Daily Papers

Structural analyses are an integral part of computational research on nucleation and supercooled water, whose accuracy and efficiency can impact the validity and feasibility of such studies. The underlying molecular mechanisms of these often elusive and computationally expensive processes can be inferred from the evolution of ice-like structures, determined using appropriate structural analysis techniques. We present d-SEAMS, a free and open-source post-processing engine for the analysis of molecular dynamics trajectories, which is specifically able to qualitatively classify ice structures, in both strong confinement and bulk systems. For the first time, recent algorithms for confined ice structure determination have been implemented, along with topological network criteria for bulk ice structure determination. Recognizing the need for customization in structural analysis, d-SEAMS has a unique code architecture, built with `nix`, employing a `YAML`-`Lua` scripting pipeline. The software has been designed to be user-friendly and easy to extend. The engine outputs are compatible with popular graphics software suites, allowing for immediate visual insights into the systems studied. We demonstrate the features of d-SEAMS by using it to analyze nucleation in the bulk regime and for quasi-one and quasi-two-dimensional systems. Structural time evolution and quantitative metrics are determined for heterogenous ice nucleation on a silver-exposed beta-AgI surface, homogenous ice nucleation, flat monolayer square ice formation and freezing of an ice nanotube.

Analysis and prediction of stock market time series data has attracted considerable interest from the research community over the last decade. Rapid development and evolution of sophisticated algorithms for statistical analysis of time series data, and availability of high-performance hardware has made it possible to process and analyze high volume stock market time series data effectively, in real-time. Among many other important characteristics and behavior of such data, forecasting is an area which has witnessed considerable focus. In this work, we have used time series of the index values of the Auto sector in India during January 2010 to December 2015 for a deeper understanding of the behavior of its three constituent components, e.g., the trend, the seasonal component, and the random component. Based on this structural analysis, we have also designed five approaches for forecasting and also computed their accuracy in prediction using suitably chosen training and test data sets. Extensive results are presented to demonstrate the effectiveness of our proposed decomposition approaches of time series and the efficiency of our forecasting techniques, even in presence of a random component and a sharply changing trend component in the time-series.

Designing efficient and robust algorithms for accurate prediction of stock market prices is one of the most exciting challenges in the field of time series analysis and forecasting. With the exponential rate of development and evolution of sophisticated algorithms and with the availability of fast computing platforms, it has now become possible to effectively and efficiently extract, store, process and analyze high volume of stock market data with diversity in its contents. Availability of complex algorithms which can execute very fast on parallel architecture over the cloud has made it possible to achieve higher accuracy in forecasting results while reducing the time required for computation. In this paper, we use the time series data of the healthcare sector of India for the period January 2010 till December 2016. We first demonstrate a decomposition approach of the time series and then illustrate how the decomposition results provide us with useful insights into the behavior and properties exhibited by the time series. Further, based on the structural analysis of the time series, we propose six different methods of forecasting for predicting the time series index of the healthcare sector. Extensive results are provided on the performance of the forecasting methods to demonstrate their effectiveness.

Building a working mental model of a protein typically requires weeks of reading, cross-referencing crystal and predicted structures, and inspecting ligand complexes, an effort that is slow, unevenly accessible, and often requires specialized computational skills. We introduce Speak to a Protein, a new capability that turns protein analysis into an interactive, multimodal dialogue with an expert co-scientist. The AI system retrieves and synthesizes relevant literature, structures, and ligand data; grounds answers in a live 3D scene; and can highlight, annotate, manipulate and see the visualization. It also generates and runs code when needed, explaining results in both text and graphics. We demonstrate these capabilities on relevant proteins, posing questions about binding pockets, conformational changes, or structure-activity relationships to test ideas in real-time. Speak to a Protein reduces the time from question to evidence, lowers the barrier to advanced structural analysis, and enables hypothesis generation by tightly coupling language, code, and 3D structures. Speak to a Protein is freely accessible at https://open.playmolecule.org.

The computational analysis of poetry is limited by the scarcity of tools to automatically analyze and scan poems. In a multilingual settings, the problem is exacerbated as scansion and rhyme systems only exist for individual languages, making comparative studies very challenging and time consuming. In this work, we present Alberti, the first multilingual pre-trained large language model for poetry. Through domain-specific pre-training (DSP), we further trained multilingual BERT on a corpus of over 12 million verses from 12 languages. We evaluated its performance on two structural poetry tasks: Spanish stanza type classification, and metrical pattern prediction for Spanish, English and German. In both cases, Alberti outperforms multilingual BERT and other transformers-based models of similar sizes, and even achieves state-of-the-art results for German when compared to rule-based systems, demonstrating the feasibility and effectiveness of DSP in the poetry domain.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

With the rapid development and evolution of sophisticated algorithms for statistical analysis of time series data, the research community has started spending considerable effort in technical analysis of such data. Forecasting is also an area which has witnessed a paradigm shift in its approach. In this work, we have used the time series of the index values of the Auto sector in India during January 2010 to December 2015 for a deeper understanding of the behavior of its three constituent components, e.g., the Trend, the Seasonal component, and the Random component. Based on this structural analysis, we have also designed three approaches for forecasting and also computed their accuracy in prediction using suitably chosen training and test data sets. The results clearly demonstrate the accuracy of our decomposition results and efficiency of our forecasting techniques, even in presence of a dominant Random component in the time series.

When language models correctly parse "The cat that the dog chased meowed," are they analyzing syntax or simply familiar with dogs chasing cats? Despite extensive benchmarking, we lack methods to distinguish structural understanding from semantic pattern matching. We introduce CenterBench, a dataset of 9,720 comprehension questions on center-embedded sentences (like "The cat [that the dog chased] meowed") where relative clauses nest recursively, creating processing demands from simple to deeply nested structures. Each sentence has a syntactically identical but semantically implausible counterpart (e.g., mailmen prescribe medicine, doctors deliver mail) and six comprehension questions testing surface understanding, syntactic dependencies, and causal reasoning. Testing six models reveals that performance gaps between plausible and implausible sentences widen systematically with complexity, with models showing median gaps up to 26.8 percentage points, quantifying when they abandon structural analysis for semantic associations. Notably, semantic plausibility harms performance on questions about resulting actions, where following causal relationships matters more than semantic coherence. Reasoning models improve accuracy but their traces show semantic shortcuts, overthinking, and answer refusal. Unlike models whose plausibility advantage systematically widens with complexity, humans shows variable semantic effects. CenterBench provides the first framework to identify when models shift from structural analysis to pattern matching.

One of the challenging research problems in the domain of time series analysis and forecasting is making efficient and robust prediction of stock market prices. With rapid development and evolution of sophisticated algorithms and with the availability of extremely fast computing platforms, it has now become possible to effectively extract, store, process and analyze high volume stock market time series data. Complex algorithms for forecasting are now available for speedy execution over parallel architecture leading to fairly accurate results. In this paper, we have used time series data of the two sectors of the Indian economy: Consumer Durables sector and the Small Cap sector for the period January 2010 to December 2015 and proposed a decomposition approach for better understanding of the behavior of each of the time series. Our contention is that various sectors reveal different time series patterns and understanding them is essential for portfolio formation. Further, based on this structural analysis, we have also proposed several robust forecasting techniques and analyzed their accuracy in prediction using suitably chosen training and test data sets. Extensive results are presented to demonstrate the effectiveness of our propositions.

Influenced by the complexity of volumetric imaging, there is a shortage of established datasets useful for benchmarking volumetric deep-learning models. As a consequence, new and existing models are not easily comparable, limiting the development of architectures optimized specifically for volumetric data. To counteract this trend, we introduce MozzaVID - a large, clean, and versatile volumetric classification dataset. Our dataset contains X-ray computed tomography (CT) images of mozzarella microstructure and enables the classification of 25 cheese types and 149 cheese samples. We provide data in three different resolutions, resulting in three dataset instances containing from 591 to 37,824 images. While being general-purpose, the dataset also facilitates investigating mozzarella structure properties. The structure of food directly affects its functional properties and thus its consumption experience. Understanding food structure helps tune the production and mimicking it enables sustainable alternatives to animal-derived food products. The complex and disordered nature of food structures brings a unique challenge, where a choice of appropriate imaging method, scale, and sample size is not trivial. With this dataset we aim to address these complexities, contributing to more robust structural analysis models. The dataset can be downloaded from: https://archive.compute.dtu.dk/files/public/projects/MozzaVID/.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

Machine learning (ML) and deep learning (DL) techniques have gained significant attention as reduced order models (ROMs) to computationally expensive structural analysis methods, such as finite element analysis (FEA). Graph neural network (GNN) is a particular type of neural network which processes data that can be represented as graphs. This allows for efficient representation of complex geometries that can change during conceptual design of a structure or a product. In this study, we propose a novel graph embedding technique for efficient representation of 3D stiffened panels by considering separate plate domains as vertices. This approach is considered using Graph Sampling and Aggregation (GraphSAGE) to predict stress distributions in stiffened panels with varying geometries. A comparison between a finite-element-vertex graph representation is conducted to demonstrate the effectiveness of the proposed approach. A comprehensive parametric study is performed to examine the effect of structural geometry on the prediction performance. Our results demonstrate the immense potential of graph neural networks with the proposed graph embedding method as robust reduced-order models for 3D structures.

Large Language Models (LLMs) have made significant strides in natural language generation but often face challenges in tasks requiring precise calculations and structural analysis. This paper investigates the performance of state-of-the-art LLMs on language complexity measurement tasks, through the computation of the LIX readability metric and Average Dependency Distance (ADD). Using Swedish high school and university-level essays, we evaluate the models' abilities to compute LIX scores and perform dependency parsing, comparing their results to established ground truths. Our findings reveal that while all models demonstrate some capacity for these tasks, ChatGPT-o1-mini performs most consistently, achieving the highest accuracy in both LIX computation and dependency parsing. Additionally, we observe a strong significant correlation -0.875 p 0.026 (N=6) between the models' accuracy in computing LIX and their overall performance on the Massive Multitask Language Understanding (MMLU) benchmark. These results suggest that language complexity measurement abilities can serve as a noisy zero-shot proxies for assessing the general capabilities of LLMs, providing a practical method for model evaluation without the need for extensive benchmarking datasets.

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

The application of artificial intelligence (AI) in three-dimensional (3D) agricultural research, particularly for maize, has been limited by the scarcity of large-scale, diverse datasets. While 2D image datasets are abundant, they fail to capture essential structural details such as leaf architecture, plant volume, and spatial arrangements that 3D data provide. To address this limitation, we present AgriField3D (https://baskargroup.github.io/AgriField3D/), a curated dataset of 3D point clouds of field-grown maize plants from a diverse genetic panel, designed to be AI-ready for advancing agricultural research. Our dataset comprises over 1,000 high-quality point clouds collected using a Terrestrial Laser Scanner, complemented by procedural models that provide structured, parametric representations of maize plants. These procedural models, generated using Non-Uniform Rational B-Splines (NURBS) and optimized via a two-step process combining Particle Swarm Optimization (PSO) and differentiable programming, enable precise, scalable reconstructions of leaf surfaces and plant architectures. To enhance usability, we performed graph-based segmentation to isolate individual leaves and stalks, ensuring consistent labeling across all samples. We also conducted rigorous manual quality control on all datasets, correcting errors in segmentation, ensuring accurate leaf ordering, and validating metadata annotations. The dataset further includes metadata detailing plant morphology and quality, alongside multi-resolution subsampled versions (100k, 50k, 10k points) optimized for various computational needs. By integrating point cloud data of field grown plants with high-fidelity procedural models and ensuring meticulous manual validation, AgriField3D provides a comprehensive foundation for AI-driven phenotyping, plant structural analysis, and 3D applications in agricultural research.

Quantum algorithms, represented as quantum circuits, can be used as benchmarks for assessing the performance of quantum systems. Existing datasets, widely utilized in the field, suffer from limitations in size and versatility, leading researchers to employ randomly generated circuits. Random circuits are, however, not representative benchmarks as they lack the inherent properties of real quantum algorithms for which the quantum systems are manufactured. This shortage of `useful' quantum benchmarks poses a challenge to advancing the development and comparison of quantum compilers and hardware. This research aims to enhance the existing quantum circuit datasets by generating what we refer to as `realistic-looking' circuits by employing the Transformer machine learning architecture. For this purpose, we introduce KetGPT, a tool that generates synthetic circuits in OpenQASM language, whose structure is based on quantum circuits derived from existing quantum algorithms and follows the typical patterns of human-written algorithm-based code (e.g., order of gates and qubits). Our three-fold verification process, involving manual inspection and Qiskit framework execution, transformer-based classification, and structural analysis, demonstrates the efficacy of KetGPT in producing large amounts of additional circuits that closely align with algorithm-based structures. Beyond benchmarking, we envision KetGPT contributing substantially to AI-driven quantum compilers and systems.

