produced by multiple-choice question-answering have high predictive signal but are widely miscalibrated. Base models consistently overestimate outcome uncertainty, while instruction-tuned models underestimate uncertainty and produce over-confident risk scores. In fact, instruction-tuning polarizes answer distribution regardless of true underlying data uncertainty. This reveals a general inability of instruction-tuned LLMs to express data uncertainty using multiple-choice answers. A separate experiment using verbalized chat-style risk queries yields substantially improved calibration across instruction-tuned models. These differences in ability to quantify data uncertainty cannot be revealed in realizable settings, and highlight a blind-spot in the current evaluation ecosystem that folktexts covers.

Accuracy and timeliness are indeed often conflicting goals in prediction tasks. Premature predictions may yield a higher rate of false alarms, whereas delaying predictions to gather more information can render them too late to be useful. In applications such as wildfires, crimes, and traffic jams, timely forecasting are vital for safeguarding human life and property. Consequently, finding a balance between accuracy and timeliness is crucial. In this paper, we propose an early spatio-temporal forecasting model based on Multi-Objective reinforcement learning that can either implement an optimal policy given a preference or infer the preference based on a small number of samples. The model addresses two primary challenges: 1) enhancing the accuracy of early forecasting and 2) providing the optimal policy for determining the most suitable prediction time for each area. Our method demonstrates superior performance on three large-scale real-world datasets, surpassing existing methods in early spatio-temporal forecasting tasks.

Perception systems in modern autonomous driving vehicles typically take inputs from complementary multi-modal sensors, e.g., LiDAR and cameras. However, in real-world applications, sensor corruptions and failures lead to inferior performances, thus compromising autonomous safety. In this paper, we propose a robust framework, called MetaBEV, to address extreme real-world environments involving overall six sensor corruptions and two extreme sensor-missing situations. In MetaBEV, signals from multiple sensors are first processed by modal-specific encoders. Subsequently, a set of dense BEV queries are initialized, termed meta-BEV. These queries are then processed iteratively by a BEV-Evolving decoder, which selectively aggregates deep features from either LiDAR, cameras, or both modalities. The updated BEV representations are further leveraged for multiple 3D prediction tasks. Additionally, we introduce a new M2oE structure to alleviate the performance drop on distinct tasks in multi-task joint learning. Finally, MetaBEV is evaluated on the nuScenes dataset with 3D object detection and BEV map segmentation tasks. Experiments show MetaBEV outperforms prior arts by a large margin on both full and corrupted modalities. For instance, when the LiDAR signal is missing, MetaBEV improves 35.5% detection NDS and 17.7% segmentation mIoU upon the vanilla BEVFusion model; and when the camera signal is absent, MetaBEV still achieves 69.2% NDS and 53.7% mIoU, which is even higher than previous works that perform on full-modalities. Moreover, MetaBEV performs fairly against previous methods in both canonical perception and multi-task learning settings, refreshing state-of-the-art nuScenes BEV map segmentation with 70.4% mIoU.

We present a simple but effective pixel-level self-supervised distillation framework friendly to dense prediction tasks. Our method, called Pixel-Wise Contrastive Distillation (PCD), distills knowledge by attracting the corresponding pixels from student's and teacher's output feature maps. PCD includes a novel design called SpatialAdaptor which ``reshapes'' a part of the teacher network while preserving the distribution of its output features. Our ablation experiments suggest that this reshaping behavior enables more informative pixel-to-pixel distillation. Moreover, we utilize a plug-in multi-head self-attention module that explicitly relates the pixels of student's feature maps to enhance the effective receptive field, leading to a more competitive student. PCD outperforms previous self-supervised distillation methods on various dense prediction tasks. A backbone of ResNet-18-FPN distilled by PCD achieves 37.4 AP^bbox and 34.0 AP^mask on COCO dataset using the detector of Mask R-CNN. We hope our study will inspire future research on how to pre-train a small model friendly to dense prediction tasks in a self-supervised fashion.

With the growing prominence of the Mixture of Experts (MoE) architecture in developing large-scale foundation models, we investigate the Hierarchical Mixture of Experts (HMoE), a specialized variant of MoE that excels in handling complex inputs and improving performance on targeted tasks. Our analysis highlights the advantages of using the Laplace gating function over the traditional Softmax gating within the HMoE frameworks. We theoretically demonstrate that applying the Laplace gating function at both levels of the HMoE model helps eliminate undesirable parameter interactions caused by the Softmax gating and, therefore, accelerates the expert convergence as well as enhances the expert specialization. Empirical validation across diverse scenarios supports these theoretical claims. This includes large-scale multimodal tasks, image classification, and latent domain discovery and prediction tasks, where our modified HMoE models show great performance improvements compared to the conventional HMoE models.

Self-supervised learning of graph neural networks (GNNs) aims to learn an accurate representation of the graphs in an unsupervised manner, to obtain transferable representations of them for diverse downstream tasks. Predictive learning and contrastive learning are the two most prevalent approaches for graph self-supervised learning. However, they have their own drawbacks. While the predictive learning methods can learn the contextual relationships between neighboring nodes and edges, they cannot learn global graph-level similarities. Contrastive learning, while it can learn global graph-level similarities, its objective to maximize the similarity between two differently perturbed graphs may result in representations that cannot discriminate two similar graphs with different properties. To tackle such limitations, we propose a framework that aims to learn the exact discrepancy between the original and the perturbed graphs, coined as Discrepancy-based Self-supervised LeArning (D-SLA). Specifically, we create multiple perturbations of the given graph with varying degrees of similarity, and train the model to predict whether each graph is the original graph or the perturbed one. Moreover, we further aim to accurately capture the amount of discrepancy for each perturbed graph using the graph edit distance. We validate our D-SLA on various graph-related downstream tasks, including molecular property prediction, protein function prediction, and link prediction tasks, on which ours largely outperforms relevant baselines.

Evaluation is crucial in the development process of task-oriented dialogue systems. As an evaluation method, user simulation allows us to tackle issues such as scalability and cost-efficiency, making it a viable choice for large-scale automatic evaluation. To help build a human-like user simulator that can measure the quality of a dialogue, we propose the following task: simulating user satisfaction for the evaluation of task-oriented dialogue systems. The purpose of the task is to increase the evaluation power of user simulations and to make the simulation more human-like. To overcome a lack of annotated data, we propose a user satisfaction annotation dataset, USS, that includes 6,800 dialogues sampled from multiple domains, spanning real-world e-commerce dialogues, task-oriented dialogues constructed through Wizard-of-Oz experiments, and movie recommendation dialogues. All user utterances in those dialogues, as well as the dialogues themselves, have been labeled based on a 5-level satisfaction scale. We also share three baseline methods for user satisfaction prediction and action prediction tasks. Experiments conducted on the USS dataset suggest that distributed representations outperform feature-based methods. A model based on hierarchical GRUs achieves the best performance in in-domain user satisfaction prediction, while a BERT-based model has better cross-domain generalization ability.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

While the general machine learning (ML) community has benefited from public datasets, tasks, and models, the progress of ML in healthcare has been hampered by a lack of such shared assets. The success of foundation models creates new challenges for healthcare ML by requiring access to shared pretrained models to validate performance benefits. We help address these challenges through three contributions. First, we publish a new dataset, EHRSHOT, which contains deidentified structured data from the electronic health records (EHRs) of 6,739 patients from Stanford Medicine. Unlike MIMIC-III/IV and other popular EHR datasets, EHRSHOT is longitudinal and not restricted to ICU/ED patients. Second, we publish the weights of CLMBR-T-base, a 141M parameter clinical foundation model pretrained on the structured EHR data of 2.57M patients. We are one of the first to fully release such a model for coded EHR data; in contrast, most prior models released for clinical data (e.g. GatorTron, ClinicalBERT) only work with unstructured text and cannot process the rich, structured data within an EHR. We provide an end-to-end pipeline for the community to validate and build upon its performance. Third, we define 15 few-shot clinical prediction tasks, enabling evaluation of foundation models on benefits such as sample efficiency and task adaptation. Our model and dataset are available via a research data use agreement from the Stanford AIMI Center. Code to reproduce our results are available at our Github repo: https://github.com/som-shahlab/ehrshot-benchmark

Understanding urban socioeconomic conditions through visual data is a challenging yet essential task for sustainable urban development and policy planning. In this work, we introduce CityLens, a comprehensive benchmark designed to evaluate the capabilities of large language-vision models (LLVMs) in predicting socioeconomic indicators from satellite and street view imagery. We construct a multi-modal dataset covering a total of 17 globally distributed cities, spanning 6 key domains: economy, education, crime, transport, health, and environment, reflecting the multifaceted nature of urban life. Based on this dataset, we define 11 prediction tasks and utilize three evaluation paradigms: Direct Metric Prediction, Normalized Metric Estimation, and Feature-Based Regression. We benchmark 17 state-of-the-art LLVMs across these tasks. Our results reveal that while LLVMs demonstrate promising perceptual and reasoning capabilities, they still exhibit limitations in predicting urban socioeconomic indicators. CityLens provides a unified framework for diagnosing these limitations and guiding future efforts in using LLVMs to understand and predict urban socioeconomic patterns. Our codes and datasets are open-sourced via https://github.com/tsinghua-fib-lab/CityLens.

Developing models that can learn to reason is a notoriously challenging problem. We focus on reasoning in relational domains, where the use of Graph Neural Networks (GNNs) seems like a natural choice. However, previous work has shown that regular GNNs lack the ability to systematically generalize from training examples on test graphs requiring longer inference chains, which fundamentally limits their reasoning abilities. A common solution relies on neuro-symbolic methods that systematically reason by learning rules, but their scalability is often limited and they tend to make unrealistically strong assumptions, e.g.\ that the answer can always be inferred from a single relational path. We propose the Epistemic GNN (EpiGNN), a novel parameter-efficient and scalable GNN architecture with an epistemic inductive bias for systematic reasoning. Node embeddings in EpiGNNs are treated as epistemic states, and message passing is implemented accordingly. We show that EpiGNNs achieve state-of-the-art results on link prediction tasks that require systematic reasoning. Furthermore, for inductive knowledge graph completion, EpiGNNs rival the performance of state-of-the-art specialized approaches. Finally, we introduce two new benchmarks that go beyond standard relational reasoning by requiring the aggregation of information from multiple paths. Here, existing neuro-symbolic approaches fail, yet EpiGNNs learn to reason accurately. Code and datasets are available at https://github.com/erg0dic/gnn-sg.

Vision transformers (ViTs) have pushed the state-of-the-art for visual perception tasks. The self-attention mechanism underpinning the strength of ViTs has a quadratic complexity in both computation and memory usage. This motivates the development of approximating the self-attention at linear complexity. However, an in-depth analysis in this work reveals that existing methods are either theoretically flawed or empirically ineffective for visual recognition. We identify that their limitations are rooted in the inheritance of softmax-based self-attention during approximations, that is, normalizing the scaled dot-product between token feature vectors using the softmax function. As preserving the softmax operation challenges any subsequent linearization efforts. By this insight, a family of Softmax-Free Transformers (SOFT) are proposed. Specifically, a Gaussian kernel function is adopted to replace the dot-product similarity, enabling a full self-attention matrix to be approximated under low-rank matrix decomposition. For computational robustness, we estimate the Moore-Penrose inverse using an iterative Newton-Raphson method in the forward process only, while calculating its theoretical gradients only once in the backward process. To further expand applicability (e.g., dense prediction tasks), an efficient symmetric normalization technique is introduced. Extensive experiments on ImageNet, COCO, and ADE20K show that our SOFT significantly improves the computational efficiency of existing ViT variants. With linear complexity, much longer token sequences are permitted by SOFT, resulting in superior trade-off between accuracy and complexity. Code and models are available at https://github.com/fudan-zvg/SOFT.

Vision transformers have been widely explored in various vision tasks. Due to heavy computational cost, much interest has aroused for compressing vision transformer dynamically in the aspect of tokens. Current methods mainly pay attention to token pruning or merging to reduce token numbers, in which tokens are compressed exclusively, causing great information loss and therefore post-training is inevitably required to recover the performance. In this paper, we rethink token reduction and unify the process as an explicit form of token matrix transformation, in which all existing methods are constructing special forms of matrices within the framework. Furthermore, we propose a many-to-many Token Transforming framework that serves as a generalization of all existing methods and reserves the most information, even enabling training-free acceleration. We conduct extensive experiments to validate our framework. Specifically, we reduce 40% FLOPs and accelerate DeiT-S by times1.5 with marginal 0.1% accuracy drop. Furthermore, we extend the method to dense prediction tasks including segmentation, object detection, depth estimation, and language model generation. Results demonstrate that the proposed method consistently achieves substantial improvements, offering a better computation-performance trade-off, impressive budget reduction and inference acceleration.

Dense contrastive representation learning (DCRL) has greatly improved the learning efficiency for image-dense prediction tasks, showing its great potential to reduce the large costs of medical image collection and dense annotation. However, the properties of medical images make unreliable correspondence discovery, bringing an open problem of large-scale false positive and negative (FP&N) pairs in DCRL. In this paper, we propose GEoMetric vIsual deNse sImilarity (GEMINI) learning which embeds the homeomorphism prior to DCRL and enables a reliable correspondence discovery for effective dense contrast. We propose a deformable homeomorphism learning (DHL) which models the homeomorphism of medical images and learns to estimate a deformable mapping to predict the pixels' correspondence under topological preservation. It effectively reduces the searching space of pairing and drives an implicit and soft learning of negative pairs via a gradient. We also propose a geometric semantic similarity (GSS) which extracts semantic information in features to measure the alignment degree for the correspondence learning. It will promote the learning efficiency and performance of deformation, constructing positive pairs reliably. We implement two practical variants on two typical representation learning tasks in our experiments. Our promising results on seven datasets which outperform the existing methods show our great superiority. We will release our code on a companion link: https://github.com/YutingHe-list/GEMINI.

Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

Tokenization methods like Byte-Pair Encoding (BPE) enhance computational efficiency in large language models (LLMs) but often obscure internal character structures within tokens. This limitation hinders LLMs' ability to predict precise character positions, which is crucial in tasks like Chinese Spelling Correction (CSC) where identifying the positions of misspelled characters accelerates correction processes. We propose Token Internal Position Awareness (TIPA), a method that significantly improves models' ability to capture character positions within tokens by training them on reverse character prediction tasks using the tokenizer's vocabulary. Experiments demonstrate that TIPA enhances position prediction accuracy in LLMs, enabling more precise identification of target characters in original text. Furthermore, when applied to downstream tasks that do not require exact position prediction, TIPA still boosts performance in tasks needing character-level information, validating its versatility and effectiveness.

We have witnessed impressive advances in video action understanding. Increased dataset sizes, variability, and computation availability have enabled leaps in performance and task diversification. Current systems can provide coarse- and fine-grained descriptions of video scenes, extract segments corresponding to queries, synthesize unobserved parts of videos, and predict context. This survey comprehensively reviews advances in uni- and multi-modal action understanding across a range of tasks. We focus on prevalent challenges, overview widely adopted datasets, and survey seminal works with an emphasis on recent advances. We broadly distinguish between three temporal scopes: (1) recognition tasks of actions observed in full, (2) prediction tasks for ongoing partially observed actions, and (3) forecasting tasks for subsequent unobserved action. This division allows us to identify specific action modeling and video representation challenges. Finally, we outline future directions to address current shortcomings.

Predicting future international events from textual information, such as news articles, has tremendous potential for applications in global policy, strategic decision-making, and geopolitics. However, existing datasets available for this task are often limited in quality, hindering the progress of related research. In this paper, we introduce WORLDREP (WORLD Relationship and Event Prediction), a novel dataset designed to address these limitations by leveraging the advanced reasoning capabilities of large-language models (LLMs). Our dataset features high-quality scoring labels generated through advanced prompt modeling and rigorously validated by domain experts in political science. We showcase the quality and utility of WORLDREP for real-world event prediction tasks, demonstrating its effectiveness through extensive experiments and analysis. Furthermore, we publicly release our dataset along with the full automation source code for data collection, labeling, and benchmarking, aiming to support and advance research in text-based event prediction.

There are many settings where it is useful to predict and explain the success or failure of a dialogue. Circumplex theory from psychology models the social orientations (e.g., Warm-Agreeable, Arrogant-Calculating) of conversation participants and can be used to predict and explain the outcome of social interactions. Our work is novel in its systematic application of social orientation tags to modeling conversation outcomes. In this paper, we introduce a new data set of dialogue utterances machine-labeled with social orientation tags. We show that social orientation tags improve task performance, especially in low-resource settings, on both English and Chinese language benchmarks. We also demonstrate how social orientation tags help explain the outcomes of social interactions when used in neural models. Based on these results showing the utility of social orientation tags for dialogue outcome prediction tasks, we release our data sets, code, and models that are fine-tuned to predict social orientation tags on dialogue utterances.

Deep sparse networks are widely investigated as a neural network architecture for prediction tasks with high-dimensional sparse features, with which feature interaction selection is a critical component. While previous methods primarily focus on how to search feature interaction in a coarse-grained space, less attention has been given to a finer granularity. In this work, we introduce a hybrid-grained feature interaction selection approach that targets both feature field and feature value for deep sparse networks. To explore such expansive space, we propose a decomposed space which is calculated on the fly. We then develop a selection algorithm called OptFeature, which efficiently selects the feature interaction from both the feature field and the feature value simultaneously. Results from experiments on three large real-world benchmark datasets demonstrate that OptFeature performs well in terms of accuracy and efficiency. Additional studies support the feasibility of our method.

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

Recent studies have shown promising results on utilizing pre-trained image-language models for video question answering. While these image-language models can efficiently bootstrap the representation learning of video-language models, they typically concatenate uniformly sampled video frames as visual inputs without explicit language-aware, temporal modeling. When only a portion of a video input is relevant to the language query, such uniform frame sampling can often lead to missing important visual cues. Although humans often find a video moment to focus on and rewind the moment to answer questions, training a query-aware video moment localizer often requires expensive annotations and high computational costs. To address this issue, we propose Self-Chained Video Localization-Answering (SeViLA), a novel framework that leverages a single image-language model (BLIP-2) to tackle both temporal keyframe localization and QA on videos. SeViLA framework consists of two modules: Localizer and Answerer, where both are parameter-efficiently fine-tuned from BLIP-2. We chain these modules for cascaded inference and self-refinement. First, in the forward chain, the Localizer finds multiple language-aware keyframes in a video, which the Answerer uses to predict the answer. Second, in the reverse chain, the Answerer generates keyframe pseudo-labels to refine the Localizer, alleviating the need for expensive video moment localization annotations. SeViLA outperforms several strong baselines/previous works on five video QA and event prediction tasks, and achieves the state-of-the-art in both fine-tuning (NExT-QA, STAR) and zero-shot (NExT-QA, STAR, How2QA, VLEP) settings. We show a comprehensive analysis, e.g., the impact of Localizer, comparisons of Localizer with other temporal localization models, pre-training/self-refinement of Localizer, and varying the number of keyframes.

We present a self-supervised, time-to-event (TTE) foundation model called MOTOR (Many Outcome Time Oriented Representations) which is pretrained on timestamped sequences of events in electronic health records (EHR) and health insurance claims. TTE models are used for estimating the probability distribution of the time until a specific event occurs, which is an important task in medical settings. TTE models provide many advantages over classification using fixed time horizons, including naturally handling censored observations, but are challenging to train with limited labeled data. MOTOR addresses this challenge by pretraining on up to 55M patient records (9B clinical events). We evaluate MOTOR's transfer learning performance on 19 tasks, across 3 patient databases (a private EHR system, MIMIC-IV, and Merative claims data). Task-specific models adapted from MOTOR improve time-dependent C statistics by 4.6% over state-of-the-art, improve label efficiency by up to 95% ,and are more robust to temporal distributional shifts. We further evaluate cross-site portability by adapting our MOTOR foundation model for six prediction tasks on the MIMIC-IV dataset, where it outperforms all baselines. MOTOR is the first foundation model for medical TTE predictions and we release a 143M parameter pretrained model for research use at [redacted URL].

Recent work attributes progress in NLP to large language models (LMs) with increased model size and large quantities of pretraining data. Despite this, current state-of-the-art LMs for Hebrew are both under-parameterized and under-trained compared to LMs in other languages. Additionally, previous work on pretrained Hebrew LMs focused on encoder-only models. While the encoder-only architecture is beneficial for classification tasks, it does not cater well for sub-word prediction tasks, such as Named Entity Recognition, when considering the morphologically rich nature of Hebrew. In this paper we argue that sequence-to-sequence generative architectures are more suitable for LLMs in the case of morphologically rich languages (MRLs) such as Hebrew. We demonstrate that by casting tasks in the Hebrew NLP pipeline as text-to-text tasks, we can leverage powerful multilingual, pretrained sequence-to-sequence models as mT5, eliminating the need for a specialized, morpheme-based, separately fine-tuned decoder. Using this approach, our experiments show substantial improvements over previously published results on existing Hebrew NLP benchmarks. These results suggest that multilingual sequence-to-sequence models present a promising building block for NLP for MRLs.

Recent works in self-supervised learning have demonstrated strong performance on scene-level dense prediction tasks by pretraining with object-centric or region-based correspondence objectives. In this paper, we present Region-to-Object Representation Learning (R2O) which unifies region-based and object-centric pretraining. R2O operates by training an encoder to dynamically refine region-based segments into object-centric masks and then jointly learns representations of the contents within the mask. R2O uses a "region refinement module" to group small image regions, generated using a region-level prior, into larger regions which tend to correspond to objects by clustering region-level features. As pretraining progresses, R2O follows a region-to-object curriculum which encourages learning region-level features early on and gradually progresses to train object-centric representations. Representations learned using R2O lead to state-of-the art performance in semantic segmentation for PASCAL VOC (+0.7 mIOU) and Cityscapes (+0.4 mIOU) and instance segmentation on MS COCO (+0.3 mask AP). Further, after pretraining on ImageNet, R2O pretrained models are able to surpass existing state-of-the-art in unsupervised object segmentation on the Caltech-UCSD Birds 200-2011 dataset (+2.9 mIoU) without any further training. We provide the code/models from this work at https://github.com/KKallidromitis/r2o.

To provide consistent emotional interaction with users, dialog systems should be capable to automatically select appropriate emotions for responses like humans. However, most existing works focus on rendering specified emotions in responses or empathetically respond to the emotion of users, yet the individual difference in emotion expression is overlooked. This may lead to inconsistent emotional expressions and disinterest users. To tackle this issue, we propose to equip the dialog system with personality and enable it to automatically select emotions in responses by simulating the emotion transition of humans in conversation. In detail, the emotion of the dialog system is transitioned from its preceding emotion in context. The transition is triggered by the preceding dialog context and affected by the specified personality trait. To achieve this, we first model the emotion transition in the dialog system as the variation between the preceding emotion and the response emotion in the Valence-Arousal-Dominance (VAD) emotion space. Then, we design neural networks to encode the preceding dialog context and the specified personality traits to compose the variation. Finally, the emotion for response is selected from the sum of the preceding emotion and the variation. We construct a dialog dataset with emotion and personality labels and conduct emotion prediction tasks for evaluation. Experimental results validate the effectiveness of the personality-affected emotion transition.

Combining satellite imagery with machine learning (SIML) has the potential to address global challenges by remotely estimating socioeconomic and environmental conditions in data-poor regions, yet the resource requirements of SIML limit its accessibility and use. We show that a single encoding of satellite imagery can generalize across diverse prediction tasks (e.g. forest cover, house price, road length). Our method achieves accuracy competitive with deep neural networks at orders of magnitude lower computational cost, scales globally, delivers label super-resolution predictions, and facilitates characterizations of uncertainty. Since image encodings are shared across tasks, they can be centrally computed and distributed to unlimited researchers, who need only fit a linear regression to their own ground truth data in order to achieve state-of-the-art SIML performance.

While deep learning models have achieved state-of-the-art accuracies for many prediction tasks, understanding these models remains a challenge. Despite the recent interest in developing visual tools to help users interpret deep learning models, the complexity and wide variety of models deployed in industry, and the large-scale datasets that they used, pose unique design challenges that are inadequately addressed by existing work. Through participatory design sessions with over 15 researchers and engineers at Facebook, we have developed, deployed, and iteratively improved ActiVis, an interactive visualization system for interpreting large-scale deep learning models and results. By tightly integrating multiple coordinated views, such as a computation graph overview of the model architecture, and a neuron activation view for pattern discovery and comparison, users can explore complex deep neural network models at both the instance- and subset-level. ActiVis has been deployed on Facebook's machine learning platform. We present case studies with Facebook researchers and engineers, and usage scenarios of how ActiVis may work with different models.

We introduce a new approach to generative data-driven dialogue systems (e.g. chatbots) called TransferTransfo which is a combination of a Transfer learning based training scheme and a high-capacity Transformer model. Fine-tuning is performed by using a multi-task objective which combines several unsupervised prediction tasks. The resulting fine-tuned model shows strong improvements over the current state-of-the-art end-to-end conversational models like memory augmented seq2seq and information-retrieval models. On the privately held PERSONA-CHAT dataset of the Conversational Intelligence Challenge 2, this approach obtains a new state-of-the-art, with respective perplexity, Hits@1 and F1 metrics of 16.28 (45 % absolute improvement), 80.7 (46 % absolute improvement) and 19.5 (20 % absolute improvement).

Graph embedding methods such as Graph Neural Networks (GNNs) and Graph Transformers have contributed to the development of graph reasoning algorithms for various tasks on knowledge graphs. However, the lack of interpretability and explainability of graph embedding methods has limited their applicability in scenarios requiring explicit reasoning. In this paper, we introduce the Graph Agent (GA), an intelligent agent methodology of leveraging large language models (LLMs), inductive-deductive reasoning modules, and long-term memory for knowledge graph reasoning tasks. GA integrates aspects of symbolic reasoning and existing graph embedding methods to provide an innovative approach for complex graph reasoning tasks. By converting graph structures into textual data, GA enables LLMs to process, reason, and provide predictions alongside human-interpretable explanations. The effectiveness of the GA was evaluated on node classification and link prediction tasks. Results showed that GA reached state-of-the-art performance, demonstrating accuracy of 90.65%, 95.48%, and 89.32% on Cora, PubMed, and PrimeKG datasets, respectively. Compared to existing GNN and transformer models, GA offered advantages of explicit reasoning ability, free-of-training, easy adaption to various graph reasoning tasks

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.

Machine learning models are routinely used to support decisions that affect individuals -- be it to screen a patient for a serious illness or to gauge their response to treatment. In these tasks, we are limited to learning models from datasets with noisy labels. In this paper, we study the instance-level impact of learning under label noise. We introduce a notion of regret for this regime, which measures the number of unforeseen mistakes due to noisy labels. We show that standard approaches to learning under label noise can return models that perform well at a population-level while subjecting individuals to a lottery of mistakes. We present a versatile approach to estimate the likelihood of mistakes at the individual-level from a noisy dataset by training models over plausible realizations of datasets without label noise. This is supported by a comprehensive empirical study of label noise in clinical prediction tasks. Our results reveal how failure to anticipate mistakes can compromise model reliability and adoption -- we demonstrate how we can address these challenges by anticipating and avoiding regretful decisions.

Temporal Point Processes (TPP) are probabilistic generative frameworks. They model discrete event sequences localized in continuous time. Generally, real-life events reveal descriptive information, known as marks. Marked TPPs model time and marks of the event together for practical relevance. Conditioned on past events, marked TPPs aim to learn the joint distribution of the time and the mark of the next event. For simplicity, conditionally independent TPP models assume time and marks are independent given event history. They factorize the conditional joint distribution of time and mark into the product of individual conditional distributions. This structural limitation in the design of TPP models hurt the predictive performance on entangled time and mark interactions. In this work, we model the conditional inter-dependence of time and mark to overcome the limitations of conditionally independent models. We construct a multivariate TPP conditioning the time distribution on the current event mark in addition to past events. Besides the conventional intensity-based models for conditional joint distribution, we also draw on flexible intensity-free TPP models from the literature. The proposed TPP models outperform conditionally independent and dependent models in standard prediction tasks. Our experimentation on various datasets with multiple evaluation metrics highlights the merit of the proposed approach.

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.

Safe deployment of large language models (LLMs) may benefit from a reliable method for assessing their generated content to determine when to abstain or to selectively generate. While likelihood-based metrics such as perplexity are widely employed, recent research has demonstrated the limitations of using sequence-level probability estimates given by LLMs as reliable indicators of generation quality. Conversely, LLMs have demonstrated strong calibration at the token level, particularly when it comes to choosing correct answers in multiple-choice questions or evaluating true/false statements. In this work, we reformulate open-ended generation tasks into token-level prediction tasks, and leverage LLMs' superior calibration at the token level. We instruct an LLM to self-evaluate its answers, employing either a multi-way comparison or a point-wise evaluation approach, with the option to include a ``None of the above'' option to express the model's uncertainty explicitly. We benchmark a range of scoring methods based on self-evaluation and evaluate their performance in selective generation using TruthfulQA and TL;DR. Through experiments with PaLM-2 and GPT-3, we demonstrate that self-evaluation based scores not only improve accuracy, but also correlate better with the overall quality of generated content.

In order to understand the in-context learning phenomenon, recent works have adopted a stylized experimental framework and demonstrated that Transformers can learn gradient-based learning algorithms for various classes of real-valued functions. However, the limitations of Transformers in implementing learning algorithms, and their ability to learn other forms of algorithms are not well understood. Additionally, the degree to which these capabilities are confined to attention-based models is unclear. Furthermore, it remains to be seen whether the insights derived from these stylized settings can be extrapolated to pretrained Large Language Models (LLMs). In this work, we take a step towards answering these questions by demonstrating the following: (a) On a test-bed with a variety of Boolean function classes, we find that Transformers can nearly match the optimal learning algorithm for 'simpler' tasks, while their performance deteriorates on more 'complex' tasks. Additionally, we find that certain attention-free models perform (almost) identically to Transformers on a range of tasks. (b) When provided a teaching sequence, i.e. a set of examples that uniquely identifies a function in a class, we show that Transformers learn more sample-efficiently. Interestingly, our results show that Transformers can learn to implement two distinct algorithms to solve a single task, and can adaptively select the more sample-efficient algorithm depending on the sequence of in-context examples. (c) Lastly, we show that extant LLMs, e.g. LLaMA-2, GPT-4, can compete with nearest-neighbor baselines on prediction tasks that are guaranteed to not be in their training set.