The Handwritten Mathematical Expression Recognition (HMER) task is a critical branch in the field of OCR. Recent studies have demonstrated that incorporating bidirectional context information significantly improves the performance of HMER models. However, existing methods fail to effectively utilize bidirectional context information during the inference stage. Furthermore, current bidirectional training methods are primarily designed for string decoders and cannot adequately generalize to tree decoders, which offer superior generalization capabilities and structural analysis capacity. In order to overcome these limitations, we propose the Mirror-Flipped Symbol Layout Tree (MF-SLT) and Bidirectional Asynchronous Training (BAT) structure. Our method extends the bidirectional training strategy to the tree decoder, allowing for more effective training by leveraging bidirectional information. Additionally, we analyze the impact of the visual and linguistic perception of the HMER model separately and introduce the Shared Language Modeling (SLM) mechanism. Through the SLM, we enhance the model's robustness and generalization when dealing with visual ambiguity, particularly in scenarios with abundant training data. Our approach has been validated through extensive experiments, demonstrating its ability to achieve new state-of-the-art results on the CROHME 2014, 2016, and 2019 datasets, as well as the HME100K dataset. The code used in our experiments will be publicly available.

Super-resolution (SR) advances astronomical imaging by enabling cost-effective high-resolution capture, crucial for detecting faraway celestial objects and precise structural analysis. However, existing datasets for astronomical SR (ASR) exhibit three critical limitations: flux inconsistency, object-crop setting, and insufficient data diversity, significantly impeding ASR development. We propose STAR, a large-scale astronomical SR dataset containing 54,738 flux-consistent star field image pairs covering wide celestial regions. These pairs combine Hubble Space Telescope high-resolution observations with physically faithful low-resolution counterparts generated through a flux-preserving data generation pipeline, enabling systematic development of field-level ASR models. To further empower the ASR community, STAR provides a novel Flux Error (FE) to evaluate SR models in physical view. Leveraging this benchmark, we propose a Flux-Invariant Super Resolution (FISR) model that could accurately infer the flux-consistent high-resolution images from input photometry, suppressing several SR state-of-the-art methods by 24.84% on a novel designed flux consistency metric, showing the priority of our method for astrophysics. Extensive experiments demonstrate the effectiveness of our proposed method and the value of our dataset. Code and models are available at https://github.com/GuoCheng12/STAR.

A crucial part of any home is the roof over our heads to protect us from the elements. In this paper we present the Zeitview Rooftop Geometry (ZRG) dataset for residential rooftop understanding. ZRG is a large-scale residential rooftop dataset of over 20k properties collected through roof inspections from across the U.S. and contains multiple modalities including high resolution aerial orthomosaics, digital surface models (DSM), colored point clouds, and 3D roof wireframe annotations. We provide an in-depth analysis and perform several experimental baselines including roof outline extraction, monocular height estimation, and planar roof structure extraction, to illustrate a few of the numerous potential applications unlocked by this dataset.

Tactile graphics are essential for providing access to visual information for the 43 million people globally living with vision loss. Traditional methods for creating these graphics are labor-intensive and cannot meet growing demand. We introduce TactileNet, the first comprehensive dataset and AI-driven framework for generating embossing-ready 2D tactile templates using text-to-image Stable Diffusion (SD) models. By integrating Low-Rank Adaptation (LoRA) and DreamBooth, our method fine-tunes SD models to produce high-fidelity, guideline-compliant graphics while reducing computational costs. Quantitative evaluations with tactile experts show 92.86% adherence to accessibility standards. Structural fidelity analysis revealed near-human design similarity, with an SSIM of 0.538 between generated graphics and expert-designed tactile images. Notably, our method preserves object silhouettes better than human designs (SSIM = 0.259 vs. 0.215 for binary masks), addressing a key limitation of manual tactile abstraction. The framework scales to 32,000 images (7,050 high-quality) across 66 classes, with prompt editing enabling customizable outputs (e.g., adding or removing details). By automating the 2D template generation step-compatible with standard embossing workflows-TactileNet accelerates production while preserving design flexibility. This work demonstrates how AI can augment (not replace) human expertise to bridge the accessibility gap in education and beyond. Code, data, and models will be publicly released to foster further research.

In this report, we introduce Qwen2.5, a comprehensive series of large language models (LLMs) designed to meet diverse needs. Compared to previous iterations, Qwen 2.5 has been significantly improved during both the pre-training and post-training stages. In terms of pre-training, we have scaled the high-quality pre-training datasets from the previous 7 trillion tokens to 18 trillion tokens. This provides a strong foundation for common sense, expert knowledge, and reasoning capabilities. In terms of post-training, we implement intricate supervised finetuning with over 1 million samples, as well as multistage reinforcement learning. Post-training techniques enhance human preference, and notably improve long text generation, structural data analysis, and instruction following. To handle diverse and varied use cases effectively, we present Qwen2.5 LLM series in rich sizes. Open-weight offerings include base and instruction-tuned models, with quantized versions available. In addition, for hosted solutions, the proprietary models currently include two mixture-of-experts (MoE) variants: Qwen2.5-Turbo and Qwen2.5-Plus, both available from Alibaba Cloud Model Studio. Qwen2.5 has demonstrated top-tier performance on a wide range of benchmarks evaluating language understanding, reasoning, mathematics, coding, human preference alignment, etc. Specifically, the open-weight flagship Qwen2.5-72B-Instruct outperforms a number of open and proprietary models and demonstrates competitive performance to the state-of-the-art open-weight model, Llama-3-405B-Instruct, which is around 5 times larger. Qwen2.5-Turbo and Qwen2.5-Plus offer superior cost-effectiveness while performing competitively against GPT-4o-mini and GPT-4o respectively. Additionally, as the foundation, Qwen2.5 models have been instrumental in training specialized models such as Qwen2.5-Math, Qwen2.5-Coder, QwQ, and multimodal models.

Retrieval-Augmented Generation (RAG) offers a promising solution to address various limitations of Large Language Models (LLMs), such as hallucination and difficulties in keeping up with real-time updates. This approach is particularly critical in expert and domain-specific applications where LLMs struggle to cover expert knowledge. Therefore, evaluating RAG models in such scenarios is crucial, yet current studies often rely on general knowledge sources like Wikipedia to assess the models' abilities in solving common-sense problems. In this paper, we evaluated LLMs by RAG settings in a domain-specific context, college enrollment. We identified six required abilities for RAG models, including the ability in conversational RAG, analyzing structural information, faithfulness to external knowledge, denoising, solving time-sensitive problems, and understanding multi-document interactions. Each ability has an associated dataset with shared corpora to evaluate the RAG models' performance. We evaluated popular LLMs such as Llama, Baichuan, ChatGLM, and GPT models. Experimental results indicate that existing closed-book LLMs struggle with domain-specific questions, highlighting the need for RAG models to solve expert problems. Moreover, there is room for RAG models to improve their abilities in comprehending conversational history, analyzing structural information, denoising, processing multi-document interactions, and faithfulness in expert knowledge. We expect future studies could solve these problems better.

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

Recently, contrastive learning has found impressive success in advancing the state of the art in solving various machine learning tasks. However, the existing generalization analysis is very limited or even not meaningful. In particular, the existing generalization error bounds depend linearly on the number k of negative examples while it was widely shown in practice that choosing a large k is necessary to guarantee good generalization of contrastive learning in downstream tasks. In this paper, we establish novel generalization bounds for contrastive learning which do not depend on k, up to logarithmic terms. Our analysis uses structural results on empirical covering numbers and Rademacher complexities to exploit the Lipschitz continuity of loss functions. For self-bounding Lipschitz loss functions, we further improve our results by developing optimistic bounds which imply fast rates in a low noise condition. We apply our results to learning with both linear representation and nonlinear representation by deep neural networks, for both of which we derive Rademacher complexity bounds to get improved generalization bounds.

We propose a structural default model for portfolio-wide valuation adjustments (xVAs) and represent it as a system of coupled backward stochastic differential equations. The framework is divided into four layers, each capturing a key component: (i) clean values, (ii) initial margin and Collateral Valuation Adjustment (ColVA), (iii) Credit/Debit Valuation Adjustments (CVA/DVA) together with Margin Valuation Adjustment (MVA), and (iv) Funding Valuation Adjustment (FVA). Because these layers depend on one another through collateral and default effects, a naive Monte Carlo approach would require deeply nested simulations, making the problem computationally intractable. To address this challenge, we use an iterative deep BSDE approach, handling each layer sequentially so that earlier outputs serve as inputs to the subsequent layers. Initial margin is computed via deep quantile regression to reflect margin requirements over the Margin Period of Risk. We also adopt a change-of-measure method that highlights rare but significant defaults of the bank or counterparty, ensuring that these events are accurately captured in the training process. We further extend Han and Long's (2020) a posteriori error analysis to BSDEs on bounded domains. Due to the random exit from the domain, we obtain an order of convergence of O(h^{1/4-epsilon}) rather than the usual O(h^{1/2}). Numerical experiments illustrate that this method drastically reduces computational demands and successfully scales to high-dimensional, non-symmetric portfolios. The results confirm its effectiveness and accuracy, offering a practical alternative to nested Monte Carlo simulations in multi-counterparty xVA analyses.

ImageNet has become a reputable resource for transfer learning, allowing the development of efficient ML models with reduced training time and data requirements. However, vibration analysis in predictive maintenance, structural health monitoring, and fault diagnosis, lacks a comparable large-scale, annotated dataset to facilitate similar advancements. To address this, a dataset framework is proposed that begins with bearing vibration data as an initial step towards creating a universal dataset for vibration-based spectrogram analysis for all machinery. The initial framework includes a collection of bearing vibration signals from various publicly available datasets. To demonstrate the advantages of this framework, experiments were conducted using a deep learning architecture, showing improvements in model performance when pre-trained on bearing vibration data and fine-tuned on a smaller, domain-specific dataset. These findings highlight the potential to parallel the success of ImageNet in visual computing but for vibration analysis. For future work, this research will include a broader range of vibration signals from multiple types of machinery, emphasizing spectrogram-based representations of the data. Each sample will be labeled according to machinery type, operational status, and the presence or type of faults, ensuring its utility for supervised and unsupervised learning tasks. Additionally, a framework for data preprocessing, feature extraction, and model training specific to vibration data will be developed. This framework will standardize methodologies across the research community, allowing for collaboration and accelerating progress in predictive maintenance, structural health monitoring, and related fields. By mirroring the success of ImageNet in visual computing, this dataset has the potential to improve the development of intelligent systems in industrial applications.

Models need appropriate inductive biases to effectively learn from small amounts of data and generalize systematically outside of the training distribution. While Transformers are highly versatile and powerful, they can still benefit from enhanced structural inductive biases for seq2seq tasks, especially those involving syntactic transformations, such as converting active to passive voice or semantic parsing. In this paper, we propose to strengthen the structural inductive bias of a Transformer by intermediate pre-training to perform synthetically generated syntactic transformations of dependency trees given a description of the transformation. Our experiments confirm that this helps with few-shot learning of syntactic tasks such as chunking, and also improves structural generalization for semantic parsing. Our analysis shows that the intermediate pre-training leads to attention heads that keep track of which syntactic transformation needs to be applied to which token, and that the model can leverage these attention heads on downstream tasks.

Large language model (LLM) agents increasingly rely on external tools such as search engines to solve complex, multi-step problems, and reinforcement learning (RL) has become a key paradigm for training them. However, the trajectories of search agents are structurally heterogeneous, where variations in the number, placement, and outcomes of search calls lead to fundamentally different answer directions and reward distributions. Standard policy gradient methods, which use a single global baseline, suffer from what we identify and formalize as cross-stratum bias-an "apples-to-oranges" comparison of heterogeneous trajectories. This cross-stratum bias distorts credit assignment and hinders exploration of complex, multi-step search strategies. To address this, we propose Stratified GRPO, whose central component, Stratified Advantage Normalization (SAN), partitions trajectories into homogeneous strata based on their structural properties and computes advantages locally within each stratum. This ensures that trajectories are evaluated only against their true peers. Our analysis proves that SAN eliminates cross-stratum bias, yields conditionally unbiased unit-variance estimates inside each stratum, and retains the global unbiasedness and unit-variance properties enjoyed by standard normalization, resulting in a more pure and scale-stable learning signal. To improve practical stability under finite-sample regimes, we further linearly blend SAN with the global estimator. Extensive experiments on diverse single-hop and multi-hop question-answering benchmarks demonstrate that Stratified GRPO consistently and substantially outperforms GRPO by up to 11.3 points, achieving higher training rewards, greater training stability, and more effective search policies. These results establish stratification as a principled remedy for structural heterogeneity in RL for LLM search agents.