Although Large Language Models (LLMs) have demonstrated remarkable progress, their proficiency in graph-related tasks remains notably limited, hindering the development of truly general-purpose models. Previous attempts, including pretraining graph foundation models or employing supervised fine-tuning, often face challenges such as the scarcity of large-scale, universally represented graph data. We introduce G1, a simple yet effective approach demonstrating that Reinforcement Learning (RL) on synthetic graph-theoretic tasks can significantly scale LLMs' graph reasoning abilities. To enable RL training, we curate Erd\~os, the largest graph reasoning dataset to date comprising 50 diverse graph-theoretic tasks of varying difficulty levels, 100k training data and 5k test data, all drived from real-world graphs. With RL on Erd\~os, G1 obtains substantial improvements in graph reasoning, where our finetuned 3B model even outperforms Qwen2.5-72B-Instruct (24x size). RL-trained models also show strong zero-shot generalization to unseen tasks, domains, and graph encoding schemes, including other graph-theoretic benchmarks as well as real-world node classification and link prediction tasks, without compromising general reasoning abilities. Our findings offer an efficient, scalable path for building strong graph reasoners by finetuning LLMs with RL on graph-theoretic tasks, which combines the strengths of pretrained LLM capabilities with abundant, automatically generated synthetic data, suggesting that LLMs possess graph understanding abilities that RL can elicit successfully.

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.

Self-supervised visual representation learning has seen huge progress recently, but no large scale evaluation has compared the many models now available. We evaluate the transfer performance of 13 top self-supervised models on 40 downstream tasks, including many-shot and few-shot recognition, object detection, and dense prediction. We compare their performance to a supervised baseline and show that on most tasks the best self-supervised models outperform supervision, confirming the recently observed trend in the literature. We find ImageNet Top-1 accuracy to be highly correlated with transfer to many-shot recognition, but increasingly less so for few-shot, object detection and dense prediction. No single self-supervised method dominates overall, suggesting that universal pre-training is still unsolved. Our analysis of features suggests that top self-supervised learners fail to preserve colour information as well as supervised alternatives, but tend to induce better classifier calibration, and less attentive overfitting than supervised learners.

This paper introduces Graph Convolutional Recurrent Network (GCRN), a deep learning model able to predict structured sequences of data. Precisely, GCRN is a generalization of classical recurrent neural networks (RNN) to data structured by an arbitrary graph. Such structured sequences can represent series of frames in videos, spatio-temporal measurements on a network of sensors, or random walks on a vocabulary graph for natural language modeling. The proposed model combines convolutional neural networks (CNN) on graphs to identify spatial structures and RNN to find dynamic patterns. We study two possible architectures of GCRN, and apply the models to two practical problems: predicting moving MNIST data, and modeling natural language with the Penn Treebank dataset. Experiments show that exploiting simultaneously graph spatial and dynamic information about data can improve both precision and learning speed.

Unsupervised domain adaptation for semantic segmentation (DASS) aims to transfer knowledge from a label-rich source domain to a target domain with no labels. Two key approaches in DASS are (1) vision-only approaches using masking or multi-resolution crops, and (2) language-based approaches that use generic class-wise prompts informed by target domain (e.g. "a {snowy} photo of a {class}"). However, the former is susceptible to noisy pseudo-labels that are biased to the source domain. The latter does not fully capture the intricate spatial relationships of objects -- key for dense prediction tasks. To this end, we propose LangDA. LangDA addresses these challenges by, first, learning contextual relationships between objects via VLM-generated scene descriptions (e.g. "a pedestrian is on the sidewalk, and the street is lined with buildings."). Second, LangDA aligns the entire image features with text representation of this context-aware scene caption and learns generalized representations via text. With this, LangDA sets the new state-of-the-art across three DASS benchmarks, outperforming existing methods by 2.6%, 1.4% and 3.9%.

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation, PAAG, a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a significant increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 22.0% in the immunoglobulin domain) in comparison to the existing model. We anticipate that PAAG will broaden the horizons of protein design by leveraging the knowledge from between textual annotation and proteins.

One of the grand challenges of artificial general intelligence is developing agents capable of conducting scientific research and discovering new knowledge. While frontier models have already been used as aids to human scientists, e.g. for brainstorming ideas, writing code, or prediction tasks, they still conduct only a small part of the scientific process. This paper presents the first comprehensive framework for fully automatic scientific discovery, enabling frontier large language models to perform research independently and communicate their findings. We introduce The AI Scientist, which generates novel research ideas, writes code, executes experiments, visualizes results, describes its findings by writing a full scientific paper, and then runs a simulated review process for evaluation. In principle, this process can be repeated to iteratively develop ideas in an open-ended fashion, acting like the human scientific community. We demonstrate its versatility by applying it to three distinct subfields of machine learning: diffusion modeling, transformer-based language modeling, and learning dynamics. Each idea is implemented and developed into a full paper at a cost of less than $15 per paper. To evaluate the generated papers, we design and validate an automated reviewer, which we show achieves near-human performance in evaluating paper scores. The AI Scientist can produce papers that exceed the acceptance threshold at a top machine learning conference as judged by our automated reviewer. This approach signifies the beginning of a new era in scientific discovery in machine learning: bringing the transformative benefits of AI agents to the entire research process of AI itself, and taking us closer to a world where endless affordable creativity and innovation can be unleashed on the world's most challenging problems. Our code is open-sourced at https://github.com/SakanaAI/AI-Scientist

Recent advancements in Large Language Models (LLMs) have empowered LLM agents to autonomously collect world information, over which to conduct reasoning to solve complex problems. Given this capability, increasing interests have been put into employing LLM agents for predicting international events, which can influence decision-making and shape policy development on an international scale. Despite such a growing interest, there is a lack of a rigorous benchmark of LLM agents' forecasting capability and reliability. To address this gap, we introduce MIRAI, a novel benchmark designed to systematically evaluate LLM agents as temporal forecasters in the context of international events. Our benchmark features an agentic environment with tools for accessing an extensive database of historical, structured events and textual news articles. We refine the GDELT event database with careful cleaning and parsing to curate a series of relational prediction tasks with varying forecasting horizons, assessing LLM agents' abilities from short-term to long-term forecasting. We further implement APIs to enable LLM agents to utilize different tools via a code-based interface. In summary, MIRAI comprehensively evaluates the agents' capabilities in three dimensions: 1) autonomously source and integrate critical information from large global databases; 2) write codes using domain-specific APIs and libraries for tool-use; and 3) jointly reason over historical knowledge from diverse formats and time to accurately predict future events. Through comprehensive benchmarking, we aim to establish a reliable framework for assessing the capabilities of LLM agents in forecasting international events, thereby contributing to the development of more accurate and trustworthy models for international relation analysis.

Deep features are a cornerstone of computer vision research, capturing image semantics and enabling the community to solve downstream tasks even in the zero- or few-shot regime. However, these features often lack the spatial resolution to directly perform dense prediction tasks like segmentation and depth prediction because models aggressively pool information over large areas. In this work, we introduce FeatUp, a task- and model-agnostic framework to restore lost spatial information in deep features. We introduce two variants of FeatUp: one that guides features with high-resolution signal in a single forward pass, and one that fits an implicit model to a single image to reconstruct features at any resolution. Both approaches use a multi-view consistency loss with deep analogies to NeRFs. Our features retain their original semantics and can be swapped into existing applications to yield resolution and performance gains even without re-training. We show that FeatUp significantly outperforms other feature upsampling and image super-resolution approaches in class activation map generation, transfer learning for segmentation and depth prediction, and end-to-end training for semantic segmentation.

This paper presents a new vision Transformer, called Swin Transformer, that capably serves as a general-purpose backbone for computer vision. Challenges in adapting Transformer from language to vision arise from differences between the two domains, such as large variations in the scale of visual entities and the high resolution of pixels in images compared to words in text. To address these differences, we propose a hierarchical Transformer whose representation is computed with Shifted windows. The shifted windowing scheme brings greater efficiency by limiting self-attention computation to non-overlapping local windows while also allowing for cross-window connection. This hierarchical architecture has the flexibility to model at various scales and has linear computational complexity with respect to image size. These qualities of Swin Transformer make it compatible with a broad range of vision tasks, including image classification (87.3 top-1 accuracy on ImageNet-1K) and dense prediction tasks such as object detection (58.7 box AP and 51.1 mask AP on COCO test-dev) and semantic segmentation (53.5 mIoU on ADE20K val). Its performance surpasses the previous state-of-the-art by a large margin of +2.7 box AP and +2.6 mask AP on COCO, and +3.2 mIoU on ADE20K, demonstrating the potential of Transformer-based models as vision backbones. The hierarchical design and the shifted window approach also prove beneficial for all-MLP architectures. The code and models are publicly available at~https://github.com/microsoft/Swin-Transformer.

The development of emotion recognition in dialogue (ERC) has been consistently hindered by the complexity of pipeline designs, leading to ERC models that often overfit to specific datasets and dialogue patterns. In this study, we propose a novel approach, namely InstructERC, to reformulates the ERC task from a discriminative framework to a generative framework based on Large Language Models (LLMs) . InstructERC has two significant contributions: Firstly, InstructERC introduces a simple yet effective retrieval template module, which helps the model explicitly integrate multi-granularity dialogue supervision information by concatenating the historical dialog content, label statement, and emotional domain demonstrations with high semantic similarity. Furthermore, we introduce two additional emotion alignment tasks, namely speaker identification and emotion prediction tasks, to implicitly model the dialogue role relationships and future emotional tendencies in conversations. Our LLM-based plug-and-play plugin framework significantly outperforms all previous models and achieves comprehensive SOTA on three commonly used ERC datasets. Extensive analysis of parameter-efficient and data-scaling experiments provide empirical guidance for applying InstructERC in practical scenarios. Our code will be released after blind review.

Attention mechanisms have been widely used to capture long-range dependencies among nodes in Graph Transformers. Bottlenecked by the quadratic computational cost, attention mechanisms fail to scale in large graphs. Recent improvements in computational efficiency are mainly achieved by attention sparsification with random or heuristic-based graph subsampling, which falls short in data-dependent context reasoning. State space models (SSMs), such as Mamba, have gained prominence for their effectiveness and efficiency in modeling long-range dependencies in sequential data. However, adapting SSMs to non-sequential graph data presents a notable challenge. In this work, we introduce Graph-Mamba, the first attempt to enhance long-range context modeling in graph networks by integrating a Mamba block with the input-dependent node selection mechanism. Specifically, we formulate graph-centric node prioritization and permutation strategies to enhance context-aware reasoning, leading to a substantial improvement in predictive performance. Extensive experiments on ten benchmark datasets demonstrate that Graph-Mamba outperforms state-of-the-art methods in long-range graph prediction tasks, with a fraction of the computational cost in both FLOPs and GPU memory consumption. The code and models are publicly available at https://github.com/bowang-lab/Graph-Mamba.

Text entry is an essential task in our day-to-day digital interactions. Numerous intelligent features have been developed to streamline this process, making text entry more effective, efficient, and fluid. These improvements include sentence prediction and user personalization. However, as deep learning-based language models become the norm for these advanced features, the necessity for data collection and model fine-tuning increases. These challenges can be mitigated by harnessing the in-context learning capability of large language models such as GPT-3.5. This unique feature allows the language model to acquire new skills through prompts, eliminating the need for data collection and fine-tuning. Consequently, large language models can learn various text prediction techniques. We initially showed that, for a sentence prediction task, merely prompting GPT-3.5 surpassed a GPT-2 backed system and is comparable with a fine-tuned GPT-3.5 model, with the latter two methods requiring costly data collection, fine-tuning and post-processing. However, the task of prompting large language models to specialize in specific text prediction tasks can be challenging, particularly for designers without expertise in prompt engineering. To address this, we introduce Promptor, a conversational prompt generation agent designed to engage proactively with designers. Promptor can automatically generate complex prompts tailored to meet specific needs, thus offering a solution to this challenge. We conducted a user study involving 24 participants creating prompts for three intelligent text entry tasks, half of the participants used Promptor while the other half designed prompts themselves. The results show that Promptor-designed prompts result in a 35% increase in similarity and 22% in coherence over those by designers.

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

Recent imitation learning policies, often framed as time series prediction tasks, directly map robotic observations-such as high-dimensional visual data and proprioception-into the action space. While time series prediction primarily relies on spatial domain modeling, the underutilization of frequency domain analysis in robotic manipulation trajectory prediction may lead to neglecting the inherent temporal information embedded within action sequences. To address this, we reframe imitation learning policies through the lens of the frequency domain and introduce the Wavelet Policy. This novel approach employs wavelet transforms (WT) for feature preprocessing and extracts multi-scale features from the frequency domain using the SE2MD (Single Encoder to Multiple Decoder) architecture. Furthermore, to enhance feature mapping in the frequency domain and increase model capacity, we introduce a Learnable Frequency-Domain Filter (LFDF) after each frequency decoder, improving adaptability under different visual conditions. Our results show that the Wavelet Policy outperforms state-of-the-art (SOTA) end-to-end methods by over 10% on four challenging robotic arm tasks, while maintaining a comparable parameter count. In long-range settings, its performance declines more slowly as task volume increases. The source code is available at https://github.com/lurenjia384/Wavelet_Policy.

Domain generalization is critical for real-world applications of machine learning to microscopy images, including histopathology and fluorescence imaging. Artifacts in these modalities arise through a complex combination of factors relating to tissue collection and laboratory processing, as well as factors intrinsic to patient samples. In fluorescence imaging, these artifacts stem from variations across experimental batches. The complexity and subtlety of these artifacts make the enumeration of data domains intractable. Therefore, augmentation-based methods of domain generalization that require domain identifiers and manual fine-tuning are inadequate in this setting. To overcome this challenge, we introduce ContriMix, a domain generalization technique that learns to generate synthetic images by disentangling and permuting the biological content ("content") and technical variations ("attributes") in microscopy images. ContriMix does not rely on domain identifiers or handcrafted augmentations and makes no assumptions about the input characteristics of images. We assess the performance of ContriMix on two pathology datasets dealing with patch classification and Whole Slide Image label prediction tasks respectively (Camelyon17-WILDS and RCC subtyping), and one fluorescence microscopy dataset (RxRx1-WILDS). Without any access to domain identifiers at train or test time, ContriMix performs similar or better than current state-of-the-art methods in all these datasets, motivating its usage for microscopy image analysis in real-world settings where domain information is hard to come by. The code for ContriMix can be found at https://gitlab.com/huutan86/contrimix

The rise of big data has amplified the need for efficient, user-friendly automated machine learning (AutoML) tools. However, the intricacy of understanding domain-specific data and defining prediction tasks necessitates human intervention making the process time-consuming while preventing full automation. Instead, envision an intelligent agent capable of assisting users in conducting AutoML tasks through intuitive, natural conversations without requiring in-depth knowledge of the underlying machine learning (ML) processes. This agent's key challenge is to accurately comprehend the user's prediction goals and, consequently, formulate precise ML tasks, adjust data sets and model parameters accordingly, and articulate results effectively. In this paper, we take a pioneering step towards this ambitious goal by introducing a ChatGPT-based conversational data-science framework to act as a "personal data scientist". Precisely, we utilize Large Language Models (ChatGPT) to build a natural interface between the users and the ML models (Scikit-Learn), which in turn, allows us to approach this ambitious problem with a realistic solution. Our model pivots around four dialogue states: Data Visualization, Task Formulation, Prediction Engineering, and Result Summary and Recommendation. Each state marks a unique conversation phase, impacting the overall user-system interaction. Multiple LLM instances, serving as "micro-agents", ensure a cohesive conversation flow, granting us granular control over the conversation's progression. In summary, we developed an end-to-end system that not only proves the viability of the novel concept of conversational data science but also underscores the potency of LLMs in solving complex tasks. Interestingly, its development spotlighted several critical weaknesses in the current LLMs (ChatGPT) and highlighted substantial opportunities for improvement.

Autoregressive (AR) models have long dominated the landscape of large language models, driving progress across a wide range of tasks. Recently, diffusion-based language models have emerged as a promising alternative, though their advantages over AR models remain underexplored. In this paper, we systematically study masked diffusion models in data-constrained settings-where training involves repeated passes over limited data-and find that they significantly outperform AR models when compute is abundant but data is scarce. Diffusion models make better use of repeated data, achieving lower validation loss and superior downstream performance. We interpret this advantage as implicit data augmentation: masked diffusion exposes the model to a diverse distribution of token orderings and prediction tasks, unlike AR's fixed left-to-right factorization. We find new scaling laws for diffusion models and derive a closed-form expression for the critical compute threshold at which diffusion begins to outperform AR. These results suggest that when data, not compute, is the bottleneck, diffusion models offer a compelling alternative to the standard AR paradigm. Our code is available at: https://diffusion-scaling.github.io.

Training large neural networks on large-scale datasets requires substantial computational resources, particularly for dense prediction tasks such as object detection. Although dataset distillation (DD) has been proposed to alleviate these demands by synthesizing compact datasets from larger ones, most existing work focuses solely on image classification, leaving the more complex detection setting largely unexplored. In this paper, we introduce OD3, a novel optimization-free data distillation framework specifically designed for object detection. Our approach involves two stages: first, a candidate selection process in which object instances are iteratively placed in synthesized images based on their suitable locations, and second, a candidate screening process using a pre-trained observer model to remove low-confidence objects. We perform our data synthesis framework on MS COCO and PASCAL VOC, two popular detection datasets, with compression ratios ranging from 0.25% to 5%. Compared to the prior solely existing dataset distillation method on detection and conventional core set selection methods, OD3 delivers superior accuracy, establishes new state-of-the-art results, surpassing prior best method by more than 14% on COCO mAP50 at a compression ratio of 1.0%. Code and condensed datasets are available at: https://github.com/VILA-Lab/OD3.

Contrastive Language-Image Pre-training (CLIP) excels in global alignment with language but exhibits limited sensitivity to spatial information, leading to strong performance in zero-shot classification tasks but underperformance in tasks requiring precise spatial understanding. Recent approaches have introduced Region-Language Alignment (RLA) to enhance CLIP's performance in dense multimodal tasks by aligning regional visual representations with corresponding text inputs. However, we find that CLIP ViTs fine-tuned with RLA suffer from notable loss in spatial awareness, which is crucial for dense prediction tasks. To address this, we propose the Spatial Correlation Distillation (SCD) framework, which preserves CLIP's inherent spatial structure and mitigates the above degradation. To further enhance spatial correlations, we introduce a lightweight Refiner that extracts refined correlations directly from CLIP before feeding them into SCD, based on an intriguing finding that CLIP naturally captures high-quality dense features. Together, these components form a robust distillation framework that enables CLIP ViTs to integrate both visual-language and visual-centric improvements, achieving state-of-the-art results across various open-vocabulary dense prediction benchmarks.

We introduce a novel contextual embedding model med-gte-hybrid that was derived from the gte-large sentence transformer to extract information from unstructured clinical narratives. Our model tuning strategy for med-gte-hybrid combines contrastive learning and a denoising autoencoder. To evaluate the performance of med-gte-hybrid, we investigate several clinical prediction tasks in large patient cohorts extracted from the MIMIC-IV dataset, including Chronic Kidney Disease (CKD) patient prognosis, estimated glomerular filtration rate (eGFR) prediction, and patient mortality prediction. Furthermore, we demonstrate that the med-gte-hybrid model improves patient stratification, clustering, and text retrieval, thus outperforms current state-of-the-art models on the Massive Text Embedding Benchmark (MTEB). While some of our evaluations focus on CKD, our hybrid tuning of sentence transformers could be transferred to other medical domains and has the potential to improve clinical decision-making and personalised treatment pathways in various healthcare applications.

Multi-task dense scene understanding, which trains a model for multiple dense prediction tasks, has a wide range of application scenarios. Capturing long-range dependency and enhancing cross-task interactions are crucial to multi-task dense prediction. In this paper, we propose MTMamba++, a novel architecture for multi-task scene understanding featuring with a Mamba-based decoder. It contains two types of core blocks: self-task Mamba (STM) block and cross-task Mamba (CTM) block. STM handles long-range dependency by leveraging state-space models, while CTM explicitly models task interactions to facilitate information exchange across tasks. We design two types of CTM block, namely F-CTM and S-CTM, to enhance cross-task interaction from feature and semantic perspectives, respectively. Experiments on NYUDv2, PASCAL-Context, and Cityscapes datasets demonstrate the superior performance of MTMamba++ over CNN-based and Transformer-based methods. The code is available at https://github.com/EnVision-Research/MTMamba.

Multi-task dense scene understanding, which learns a model for multiple dense prediction tasks, has a wide range of application scenarios. Modeling long-range dependency and enhancing cross-task interactions are crucial to multi-task dense prediction. In this paper, we propose MTMamba, a novel Mamba-based architecture for multi-task scene understanding. It contains two types of core blocks: self-task Mamba (STM) block and cross-task Mamba (CTM) block. STM handles long-range dependency by leveraging Mamba, while CTM explicitly models task interactions to facilitate information exchange across tasks. Experiments on NYUDv2 and PASCAL-Context datasets demonstrate the superior performance of MTMamba over Transformer-based and CNN-based methods. Notably, on the PASCAL-Context dataset, MTMamba achieves improvements of +2.08, +5.01, and +4.90 over the previous best methods in the tasks of semantic segmentation, human parsing, and object boundary detection, respectively. The code is available at https://github.com/EnVision-Research/MTMamba.

Numerous crucial tasks in real-world decision-making rely on machine learning algorithms with calibrated uncertainty estimates. However, modern methods often yield overconfident and uncalibrated predictions. Various approaches involve training an ensemble of separate models to quantify the uncertainty related to the model itself, known as epistemic uncertainty. In an explicit implementation, the ensemble approach has high computational cost and high memory requirements. This particular challenge is evident in state-of-the-art neural networks such as transformers, where even a single network is already demanding in terms of compute and memory. Consequently, efforts are made to emulate the ensemble model without actually instantiating separate ensemble members, referred to as implicit ensembling. We introduce LoRA-Ensemble, a parameter-efficient deep ensemble method for self-attention networks, which is based on Low-Rank Adaptation (LoRA). Initially developed for efficient LLM fine-tuning, we extend LoRA to an implicit ensembling approach. By employing a single pre-trained self-attention network with weights shared across all members, we train member-specific low-rank matrices for the attention projections. Our method exhibits superior calibration compared to explicit ensembles and achieves similar or better accuracy across various prediction tasks and datasets.

We present DySample, an ultra-lightweight and effective dynamic upsampler. While impressive performance gains have been witnessed from recent kernel-based dynamic upsamplers such as CARAFE, FADE, and SAPA, they introduce much workload, mostly due to the time-consuming dynamic convolution and the additional sub-network used to generate dynamic kernels. Further, the need for high-res feature guidance of FADE and SAPA somehow limits their application scenarios. To address these concerns, we bypass dynamic convolution and formulate upsampling from the perspective of point sampling, which is more resource-efficient and can be easily implemented with the standard built-in function in PyTorch. We first showcase a naive design, and then demonstrate how to strengthen its upsampling behavior step by step towards our new upsampler, DySample. Compared with former kernel-based dynamic upsamplers, DySample requires no customized CUDA package and has much fewer parameters, FLOPs, GPU memory, and latency. Besides the light-weight characteristics, DySample outperforms other upsamplers across five dense prediction tasks, including semantic segmentation, object detection, instance segmentation, panoptic segmentation, and monocular depth estimation. Code is available at https://github.com/tiny-smart/dysample.

Adapting pretrained language models to novel domains, such as clinical applications, traditionally involves retraining their entire set of parameters. Parameter-Efficient Fine-Tuning (PEFT) techniques for fine-tuning language models significantly reduce computational requirements by selectively fine-tuning small subsets of parameters. In this study, we propose a two-step PEFT framework and evaluate it in the clinical domain. Our approach combines a specialised PEFT adapter layer designed for clinical domain adaptation with another adapter specialised for downstream tasks. We evaluate the framework on multiple clinical outcome prediction datasets, comparing it to clinically trained language models. Our framework achieves a better AUROC score averaged across all clinical downstream tasks compared to clinical language models. In particular, we observe large improvements of 4-5% AUROC in large-scale multilabel classification tasks, such as diagnoses and procedures classification. To our knowledge, this study is the first to provide an extensive empirical analysis of the interplay between PEFT techniques and domain adaptation in an important real-world domain of clinical applications.

When dealing with electro or magnetoencephalography records, many supervised prediction tasks are solved by working with covariance matrices to summarize the signals. Learning with these matrices requires using Riemanian geometry to account for their structure. In this paper, we propose a new method to deal with distributions of covariance matrices and demonstrate its computational efficiency on M/EEG multivariate time series. More specifically, we define a Sliced-Wasserstein distance between measures of symmetric positive definite matrices that comes with strong theoretical guarantees. Then, we take advantage of its properties and kernel methods to apply this distance to brain-age prediction from MEG data and compare it to state-of-the-art algorithms based on Riemannian geometry. Finally, we show that it is an efficient surrogate to the Wasserstein distance in domain adaptation for Brain Computer Interface applications.

Recently, dense contrastive learning has shown superior performance on dense prediction tasks compared to instance-level contrastive learning. Despite its supremacy, the properties of dense contrastive representations have not yet been carefully studied. Therefore, we analyze the theoretical ideas of dense contrastive learning using a standard CNN and straightforward feature matching scheme rather than propose a new complex method. Inspired by the analysis of the properties of instance-level contrastive representations through the lens of alignment and uniformity on the hypersphere, we employ and extend the same lens for the dense contrastive representations to analyze their underexplored properties. We discover the core principle in constructing a positive pair of dense features and empirically proved its validity. Also, we introduces a new scalar metric that summarizes the correlation between alignment-and-uniformity and downstream performance. Using this metric, we study various facets of densely learned contrastive representations such as how the correlation changes over single- and multi-object datasets or linear evaluation and dense prediction tasks. The source code is publicly available at: https://github.com/SuperSupermoon/DenseCL-analysis

In this paper, we cast the problem of task underspecification in causal terms, and develop a method for empirical measurement of spurious associations between gender and gender-neutral entities for unmodified large language models, detecting previously unreported spurious correlations. We then describe a lightweight method to exploit the resulting spurious associations for prediction task uncertainty classification, achieving over 90% accuracy on a Winogender Schemas challenge set. Finally, we generalize our approach to address a wider range of prediction tasks and provide open-source demos for each method described here.

Machine learning especially deep neural networks have achieved great success but many of them often rely on a number of labeled samples for supervision. As sufficient labeled training data are not always ready due to e.g., continuously emerging prediction targets and costly sample annotation in real world applications, machine learning with sample shortage is now being widely investigated. Among all these studies, many prefer to utilize auxiliary information including those in the form of Knowledge Graph (KG) to reduce the reliance on labeled samples. In this survey, we have comprehensively reviewed over 90 papers about KG-aware research for two major sample shortage settings -- zero-shot learning (ZSL) where some classes to be predicted have no labeled samples, and few-shot learning (FSL) where some classes to be predicted have only a small number of labeled samples that are available. We first introduce KGs used in ZSL and FSL as well as their construction methods, and then systematically categorize and summarize KG-aware ZSL and FSL methods, dividing them into different paradigms such as the mapping-based, the data augmentation, the propagation-based and the optimization-based. We next present different applications, including not only KG augmented prediction tasks such as image classification, question answering, text classification and knowledge extraction, but also KG completion tasks, and some typical evaluation resources for each task. We eventually discuss some challenges and open problems from different perspectives.

Very recently, a variety of vision transformer architectures for dense prediction tasks have been proposed and they show that the design of spatial attention is critical to their success in these tasks. In this work, we revisit the design of the spatial attention and demonstrate that a carefully-devised yet simple spatial attention mechanism performs favourably against the state-of-the-art schemes. As a result, we propose two vision transformer architectures, namely, Twins-PCPVT and Twins-SVT. Our proposed architectures are highly-efficient and easy to implement, only involving matrix multiplications that are highly optimized in modern deep learning frameworks. More importantly, the proposed architectures achieve excellent performance on a wide range of visual tasks, including image level classification as well as dense detection and segmentation. The simplicity and strong performance suggest that our proposed architectures may serve as stronger backbones for many vision tasks. Our code is released at https://github.com/Meituan-AutoML/Twins .

Self-supervised learning is an empirically successful approach to unsupervised learning based on creating artificial supervised learning problems. A popular self-supervised approach to representation learning is contrastive learning, which leverages naturally occurring pairs of similar and dissimilar data points, or multiple views of the same data. This work provides a theoretical analysis of contrastive learning in the multi-view setting, where two views of each datum are available. The main result is that linear functions of the learned representations are nearly optimal on downstream prediction tasks whenever the two views provide redundant information about the label.

Neural networks trained on datasets such as ImageNet have led to major advances in visual object classification. One obstacle that prevents networks from reasoning more deeply about complex scenes and situations, and from integrating visual knowledge with natural language, like humans do, is their lack of common sense knowledge about the physical world. Videos, unlike still images, contain a wealth of detailed information about the physical world. However, most labelled video datasets represent high-level concepts rather than detailed physical aspects about actions and scenes. In this work, we describe our ongoing collection of the "something-something" database of video prediction tasks whose solutions require a common sense understanding of the depicted situation. The database currently contains more than 100,000 videos across 174 classes, which are defined as caption-templates. We also describe the challenges in crowd-sourcing this data at scale.

Pose Machines provide a sequential prediction framework for learning rich implicit spatial models. In this work we show a systematic design for how convolutional networks can be incorporated into the pose machine framework for learning image features and image-dependent spatial models for the task of pose estimation. The contribution of this paper is to implicitly model long-range dependencies between variables in structured prediction tasks such as articulated pose estimation. We achieve this by designing a sequential architecture composed of convolutional networks that directly operate on belief maps from previous stages, producing increasingly refined estimates for part locations, without the need for explicit graphical model-style inference. Our approach addresses the characteristic difficulty of vanishing gradients during training by providing a natural learning objective function that enforces intermediate supervision, thereby replenishing back-propagated gradients and conditioning the learning procedure. We demonstrate state-of-the-art performance and outperform competing methods on standard benchmarks including the MPII, LSP, and FLIC datasets.

We introduce SigLIP 2, a family of new multilingual vision-language encoders that build on the success of the original SigLIP. In this second iteration, we extend the original image-text training objective with several prior, independently developed techniques into a unified recipe -- this includes captioning-based pretraining, self-supervised losses (self-distillation, masked prediction) and online data curation. With these changes, SigLIP 2 models outperform their SigLIP counterparts at all model scales in core capabilities, including zero-shot classification, image-text retrieval, and transfer performance when extracting visual representations for Vision-Language Models (VLMs). Furthermore, the new training recipe leads to significant improvements on localization and dense prediction tasks. We also train variants which support multiple resolutions and preserve the input's native aspect ratio. Finally, we train on a more diverse data-mixture that includes de-biasing techniques, leading to much better multilingual understanding and improved fairness. To allow users to trade off inference cost with performance, we release model checkpoints at four sizes: ViT-B (86M), L (303M), So400m (400M), and g (1B).