Mathematical researchers, especially those in early-career positions, face critical decisions about topic specialization with limited information about the collaborative environments of different research areas. The aim of this paper is to study how the popularity of a research topic is associated with the structure of that topic's collaboration network, as observed by a suite of measures capturing organizational structure at several scales. We apply these measures to 1,938 algorithmically discovered topics across 121,391 papers sourced from arXiv metadata during the period 2020--2025. Our analysis, which controls for the confounding effects of network size, reveals a structural dichotomy--we find that popular topics organize into modular "schools of thought," while niche topics maintain hierarchical core-periphery structures centered around established experts. This divide is not an artifact of scale, but represents a size-independent structural pattern correlated with popularity. We also document a "constraint reversal": after controlling for size, researchers in popular fields face greater structural constraints on collaboration opportunities, contrary to conventional expectations. Our findings suggest that topic selection is an implicit choice between two fundamentally different collaborative environments, each with distinct implications for a researcher's career. To make these structural patterns transparent to the research community, we developed the Math Research Compass (https://mathresearchcompass.com), an interactive platform providing data on topic popularity and collaboration patterns across mathematical topics.

Dwarf galaxies serve as powerful laboratories for investigating the underlying physics of galaxy evolution including the impact of baryonic feedback processes and environmental influences. We compare the visual and structural properties of dwarf galaxies in ultra-deep HSC-SSP imaging of the COSMOS field with those measured from realistic HSC-like synthetic observations of dwarfs generated by the Illustris TNG50 and NewHorizon simulations. Using S\'ersic profile fitting and non-parametric morphological metrics (Gini, M_{20}, asymmetry, and concentration), we evaluate the diversity of structural properties in observed and simulated galaxies. Our analysis shows that NewHorizon and TNG50 galaxies lie at opposite extremes of observed structural trends: NewHorizon produces diffuse, extended galaxies with shallow S\'ersic indices, while TNG50 yields compact, concentrated systems with steep indices. Both simulations reproduce observed structural trends more closely at higher stellar masses (M_{star}sim10^{9.5} {rm M_{odot}}) but fail to capture the full diversity of COSMOS dwarfs at lower masses. Non-parametric metrics further show that NewHorizon galaxies exhibit more uneven, clumpy light distributions while TNG50 galaxies have smoother but excessively concentrated profiles. These structural differences reflect underlying differences in their physical prescriptions and are likely driven by differing approaches to ISM physics, supernova feedback and star formation in addition to differences in numerical resolution. Our findings highlight the unique power of low-mass galaxies to constrain differences in simulation physics, especially star formation and feedback. Upcoming surveys from facilities like the Vera C. Rubin Observatory and Euclid will enable more rigorous comparisons with simulations, offering deeper insights into the physical processes shaping galaxy evolution.

Deep Learning of neural networks has gained prominence in multiple life-critical applications like medical diagnoses and autonomous vehicle accident investigations. However, concerns about model transparency and biases persist. Explainable methods are viewed as the solution to address these challenges. In this study, we introduce the Occlusion Sensitivity Analysis with Deep Feature Augmentation Subspace (OSA-DAS), a novel perturbation-based interpretability approach for computer vision. While traditional perturbation methods make only use of occlusions to explain the model predictions, OSA-DAS extends standard occlusion sensitivity analysis by enabling the integration with diverse image augmentations. Distinctly, our method utilizes the output vector of a DNN to build low-dimensional subspaces within the deep feature vector space, offering a more precise explanation of the model prediction. The structural similarity between these subspaces encompasses the influence of diverse augmentations and occlusions. We test extensively on the ImageNet-1k, and our class- and model-agnostic approach outperforms commonly used interpreters, setting it apart in the realm of explainable AI.

Strong inductive biases enable learning from little data and help generalization outside of the training distribution. Popular neural architectures such as Transformers lack strong structural inductive biases for seq2seq NLP tasks on their own. Consequently, they struggle with systematic generalization beyond the training distribution, e.g. with extrapolating to longer inputs, even when pre-trained on large amounts of text. We show how a structural inductive bias can be efficiently injected into a seq2seq model by pre-training it to simulate structural transformations on synthetic data. Specifically, we inject an inductive bias towards Finite State Transducers (FSTs) into a Transformer by pre-training it to simulate FSTs given their descriptions. Our experiments show that our method imparts the desired inductive bias, resulting in improved systematic generalization and better few-shot learning for FST-like tasks. Our analysis shows that fine-tuned models accurately capture the state dynamics of the unseen underlying FSTs, suggesting that the simulation process is internalized by the fine-tuned model.

Fine-tuning pre-trained large language models (LLMs) presents a dual challenge of balancing parameter efficiency and model capacity. Existing methods like low-rank adaptations (LoRA) are efficient but lack flexibility, while Mixture-of-Experts (MoE) architectures enhance model capacity at the cost of more & under-utilized parameters. To address these limitations, we propose Structural Mixture of Residual Experts (S'MoRE), a novel framework that seamlessly integrates the efficiency of LoRA with the flexibility of MoE. Specifically, S'MoRE employs hierarchical low-rank decomposition of expert weights, yielding residuals of varying orders interconnected in a multi-layer structure. By routing input tokens through sub-trees of residuals, S'MoRE emulates the capacity of many experts by instantiating and assembling just a few low-rank matrices. We craft the inter-layer propagation of S'MoRE's residuals as a special type of Graph Neural Network (GNN), and prove that under similar parameter budget, S'MoRE improves "structural flexibility" of traditional MoE (or Mixture-of-LoRA) by exponential order. Comprehensive theoretical analysis and empirical results demonstrate that S'MoRE achieves superior fine-tuning performance, offering a transformative approach for efficient LLM adaptation.

Recently, machine unlearning, which seeks to erase specific data stored in the pre-trained or fine-tuned models, has emerged as a crucial protective measure for LLMs. However, unlearning approaches for LLMs that have been considered thus far have focused on the removal of independent data points and have not taken into account that the stored facts are logically connected to one another and form an implicit knowledge graph. To facilitate the development of structural unlearning methods, which are essential for the practical application of unlearning, we propose PISTOL, a pipeline for compiling multi-scenario datasets for benchmarking structural LLM unlearning. Additionally, leveraging sample datasets synthesized using PISTOL, we conducted benchmarks with four distinct unlearning methods on both Llama2-7B and Mistral-7B models. This analysis helps to illustrate the prevailing challenges in effectively and robustly removing highly inter-connected data, batched data, or data skewed towards a specific domain. It also highlights the choice of pre-trained model can impact unlearning performance. This work not only advances our understandings on the limitation of current LLMs unlearning methods and proposes future research directions, but also provides a replicable framework for ongoing exploration and validation in the field.

Time series analysis and forecasting of stock market prices has been a very active area of research over the last two decades. Availability of extremely fast and parallel architecture of computing and sophisticated algorithms has made it possible to extract, store, process and analyze high volume stock market time series data very efficiently. In this paper, we have used time series data of the two sectors of the Indian economy: Information Technology and Capital Goods for the period January 2009 till April 2016 and have studied the relationships of these two time series with the time series of DJIA index, NIFTY index and the US Dollar to Indian Rupee exchange rate. We establish by graphical and statistical tests that while the IT sector of India has a strong association with DJIA index and the Dollar to Rupee exchange rate, the Indian CG sector exhibits a strong association with the NIFTY index. We contend that these observations corroborate our hypotheses that the Indian IT sector is strongly coupled with the world economy whereas the CG sector of India reflects internal economic growth of India. We also present several models of regression between the time series which exhibit strong association among them. The effectiveness of these models have been demonstrated by very low values of their forecasting errors.

To characterize the location (mean, median) of a set of graphs, one needs a notion of centrality that is adapted to metric spaces, since graph sets are not Euclidean spaces. A standard approach is to consider the Frechet mean. In this work, we equip a set of graphs with the pseudometric defined by the norm between the eigenvalues of their respective adjacency matrix. Unlike the edit distance, this pseudometric reveals structural changes at multiple scales, and is well adapted to studying various statistical problems for graph-valued data. We describe an algorithm to compute an approximation to the sample Frechet mean of a set of undirected unweighted graphs with a fixed size using this pseudometric.

This paper presents an annotated dataset of brain MRI images designed to advance the field of brain symmetry study. Magnetic resonance imaging (MRI) has gained interest in analyzing brain symmetry in neonatal infants, and challenges remain due to the vast size differences between fetal and adult brains. Classification methods for brain structural MRI use scales and visual cues to assess hemisphere symmetry, which can help diagnose neonatal patients by comparing hemispheres and anatomical regions of interest in the brain. Using the Developing Human Connectome Project dataset, this work presents a dataset comprising cerebral images extracted as slices across selected portions of interest for clinical evaluation . All the extracted images are annotated with the brain's midline. All the extracted images are annotated with the brain's midline. From the assumption that a decrease in symmetry is directly related to possible clinical pathologies, the dataset can contribute to a more precise diagnosis because it can be used to train deep learning model application in neonatal cerebral MRI anomaly detection from postnatal infant scans thanks to computer vision. Such models learn to identify and classify anomalies by identifying potential asymmetrical patterns in medical MRI images. Furthermore, this dataset can contribute to the research and development of methods using the relative symmetry of the two brain hemispheres for crucial diagnosis and treatment planning.

We present Datarus-R1-14B, a 14 B-parameter open-weights language model fine-tuned from Qwen 2.5-14B-Instruct to act as a virtual data analyst and graduate-level problem solver. Datarus is trained not on isolated question-answer pairs but on full analytical trajectories including reasoning steps, code execution, error traces, self-corrections, and final conclusions, all captured in a ReAct-style notebook format spanning finance, medicine, numerical analysis, and other quantitative domains. Our training pipeline combines (i) a trajectory-centric synthetic data generator that yielded 144 000 tagged notebook episodes, (ii) a dual-reward framework blending a lightweight tag-based structural signal with a Hierarchical Reward Model (HRM) that scores both single-step soundness and end-to-end coherence, and (iii) a memory-optimized implementation of Group Relative Policy Optimization (GRPO) featuring KV-cache reuse, sequential generation, and reference-model sharding. A cosine curriculum smoothly shifts emphasis from structural fidelity to semantic depth, reducing the format collapse and verbosity that often plague RL-aligned LLMs. A central design choice in Datarus is it dual reasoning interface. In agentic mode the model produces ReAct-tagged steps that invoke Python tools to execute real code; in reflection mode it outputs compact Chain-of-Thought (CoT) traces delimited by <think> and <answer> tags. On demanding postgraduate-level problems, Datarus exhibits an "AHA-moment" pattern: it sketches hypotheses, revises them once or twice, and converges avoiding the circular, token-inflating loops common to contemporary systems. Across standard public benchmarks Datarus surpasses similar size models and even reaches the level of larger reasoning models such as QwQ-32B achieving up to 30% higher accuracy on AIME 2024/2025 and LiveCodeBench while emitting 18-49% fewer tokens per solution.

Large Language Models (LLMs) have garnered considerable interest within both academic and industrial. Yet, the application of LLMs to graph data remains under-explored. In this study, we evaluate the capabilities of four LLMs in addressing several analytical problems with graph data. We employ four distinct evaluation metrics: Comprehension, Correctness, Fidelity, and Rectification. Our results show that: 1) LLMs effectively comprehend graph data in natural language and reason with graph topology. 2) GPT models can generate logical and coherent results, outperforming alternatives in correctness. 3) All examined LLMs face challenges in structural reasoning, with techniques like zero-shot chain-of-thought and few-shot prompting showing diminished efficacy. 4) GPT models often produce erroneous answers in multi-answer tasks, raising concerns in fidelity. 5) GPT models exhibit elevated confidence in their outputs, potentially hindering their rectification capacities. Notably, GPT-4 has demonstrated the capacity to rectify responses from GPT-3.5-turbo and its own previous iterations. The code is available at: https://github.com/Ayame1006/LLMtoGraph.

Large deployable mesh reflectors are essential for space applications, providing precise reflecting surfaces for high-gain antennas used in satellite communications, Earth observation, and deep-space missions. During on-orbit missions, active shape adjustment and attitude control are crucial for maintaining surface accuracy and proper orientation for these reflectors, ensuring optimal performance. Preventing resonance through thorough dynamic modeling and vibration analysis is vital to avoid structural damage and ensure stability and reliability. Existing dynamic modeling approaches, such as wave and finite element methods, often fail to accurately predict dynamic responses due to the limited capability of handling three-dimensional reflectors or the oversimplification of cable members of a reflector. This paper proposes the Cartesian spatial discretization method for dynamic modeling and vibration analysis of cable-network structures in large deployable mesh reflectors. This method defines cable member positions as a summation of internal and boundary-induced terms within a global Cartesian coordinate system. Numerical simulation on a two-dimensional cable-network structure and a center-feed mesh reflector demonstrates the superiority of the proposed method over traditional approaches, highlighting its accuracy and versatility, and establishing it as a robust tool for analyzing three-dimensional complex reflector configurations.

Identifying the intent of a citation in scientific papers (e.g., background information, use of methods, comparing results) is critical for machine reading of individual publications and automated analysis of the scientific literature. We propose structural scaffolds, a multitask model to incorporate structural information of scientific papers into citations for effective classification of citation intents. Our model achieves a new state-of-the-art on an existing ACL anthology dataset (ACL-ARC) with a 13.3% absolute increase in F1 score, without relying on external linguistic resources or hand-engineered features as done in existing methods. In addition, we introduce a new dataset of citation intents (SciCite) which is more than five times larger and covers multiple scientific domains compared with existing datasets. Our code and data are available at: https://github.com/allenai/scicite.