Tabular in-context learning (ICL) has recently achieved state-of-the-art (SOTA) performance on several tabular prediction tasks. Previously restricted to classification problems on small tables, recent advances such as TabPFN and TabICL have extended its use to larger datasets. While being architecturally efficient and well-adapted to tabular data structures, current table-native ICL architectures, being trained exclusively on synthetic data, do not fully leverage the rich semantics and world knowledge contained in real-world tabular data. On another end of this spectrum, tabular ICL models based on pretrained large language models such as TabuLa-8B integrate deep semantic understanding and world knowledge but are only able to make use of a small amount of context due to inherent architectural limitations. With the aim to combine the best of both these worlds, we introduce ConTextTab, integrating semantic understanding and alignment into a table-native ICL framework. By employing specialized embeddings for different data modalities and by training on large-scale real-world tabular data, our model is competitive with SOTA across a broad set of benchmarks while setting a new standard on the semantically rich CARTE benchmark.

Automated computational analysis of the vast chemical space is critical for numerous fields of research such as drug discovery and material science. Representation learning techniques have recently been employed with the primary objective of generating compact and informative numerical expressions of complex data. One approach to efficiently learn molecular representations is processing string-based notations of chemicals via natural language processing (NLP) algorithms. Majority of the methods proposed so far utilize SMILES notations for this purpose; however, SMILES is associated with numerous problems related to validity and robustness, which may prevent the model from effectively uncovering the knowledge hidden in the data. In this study, we propose SELFormer, a transformer architecture-based chemical language model that utilizes a 100% valid, compact and expressive notation, SELFIES, as input, in order to learn flexible and high-quality molecular representations. SELFormer is pre-trained on two million drug-like compounds and fine-tuned for diverse molecular property prediction tasks. Our performance evaluation has revealed that, SELFormer outperforms all competing methods, including graph learning-based approaches and SMILES-based chemical language models, on predicting aqueous solubility of molecules and adverse drug reactions. We also visualized molecular representations learned by SELFormer via dimensionality reduction, which indicated that even the pre-trained model can discriminate molecules with differing structural properties. We shared SELFormer as a programmatic tool, together with its datasets and pre-trained models. Overall, our research demonstrates the benefit of using the SELFIES notations in the context of chemical language modeling and opens up new possibilities for the design and discovery of novel drug candidates with desired features.

Foundation models (FMs) trained on electronic health records (EHRs) have shown strong performance on a range of clinical prediction tasks. However, adapting these models to local health systems remains challenging due to limited data availability and resource constraints. In this study, we investigated what these models learn and evaluated the transferability of an FM trained on MIMIC-IV to an institutional EHR dataset at the University of Chicago Medical Center. We assessed their ability to identify outlier patients and examined representation-space patient trajectories in relation to future clinical outcomes. We also evaluated the performance of supervised fine-tuned classifiers on both source and target datasets. Our findings offer insights into the adaptability of FMs across different healthcare systems, highlight considerations for their effective implementation, and provide an empirical analysis of the underlying factors that contribute to their predictive performance.

Deep recommender systems rely heavily on large embedding tables to handle high-cardinality categorical features such as user/item identifiers, and face significant memory constraints at scale. To tackle this challenge, hashing techniques are often employed to map multiple entities to the same embedding and thus reduce the size of the embedding tables. Concurrently, graph-based collaborative signals have emerged as powerful tools in recommender systems, yet their potential for optimizing embedding table reduction remains unexplored. This paper introduces GraphHash, the first graph-based approach that leverages modularity-based bipartite graph clustering on user-item interaction graphs to reduce embedding table sizes. We demonstrate that the modularity objective has a theoretical connection to message-passing, which provides a foundation for our method. By employing fast clustering algorithms, GraphHash serves as a computationally efficient proxy for message-passing during preprocessing and a plug-and-play graph-based alternative to traditional ID hashing. Extensive experiments show that GraphHash substantially outperforms diverse hashing baselines on both retrieval and click-through-rate prediction tasks. In particular, GraphHash achieves on average a 101.52% improvement in recall when reducing the embedding table size by more than 75%, highlighting the value of graph-based collaborative information for model reduction. Our code is available at https://github.com/snap-research/GraphHash.

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

Name-based gender prediction has traditionally categorized individuals as either female or male based on their names, using a binary classification system. That binary approach can be problematic in the cases of gender-neutral names that do not align with any one gender, among other reasons. Relying solely on binary gender categories without recognizing gender-neutral names can reduce the inclusiveness of gender prediction tasks. We introduce an additional gender category, i.e., "neutral", to study and address potential gender biases in Large Language Models (LLMs). We evaluate the performance of several foundational and large language models in predicting gender based on first names only. Additionally, we investigate the impact of adding birth years to enhance the accuracy of gender prediction, accounting for shifting associations between names and genders over time. Our findings indicate that most LLMs identify male and female names with high accuracy (over 80%) but struggle with gender-neutral names (under 40%), and the accuracy of gender prediction is higher for English-based first names than non-English names. The experimental results show that incorporating the birth year does not improve the overall accuracy of gender prediction, especially for names with evolving gender associations. We recommend using caution when applying LLMs for gender identification in downstream tasks, particularly when dealing with non-binary gender labels.

Adapting models pre-trained on large-scale datasets to a variety of downstream tasks is a common strategy in deep learning. Consequently, parameter-efficient fine-tuning methods have emerged as a promising way to adapt pre-trained models to different tasks while training only a minimal number of parameters. While most of these methods are designed for single-task adaptation, parameter-efficient training in Multi-Task Learning (MTL) architectures is still unexplored. In this paper, we introduce MTLoRA, a novel framework for parameter-efficient training of MTL models. MTLoRA employs Task-Agnostic and Task-Specific Low-Rank Adaptation modules, which effectively disentangle the parameter space in MTL fine-tuning, thereby enabling the model to adeptly handle both task specialization and interaction within MTL contexts. We applied MTLoRA to hierarchical-transformer-based MTL architectures, adapting them to multiple downstream dense prediction tasks. Our extensive experiments on the PASCAL dataset show that MTLoRA achieves higher accuracy on downstream tasks compared to fully fine-tuning the MTL model while reducing the number of trainable parameters by 3.6x. Furthermore, MTLoRA establishes a Pareto-optimal trade-off between the number of trainable parameters and the accuracy of the downstream tasks, outperforming current state-of-the-art parameter-efficient training methods in both accuracy and efficiency. Our code is publicly available.

Tabular data prediction is a fundamental machine learning task for many applications. Existing methods predominantly employ discriminative modeling and operate under the assumption of a fixed target column, necessitating re-training for every new predictive task. Inspired by the generative power of large language models (LLMs), this paper exploits the idea of building universal tabular data predictors based on generative modeling, namely UniPredict. Here, we demonstrate the scalability of an LLM to extensive tabular datasets, enabling it to comprehend diverse tabular inputs and predict target variables following the provided instructions. Specifically, we train a single LLM on an aggregation of 169 tabular datasets with diverse targets and compare its performance against baselines that are trained on each dataset separately. We observe this versatile UniPredict model demonstrates an advantage over other models, ranging from 5.4% to 13.4%, when compared with the best tree-boosting baseline and the best neural network baseline, respectively. We further test UniPredict in few-shot learning settings on another 62 tabular datasets. Our method achieves strong performance in quickly adapting to new tasks. In low-resource few-shot setup, we observed a 100%+ performance advantage compared with XGBoost, and significant margin over all baselines. We envision that UniPredict sheds light on developing a universal tabular data prediction system that learns from data at scale and serves a wide range of prediction tasks.

The use of artificial intelligence to enable precision medicine and decision support systems through the analysis of pathology images has the potential to revolutionize the diagnosis and treatment of cancer. Such applications will depend on models' abilities to capture the diverse patterns observed in pathology images. To address this challenge, we present Virchow, a foundation model for computational pathology. Using self-supervised learning empowered by the DINOv2 algorithm, Virchow is a vision transformer model with 632 million parameters trained on 1.5 million hematoxylin and eosin stained whole slide images from diverse tissue and specimen types, which is orders of magnitude more data than previous works. The Virchow model enables the development of a pan-cancer detection system with 0.949 overall specimen-level AUC across 17 different cancer types, while also achieving 0.937 AUC on 7 rare cancer types. The Virchow model sets the state-of-the-art on the internal and external image tile level benchmarks and slide level biomarker prediction tasks. The gains in performance highlight the importance of training on massive pathology image datasets, suggesting scaling up the data and network architecture can improve the accuracy for many high-impact computational pathology applications where limited amounts of training data are available.

In populous countries, pending legal cases have been growing exponentially. There is a need for developing techniques for processing and organizing legal documents. In this paper, we introduce a new corpus for structuring legal documents. In particular, we introduce a corpus of legal judgment documents in English that are segmented into topical and coherent parts. Each of these parts is annotated with a label coming from a list of pre-defined Rhetorical Roles. We develop baseline models for automatically predicting rhetorical roles in a legal document based on the annotated corpus. Further, we show the application of rhetorical roles to improve performance on the tasks of summarization and legal judgment prediction. We release the corpus and baseline model code along with the paper.

Speech summarization is typically performed by using a cascade of speech recognition and text summarization models. End-to-end modeling of speech summarization models is challenging due to memory and compute constraints arising from long input audio sequences. Recent work in document summarization has inspired methods to reduce the complexity of self-attentions, which enables transformer models to handle long sequences. In this work, we introduce a single model optimized end-to-end for speech summarization. We apply the restricted self-attention technique from text-based models to speech models to address the memory and compute constraints. We demonstrate that the proposed model learns to directly summarize speech for the How-2 corpus of instructional videos. The proposed end-to-end model outperforms the previously proposed cascaded model by 3 points absolute on ROUGE. Further, we consider the spoken language understanding task of predicting concepts from speech inputs and show that the proposed end-to-end model outperforms the cascade model by 4 points absolute F-1.

Memory Mosaics are networks of associative memories working in concert to achieve a prediction task of interest. Like transformers, memory mosaics possess compositional capabilities and in-context learning capabilities. Unlike transformers, memory mosaics achieve these capabilities in comparatively transparent ways. We demonstrate these capabilities on toy examples and we also show that memory mosaics perform as well or better than transformers on medium-scale language modeling tasks.

Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector. Such a shallow lookup results in a linear growth of memory consumption for storing the embedding matrix and incurs high computational costs when working with real-world KGs. Drawing parallels with subword tokenization commonly used in NLP, we explore the landscape of more parameter-efficient node embedding strategies with possibly sublinear memory requirements. To this end, we propose NodePiece, an anchor-based approach to learn a fixed-size entity vocabulary. In NodePiece, a vocabulary of subword/sub-entity units is constructed from anchor nodes in a graph with known relation types. Given such a fixed-size vocabulary, it is possible to bootstrap an encoding and embedding for any entity, including those unseen during training. Experiments show that NodePiece performs competitively in node classification, link prediction, and relation prediction tasks while retaining less than 10% of explicit nodes in a graph as anchors and often having 10x fewer parameters. To this end, we show that a NodePiece-enabled model outperforms existing shallow models on a large OGB WikiKG 2 graph having 70x fewer parameters.

In this paper, we present the practical problems and the lessons learned at short-video services from Kuaishou. In industry, a widely-used multi-task framework is the Mixture-of-Experts (MoE) paradigm, which always introduces some shared and specific experts for each task and then uses gate networks to measure related experts' contributions. Although the MoE achieves remarkable improvements, we still observe three anomalies that seriously affect model performances in our iteration: (1) Expert Collapse: We found that experts' output distributions are significantly different, and some experts have over 90% zero activations with ReLU, making it hard for gate networks to assign fair weights to balance experts. (2) Expert Degradation: Ideally, the shared-expert aims to provide predictive information for all tasks simultaneously. Nevertheless, we find that some shared-experts are occupied by only one task, which indicates that shared-experts lost their ability but degenerated into some specific-experts. (3) Expert Underfitting: In our services, we have dozens of behavior tasks that need to be predicted, but we find that some data-sparse prediction tasks tend to ignore their specific-experts and assign large weights to shared-experts. The reason might be that the shared-experts can perceive more gradient updates and knowledge from dense tasks, while specific-experts easily fall into underfitting due to their sparse behaviors. Motivated by those observations, we propose HoME to achieve a simple, efficient and balanced MoE system for multi-task learning.

This paper introduces WeatherFormer, a transformer encoder-based model designed to learn robust weather features from minimal observations. It addresses the challenge of modeling complex weather dynamics from small datasets, a bottleneck for many prediction tasks in agriculture, epidemiology, and climate science. WeatherFormer was pretrained on a large pretraining dataset comprised of 39 years of satellite measurements across the Americas. With a novel pretraining task and fine-tuning, WeatherFormer achieves state-of-the-art performance in county-level soybean yield prediction and influenza forecasting. Technical innovations include a unique spatiotemporal encoding that captures geographical, annual, and seasonal variations, adapting the transformer architecture to continuous weather data, and a pretraining strategy to learn representations that are robust to missing weather features. This paper for the first time demonstrates the effectiveness of pretraining large transformer encoder models for weather-dependent applications across multiple domains.

Climate models have been key for assessing the impact of climate change and simulating future climate scenarios. The machine learning (ML) community has taken an increased interest in supporting climate scientists' efforts on various tasks such as climate model emulation, downscaling, and prediction tasks. Many of those tasks have been addressed on datasets created with single climate models. However, both the climate science and ML communities have suggested that to address those tasks at scale, we need large, consistent, and ML-ready climate model datasets. Here, we introduce ClimateSet, a dataset containing the inputs and outputs of 36 climate models from the Input4MIPs and CMIP6 archives. In addition, we provide a modular dataset pipeline for retrieving and preprocessing additional climate models and scenarios. We showcase the potential of our dataset by using it as a benchmark for ML-based climate model emulation. We gain new insights about the performance and generalization capabilities of the different ML models by analyzing their performance across different climate models. Furthermore, the dataset can be used to train an ML emulator on several climate models instead of just one. Such a "super emulator" can quickly project new climate change scenarios, complementing existing scenarios already provided to policymakers. We believe ClimateSet will create the basis needed for the ML community to tackle climate-related tasks at scale.

Self-supervised learning on large-scale Vision Transformers (ViTs) as pre-training methods has achieved promising downstream performance. Yet, how much these pre-training paradigms promote lightweight ViTs' performance is considerably less studied. In this work, we develop and benchmark several self-supervised pre-training methods on image classification tasks and some downstream dense prediction tasks. We surprisingly find that if proper pre-training is adopted, even vanilla lightweight ViTs show comparable performance to previous SOTA networks with delicate architecture design. It breaks the recently popular conception that vanilla ViTs are not suitable for vision tasks in lightweight regimes. We also point out some defects of such pre-training, e.g., failing to benefit from large-scale pre-training data and showing inferior performance on data-insufficient downstream tasks. Furthermore, we analyze and clearly show the effect of such pre-training by analyzing the properties of the layer representation and attention maps for related models. Finally, based on the above analyses, a distillation strategy during pre-training is developed, which leads to further downstream performance improvement for MAE-based pre-training. Code is available at https://github.com/wangsr126/mae-lite.