Disassembly is a crucial yet challenging step in binary analysis. While emerging neural disassemblers show promise for efficiency and accuracy, they frequently generate outputs violating fundamental structural constraints, which significantly compromise their practical usability. To address this critical problem, we regularize the disassembly solution space by formalizing and applying key structural constraints based on post-dominance relations. This approach systematically detects widespread errors in existing neural disassemblers' outputs. These errors often originate from models' limited context modeling and instruction-level decoding that neglect global structural integrity. We introduce Tady, a novel neural disassembler featuring an improved model architecture and a dedicated post-processing algorithm, specifically engineered to address these deficiencies. Comprehensive evaluations on diverse binaries demonstrate that Tady effectively eliminates structural constraint violations and functions with high efficiency, while maintaining instruction-level accuracy.

Artificial intelligence has become a crucial tool for medical image analysis. As an advanced cerebral angiography technique, Digital Subtraction Angiography (DSA) poses a challenge where the radiation dose to humans is proportional to the image count. By reducing images and using AI interpolation instead, the radiation can be cut significantly. However, DSA images present more complex motion and structural features than natural scenes, making interpolation more challenging. We propose MoSt-DSA, the first work that uses deep learning for DSA frame interpolation. Unlike natural scene Video Frame Interpolation (VFI) methods that extract unclear or coarse-grained features, we devise a general module that models motion and structural context interactions between frames in an efficient full convolution manner by adjusting optimal context range and transforming contexts into linear functions. Benefiting from this, MoSt-DSA is also the first method that directly achieves any number of interpolations at any time steps with just one forward pass during both training and testing. We conduct extensive comparisons with 7 representative VFI models for interpolating 1 to 3 frames, MoSt-DSA demonstrates robust results across 470 DSA image sequences (each typically 152 images), with average SSIM over 0.93, average PSNR over 38 (standard deviations of less than 0.030 and 3.6, respectively), comprehensively achieving state-of-the-art performance in accuracy, speed, visual effect, and memory usage. Our code is available at https://github.com/ZyoungXu/MoSt-DSA.

Earth system models suffer from various structural and parametric errors in their representation of nonlinear, multi-scale processes, leading to uncertainties in their long-term projections. The effects of many of these errors (particularly those due to fast physics) can be quantified in short-term simulations, e.g., as differences between the predicted and observed states (analysis increments). With the increase in the availability of high-quality observations and simulations, learning nudging from these increments to correct model errors has become an active research area. However, most studies focus on using neural networks, which while powerful, are hard to interpret, are data-hungry, and poorly generalize out-of-distribution. Here, we show the capabilities of Model Error Discovery with Interpretability and Data Assimilation (MEDIDA), a general, data-efficient framework that uses sparsity-promoting equation-discovery techniques to learn model errors from analysis increments. Using two-layer quasi-geostrophic turbulence as the test case, MEDIDA is shown to successfully discover various linear and nonlinear structural/parametric errors when full observations are available. Discovery from spatially sparse observations is found to require highly accurate interpolation schemes. While NNs have shown success as interpolators in recent studies, here, they are found inadequate due to their inability to accurately represent small scales, a phenomenon known as spectral bias. We show that a general remedy, adding a random Fourier feature layer to the NN, resolves this issue enabling MEDIDA to successfully discover model errors from sparse observations. These promising results suggest that with further development, MEDIDA could be scaled up to models of the Earth system and real observations.

The local structure of V_{2}O_{3}, an archetypal strongly correlated electron system that displays a metal-insulator transition around 160 K, has been investigated via pair distribution function (PDF) analysis of neutron and x-ray total scattering data. The rhombohedral-to-monoclinic structural phase transition manifests as an abrupt change on all length scales in the observed PDF. No monoclinic distortions of the local structure are found above the transition, although coexisting regions of phase-separated rhombohedral and monoclinic symmetry are observed between 150 K and 160 K. This lack of structural fluctuations above the transition contrasts with the known presence of magnetic fluctuations in the high-temperature state, suggesting that the lattice degree of freedom plays a secondary role behind the spin degree of freedom in the transition mechanism.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

The Milky Way is known to contain a stellar bar, as are a significant fraction of disc galaxies across the universe. Our understanding of bar evolution, both theoretically and through analysis of simulations indicates that bars both grow in amplitude and slow down over time through interaction and angular momentum exchange with the galaxy's dark matter halo. Understanding the physical mechanisms underlying this coupling requires modelling of the structural deformations to the potential that are mutually induced between components. In this work we use Basis Function Expansion (BFE) in combination with multichannel Singular Spectral Analysis (mSSA) as a non-parametric analysis tool to illustrate the coupling between the bar and the dark halo in a single high-resolution isolated barred disc galaxy simulation. We demonstrate the power of mSSA to extract and quantify explicitly coupled dynamical modes, determining growth rates, pattern speeds and phase lags for different stages of evolution of the stellar bar and the dark matter response. BFE & mSSA together grant us the ability to explore the importance and physical mechanisms of bar-halo coupling, and other dynamically coupled structures across a wide range of dynamical environments.

Evaluating tabular generators remains a challenging problem, as the unique causal structural prior of heterogeneous tabular data does not lend itself to intuitive human inspection. Recent work has introduced structural fidelity as a tabular-specific evaluation dimension to assess whether synthetic data complies with the causal structures of real data. However, existing benchmarks often neglect the interplay between structural fidelity and conventional evaluation dimensions, thus failing to provide a holistic understanding of model performance. Moreover, they are typically limited to toy datasets, as quantifying existing structural fidelity metrics requires access to ground-truth causal structures, which are rarely available for real-world datasets. In this paper, we propose a novel evaluation framework that jointly considers structural fidelity and conventional evaluation dimensions. We introduce a new evaluation metric, global utility, which enables the assessment of structural fidelity even in the absence of ground-truth causal structures. In addition, we present TabStruct, a comprehensive evaluation benchmark offering large-scale quantitative analysis on 13 tabular generators from nine distinct categories, across 29 datasets. Our results demonstrate that global utility provides a task-independent, domain-agnostic lens for tabular generator performance. We release the TabStruct benchmark suite, including all datasets, evaluation pipelines, and raw results. Code is available at https://github.com/SilenceX12138/TabStruct.

Finite Element Analysis (FEA) is a powerful but computationally intensive method for simulating physical phenomena. Recent advancements in machine learning have led to surrogate models capable of accelerating FEA. Yet there are still limitations in developing surrogates of transient FEA models that can simultaneously predict the solutions for both nodes and elements with applicability on both the 2D and 3D domains. Motivated by this research gap, this study proposes DeepFEA, a deep learning-based framework that leverages a multilayer Convolutional Long Short-Term Memory (ConvLSTM) network branching into two parallel convolutional neural networks to predict the solutions for both nodes and elements of FEA models. The proposed network is optimized using a novel adaptive learning algorithm, called Node-Element Loss Optimization (NELO). NELO minimizes the error occurring at both branches of the network enabling the prediction of solutions for transient FEA simulations. The experimental evaluation of DeepFEA is performed on three datasets in the context of structural mechanics, generated to serve as publicly available reference datasets. The results show that DeepFEA can achieve less than 3% normalized mean and root mean squared error for 2D and 3D simulation scenarios, and inference times that are two orders of magnitude faster than FEA. In contrast, relevant state-of-the-art methods face challenges with multi-dimensional output and dynamic input prediction. Furthermore, DeepFEA's robustness was demonstrated in a real-life biomedical scenario, confirming its suitability for accurate and efficient predictions of FEA simulations.

Cross-lingual transfer-learning is widely used in Event Extraction for low-resource languages and involves a Multilingual Language Model that is trained in a source language and applied to the target language. This paper studies whether the typological similarity between source and target languages impacts the performance of cross-lingual transfer, an under-explored topic. We first focus on Basque as the target language, which is an ideal target language because it is typologically different from surrounding languages. Our experiments on three Event Extraction tasks show that the shared linguistic characteristic between source and target languages does have an impact on transfer quality. Further analysis of 72 language pairs reveals that for tasks that involve token classification such as entity and event trigger identification, common writing script and morphological features produce higher quality cross-lingual transfer. In contrast, for tasks involving structural prediction like argument extraction, common word order is the most relevant feature. In addition, we show that when increasing the training size, not all the languages scale in the same way in the cross-lingual setting. To perform the experiments we introduce EusIE, an event extraction dataset for Basque, which follows the Multilingual Event Extraction dataset (MEE). The dataset and code are publicly available.

Conventional music structure analysis algorithms aim to divide a song into segments and to group them with abstract labels (e.g., 'A', 'B', and 'C'). However, explicitly identifying the function of each segment (e.g., 'verse' or 'chorus') is rarely attempted, but has many applications. We introduce a multi-task deep learning framework to model these structural semantic labels directly from audio by estimating "verseness," "chorusness," and so forth, as a function of time. We propose a 7-class taxonomy (i.e., intro, verse, chorus, bridge, outro, instrumental, and silence) and provide rules to consolidate annotations from four disparate datasets. We also propose to use a spectral-temporal Transformer-based model, called SpecTNT, which can be trained with an additional connectionist temporal localization (CTL) loss. In cross-dataset evaluations using four public datasets, we demonstrate the effectiveness of the SpecTNT model and CTL loss, and obtain strong results overall: the proposed system outperforms state-of-the-art chorus-detection and boundary-detection methods at detecting choruses and boundaries, respectively.

Models of many engineering and natural systems are imperfect. The discrepancy between the mathematical representations of a true physical system and its imperfect model is called the model error. These model errors can lead to substantial differences between the numerical solutions of the model and the state of the system, particularly in those involving nonlinear, multi-scale phenomena. Thus, there is increasing interest in reducing model errors, particularly by leveraging the rapidly growing observational data to understand their physics and sources. Here, we introduce a framework named MEDIDA: Model Error Discovery with Interpretability and Data Assimilation. MEDIDA only requires a working numerical solver of the model and a small number of noise-free or noisy sporadic observations of the system. In MEDIDA, first the model error is estimated from differences between the observed states and model-predicted states (the latter are obtained from a number of one-time-step numerical integrations from the previous observed states). If observations are noisy, a data assimilation (DA) technique such as ensemble Kalman filter (EnKF) is employed to provide the analysis state of the system, which is then used to estimate the model error. Finally, an equation-discovery technique, here the relevance vector machine (RVM), a sparsity-promoting Bayesian method, is used to identify an interpretable, parsimonious, and closed-form representation of the model error. Using the chaotic Kuramoto-Sivashinsky (KS) system as the test case, we demonstrate the excellent performance of MEDIDA in discovering different types of structural/parametric model errors, representing different types of missing physics, using noise-free and noisy observations.

Human sciences have traditionally relied on human reasoning and intelligence to infer knowledge from a wide range of sources, such as oral and written narrations, reports, and traditions. Here we develop an extension of classical social network analysis approaches to incorporate the concept of meaning in each actor, as a mean to quantify and infer further knowledge from the original source of the network. This extension is based on a new affinity function, the semantic affinity, that establishes fuzzy-like relationships between the different actors in the network, using combinations of affinity functions. We also propose a new heuristic algorithm based on the shortest capacity problem to compute this affinity function. We use these concept of meaning and semantic affinity to analyze and compare the gods and heroes from three different classical mythologies: Greek, Celtic and Nordic. We study the relationships of each individual mythology and those of common structure that is formed when we fuse the three of them. We show a strong connection between the Celtic and Nordic gods and that Greeks put more emphasis on heroic characters rather than deities. Our approach provides a technique to highlight and quantify important relationships in the original domain of the network not deducible from its structural properties.

Dual-system VLA (Vision-Language-Action) architectures have become a hot topic in embodied intelligence research, but there is a lack of sufficient open-source work for further performance analysis and optimization. To address this problem, this paper will summarize and compare the structural designs of existing dual-system architectures, and conduct systematic empirical evaluations on the core design elements of existing dual-system architectures. Ultimately, it will provide a low-cost open-source model for further exploration. Of course, this project will continue to update with more experimental conclusions and open-source models with improved performance for everyone to choose from. Project page: https://openhelix-robot.github.io/.

Large language models (LLMs) have been widely adopted across diverse software engineering domains, such as code generation, program repair, and vulnerability detection. These applications require understanding beyond surface-level code patterns: value propagation, control flow, and interdependence between program elements. However, existing benchmarks primarily evaluate end-to-end outcomes, such as whether code is correctly repaired or generated, leaving the models ability for program semantic reasoning underexplored. This work presents CoRe, a high-quality, human-verified benchmark designed to evaluate LLMs on fundamental static analysis tasks. CoRe includes 12,553 task instances spanning data dependency, control dependency, and information flow across programs written in C/C++, Java, and Python. To ensure semantic diversity and reasoning complexity, we propose a semantics-aware diverse sampling strategy that selects targets and task instances based on structural coverage and dependency depth. We evaluate 10 mainstream LLMs and show that, while they perform well at identifying dependencies, models still struggle with tasks that require deeper semantic understanding and multi-step reasoning. We further conduct qualitative analyses to uncover key challenges, such as complex control structures and backward dependency patterns, offering insights into improving LLMs code reasoning capabilities.