Convolutional networks are powerful visual models that yield hierarchies of features. We show that convolutional networks by themselves, trained end-to-end, pixels-to-pixels, improve on the previous best result in semantic segmentation. Our key insight is to build "fully convolutional" networks that take input of arbitrary size and produce correspondingly-sized output with efficient inference and learning. We define and detail the space of fully convolutional networks, explain their application to spatially dense prediction tasks, and draw connections to prior models. We adapt contemporary classification networks (AlexNet, the VGG net, and GoogLeNet) into fully convolutional networks and transfer their learned representations by fine-tuning to the segmentation task. We then define a skip architecture that combines semantic information from a deep, coarse layer with appearance information from a shallow, fine layer to produce accurate and detailed segmentations. Our fully convolutional network achieves improved segmentation of PASCAL VOC (30% relative improvement to 67.2% mean IU on 2012), NYUDv2, SIFT Flow, and PASCAL-Context, while inference takes one tenth of a second for a typical image.

Convolutional networks are powerful visual models that yield hierarchies of features. We show that convolutional networks by themselves, trained end-to-end, pixels-to-pixels, exceed the state-of-the-art in semantic segmentation. Our key insight is to build "fully convolutional" networks that take input of arbitrary size and produce correspondingly-sized output with efficient inference and learning. We define and detail the space of fully convolutional networks, explain their application to spatially dense prediction tasks, and draw connections to prior models. We adapt contemporary classification networks (AlexNet, the VGG net, and GoogLeNet) into fully convolutional networks and transfer their learned representations by fine-tuning to the segmentation task. We then define a novel architecture that combines semantic information from a deep, coarse layer with appearance information from a shallow, fine layer to produce accurate and detailed segmentations. Our fully convolutional network achieves state-of-the-art segmentation of PASCAL VOC (20% relative improvement to 62.2% mean IU on 2012), NYUDv2, and SIFT Flow, while inference takes one third of a second for a typical image.

Transformers have recently emerged as a powerful tool for learning visual representations. In this paper, we identify and characterize artifacts in feature maps of both supervised and self-supervised ViT networks. The artifacts correspond to high-norm tokens appearing during inference primarily in low-informative background areas of images, that are repurposed for internal computations. We propose a simple yet effective solution based on providing additional tokens to the input sequence of the Vision Transformer to fill that role. We show that this solution fixes that problem entirely for both supervised and self-supervised models, sets a new state of the art for self-supervised visual models on dense visual prediction tasks, enables object discovery methods with larger models, and most importantly leads to smoother feature maps and attention maps for downstream visual processing.

The rapid evolution of software libraries presents a significant challenge for code generation models, which must adapt to frequent version updates while maintaining compatibility with previous versions. Existing code completion benchmarks often overlook this dynamic aspect, and the one that does consider it relies on static code prediction tasks without execution-based evaluation, offering a limited perspective on a model's practical usability. To address this gap, we introduce \GitChameleon{}, a novel, manually curated dataset comprising 116 Python code completion problems, each conditioned on specific library versions and accompanied by executable unit tests. is designed to rigorously assess the ability of modern large language models (LLMs) to generate version-specific code that is not only syntactically correct but also functionally accurate upon execution. Our comprehensive evaluations reveal that state-of-the-art LLMs struggle with this task; for instance, GPT-4o achieves a pass@10 of only 39.9\% (43.7\% when provided with error feedback), highlighting the complexity of the problem and the limitations of current models. By providing an execution-based benchmark that emphasizes the dynamic nature of code libraries, serves as a critical tool to advance the development of more adaptable and reliable code generation models. For facilitation for further exploration of version-conditioned code generation, we make our code repository publicly accessible at https://github.com/NizarIslah/GitChameleon.

Learning visual representations is foundational for a broad spectrum of downstream tasks. Although recent vision-language contrastive models, such as CLIP and SigLIP, have achieved impressive zero-shot performance via large-scale vision-language alignment, their reliance on global representations constrains their effectiveness for dense prediction tasks, such as grounding, OCR, and segmentation. To address this gap, we introduce Region-Aware Cluster Discrimination (RICE), a novel method that enhances region-level visual and OCR capabilities. We first construct a billion-scale candidate region dataset and propose a Region Transformer layer to extract rich regional semantics. We further design a unified region cluster discrimination loss that jointly supports object and OCR learning within a single classification framework, enabling efficient and scalable distributed training on large-scale data. Extensive experiments show that RICE consistently outperforms previous methods on tasks, including segmentation, dense detection, and visual perception for Multimodal Large Language Models (MLLMs). The pre-trained models have been released at https://github.com/deepglint/MVT.

We introduce D-FINE, a powerful real-time object detector that achieves outstanding localization precision by redefining the bounding box regression task in DETR models. D-FINE comprises two key components: Fine-grained Distribution Refinement (FDR) and Global Optimal Localization Self-Distillation (GO-LSD). FDR transforms the regression process from predicting fixed coordinates to iteratively refining probability distributions, providing a fine-grained intermediate representation that significantly enhances localization accuracy. GO-LSD is a bidirectional optimization strategy that transfers localization knowledge from refined distributions to shallower layers through self-distillation, while also simplifying the residual prediction tasks for deeper layers. Additionally, D-FINE incorporates lightweight optimizations in computationally intensive modules and operations, achieving a better balance between speed and accuracy. Specifically, D-FINE-L / X achieves 54.0% / 55.8% AP on the COCO dataset at 124 / 78 FPS on an NVIDIA T4 GPU. When pretrained on Objects365, D-FINE-L / X attains 57.1% / 59.3% AP, surpassing all existing real-time detectors. Furthermore, our method significantly enhances the performance of a wide range of DETR models by up to 5.3% AP with negligible extra parameters and training costs. Our code and pretrained models: https://github.com/Peterande/D-FINE.

Recent vision transformers, large-kernel CNNs and MLPs have attained remarkable successes in broad vision tasks thanks to their effective information fusion in the global scope. However, their efficient deployments, especially on mobile devices, still suffer from noteworthy challenges due to the heavy computational costs of self-attention mechanisms, large kernels, or fully connected layers. In this work, we apply conventional convolution theorem to deep learning for addressing this and reveal that adaptive frequency filters can serve as efficient global token mixers. With this insight, we propose Adaptive Frequency Filtering (AFF) token mixer. This neural operator transfers a latent representation to the frequency domain via a Fourier transform and performs semantic-adaptive frequency filtering via an elementwise multiplication, which mathematically equals to a token mixing operation in the original latent space with a dynamic convolution kernel as large as the spatial resolution of this latent representation. We take AFF token mixers as primary neural operators to build a lightweight neural network, dubbed AFFNet. Extensive experiments demonstrate the effectiveness of our proposed AFF token mixer and show that AFFNet achieve superior accuracy and efficiency trade-offs compared to other lightweight network designs on broad visual tasks, including visual recognition and dense prediction tasks.

Temporal consistency is critical in video prediction to ensure that outputs are coherent and free of artifacts. Traditional methods, such as temporal attention and 3D convolution, may struggle with significant object motion and may not capture long-range temporal dependencies in dynamic scenes. To address this gap, we propose the Tracktention Layer, a novel architectural component that explicitly integrates motion information using point tracks, i.e., sequences of corresponding points across frames. By incorporating these motion cues, the Tracktention Layer enhances temporal alignment and effectively handles complex object motions, maintaining consistent feature representations over time. Our approach is computationally efficient and can be seamlessly integrated into existing models, such as Vision Transformers, with minimal modification. It can be used to upgrade image-only models to state-of-the-art video ones, sometimes outperforming models natively designed for video prediction. We demonstrate this on video depth prediction and video colorization, where models augmented with the Tracktention Layer exhibit significantly improved temporal consistency compared to baselines.

Automated medical image analysis systems often require large amounts of training data with high quality labels, which are difficult and time consuming to generate. This paper introduces Radiology Object in COntext version 2 (ROCOv2), a multimodal dataset consisting of radiological images and associated medical concepts and captions extracted from the PMC Open Access subset. It is an updated version of the ROCO dataset published in 2018, and adds 35,705 new images added to PMC since 2018. It further provides manually curated concepts for imaging modalities with additional anatomical and directional concepts for X-rays. The dataset consists of 79,789 images and has been used, with minor modifications, in the concept detection and caption prediction tasks of ImageCLEFmedical Caption 2023. The dataset is suitable for training image annotation models based on image-caption pairs, or for multi-label image classification using Unified Medical Language System (UMLS) concepts provided with each image. In addition, it can serve for pre-training of medical domain models, and evaluation of deep learning models for multi-task learning.

Fine-tuning pre-trained Vision Transformers (ViT) has consistently demonstrated promising performance in the realm of visual recognition. However, adapting large pre-trained models to various tasks poses a significant challenge. This challenge arises from the need for each model to undergo an independent and comprehensive fine-tuning process, leading to substantial computational and memory demands. While recent advancements in Parameter-efficient Transfer Learning (PETL) have demonstrated their ability to achieve superior performance compared to full fine-tuning with a smaller subset of parameter updates, they tend to overlook dense prediction tasks such as object detection and segmentation. In this paper, we introduce Hierarchical Side-Tuning (HST), a novel PETL approach that enables ViT transfer to various downstream tasks effectively. Diverging from existing methods that exclusively fine-tune parameters within input spaces or certain modules connected to the backbone, we tune a lightweight and hierarchical side network (HSN) that leverages intermediate activations extracted from the backbone and generates multi-scale features to make predictions. To validate HST, we conducted extensive experiments encompassing diverse visual tasks, including classification, object detection, instance segmentation, and semantic segmentation. Notably, our method achieves state-of-the-art average Top-1 accuracy of 76.0% on VTAB-1k, all while fine-tuning a mere 0.78M parameters. When applied to object detection tasks on COCO testdev benchmark, HST even surpasses full fine-tuning and obtains better performance with 49.7 box AP and 43.2 mask AP using Cascade Mask R-CNN.

Recently, MLP-based vision backbones have achieved promising performance in several visual recognition tasks. However, the existing MLP-based methods directly aggregate tokens with static weights, leaving the adaptability to different images untouched. Moreover, Recent research demonstrates that MLP-Transformer is great at creating long-range dependencies but ineffective at catching high frequencies that primarily transmit local information, which prevents it from applying to the downstream dense prediction tasks, such as semantic segmentation. To address these challenges, we propose a content-adaptive yet computationally efficient structure, dubbed Dynamic Spectrum Mixer (DSM). The DSM represents token interactions in the frequency domain by employing the Discrete Cosine Transform, which can learn long-term spatial dependencies with log-linear complexity. Furthermore, a dynamic spectrum weight generation layer is proposed as the spectrum bands selector, which could emphasize the informative frequency bands while diminishing others. To this end, the technique can efficiently learn detailed features from visual input that contains both high- and low-frequency information. Extensive experiments show that DSM is a powerful and adaptable backbone for a range of visual recognition tasks. Particularly, DSM outperforms previous transformer-based and MLP-based models, on image classification, object detection, and semantic segmentation tasks, such as 83.8 \% top-1 accuracy on ImageNet, and 49.9 \% mIoU on ADE20K.

We report a series of deep learning models to solve complex forward and inverse design problems in molecular modeling and design. Using both diffusion models inspired by nonequilibrium thermodynamics and attention-based transformer architectures, we demonstrate a flexible framework to capture complex chemical structures. First trained on the QM9 dataset and a series of quantum mechanical properties (e.g. homo, lumo, free energy, heat capacity, etc.), we then generalize the model to study and design key properties of deep eutectic solvents. In addition to separate forward and inverse models, we also report an integrated fully prompt-based multi-task generative pretrained transformer model that solves multiple forward, inverse design, and prediction tasks, flexibly and within one model. We show that the multi-task generative model has the overall best performance and allows for flexible integration of multiple objectives, within one model, and for distinct chemistries, suggesting that synergies emerge during training of this large language model. Trained jointly in tasks related to the QM9 dataset and deep eutectic solvents (DESs), the model can predict various quantum mechanical properties and critical properties to achieve deep eutectic solvent behavior. Several novel combinations of DESs are proposed based on this framework.

Learning self-supervised representations that are invariant and equivariant to transformations is crucial for advancing beyond traditional visual classification tasks. However, many methods rely on predictor architectures to encode equivariance, despite evidence that architectural choices, such as capsule networks, inherently excel at learning interpretable pose-aware representations. To explore this, we introduce EquiCaps (Equivariant Capsule Network), a capsule-based approach to pose-aware self-supervision that eliminates the need for a specialised predictor for enforcing equivariance. Instead, we leverage the intrinsic pose-awareness capabilities of capsules to improve performance in pose estimation tasks. To further challenge our assumptions, we increase task complexity via multi-geometric transformations to enable a more thorough evaluation of invariance and equivariance by introducing 3DIEBench-T, an extension of a 3D object-rendering benchmark dataset. Empirical results demonstrate that EquiCaps outperforms prior state-of-the-art equivariant methods on rotation prediction, achieving a supervised-level R^2 of 0.78 on the 3DIEBench rotation prediction benchmark and improving upon SIE and CapsIE by 0.05 and 0.04 R^2, respectively. Moreover, in contrast to non-capsule-based equivariant approaches, EquiCaps maintains robust equivariant performance under combined geometric transformations, underscoring its generalisation capabilities and the promise of predictor-free capsule architectures.

Remote sensing (RS) visual grounding aims to use natural language expression to locate specific objects (in the form of the bounding box or segmentation mask) in RS images, enhancing human interaction with intelligent RS interpretation systems. Early research in this area was primarily based on horizontal bounding boxes (HBBs), but as more diverse RS datasets have become available, tasks involving oriented bounding boxes (OBBs) and segmentation masks have emerged. In practical applications, different targets require different grounding types: HBB can localize an object's position, OBB provides its orientation, and mask depicts its shape. However, existing specialized methods are typically tailored to a single type of RS visual grounding task and are hard to generalize across tasks. In contrast, large vision-language models (VLMs) exhibit powerful multi-task learning capabilities but struggle to handle dense prediction tasks like segmentation. This paper proposes GeoGround, a novel framework that unifies support for HBB, OBB, and mask RS visual grounding tasks, allowing flexible output selection. Rather than customizing the architecture of VLM, our work aims to elegantly support pixel-level visual grounding output through the Text-Mask technique. We define prompt-assisted and geometry-guided learning to enhance consistency across different signals. To support model training, we present refGeo, a large-scale RS visual instruction-following dataset containing 161k image-text pairs. Experimental results show that GeoGround demonstrates strong performance across four RS visual grounding tasks, matching or surpassing the performance of specialized methods on multiple benchmarks. Code available at https://github.com/zytx121/GeoGround

Distillation-based self-supervised learning typically leads to more compressed representations due to its radical clustering process and the implementation of a sharper target distribution. To overcome this limitation and preserve more information from input, we introduce UDI, conceptualized as Unsqueezed Distillation-based self-supervised learning (SSL). UDI enriches the learned representation by encouraging multimodal prediction distilled from a consolidated profile of local predictions that are derived via stratified sampling. Our evaluations show that UDI not only promotes semantically meaningful representations at instance level, delivering superior or competitive results to state-of-the-art SSL methods in image classification, but also effectively preserves the nuisance of input, which yields significant improvement in dense prediction tasks, including object detection and segmentation. Additionally, UDI performs competitively in low-shot image classification, improving the scalability of joint-embedding pipelines. Various visualizations and ablation studies are presented to further elucidate the mechanisms behind UDI. Our source code is available at https://github.com/ISL-CV/udi.