Whole slide image (WSI) analysis has become increasingly important in the medical imaging community, enabling automated and objective diagnosis, prognosis, and therapeutic-response prediction. However, in clinical practice, the ever-evolving environment hamper the utility of WSI analysis models. In this paper, we propose the FIRST continual learning framework for WSI analysis, named ConSlide, to tackle the challenges of enormous image size, utilization of hierarchical structure, and catastrophic forgetting by progressive model updating on multiple sequential datasets. Our framework contains three key components. The Hierarchical Interaction Transformer (HIT) is proposed to model and utilize the hierarchical structural knowledge of WSI. The Breakup-Reorganize (BuRo) rehearsal method is developed for WSI data replay with efficient region storing buffer and WSI reorganizing operation. The asynchronous updating mechanism is devised to encourage the network to learn generic and specific knowledge respectively during the replay stage, based on a nested cross-scale similarity learning (CSSL) module. We evaluated the proposed ConSlide on four public WSI datasets from TCGA projects. It performs best over other state-of-the-art methods with a fair WSI-based continual learning setting and achieves a better trade-off of the overall performance and forgetting on previous task

Logs, being run-time information automatically generated by software, record system events and activities with their timestamps. Before obtaining more insights into the run-time status of the software, a fundamental step of log analysis, called log parsing, is employed to extract structured templates and parameters from the semi-structured raw log messages. However, current log parsers are all syntax-based and regard each message as a character string, ignoring the semantic information included in parameters and templates. Thus, we propose the semantic-based parser SemParser to unlock the critical bottleneck of mining semantics from log messages. It contains two steps, an end-to-end semantic miner and a joint parser. Specifically, the first step aims to identify explicit semantics inside a single log, and the second step is responsible for jointly inferring implicit semantics and computing structural outputs based on the contextual knowledge base. To analyze the effectiveness of our semantic parser, we first demonstrate that it can derive rich semantics from log messages collected from six widely-applied systems with an average F1 score of 0.985. Then, we conduct two representative downstream tasks, showing that current downstream models improve their performance with appropriately extracted semantics by 1.2%-11.7% and 8.65% on two anomaly detection datasets and a failure identification dataset, respectively. We believe these findings provide insights into semantically understanding log messages for the log analysis community.

One billion people live in informal settlements worldwide. The complex and multilayered spaces that characterize this unplanned form of urbanization pose a challenge to traditional approaches to mapping and morphological analysis. This study proposes a methodology to study the morphological properties of informal settlements based on terrestrial LiDAR (Light Detection and Ranging) data collected in Rocinha, the largest favela in Rio de Janeiro, Brazil. Our analysis operates at two resolutions, including a global analysis focused on comparing different streets of the favela to one another, and a local analysis unpacking the variation of morphological metrics within streets. We show that our methodology reveals meaningful differences and commonalities both in terms of the global morphological characteristics across streets and their local distributions. Finally, we create morphological maps at high spatial resolution from LiDAR data, which can inform urban planning assessments of concerns related to crowding, structural safety, air quality, and accessibility in the favela. The methods for this study are automated and can be easily scaled to analyze entire informal settlements, leveraging the increasing availability of inexpensive LiDAR scanners on portable devices such as cellphones.

Task-oriented dialogue systems often face difficulties when user utterances seem semantically complete but lack necessary structural information for appropriate system action. This arises because users frequently do not fully understand their own needs, while systems require precise intent definitions. Current LLM-based agents cannot effectively distinguish between linguistically complete and contextually triggerable expressions, lacking frameworks for collaborative intent formation. We present STORM, a framework modeling asymmetric information dynamics through conversations between UserLLM (full internal access) and AgentLLM (observable behavior only). STORM produces annotated corpora capturing expression trajectories and latent cognitive transitions, enabling systematic analysis of collaborative understanding development. Our contributions include: (1) formalizing asymmetric information processing in dialogue systems; (2) modeling intent formation tracking collaborative understanding evolution; and (3) evaluation metrics measuring internal cognitive improvements alongside task performance. Experiments across four language models reveal that moderate uncertainty (40-60%) can outperform complete transparency in certain scenarios, with model-specific patterns suggesting reconsideration of optimal information completeness in human-AI collaboration. These findings contribute to understanding asymmetric reasoning dynamics and inform uncertainty-calibrated dialogue system design.

Instruction-tuned Large Language Models (It-LLMs) have been exhibiting outstanding abilities to reason around cognitive states, intentions, and reactions of all people involved, letting humans guide and comprehend day-to-day social interactions effectively. In fact, several multiple-choice questions (MCQ) benchmarks have been proposed to construct solid assessments of the models' abilities. However, earlier works are demonstrating the presence of inherent "order bias" in It-LLMs, posing challenges to the appropriate evaluation. In this paper, we investigate It-LLMs' resilience abilities towards a series of probing tests using four MCQ benchmarks. Introducing adversarial examples, we show a significant performance gap, mainly when varying the order of the choices, which reveals a selection bias and brings into discussion reasoning abilities. Following a correlation between first positions and model choices due to positional bias, we hypothesized the presence of structural heuristics in the decision-making process of the It-LLMs, strengthened by including significant examples in few-shot scenarios. Finally, by using the Chain-of-Thought (CoT) technique, we elicit the model to reason and mitigate the bias by obtaining more robust models.

While recent text-to-image (T2I) models show impressive capabilities in synthesizing images from brief descriptions, their performance significantly degrades when confronted with long, detail-intensive prompts required in professional applications. We present DetailMaster, the first comprehensive benchmark specifically designed to evaluate T2I models' systematical abilities to handle extended textual inputs that contain complex compositional requirements. Our benchmark introduces four critical evaluation dimensions: Character Attributes, Structured Character Locations, Multi-Dimensional Scene Attributes, and Explicit Spatial/Interactive Relationships. The benchmark comprises long and detail-rich prompts averaging 284.89 tokens, with high quality validated by expert annotators. Evaluation on 7 general-purpose and 5 long-prompt-optimized T2I models reveals critical performance limitations: state-of-the-art models achieve merely ~50% accuracy in key dimensions like attribute binding and spatial reasoning, while all models showing progressive performance degradation as prompt length increases. Our analysis highlights systemic failures in structural comprehension and detail overload handling, motivating future research into architectures with enhanced compositional reasoning. We open-source the dataset, data curation code, and evaluation tools to advance detail-rich T2I generation and enable broad applications that would otherwise be infeasible due to the lack of a dedicated benchmark.

Agentic coding tools receive goals written in natural language as input, break them down into specific tasks, and write/execute the actual code with minimal human intervention. Key to this process are agent manifests, configuration files (such as Claude.md) that provide agents with essential project context, identity, and operational rules. However, the lack of comprehensive and accessible documentation for creating these manifests presents a significant challenge for developers. We analyzed 253 Claude.md files from 242 repositories to identify structural patterns and common content. Our findings show that manifests typically have shallow hierarchies with one main heading and several subsections, with content dominated by operational commands, technical implementation notes, and high-level architecture.

Relational databases (RDBs) are composed of interconnected tables, where relationships between them are defined through foreign keys. Recent research on applying machine learning to RDBs has explored graph-based representations of RDBs, where rows of tables are modeled as nodes, and foreign key relationships are modeled as edges. RDB-to-graph modeling helps capture cross-table dependencies, ultimately leading to enhanced performance across diverse tasks. However, there are numerous ways to model RDBs as graphs, and performance varies significantly depending on the chosen graph model. In our analysis, applying a common heuristic rule for graph modeling leads to up to a 10% drop in performance compared to the best-performing graph model, which remains non-trivial to identify. To foster research on intelligent RDB-to-graph modeling, we introduce RDB2G-Bench, the first benchmark framework for evaluating such methods. We construct extensive datasets covering 5 real-world RDBs and 12 predictive tasks, resulting in around 50k graph-performance pairs for efficient and reproducible evaluations. Thanks to our precomputed datasets, we were able to benchmark 9 automatic RDB-to-graph modeling methods on the 12 tasks over 600x faster than on-the-fly evaluation, which requires repeated model training. Our analysis of the datasets and benchmark results reveals key structural patterns affecting graph model effectiveness, along with practical implications for effective graph modeling.

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

Demand for 2K video synthesis is rising with increasing consumer expectations for ultra-clear visuals. While diffusion transformers (DiTs) have demonstrated remarkable capabilities in high-quality video generation, scaling them to 2K resolution remains computationally prohibitive due to quadratic growth in memory and processing costs. In this work, we propose Turbo2K, an efficient and practical framework for generating detail-rich 2K videos while significantly improving training and inference efficiency. First, Turbo2K operates in a highly compressed latent space, reducing computational complexity and memory footprint, making high-resolution video synthesis feasible. However, the high compression ratio of the VAE and limited model size impose constraints on generative quality. To mitigate this, we introduce a knowledge distillation strategy that enables a smaller student model to inherit the generative capacity of a larger, more powerful teacher model. Our analysis reveals that, despite differences in latent spaces and architectures, DiTs exhibit structural similarities in their internal representations, facilitating effective knowledge transfer. Second, we design a hierarchical two-stage synthesis framework that first generates multi-level feature at lower resolutions before guiding high-resolution video generation. This approach ensures structural coherence and fine-grained detail refinement while eliminating redundant encoding-decoding overhead, further enhancing computational efficiency.Turbo2K achieves state-of-the-art efficiency, generating 5-second, 24fps, 2K videos with significantly reduced computational cost. Compared to existing methods, Turbo2K is up to 20times faster for inference, making high-resolution video generation more scalable and practical for real-world applications.

Diffusion models excel at generating high-dimensional data but fall short in training efficiency and representation quality compared to self-supervised methods. We identify a key bottleneck: the underutilization of high-quality, semantically rich representations during training notably slows down convergence. Our systematic analysis reveals a critical representation processing region -- primarily in the early layers -- where semantic and structural pattern learning takes place before generation can occur. To address this, we propose Embedded Representation Warmup (ERW), a plug-and-play framework where in the first stage we get the ERW module serves as a warmup that initializes the early layers of the diffusion model with high-quality, pretrained representations. This warmup minimizes the burden of learning representations from scratch, thereby accelerating convergence and boosting performance. Our theoretical analysis demonstrates that ERW's efficacy depends on its precise integration into specific neural network layers -- termed the representation processing region -- where the model primarily processes and transforms feature representations for later generation. We further establish that ERW not only accelerates training convergence but also enhances representation quality: empirically, our method achieves a 40times acceleration in training speed compared to REPA, the current state-of-the-art methods. Code is available at https://github.com/LINs-lab/ERW.

Molecule generation with desired properties has grown immensely in popularity by disruptively changing the way scientists design molecular structures and providing support for chemical and materials design. However, despite the promising outcome, previous machine learning-based deep generative models suffer from a reliance on complex, task-specific fine-tuning, limited dimensional latent spaces, or the quality of expert rules. In this work, we propose MolGen, a pre-trained molecular language model that effectively learns and shares knowledge across multiple generation tasks and domains. Specifically, we pre-train MolGen with the chemical language SELFIES on more than 100 million unlabelled molecules. We further propose multi-task molecular prefix tuning across several molecular generation tasks and different molecular domains (synthetic & natural products) with a self-feedback mechanism. Extensive experiments show that MolGen can obtain superior performances on well-known molecular generation benchmark datasets. The further analysis illustrates that MolGen can accurately capture the distribution of molecules, implicitly learn their structural characteristics, and efficiently explore the chemical space with the guidance of multi-task molecular prefix tuning. Codes, datasets, and the pre-trained model will be available in https://github.com/zjunlp/MolGen.

Despite extensive safety enhancements in large language models (LLMs), multi-turn "jailbreak" conversations crafted by skilled human adversaries can still breach even the most sophisticated guardrails. However, these multi-turn attacks demand considerable manual effort, limiting their scalability. In this work, we introduce a novel approach called Multi-turn-to-Single-turn (M2S) that systematically converts multi-turn jailbreak prompts into single-turn attacks. Specifically, we propose three conversion strategies - Hyphenize, Numberize, and Pythonize - each preserving sequential context yet packaging it in a single query. Our experiments on the Multi-turn Human Jailbreak (MHJ) dataset show that M2S often increases or maintains high Attack Success Rates (ASRs) compared to original multi-turn conversations. Notably, using a StrongREJECT-based evaluation of harmfulness, M2S achieves up to 95.9% ASR on Mistral-7B and outperforms original multi-turn prompts by as much as 17.5% in absolute improvement on GPT-4o. Further analysis reveals that certain adversarial tactics, when consolidated into a single prompt, exploit structural formatting cues to evade standard policy checks. These findings underscore that single-turn attacks - despite being simpler and cheaper to conduct - can be just as potent, if not more, than their multi-turn counterparts. Our findings underscore the urgent need to reevaluate and reinforce LLM safety strategies, given how adversarial queries can be compacted into a single prompt while still retaining sufficient complexity to bypass existing safety measures.

Improving the reasoning capabilities of large language models (LLMs) typically requires supervised fine-tuning with labeled data or computationally expensive sampling. We introduce Unsupervised Prefix Fine-Tuning (UPFT), which leverages the observation of Prefix Self-Consistency -- the shared initial reasoning steps across diverse solution trajectories -- to enhance LLM reasoning efficiency. By training exclusively on the initial prefix substrings (as few as 8 tokens), UPFT removes the need for labeled data or exhaustive sampling. Experiments on reasoning benchmarks show that UPFT matches the performance of supervised methods such as Rejection Sampling Fine-Tuning, while reducing training time by 75% and sampling cost by 99%. Further analysis reveals that errors tend to appear in later stages of the reasoning process and that prefix-based training preserves the model's structural knowledge. This work demonstrates how minimal unsupervised fine-tuning can unlock substantial reasoning gains in LLMs, offering a scalable and resource-efficient alternative to conventional approaches.

This paper investigates a novel lossy compression framework operating under logarithmic loss, designed to handle situations where the reconstruction distribution diverges from the source distribution. This framework is especially relevant for applications that require joint compression and retrieval, and in scenarios involving distributional shifts due to processing. We show that the proposed formulation extends the classical minimum entropy coupling framework by integrating a bottleneck, allowing for a controlled degree of stochasticity in the coupling. We explore the decomposition of the Minimum Entropy Coupling with Bottleneck (MEC-B) into two distinct optimization problems: Entropy-Bounded Information Maximization (EBIM) for the encoder, and Minimum Entropy Coupling (MEC) for the decoder. Through extensive analysis, we provide a greedy algorithm for EBIM with guaranteed performance, and characterize the optimal solution near functional mappings, yielding significant theoretical insights into the structural complexity of this problem. Furthermore, we illustrate the practical application of MEC-B through experiments in Markov Coding Games (MCGs) under rate limits. These games simulate a communication scenario within a Markov Decision Process, where an agent must transmit a compressed message from a sender to a receiver through its actions. Our experiments highlight the trade-offs between MDP rewards and receiver accuracy across various compression rates, showcasing the efficacy of our method compared to conventional compression baseline.

Document layout analysis is a critical preprocessing step in document intelligence, enabling the detection and localization of structural elements such as titles, text blocks, tables, and formulas. Despite its importance, existing layout detection models face significant challenges in generalizing across diverse document types, handling complex layouts, and achieving real-time performance for large-scale data processing. To address these limitations, we present PP-DocLayout, which achieves high precision and efficiency in recognizing 23 types of layout regions across diverse document formats. To meet different needs, we offer three models of varying scales. PP-DocLayout-L is a high-precision model based on the RT-DETR-L detector, achieving 90.4% [email protected] and an end-to-end inference time of 13.4 ms per page on a T4 GPU. PP-DocLayout-M is a balanced model, offering 75.2% [email protected] with an inference time of 12.7 ms per page on a T4 GPU. PP-DocLayout-S is a high-efficiency model designed for resource-constrained environments and real-time applications, with an inference time of 8.1 ms per page on a T4 GPU and 14.5 ms on a CPU. This work not only advances the state of the art in document layout analysis but also provides a robust solution for constructing high-quality training data, enabling advancements in document intelligence and multimodal AI systems. Code and models are available at https://github.com/PaddlePaddle/PaddleX .

We present two new classes of algorithms for efficient field integration on graphs encoding point clouds. The first class, SeparatorFactorization(SF), leverages the bounded genus of point cloud mesh graphs, while the second class, RFDiffusion(RFD), uses popular epsilon-nearest-neighbor graph representations for point clouds. Both can be viewed as providing the functionality of Fast Multipole Methods (FMMs), which have had a tremendous impact on efficient integration, but for non-Euclidean spaces. We focus on geometries induced by distributions of walk lengths between points (e.g., shortest-path distance). We provide an extensive theoretical analysis of our algorithms, obtaining new results in structural graph theory as a byproduct. We also perform exhaustive empirical evaluation, including on-surface interpolation for rigid and deformable objects (particularly for mesh-dynamics modeling), Wasserstein distance computations for point clouds, and the Gromov-Wasserstein variant.

In the deep learning (DL) era, parsing models are extremely simplified with little hurt on performance, thanks to the remarkable capability of multi-layer BiLSTMs in context representation. As the most popular graph-based dependency parser due to its high efficiency and performance, the biaffine parser directly scores single dependencies under the arc-factorization assumption, and adopts a very simple local token-wise cross-entropy training loss. This paper for the first time presents a second-order TreeCRF extension to the biaffine parser. For a long time, the complexity and inefficiency of the inside-outside algorithm hinder the popularity of TreeCRF. To address this issue, we propose an effective way to batchify the inside and Viterbi algorithms for direct large matrix operation on GPUs, and to avoid the complex outside algorithm via efficient back-propagation. Experiments and analysis on 27 datasets from 13 languages clearly show that techniques developed before the DL era, such as structural learning (global TreeCRF loss) and high-order modeling are still useful, and can further boost parsing performance over the state-of-the-art biaffine parser, especially for partially annotated training data. We release our code at https://github.com/yzhangcs/crfpar.

Recent advancements in large language models (LLMs) have demonstrated promising capabilities in code generation tasks. However, most existing benchmarks focus on isolated functions and fail to capture the complexity of real-world, class-level software structures. To address this gap, we introduce a large-scale, Python class-level dataset curated from 13{,}174 real-world open-source projects. The dataset contains over 842,000 class skeletons, each including class and method signatures, along with associated docstrings when available. We preserve structural and contextual dependencies critical to realistic software development scenarios and enrich the dataset with static code metrics to support downstream analysis. To evaluate the usefulness of this dataset, we use extracted class skeletons as prompts for GPT-4 to generate full class implementations. Results show that the LLM-generated classes exhibit strong lexical and structural similarity to human-written counterparts, with average ROUGE@L, BLEU, and TSED scores of 0.80, 0.59, and 0.73, respectively. These findings confirm that well-structured prompts derived from real-world class skeletons significantly enhance LLM performance in class-level code generation. This dataset offers a valuable resource for benchmarking, training, and improving LLMs in realistic software engineering contexts.

Reasoning large language models (RLLMs) have recently demonstrated remarkable capabilities through structured and multi-step reasoning. While prior research has primarily focused on improving their training and inference strategies, their potential for in-context learning (ICL) remains largely underexplored. To fill this gap, we propose Thinking with Nothinking Calibration (JointThinking), a new ICL paradigm that leverages the structured difference between two reasoning modes, i.e., Thinking and Nothinking, to improve reasoning accuracy. Specifically, our method prompts the model to generate two answers in parallel: one in Thinking mode and the other in Nothinking mode. A second round of Thinking is triggered only when the two initial responses are inconsistent, using a single prompt that incorporates the original question and both candidate answers. Since such disagreement occurs infrequently (e.g., only 6\% in GSM8K), our method performs just one round of reasoning in most cases, resulting in minimal latency overhead. Extensive experiments across multiple reasoning benchmarks demonstrate that JointThinking significantly outperforms few-shot chain-of-thought (CoT) and majority voting with improved answer robustness. Moreover, It achieves comparable in-distribution performance to training-based SOTA method, while substantially outperforming on out-of-distribution tasks. We further conduct a systematic analysis of the calibration mechanism, showing that leveraging different reasoning modes consistently lowers the error rate and highlights the value of structural thinking diversity. Additionally, we observe that the performance gap between actual and ideal reasoning narrows as model size increases in the second round of thinking, indicating the strong scalability of our approach. Finally, we discuss current limitations and outline promising directions for future ICL research in RLLMs.

Large language model (LLM) based knowledge graph completion (KGC) aims to predict the missing triples in the KGs with LLMs and enrich the KGs to become better web infrastructure, which can benefit a lot of web-based automatic services. However, research about LLM-based KGC is limited and lacks effective utilization of LLM's inference capabilities, which ignores the important structural information in KGs and prevents LLMs from acquiring accurate factual knowledge. In this paper, we discuss how to incorporate the helpful KG structural information into the LLMs, aiming to achieve structrual-aware reasoning in the LLMs. We first transfer the existing LLM paradigms to structural-aware settings and further propose a knowledge prefix adapter (KoPA) to fulfill this stated goal. KoPA employs structural embedding pre-training to capture the structural information of entities and relations in the KG. Then KoPA informs the LLMs of the knowledge prefix adapter which projects the structural embeddings into the textual space and obtains virtual knowledge tokens as a prefix of the input prompt. We conduct comprehensive experiments on these structural-aware LLM-based KGC methods and provide an in-depth analysis comparing how the introduction of structural information would be better for LLM's knowledge reasoning ability. Our code is released at https://github.com/zjukg/KoPA.

Text-attributed graphs are widely used across domains, offering rich opportunities for zero-shot learning via graph-text alignment. However, existing methods struggle with tasks requiring fine-grained pattern recognition, particularly on heterophilic graphs. Through empirical and theoretical analysis, we identify an over-abstraction problem: current approaches operate at excessively large hyperbolic radii, compressing multi-scale structural information into uniform high-level abstractions. This abstraction-induced information loss obscures critical local patterns essential for accurate predictions. By analyzing embeddings in hyperbolic space, we demonstrate that optimal graph learning requires faithful preservation of fine-grained structural details, better retained by representations positioned closer to the origin. To address this, we propose H4G, a framework that systematically reduces embedding radii using learnable block-diagonal scaling matrices and M\"obius matrix multiplication. This approach restores access to fine-grained patterns while maintaining global receptive ability with minimal computational overhead. Experiments show H4G achieves state-of-the-art zero-shot performance with 12.8\% improvement on heterophilic graphs and 8.4\% on homophilic graphs, confirming that radius reduction enables faithful multi-scale representation for advancing zero-shot graph learning.

As opposed to scaling-up protein language models (PLMs), we seek improving performance via protein-specific optimization. Although the proportionality between the language model size and the richness of its learned representations is validated, we prioritize accessibility and pursue a path of data-efficient, cost-reduced, and knowledge-guided optimization. Through over twenty experiments ranging from masking, architecture, and pre-training data, we derive insights from protein-specific experimentation into building a model that interprets the language of life, optimally. We present Ankh, the first general-purpose PLM trained on Google's TPU-v4 surpassing the state-of-the-art performance with fewer parameters (<10% for pre-training, <7% for inference, and <30% for the embedding dimension). We provide a representative range of structure and function benchmarks where Ankh excels. We further provide a protein variant generation analysis on High-N and One-N input data scales where Ankh succeeds in learning protein evolutionary conservation-mutation trends and introducing functional diversity while retaining key structural-functional characteristics. We dedicate our work to promoting accessibility to research innovation via attainable resources.

As there are now millions of publicly available neural networks, searching and analyzing large model repositories becomes increasingly important. Navigating so many models requires an atlas, but as most models are poorly documented charting such an atlas is challenging. To explore the hidden potential of model repositories, we chart a preliminary atlas representing the documented fraction of Hugging Face. It provides stunning visualizations of the model landscape and evolution. We demonstrate several applications of this atlas including predicting model attributes (e.g., accuracy), and analyzing trends in computer vision models. However, as the current atlas remains incomplete, we propose a method for charting undocumented regions. Specifically, we identify high-confidence structural priors based on dominant real-world model training practices. Leveraging these priors, our approach enables accurate mapping of previously undocumented areas of the atlas. We publicly release our datasets, code, and interactive atlas.

Recurrent Neural Networks (RNNs), and specifically a variant with Long Short-Term Memory (LSTM), are enjoying renewed interest as a result of successful applications in a wide range of machine learning problems that involve sequential data. However, while LSTMs provide exceptional results in practice, the source of their performance and their limitations remain rather poorly understood. Using character-level language models as an interpretable testbed, we aim to bridge this gap by providing an analysis of their representations, predictions and error types. In particular, our experiments reveal the existence of interpretable cells that keep track of long-range dependencies such as line lengths, quotes and brackets. Moreover, our comparative analysis with finite horizon n-gram models traces the source of the LSTM improvements to long-range structural dependencies. Finally, we provide analysis of the remaining errors and suggests areas for further study.

Global dependency modeling and spatial position modeling are two core issues of the foundational architecture design in current deep learning frameworks. Recently, Vision Transformers (ViTs) have achieved remarkable success in computer vision, leveraging the powerful global dependency modeling capability of the self-attention mechanism. Furthermore, Mamba2 has demonstrated its significant potential in natural language processing tasks by explicitly modeling the spatial adjacency prior through the structured mask. In this paper, we propose Polyline Path Masked Attention (PPMA) that integrates the self-attention mechanism of ViTs with an enhanced structured mask of Mamba2, harnessing the complementary strengths of both architectures. Specifically, we first ameliorate the traditional structured mask of Mamba2 by introducing a 2D polyline path scanning strategy and derive its corresponding structured mask, polyline path mask, which better preserves the adjacency relationships among image tokens. Notably, we conduct a thorough theoretical analysis on the structural characteristics of the proposed polyline path mask and design an efficient algorithm for the computation of the polyline path mask. Next, we embed the polyline path mask into the self-attention mechanism of ViTs, enabling explicit modeling of spatial adjacency prior. Extensive experiments on standard benchmarks, including image classification, object detection, and segmentation, demonstrate that our model outperforms previous state-of-the-art approaches based on both state-space models and Transformers. For example, our proposed PPMA-T/S/B models achieve 48.7%/51.1%/52.3% mIoU on the ADE20K semantic segmentation task, surpassing RMT-T/S/B by 0.7%/1.3%/0.3%, respectively. Code is available at https://github.com/zhongchenzhao/PPMA.