Tokenization algorithms that merge the units of a base vocabulary into larger, variable-rate units have become standard in natural language processing tasks. This idea, however, has been mostly overlooked when the vocabulary consists of phonemes or Discrete Acoustic Units (DAUs), an audio-based representation that is playing an increasingly important role due to the success of discrete language-modeling techniques. In this paper, we showcase the advantages of tokenization of phonetic units and of DAUs on three prediction tasks: grapheme-to-phoneme, grapheme-to-DAUs, and unsupervised speech generation using DAU language modeling. We demonstrate that tokenization yields significant improvements in terms of performance, as well as training and inference speed, across all three tasks. We also offer theoretical insights to provide some explanation for the superior performance observed.

Resource-constrained hardware, such as edge devices or cell phones, often rely on cloud servers to provide the required computational resources for inference in deep vision models. However, transferring image and video data from an edge or mobile device to a cloud server requires coding to deal with network constraints. The use of standardized codecs, such as JPEG or H.264, is prevalent and required to ensure interoperability. This paper aims to examine the implications of employing standardized codecs within deep vision pipelines. We find that using JPEG and H.264 coding significantly deteriorates the accuracy across a broad range of vision tasks and models. For instance, strong compression rates reduce semantic segmentation accuracy by more than 80% in mIoU. In contrast to previous findings, our analysis extends beyond image and action classification to localization and dense prediction tasks, thus providing a more comprehensive perspective.

Artificial intelligence is transforming computational materials science, improving the prediction of material properties, and accelerating the discovery of novel materials. Recently, publicly available material data repositories have grown rapidly. This growth encompasses not only more materials, but also a greater variety and quantity of their associated properties. Existing machine learning efforts in materials science focus primarily on single-modality tasks, i.e., relationships between materials and a single physical property, thus not taking advantage of the rich and multimodal set of material properties. Here, we introduce Multimodal Learning for Materials (MultiMat), which enables self-supervised multi-modality training of foundation models for materials. We demonstrate our framework's potential using data from the Materials Project database on multiple axes: (i) MultiMat achieves state-of-the-art performance for challenging material property prediction tasks; (ii) MultiMat enables novel and accurate material discovery via latent space similarity, enabling screening for stable materials with desired properties; and (iii) MultiMat encodes interpretable emergent features that may provide novel scientific insights.

Parameter Efficient Tuning (PET) has gained attention for reducing the number of parameters while maintaining performance and providing better hardware resource savings, but few studies investigate dense prediction tasks and interaction between modalities. In this paper, we do an investigation of efficient tuning problems on referring image segmentation. We propose a novel adapter called Bridger to facilitate cross-modal information exchange and inject task-specific information into the pre-trained model. We also design a lightweight decoder for image segmentation. Our approach achieves comparable or superior performance with only 1.61\% to 3.38\% backbone parameter updates, evaluated on challenging benchmarks. The code is available at https://github.com/kkakkkka/ETRIS.

AI explanations are often mentioned as a way to improve human-AI decision-making, but empirical studies have not found consistent evidence of explanations' effectiveness and, on the contrary, suggest that they can increase overreliance when the AI system is wrong. While many factors may affect reliance on AI support, one important factor is how decision-makers reconcile their own intuition -- beliefs or heuristics, based on prior knowledge, experience, or pattern recognition, used to make judgments -- with the information provided by the AI system to determine when to override AI predictions. We conduct a think-aloud, mixed-methods study with two explanation types (feature- and example-based) for two prediction tasks to explore how decision-makers' intuition affects their use of AI predictions and explanations, and ultimately their choice of when to rely on AI. Our results identify three types of intuition involved in reasoning about AI predictions and explanations: intuition about the task outcome, features, and AI limitations. Building on these, we summarize three observed pathways for decision-makers to apply their own intuition and override AI predictions. We use these pathways to explain why (1) the feature-based explanations we used did not improve participants' decision outcomes and increased their overreliance on AI, and (2) the example-based explanations we used improved decision-makers' performance over feature-based explanations and helped achieve complementary human-AI performance. Overall, our work identifies directions for further development of AI decision-support systems and explanation methods that help decision-makers effectively apply their intuition to achieve appropriate reliance on AI.

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.

Hypergraph neural networks (HNNs) using neural networks to encode hypergraphs provide a promising way to model higher-order relations in data and further solve relevant prediction tasks built upon such higher-order relations. However, higher-order relations in practice contain complex patterns and are often highly irregular. So, it is often challenging to design an HNN that suffices to express those relations while keeping computational efficiency. Inspired by hypergraph diffusion algorithms, this work proposes a new HNN architecture named ED-HNN, which provably represents any continuous equivariant hypergraph diffusion operators that can model a wide range of higher-order relations. ED-HNN can be implemented efficiently by combining star expansions of hypergraphs with standard message passing neural networks. ED-HNN further shows great superiority in processing heterophilic hypergraphs and constructing deep models. We evaluate ED-HNN for node classification on nine real-world hypergraph datasets. ED-HNN uniformly outperforms the best baselines over these nine datasets and achieves more than 2\%uparrow in prediction accuracy over four datasets therein.

We introduce a vision-language foundation model called VL-BEiT, which is a bidirectional multimodal Transformer learned by generative pretraining. Our minimalist solution conducts masked prediction on both monomodal and multimodal data with a shared Transformer. Specifically, we perform masked vision-language modeling on image-text pairs, masked language modeling on texts, and masked image modeling on images. VL-BEiT is learned from scratch with one unified pretraining task, one shared backbone, and one-stage training. Our method is conceptually simple and empirically effective. Experimental results show that VL-BEiT obtains strong results on various vision-language benchmarks, such as visual question answering, visual reasoning, and image-text retrieval. Moreover, our method learns transferable visual features, achieving competitive performance on image classification, and semantic segmentation.

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

Financial forecasting has been an important and active area of machine learning research because of the challenges it presents and the potential rewards that even minor improvements in prediction accuracy or forecasting may entail. Traditionally, financial forecasting has heavily relied on quantitative indicators and metrics derived from structured financial statements. Earnings conference call data, including text and audio, is an important source of unstructured data that has been used for various prediction tasks using deep earning and related approaches. However, current deep learning-based methods are limited in the way that they deal with numeric data; numbers are typically treated as plain-text tokens without taking advantage of their underlying numeric structure. This paper describes a numeric-oriented hierarchical transformer model to predict stock returns, and financial risk using multi-modal aligned earnings calls data by taking advantage of the different categories of numbers (monetary, temporal, percentages etc.) and their magnitude. We present the results of a comprehensive evaluation of NumHTML against several state-of-the-art baselines using a real-world publicly available dataset. The results indicate that NumHTML significantly outperforms the current state-of-the-art across a variety of evaluation metrics and that it has the potential to offer significant financial gains in a practical trading context.

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond lengths and angles, are available, molecular property prediction tasks can be made more accurate. However, computing of 3D molecular geometries requires quantum calculations that are computationally prohibitive. For example, accurate calculation of 3D geometries of a small molecule requires hours of computing time using density functional theory (DFT). Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods. To make this feasible, we develop a benchmark, known as Molecule3D, that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from DFT. We also provide a set of software tools for data processing, splitting, training, and evaluation, etc. Specifically, we propose to assess the error and validity of predicted geometries using four metrics. We implement two baseline methods that either predict the pairwise distance between atoms or atom coordinates in 3D space. Experimental results show that, compared with generating 3D geometries with RDKit, our method can achieve comparable prediction accuracy but with much smaller computational costs. Our Molecule3D is available as a module of the MoleculeX software library (https://github.com/divelab/MoleculeX).

Despite the proven effectiveness of Transformer neural networks across multiple domains, their performance with Electronic Health Records (EHR) can be nuanced. The unique, multidimensional sequential nature of EHR data can sometimes make even simple linear models with carefully engineered features more competitive. Thus, the advantages of Transformers, such as efficient transfer learning and improved scalability are not always fully exploited in EHR applications. Addressing these challenges, we introduce SANSformer, an attention-free sequential model designed with specific inductive biases to cater for the unique characteristics of EHR data. In this work, we aim to forecast the demand for healthcare services, by predicting the number of patient visits to healthcare facilities. The challenge amplifies when dealing with divergent patient subgroups, like those with rare diseases, which are characterized by unique health trajectories and are typically smaller in size. To address this, we employ a self-supervised pretraining strategy, Generative Summary Pretraining (GSP), which predicts future summary statistics based on past health records of a patient. Our models are pretrained on a health registry of nearly one million patients, then fine-tuned for specific subgroup prediction tasks, showcasing the potential to handle the multifaceted nature of EHR data. In evaluation, SANSformer consistently surpasses robust EHR baselines, with our GSP pretraining method notably amplifying model performance, particularly within smaller patient subgroups. Our results illuminate the promising potential of tailored attention-free models and self-supervised pretraining in refining healthcare utilization predictions across various patient demographics.

Although convolutional networks (ConvNets) have enjoyed great success in computer vision (CV), it suffers from capturing global information crucial to dense prediction tasks such as object detection and segmentation. In this work, we innovatively propose ConTNet (ConvolutionTransformer Network), combining transformer with ConvNet architectures to provide large receptive fields. Unlike the recently-proposed transformer-based models (e.g., ViT, DeiT) that are sensitive to hyper-parameters and extremely dependent on a pile of data augmentations when trained from scratch on a midsize dataset (e.g., ImageNet1k), ConTNet can be optimized like normal ConvNets (e.g., ResNet) and preserve an outstanding robustness. It is also worth pointing that, given identical strong data augmentations, the performance improvement of ConTNet is more remarkable than that of ResNet. We present its superiority and effectiveness on image classification and downstream tasks. For example, our ConTNet achieves 81.8% top-1 accuracy on ImageNet which is the same as DeiT-B with less than 40% computational complexity. ConTNet-M also outperforms ResNet50 as the backbone of both Faster-RCNN (by 2.6%) and Mask-RCNN (by 3.2%) on COCO2017 dataset. We hope that ConTNet could serve as a useful backbone for CV tasks and bring new ideas for model design

With the success of language pretraining, it is highly desirable to develop more efficient architectures of good scalability that can exploit the abundant unlabeled data at a lower cost. To improve the efficiency, we examine the much-overlooked redundancy in maintaining a full-length token-level presentation, especially for tasks that only require a single-vector presentation of the sequence. With this intuition, we propose Funnel-Transformer which gradually compresses the sequence of hidden states to a shorter one and hence reduces the computation cost. More importantly, by re-investing the saved FLOPs from length reduction in constructing a deeper or wider model, we further improve the model capacity. In addition, to perform token-level predictions as required by common pretraining objectives, Funnel-Transformer is able to recover a deep representation for each token from the reduced hidden sequence via a decoder. Empirically, with comparable or fewer FLOPs, Funnel-Transformer outperforms the standard Transformer on a wide variety of sequence-level prediction tasks, including text classification, language understanding, and reading comprehension. The code and pretrained checkpoints are available at https://github.com/laiguokun/Funnel-Transformer.

Laboratory test results are an important and generally high dimensional component of a patient's Electronic Health Record (EHR). We train embedding representations (via Word2Vec and GloVe) for LOINC codes of laboratory tests from the EHRs of about 80,000 patients at a cancer center. To include information about lab test outcomes, we also train embeddings on the concatenation of a LOINC code with a symbol indicating normality or abnormality of the result. We observe several clinically meaningful similarities among LOINC embeddings trained over our data. For the embeddings of the concatenation of LOINCs with abnormality codes, we evaluate the performance for mortality prediction tasks and the ability to preserve ordinality properties: i.e. a lab test with normal outcome should be more similar to an abnormal one than to the a very abnormal one.

Image segmentation remains a challenging task in computer vision, demanding robust mask generation and precise classification. Recent mask-based approaches yield high-quality masks by capturing global context. However, accurately classifying these masks, especially in the presence of ambiguous boundaries and imbalanced class distributions, remains an open challenge. In this work, we introduce ViT-P, a novel two-stage segmentation framework that decouples mask generation from classification. The first stage employs a proposal generator to produce class-agnostic mask proposals, while the second stage utilizes a point-based classification model built on the Vision Transformer (ViT) to refine predictions by focusing on mask central points. ViT-P serves as a pre-training-free adapter, allowing the integration of various pre-trained vision transformers without modifying their architecture, ensuring adaptability to dense prediction tasks. Furthermore, we demonstrate that coarse and bounding box annotations can effectively enhance classification without requiring additional training on fine annotation datasets, reducing annotation costs while maintaining strong performance. Extensive experiments across COCO, ADE20K, and Cityscapes datasets validate the effectiveness of ViT-P, achieving state-of-the-art results with 54.0 PQ on ADE20K panoptic segmentation, 87.4 mIoU on Cityscapes semantic segmentation, and 63.6 mIoU on ADE20K semantic segmentation. The code and pretrained models are available at: https://github.com/sajjad-sh33/ViT-P}{https://github.com/sajjad-sh33/ViT-P.

We explore the emergence of intelligent behavior in artificial systems by investigating how the complexity of rule-based systems influences the capabilities of models trained to predict these rules. Our study focuses on elementary cellular automata (ECA), simple yet powerful one-dimensional systems that generate behaviors ranging from trivial to highly complex. By training distinct Large Language Models (LLMs) on different ECAs, we evaluated the relationship between the complexity of the rules' behavior and the intelligence exhibited by the LLMs, as reflected in their performance on downstream tasks. Our findings reveal that rules with higher complexity lead to models exhibiting greater intelligence, as demonstrated by their performance on reasoning and chess move prediction tasks. Both uniform and periodic systems, and often also highly chaotic systems, resulted in poorer downstream performance, highlighting a sweet spot of complexity conducive to intelligence. We conjecture that intelligence arises from the ability to predict complexity and that creating intelligence may require only exposure to complexity.

We introduce a new class of time-continuous recurrent neural network models. Instead of declaring a learning system's dynamics by implicit nonlinearities, we construct networks of linear first-order dynamical systems modulated via nonlinear interlinked gates. The resulting models represent dynamical systems with varying (i.e., liquid) time-constants coupled to their hidden state, with outputs being computed by numerical differential equation solvers. These neural networks exhibit stable and bounded behavior, yield superior expressivity within the family of neural ordinary differential equations, and give rise to improved performance on time-series prediction tasks. To demonstrate these properties, we first take a theoretical approach to find bounds over their dynamics and compute their expressive power by the trajectory length measure in latent trajectory space. We then conduct a series of time-series prediction experiments to manifest the approximation capability of Liquid Time-Constant Networks (LTCs) compared to classical and modern RNNs. Code and data are available at https://github.com/raminmh/liquid_time_constant_networks

Dynamic knowledge graphs (DKGs) are popular structures to express different types of connections between objects over time. They can also serve as an efficient mathematical tool to represent information extracted from complex unstructured data sources, such as text or images. Within financial applications, DKGs could be used to detect trends for strategic thematic investing, based on information obtained from financial news articles. In this work, we explore the properties of large language models (LLMs) as dynamic knowledge graph generators, proposing a novel open-source fine-tuned LLM for this purpose, called the Integrated Contextual Knowledge Graph Generator (ICKG). We use ICKG to produce a novel open-source DKG from a corpus of financial news articles, called FinDKG, and we propose an attention-based GNN architecture for analysing it, called KGTransformer. We test the performance of the proposed model on benchmark datasets and FinDKG, demonstrating superior performance on link prediction tasks. Additionally, we evaluate the performance of the KGTransformer on FinDKG for thematic investing, showing it can outperform existing thematic ETFs.

Forecasting future world events is a challenging but valuable task. Forecasts of climate, geopolitical conflict, pandemics and economic indicators help shape policy and decision making. In these domains, the judgment of expert humans contributes to the best forecasts. Given advances in language modeling, can these forecasts be automated? To this end, we introduce Autocast, a dataset containing thousands of forecasting questions and an accompanying news corpus. Questions are taken from forecasting tournaments, ensuring high quality, real-world importance, and diversity. The news corpus is organized by date, allowing us to precisely simulate the conditions under which humans made past forecasts (avoiding leakage from the future). Motivated by the difficulty of forecasting numbers across orders of magnitude (e.g. global cases of COVID-19 in 2022), we also curate IntervalQA, a dataset of numerical questions and metrics for calibration. We test language models on our forecasting task and find that performance is far below a human expert baseline. However, performance improves with increased model size and incorporation of relevant information from the news corpus. In sum, Autocast poses a novel challenge for large language models and improved performance could bring large practical benefits.

Transformers have become one of the dominant architectures in deep learning, particularly as a powerful alternative to convolutional neural networks (CNNs) in computer vision. However, Transformer training and inference in previous works can be prohibitively expensive due to the quadratic complexity of self-attention over a long sequence of representations, especially for high-resolution dense prediction tasks. To this end, we present a novel Less attention vIsion Transformer (LIT), building upon the fact that the early self-attention layers in Transformers still focus on local patterns and bring minor benefits in recent hierarchical vision Transformers. Specifically, we propose a hierarchical Transformer where we use pure multi-layer perceptrons (MLPs) to encode rich local patterns in the early stages while applying self-attention modules to capture longer dependencies in deeper layers. Moreover, we further propose a learned deformable token merging module to adaptively fuse informative patches in a non-uniform manner. The proposed LIT achieves promising performance on image recognition tasks, including image classification, object detection and instance segmentation, serving as a strong backbone for many vision tasks. Code is available at: https://github.com/zhuang-group/LIT

We capitalize on large amounts of unlabeled video in order to learn a model of scene dynamics for both video recognition tasks (e.g. action classification) and video generation tasks (e.g. future prediction). We propose a generative adversarial network for video with a spatio-temporal convolutional architecture that untangles the scene's foreground from the background. Experiments suggest this model can generate tiny videos up to a second at full frame rate better than simple baselines, and we show its utility at predicting plausible futures of static images. Moreover, experiments and visualizations show the model internally learns useful features for recognizing actions with minimal supervision, suggesting scene dynamics are a promising signal for representation learning. We believe generative video models can impact many applications in video understanding and simulation.

Personalizing large language models (LLMs) to accommodate diverse user preferences is essential for enhancing alignment and user satisfaction. Traditional reinforcement learning from human feedback (RLHF) approaches often rely on monolithic value representations, limiting their ability to adapt to individual preferences. We introduce a novel framework that leverages low-rank preference modeling to efficiently learn and generalize user-specific reward functions. By representing reward functions in a low-dimensional subspace and modeling individual preferences as weighted combinations of shared basis functions, our approach avoids rigid user categorization while enabling scalability and few-shot adaptation. We validate our method on multiple preference datasets, demonstrating superior generalization to unseen users and improved accuracy in preference prediction tasks.

Understanding temporal dynamics is critical for conversational agents, enabling effective content analysis and informed decision-making. However, time-aware datasets, particularly for persona-grounded conversations, are still limited, which narrows their scope and diminishes their complexity. To address this gap, we introduce MTPChat, a multimodal, time-aware persona dialogue dataset that integrates linguistic, visual, and temporal elements within dialogue and persona memory. Leveraging MTPChat, we propose two time-sensitive tasks: Temporal Next Response Prediction (TNRP) and Temporal Grounding Memory Prediction (TGMP), both designed to assess a model's ability to understand implicit temporal cues and dynamic interactions. Additionally, we present an innovative framework featuring an adaptive temporal module to effectively integrate multimodal streams and capture temporal dependencies. Experimental results validate the challenges posed by MTPChat and demonstrate the effectiveness of our framework in multimodal time-sensitive scenarios.

RGB-D salient object detection (SOD), aiming to highlight prominent regions of a given scene by jointly modeling RGB and depth information, is one of the challenging pixel-level prediction tasks. Recently, the dual-attention mechanism has been devoted to this area due to its ability to strengthen the detection process. However, most existing methods directly fuse attentional cross-modality features under a manual-mandatory fusion paradigm without considering the inherent discrepancy between the RGB and depth, which may lead to a reduction in performance. Moreover, the long-range dependencies derived from global and local information make it difficult to leverage a unified efficient fusion strategy. Hence, in this paper, we propose the GL-DMNet, a novel dual mutual learning network with global-local awareness. Specifically, we present a position mutual fusion module and a channel mutual fusion module to exploit the interdependencies among different modalities in spatial and channel dimensions. Besides, we adopt an efficient decoder based on cascade transformer-infused reconstruction to integrate multi-level fusion features jointly. Extensive experiments on six benchmark datasets demonstrate that our proposed GL-DMNet performs better than 24 RGB-D SOD methods, achieving an average improvement of ~3% across four evaluation metrics compared to the second-best model (S3Net). Codes and results are available at https://github.com/kingkung2016/GL-DMNet.

World models integrate raw data from various modalities, such as images and language to simulate comprehensive interactions in the world, thereby displaying crucial roles in fields like mixed reality and robotics. Yet, applying the world model for accurate video prediction is quite challenging due to the complex and dynamic intentions of the various scenes in practice. In this paper, inspired by the human rethinking process, we decompose the complex video prediction into four meta-tasks that enable the world model to handle this issue in a more fine-grained manner. Alongside these tasks, we introduce a new benchmark named Embodied Video Anticipation Benchmark (EVA-Bench) to provide a well-rounded evaluation. EVA-Bench focused on evaluating the video prediction ability of human and robot actions, presenting significant challenges for both the language model and the generation model. Targeting embodied video prediction, we propose the Embodied Video Anticipator (EVA), a unified framework aiming at video understanding and generation. EVA integrates a video generation model with a visual language model, effectively combining reasoning capabilities with high-quality generation. Moreover, to enhance the generalization of our framework, we tailor-designed a multi-stage pretraining paradigm that adaptatively ensembles LoRA to produce high-fidelity results. Extensive experiments on EVA-Bench highlight the potential of EVA to significantly improve performance in embodied scenes, paving the way for large-scale pre-trained models in real-world prediction tasks.

We propose PROSE-FD, a zero-shot multimodal PDE foundational model for simultaneous prediction of heterogeneous two-dimensional physical systems related to distinct fluid dynamics settings. These systems include shallow water equations and the Navier-Stokes equations with incompressible and compressible flow, regular and complex geometries, and different buoyancy settings. This work presents a new transformer-based multi-operator learning approach that fuses symbolic information to perform operator-based data prediction, i.e. non-autoregressive. By incorporating multiple modalities in the inputs, the PDE foundation model builds in a pathway for including mathematical descriptions of the physical behavior. We pre-train our foundation model on 6 parametric families of equations collected from 13 datasets, including over 60K trajectories. Our model outperforms popular operator learning, computer vision, and multi-physics models, in benchmark forward prediction tasks. We test our architecture choices with ablation studies.

Cross-domain NER is a practical yet challenging problem since the data scarcity in the real-world scenario. A common practice is first to learn a NER model in a rich-resource general domain and then adapt the model to specific domains. Due to the mismatch problem between entity types across domains, the wide knowledge in the general domain can not effectively transfer to the target domain NER model. To this end, we model the label relationship as a probability distribution and construct label graphs in both source and target label spaces. To enhance the contextual representation with label structures, we fuse the label graph into the word embedding output by BERT. By representing label relationships as graphs, we formulate cross-domain NER as a graph matching problem. Furthermore, the proposed method has good applicability with pre-training methods and is potentially capable of other cross-domain prediction tasks. Empirical results on four datasets show that our method outperforms a series of transfer learning, multi-task learning, and few-shot learning methods.

Large pre-trained vision-language models such as CLIP provide compact and general-purpose representations of text and images that are demonstrably effective across multiple downstream zero-shot prediction tasks. However, owing to the nature of their training process, these models have the potential to 1) propagate or amplify societal biases in the training data and 2) learn to rely on spurious features. This paper proposes FairerCLIP, a general approach for making zero-shot predictions of CLIP more fair and robust to spurious correlations. We formulate the problem of jointly debiasing CLIP's image and text representations in reproducing kernel Hilbert spaces (RKHSs), which affords multiple benefits: 1) Flexibility: Unlike existing approaches, which are specialized to either learn with or without ground-truth labels, FairerCLIP is adaptable to learning in both scenarios. 2) Ease of Optimization: FairerCLIP lends itself to an iterative optimization involving closed-form solvers, which leads to 4times-10times faster training than the existing methods. 3) Sample Efficiency: Under sample-limited conditions, FairerCLIP significantly outperforms baselines when they fail entirely. And, 4) Performance: Empirically, FairerCLIP achieves appreciable accuracy gains on benchmark fairness and spurious correlation datasets over their respective baselines.

The convolutional neural network-based methods have become more and more popular for medical image segmentation due to their outstanding performance. However, they struggle with capturing long-range dependencies, which are essential for accurately modeling global contextual correlations. Thanks to the ability to model long-range dependencies by expanding the receptive field, the transformer-based methods have gained prominence. Inspired by this, we propose an advanced 2D feature extraction method by combining the convolutional neural network and Transformer architectures. More specifically, we introduce a parallelized encoder structure, where one branch uses ResNet to extract local information from images, while the other branch uses Transformer to extract global information. Furthermore, we integrate pyramid structures into the Transformer to extract global information at varying resolutions, especially in intensive prediction tasks. To efficiently utilize the different information in the parallelized encoder at the decoder stage, we use a channel attention module to merge the features of the encoder and propagate them through skip connections and bottlenecks. Intensive numerical experiments are performed on both aortic vessel tree, cardiac, and multi-organ datasets. By comparing with state-of-the-art medical image segmentation methods, our method is shown with better segmentation accuracy, especially on small organs. The code is publicly available on https://github.com/HongkunSun/ParaTransCNN.

In this work, we present Vlogger, a generic AI system for generating a minute-level video blog (i.e., vlog) of user descriptions. Different from short videos with a few seconds, vlog often contains a complex storyline with diversified scenes, which is challenging for most existing video generation approaches. To break through this bottleneck, our Vlogger smartly leverages Large Language Model (LLM) as Director and decomposes a long video generation task of vlog into four key stages, where we invoke various foundation models to play the critical roles of vlog professionals, including (1) Script, (2) Actor, (3) ShowMaker, and (4) Voicer. With such a design of mimicking human beings, our Vlogger can generate vlogs through explainable cooperation of top-down planning and bottom-up shooting. Moreover, we introduce a novel video diffusion model, ShowMaker, which serves as a videographer in our Vlogger for generating the video snippet of each shooting scene. By incorporating Script and Actor attentively as textual and visual prompts, it can effectively enhance spatial-temporal coherence in the snippet. Besides, we design a concise mixed training paradigm for ShowMaker, boosting its capacity for both T2V generation and prediction. Finally, the extensive experiments show that our method achieves state-of-the-art performance on zero-shot T2V generation and prediction tasks. More importantly, Vlogger can generate over 5-minute vlogs from open-world descriptions, without loss of video coherence on script and actor. The code and model is all available at https://github.com/zhuangshaobin/Vlogger.

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.

In this work we introduce Labrador, a pre-trained Transformer model for laboratory data. Labrador and BERT were pre-trained on a corpus of 100 million lab test results from electronic health records (EHRs) and evaluated on various downstream outcome prediction tasks. Both models demonstrate mastery of the pre-training task but neither consistently outperform XGBoost on downstream supervised tasks. Our ablation studies reveal that transfer learning shows limited effectiveness for BERT and achieves marginal success with Labrador. We explore the reasons for the failure of transfer learning and suggest that the data generating process underlying each patient cannot be characterized sufficiently using labs alone, among other factors. We encourage future work to focus on joint modeling of multiple EHR data categories and to include tree-based baselines in their evaluations.

Recently, the emergence of the large-scale vision-language model (VLM), such as CLIP, has opened the way towards open-world object perception. Many works have explored the utilization of pre-trained VLM for the challenging open-vocabulary dense prediction task that requires perceiving diverse objects with novel classes at inference time. Existing methods construct experiments based on the public datasets of related tasks, which are not tailored for open vocabulary and rarely involve imperceptible objects camouflaged in complex scenes due to data collection bias and annotation costs. To fill in the gaps, we introduce a new task, open-vocabulary camouflaged object segmentation (OVCOS), and construct a large-scale complex scene dataset (OVCamo) containing 11,483 hand-selected images with fine annotations and corresponding object classes. Further, we build a strong single-stage open-vocabulary camouflaged object segmentation transformer baseline OVCoser attached to the parameter-fixed CLIP with iterative semantic guidance and structure enhancement. By integrating the guidance of class semantic knowledge and the supplement of visual structure cues from the edge and depth information, the proposed method can efficiently capture camouflaged objects. Moreover, this effective framework also surpasses previous state-of-the-arts of open-vocabulary semantic image segmentation by a large margin on our OVCamo dataset. With the proposed dataset and baseline, we hope that this new task with more practical value can further expand the research on open-vocabulary dense prediction tasks. Our code and data can be found in the https://github.com/lartpang/OVCamo{link}.

While molecular pre-training has shown great potential in enhancing drug discovery, the lack of a solid physical interpretation in current methods raises concerns about whether the learned representation truly captures the underlying explanatory factors in observed data, ultimately resulting in limited generalization and robustness. Although denoising methods offer a physical interpretation, their accuracy is often compromised by ad-hoc noise design, leading to inaccurate learned force fields. To address this limitation, this paper proposes a new method for molecular pre-training, called sliced denoising (SliDe), which is based on the classical mechanical intramolecular potential theory. SliDe utilizes a novel noise strategy that perturbs bond lengths, angles, and torsion angles to achieve better sampling over conformations. Additionally, it introduces a random slicing approach that circumvents the computationally expensive calculation of the Jacobian matrix, which is otherwise essential for estimating the force field. By aligning with physical principles, SliDe shows a 42\% improvement in the accuracy of estimated force fields compared to current state-of-the-art denoising methods, and thus outperforms traditional baselines on various molecular property prediction tasks.

The application of machine learning (ML) in a range of geospatial tasks is increasingly common but often relies on globally available covariates such as satellite imagery that can either be expensive or lack predictive power. Here we explore the question of whether the vast amounts of knowledge found in Internet language corpora, now compressed within large language models (LLMs), can be leveraged for geospatial prediction tasks. We first demonstrate that LLMs embed remarkable spatial information about locations, but naively querying LLMs using geographic coordinates alone is ineffective in predicting key indicators like population density. We then present GeoLLM, a novel method that can effectively extract geospatial knowledge from LLMs with auxiliary map data from OpenStreetMap. We demonstrate the utility of our approach across multiple tasks of central interest to the international community, including the measurement of population density and economic livelihoods. Across these tasks, our method demonstrates a 70% improvement in performance (measured using Pearson's r^2) relative to baselines that use nearest neighbors or use information directly from the prompt, and performance equal to or exceeding satellite-based benchmarks in the literature. With GeoLLM, we observe that GPT-3.5 outperforms Llama 2 and RoBERTa by 19% and 51% respectively, suggesting that the performance of our method scales well with the size of the model and its pretraining dataset. Our experiments reveal that LLMs are remarkably sample-efficient, rich in geospatial information, and robust across the globe. Crucially, GeoLLM shows promise in mitigating the limitations of existing geospatial covariates and complementing them well. Code is available on the project website: https://rohinmanvi.github.io/GeoLLM