In an industrial group like Safran, numerical simulations of physical phenomena are integral to most design processes. At Safran's corporate research center, we enhance these processes by developing fast and reliable surrogate models for various physics. We focus here on two technologies developed in recent years. The first is a physical reduced-order modeling method for non-linear structural mechanics and thermal analysis, used for calculating the lifespan of high-pressure turbine blades and performing heat analysis of high-pressure compressors. The second technology involves learning physics simulations with non-parameterized geometrical variability using classical machine learning tools, such as Gaussian process regression. Finally, we present our contributions to the open-source and open-data community.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

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/.

We introduce MinerU2.5, a 1.2B-parameter document parsing vision-language model that achieves state-of-the-art recognition accuracy while maintaining exceptional computational efficiency. Our approach employs a coarse-to-fine, two-stage parsing strategy that decouples global layout analysis from local content recognition. In the first stage, the model performs efficient layout analysis on downsampled images to identify structural elements, circumventing the computational overhead of processing high-resolution inputs. In the second stage, guided by the global layout, it performs targeted content recognition on native-resolution crops extracted from the original image, preserving fine-grained details in dense text, complex formulas, and tables. To support this strategy, we developed a comprehensive data engine that generates diverse, large-scale training corpora for both pretraining and fine-tuning. Ultimately, MinerU2.5 demonstrates strong document parsing ability, achieving state-of-the-art performance on multiple benchmarks, surpassing both general-purpose and domain-specific models across various recognition tasks, while maintaining significantly lower computational overhead.

Graph neural networks (GNNs) have brought superb performance to various applications utilizing graph structural data, such as social analysis and fraud detection. The graph links, e.g., social relationships and transaction history, are sensitive and valuable information, which raises privacy concerns when using GNNs. To exploit these vulnerabilities, we propose VertexSerum, a novel graph poisoning attack that increases the effectiveness of graph link stealing by amplifying the link connectivity leakage. To infer node adjacency more accurately, we propose an attention mechanism that can be embedded into the link detection network. Our experiments demonstrate that VertexSerum significantly outperforms the SOTA link inference attack, improving the AUC scores by an average of 9.8% across four real-world datasets and three different GNN structures. Furthermore, our experiments reveal the effectiveness of VertexSerum in both black-box and online learning settings, further validating its applicability in real-world scenarios.

Generating professional financial reports is a labor-intensive and intellectually demanding process that current AI systems struggle to fully automate. To address this challenge, we introduce FinSight (Financial InSight), a novel multi agent framework for producing high-quality, multimodal financial reports. The foundation of FinSight is the Code Agent with Variable Memory (CAVM) architecture, which unifies external data, designed tools, and agents into a programmable variable space, enabling flexible data collection, analysis and report generation through executable code. To ensure professional-grade visualization, we propose an Iterative Vision-Enhanced Mechanism that progressively refines raw visual outputs into polished financial charts. Furthermore, a two stage Writing Framework expands concise Chain-of-Analysis segments into coherent, citation-aware, and multimodal reports, ensuring both analytical depth and structural consistency. Experiments on various company and industry-level tasks demonstrate that FinSight significantly outperforms all baselines, including leading deep research systems in terms of factual accuracy, analytical depth, and presentation quality, demonstrating a clear path toward generating reports that approach human-expert quality.

Large Language Models (LLMs) have shown to be capable of various tasks, yet their capability in interpreting and reasoning over tabular data remains an underexplored area. In this context, this study investigates from three core perspectives: the robustness of LLMs to structural perturbations in tables, the comparative analysis of textual and symbolic reasoning on tables, and the potential of boosting model performance through the aggregation of multiple reasoning pathways. We discover that structural variance of tables presenting the same content reveals a notable performance decline, particularly in symbolic reasoning tasks. This prompts the proposal of a method for table structure normalization. Moreover, textual reasoning slightly edges out symbolic reasoning, and a detailed error analysis reveals that each exhibits different strengths depending on the specific tasks. Notably, the aggregation of textual and symbolic reasoning pathways, bolstered by a mix self-consistency mechanism, resulted in achieving SOTA performance, with an accuracy of 73.6% on WIKITABLEQUESTIONS, representing a substantial advancement over previous existing table processing paradigms of LLMs.

The rapid growth of scientific literature demands robust tools for automated survey-generation. However, current large language model (LLM)-based methods often lack in-depth analysis, structural coherence, and reliable citations. To address these limitations, we introduce SciSage, a multi-agent framework employing a reflect-when-you-write paradigm. SciSage features a hierarchical Reflector agent that critically evaluates drafts at outline, section, and document levels, collaborating with specialized agents for query interpretation, content retrieval, and refinement. We also release SurveyScope, a rigorously curated benchmark of 46 high-impact papers (2020-2025) across 11 computer science domains, with strict recency and citation-based quality controls. Evaluations demonstrate that SciSage outperforms state-of-the-art baselines (LLM x MapReduce-V2, AutoSurvey), achieving +1.73 points in document coherence and +32% in citation F1 scores. Human evaluations reveal mixed outcomes (3 wins vs. 7 losses against human-written surveys), but highlight SciSage's strengths in topical breadth and retrieval efficiency. Overall, SciSage offers a promising foundation for research-assistive writing tools.

"Sure, I am happy to generate a story for you: Captain Lyra stood at the helm of her trusty ship, the Maelstrom's Fury, gazing out at the endless sea. [...] Lyra's eyes welled up with tears as she realized the bitter truth - she had sacrificed everything for fleeting riches, and lost the love of her crew, her family, and herself." Although this story, generated by a large language model, is captivating, one may wonder -- how would the story have unfolded if the model had chosen "Captain Maeve" as the protagonist instead? We cannot know. State-of-the-art large language models are stateless -- they maintain no internal memory or state. Given a prompt, they generate a sequence of tokens as an output using an autoregressive process. As a consequence, they cannot reason about counterfactual alternatives to tokens they have generated in the past. In this work, our goal is to enhance them with this functionality. To this end, we develop a causal model of token generation that builds upon the Gumbel-Max structural causal model. Our model allows any large language model to perform counterfactual token generation at almost no cost in comparison with vanilla token generation, it is embarrassingly simple to implement, and it does not require any fine-tuning nor prompt engineering. We implement our model on Llama 3 8B-Instruct and Ministral-8B-Instruct and conduct a qualitative and a quantitative analysis of counterfactually generated text. We conclude with a demonstrative application of counterfactual token generation for bias detection, unveiling interesting insights about the model of the world constructed by large language models.

Designing de novo proteins beyond those found in nature holds significant promise for advancements in both scientific and engineering applications. Current methodologies for protein design often rely on AI-based models, such as surrogate models that address end-to-end problems by linking protein structure to material properties or vice versa. However, these models frequently focus on specific material objectives or structural properties, limiting their flexibility when incorporating out-of-domain knowledge into the design process or comprehensive data analysis is required. In this study, we introduce ProtAgents, a platform for de novo protein design based on Large Language Models (LLMs), where multiple AI agents with distinct capabilities collaboratively address complex tasks within a dynamic environment. The versatility in agent development allows for expertise in diverse domains, including knowledge retrieval, protein structure analysis, physics-based simulations, and results analysis. The dynamic collaboration between agents, empowered by LLMs, provides a versatile approach to tackling protein design and analysis problems, as demonstrated through diverse examples in this study. The problems of interest encompass designing new proteins, analyzing protein structures and obtaining new first-principles data -- natural vibrational frequencies -- via physics simulations. The concerted effort of the system allows for powerful automated and synergistic design of de novo proteins with targeted mechanical properties. The flexibility in designing the agents, on one hand, and their capacity in autonomous collaboration through the dynamic LLM-based multi-agent environment on the other hand, unleashes great potentials of LLMs in addressing multi-objective materials problems and opens up new avenues for autonomous materials discovery and design.

Anomaly detection is valuable for real-world applications, such as industrial quality inspection. However, most approaches focus on detecting local structural anomalies while neglecting compositional anomalies incorporating logical constraints. In this paper, we introduce LogSAD, a novel multi-modal framework that requires no training for both Logical and Structural Anomaly Detection. First, we propose a match-of-thought architecture that employs advanced large multi-modal models (i.e. GPT-4V) to generate matching proposals, formulating interests and compositional rules of thought for anomaly detection. Second, we elaborate on multi-granularity anomaly detection, consisting of patch tokens, sets of interests, and composition matching with vision and language foundation models. Subsequently, we present a calibration module to align anomaly scores from different detectors, followed by integration strategies for the final decision. Consequently, our approach addresses both logical and structural anomaly detection within a unified framework and achieves state-of-the-art results without the need for training, even when compared to supervised approaches, highlighting its robustness and effectiveness. Code is available at https://github.com/zhang0jhon/LogSAD.

Large language models (LLMs) have achieved remarkable success across various domains, driving significant technological advancements and innovations. Despite the rapid growth in model scale and capability, systematic, data-driven research on how structural configurations affect performance remains scarce. To address this gap, we present a large-scale dataset encompassing diverse open-source LLM structures and their performance across multiple benchmarks. Leveraging this dataset, we conduct a systematic, data mining-driven analysis to validate and quantify the relationship between structural configurations and performance. Our study begins with a review of the historical development of LLMs and an exploration of potential future trends. We then analyze how various structural choices impact performance across benchmarks and further corroborate our findings using mechanistic interpretability techniques. By providing data-driven insights into LLM optimization, our work aims to guide the targeted development and application of future models. We will release our dataset at https://huggingface.co/datasets/DX0369/LLM-Structure-Performance-Dataset

We introduce the MultiLang Code Parser Dataset (MLCPD), a large-scale, language-agnostic dataset unifying syntactic and structural representations of code across ten major programming languages. MLCPD contains over seven million parsed source files normalized under our proposed universal Abstract Syntax Tree (AST) schema, enabling consistent cross-language reasoning, structural learning, and multilingual software analysis. Unlike existing corpora that focus purely on token-level code or isolated parsers, MLCPD provides both hierarchical tree representations and rich metadata for every file, ensuring lossless syntactic coverage and structural uniformity. Each entry includes a normalized schema, language-level metadata, and abstracted node semantics stored in Parquet format for scalable retrieval. Empirical analyses reveal strong cross-language structural regularities-demonstrating that syntactic graphs from languages as diverse as Python, Java, and Go can be aligned under a shared schema. We release the dataset publicly on Hugging Face and the accompanying codebase on GitHub, which includes complete pipelines for dataset reproduction, grammar compilation, and a visualization tool for exploring the unified AST across languages. Together, these resources establish MLCPD as an open, reproducible foundation for future research in cross-language representation learning and program analysis.

Using an evolutionary algorithm in combination with first-principles density functional theory calculations, we identify two-dimensional (2D) CaP_3 monolayer as a new Dirac semimetal due to inversion and nonsymmorphic spatial symmetries of the structure. This new topological material, composed of light elements, exhibits high structural stability (higher than the phase known in the literature), which is confirmed by thermodynamic and kinetic stability analysis. Moreover, it satisfies the electron filling criteria, so that its Dirac state is located near the Fermi level. The existence of the Dirac state predicted by the theoretical symmetry analysis is also confirmed by first-principles electronic band structure calculations. We find that the energy position of the Dirac state can be tuned by strain, while the Dirac state is unstable against an external electric field since it breaks the spatial inversion symmetry. Our findings should be instrumental in the development of 2D Dirac fermions based on light elements for their application in nanoelectronic devices and topological electronics.

Prompts are the interface for eliciting the capabilities of large language models (LLMs). Understanding their structure and components is critical for analyzing LLM behavior and optimizing performance. However, the field lacks a comprehensive framework for systematic prompt analysis and understanding. We introduce PromptPrism, a linguistically-inspired taxonomy that enables prompt analysis across three hierarchical levels: functional structure, semantic component, and syntactic pattern. We show the practical utility of PromptPrism by applying it to three applications: (1) a taxonomy-guided prompt refinement approach that automatically improves prompt quality and enhances model performance across a range of tasks; (2) a multi-dimensional dataset profiling method that extracts and aggregates structural, semantic, and syntactic characteristics from prompt datasets, enabling comprehensive analysis of prompt distributions and patterns; (3) a controlled experimental framework for prompt sensitivity analysis by quantifying the impact of semantic reordering and delimiter modifications on LLM performance. Our experimental results validate the effectiveness of our taxonomy across these applications, demonstrating that PromptPrism provides a foundation for refining, profiling, and analyzing prompts.

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

Document structure analysis (aka document layout analysis) is crucial for understanding the physical layout and logical structure of documents, with applications in information retrieval, document summarization, knowledge extraction, etc. In this paper, we concentrate on Hierarchical Document Structure Analysis (HDSA) to explore hierarchical relationships within structured documents created using authoring software employing hierarchical schemas, such as LaTeX, Microsoft Word, and HTML. To comprehensively analyze hierarchical document structures, we propose a tree construction based approach that addresses multiple subtasks concurrently, including page object detection (Detect), reading order prediction of identified objects (Order), and the construction of intended hierarchical structure (Construct). We present an effective end-to-end solution based on this framework to demonstrate its performance. To assess our approach, we develop a comprehensive benchmark called Comp-HRDoc, which evaluates the above subtasks simultaneously. Our end-to-end system achieves state-of-the-art performance on two large-scale document layout analysis datasets (PubLayNet and DocLayNet), a high-quality hierarchical document structure reconstruction dataset (HRDoc), and our Comp-HRDoc benchmark. The Comp-HRDoc benchmark will be released to facilitate further research in this field.

Document structure analysis, aka document layout analysis, is crucial for understanding both the physical layout and logical structure of documents, serving information retrieval, document summarization, knowledge extraction, etc. Hierarchical Document Structure Analysis (HDSA) specifically aims to restore the hierarchical structure of documents created using authoring software with hierarchical schemas. Previous research has primarily followed two approaches: one focuses on tackling specific subtasks of HDSA in isolation, such as table detection or reading order prediction, while the other adopts a unified framework that uses multiple branches or modules, each designed to address a distinct task. In this work, we propose a unified relation prediction approach for HDSA, called UniHDSA, which treats various HDSA sub-tasks as relation prediction problems and consolidates relation prediction labels into a unified label space. This allows a single relation prediction module to handle multiple tasks simultaneously, whether at a page-level or document-level structure analysis. To validate the effectiveness of UniHDSA, we develop a multimodal end-to-end system based on Transformer architectures. Extensive experimental results demonstrate that our approach achieves state-of-the-art performance on a hierarchical document structure analysis benchmark, Comp-HRDoc, and competitive results on a large-scale document layout analysis dataset, DocLayNet, effectively illustrating the superiority of our method across all sub-tasks. The Comp-HRDoc benchmark and UniHDSA's configurations are publicly available at https://github.com/microsoft/CompHRDoc.

Web search is an essential way for humans to obtain information, but it's still a great challenge for machines to understand the contents of web pages. In this paper, we introduce the task of structural reading comprehension (SRC) on web. Given a web page and a question about it, the task is to find the answer from the web page. This task requires a system not only to understand the semantics of texts but also the structure of the web page. Moreover, we proposed WebSRC, a novel Web-based Structural Reading Comprehension dataset. WebSRC consists of 400K question-answer pairs, which are collected from 6.4K web pages. Along with the QA pairs, corresponding HTML source code, screenshots, and metadata are also provided in our dataset. Each question in WebSRC requires a certain structural understanding of a web page to answer, and the answer is either a text span on the web page or yes/no. We evaluate various baselines on our dataset to show the difficulty of our task. We also investigate the usefulness of structural information and visual features. Our dataset and baselines have been publicly available at https://x-lance.github.io/WebSRC/.

Structural optimization is a popular method for designing objects such as bridge trusses, airplane wings, and optical devices. Unfortunately, the quality of solutions depends heavily on how the problem is parameterized. In this paper, we propose using the implicit bias over functions induced by neural networks to improve the parameterization of structural optimization. Rather than directly optimizing densities on a grid, we instead optimize the parameters of a neural network which outputs those densities. This reparameterization leads to different and often better solutions. On a selection of 116 structural optimization tasks, our approach produces the best design 50% more often than the best baseline method.

The statistical analysis of large scale legal corpus can provide valuable legal insights. For such analysis one needs to (1) select a subset of the corpus using document retrieval tools, (2) structuralize text using information extraction (IE) systems, and (3) visualize the data for the statistical analysis. Each process demands either specialized tools or programming skills whereas no comprehensive unified "no-code" tools have been available. Especially for IE, if the target information is not predefined in the ontology of the IE system, one needs to build their own system. Here we provide NESTLE, a no code tool for large-scale statistical analysis of legal corpus. With NESTLE, users can search target documents, extract information, and visualize the structured data all via the chat interface with accompanying auxiliary GUI for the fine-level control. NESTLE consists of three main components: a search engine, an end-to-end IE system, and a Large Language Model (LLM) that glues the whole components together and provides the chat interface. Powered by LLM and the end-to-end IE system, NESTLE can extract any type of information that has not been predefined in the IE system opening up the possibility of unlimited customizable statistical analysis of the corpus without writing a single line of code. The use of the custom end-to-end IE system also enables faster and low-cost IE on large scale corpus. We validate our system on 15 Korean precedent IE tasks and 3 legal text classification tasks from LEXGLUE. The comprehensive experiments reveal NESTLE can achieve GPT-4 comparable performance by training the internal IE module with 4 human-labeled, and 192 LLM-labeled examples. The detailed analysis provides the insight on the trade-off between accuracy, time, and cost in building such system.

We apply category theory to extract multimodal document structure which leads us to develop information theoretic measures, content summarization and extension, and self-supervised improvement of large pretrained models. We first develop a mathematical representation of a document as a category of question-answer pairs. Second, we develop an orthogonalization procedure to divide the information contained in one or more documents into non-overlapping pieces. The structures extracted in the first and second steps lead us to develop methods to measure and enumerate the information contained in a document. We also build on those steps to develop new summarization techniques, as well as to develop a solution to a new problem viz. exegesis resulting in an extension of the original document. Our question-answer pair methodology enables a novel rate distortion analysis of summarization techniques. We implement our techniques using large pretrained models, and we propose a multimodal extension of our overall mathematical framework. Finally, we develop a novel self-supervised method using RLVR to improve large pretrained models using consistency constraints such as composability and closure under certain operations that stem naturally from our category theoretic framework.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

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

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.

Structural Health Monitoring (SHM) plays an indispensable role in ensuring the longevity and safety of infrastructure. With the rapid growth of sensor technology, the volume of data generated from various structures has seen an unprecedented surge, bringing forth challenges in efficient analysis and interpretation. This paper introduces a novel deep learning algorithm tailored for the complexities inherent in multimodal vibration signals prevalent in SHM. By amalgamating convolutional and recurrent architectures, the algorithm adeptly captures both localized and prolonged structural behaviors. The pivotal integration of attention mechanisms further enhances the model's capability, allowing it to discern and prioritize salient structural responses from extraneous noise. Our results showcase significant improvements in predictive accuracy, early damage detection, and adaptability across multiple SHM scenarios. In light of the critical nature of SHM, the proposed approach not only offers a robust analytical tool but also paves the way for more transparent and interpretable AI-driven SHM solutions. Future prospects include real-time processing, integration with external environmental factors, and a deeper emphasis on model interpretability.

Adapting pre-trained foundation models for various downstream tasks has been prevalent in artificial intelligence. Due to the vast number of tasks and high costs, adjusting all parameters becomes unfeasible. To mitigate this, several fine-tuning techniques have been developed to update the pre-trained model weights in a more resource-efficient manner, such as through low-rank adjustments. Yet, almost all of these methods focus on linear weights, neglecting the intricacies of parameter spaces in higher dimensions like 4D. Alternatively, some methods can be adapted for high-dimensional parameter space by compressing changes in the original space into two dimensions and then employing low-rank matrix decomposition. However, these approaches destructs the structural integrity of the involved high-dimensional spaces. To tackle the diversity of dimensional spaces across different foundation models and provide a more precise representation of the changes within these spaces, this paper introduces a generalized parameter-efficient fine-tuning framework, FLoRA, designed for various dimensional parameter space. Specifically, utilizing Tucker decomposition, FLoRA asserts that changes in each dimensional parameter space are based on a low-rank core space which maintains the consistent topological structure with the original space. It then models the changes through this core space alongside corresponding weights to reconstruct alterations in the original space. FLoRA effectively preserves the structural integrity of the change of original N-dimensional parameter space, meanwhile decomposes it via low-rank tensor decomposition. Extensive experiments on computer vision, natural language processing and multi-modal tasks validate FLoRA's effectiveness. Codes are available at https://github.com/SJTU-DeepVisionLab/FLoRA.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

In this paper, we provide two case studies to demonstrate how artificial intelligence can empower civil engineering. In the first case, a machine learning-assisted framework, BRAILS, is proposed for city-scale building information modeling. Building information modeling (BIM) is an efficient way of describing buildings, which is essential to architecture, engineering, and construction. Our proposed framework employs deep learning technique to extract visual information of buildings from satellite/street view images. Further, a novel machine learning (ML)-based statistical tool, SURF, is proposed to discover the spatial patterns in building metadata. The second case focuses on the task of soft-story building classification. Soft-story buildings are a type of buildings prone to collapse during a moderate or severe earthquake. Hence, identifying and retrofitting such buildings is vital in the current earthquake preparedness efforts. For this task, we propose an automated deep learning-based procedure for identifying soft-story buildings from street view images at a regional scale. We also create a large-scale building image database and a semi-automated image labeling approach that effectively annotates new database entries. Through extensive computational experiments, we demonstrate the effectiveness of the proposed method.

Different from the flow semantics of natural languages, programming languages are inherently rigid in structure and grammar. Existing fine-tuning methodologies for code vulnerability detection generally treat code as long text sequences, stripping away structural elements such as newlines ('/n') and whitespace. However, this approach inadvertently results in the loss of crucial structural information, diminishing the distinct characteristics of code and impairing the accuracy of vulnerability detection. To address these challenges, we propose a novel network architecture method based on pre-trained code models, which incorporates structural information awareness. We propose an enhanced code text processing workflow that retains structural elements prior to modeling. This refinement allows the model to retain and exploit line-level structural information and semantic information during the modeling process. Furthermore, we introduce a new network architecture, the Code Structure-Aware Network through Line-level Semantic Learning (CSLS), which integrates three key components: global vulnerability awareness, line-structural awareness, and sensitive-line awareness. We have conducted comprehensive experiments using vulnerability detection datasets from real-world projects. Extensive experiments were conducted on vulnerability detection datasets derived from real-world projects. The results demonstrate that our new code pre-processing flow significantly improves existing baselines (e.g., a 3\% accuracy improvement on the Devign dataset when applied to popular models such as CoderBert and UniXcoder). The proposed network architecture also demonstrates superior accuracy in detecting vulnerabilities, surpassing newly established benchmarks. These findings underscore the importance of structural information in enhancing the efficacy of code vulnerability detection models.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

Abstractive summarization of scientific papers has always been a research focus, yet existing methods face two main challenges. First, most summarization models rely on Encoder-Decoder architectures that treat papers as sequences of words, thus fail to fully capture the structured information inherent in scientific papers. Second, existing research often use keyword mapping or feature engineering to identify the structural information, but these methods struggle with the structural flexibility of scientific papers and lack robustness across different disciplines. To address these challenges, we propose a two-stage abstractive summarization framework that leverages automatic recognition of structural functions within scientific papers. In the first stage, we standardize chapter titles from numerous scientific papers and construct a large-scale dataset for structural function recognition. A classifier is then trained to automatically identify the key structural components (e.g., Background, Methods, Results, Discussion), which provides a foundation for generating more balanced summaries. In the second stage, we employ Longformer to capture rich contextual relationships across sections and generating context-aware summaries. Experiments conducted on two domain-specific scientific paper summarization datasets demonstrate that our method outperforms advanced baselines, and generates more comprehensive summaries. The code and dataset can be accessed at https://github.com/tongbao96/code-for-SFR-AS.

This work presents a systematic investigation into the latent knowledge encoded within Network Foundation Models (NFMs) that focuses on hidden representations analysis rather than pure downstream task performance. Different from existing efforts, we analyze the models through a three-part evaluation: Embedding Geometry Analysis to assess representation space utilization, Metric Alignment Assessment to measure correspondence with domain-expert features, and Causal Sensitivity Testing to evaluate robustness to protocol perturbations. Using five diverse network datasets spanning controlled and real-world environments, we evaluate four state-of-the-art NFMs, revealing that they all exhibit significant anisotropy, inconsistent feature sensitivity patterns, an inability to separate the high-level context, payload dependency, and other properties. Our work identifies numerous limitations across all models and demonstrates that addressing them can significantly improve model performance (by up to +0.35 F_1 score without architectural changes).

The analysis of parametric and non-parametric uncertainties of very large dynamical systems requires the construction of a stochastic model of said system. Linear approaches relying on random matrix theory and principal componant analysis can be used when systems undergo low-frequency vibrations. In the case of fast dynamics and wave propagation, we investigate a random generator of boundary conditions for fast submodels by using machine learning. We show that the use of non-linear techniques in machine learning and data-driven methods is highly relevant. Physics-informed neural networks is a possible choice for a data-driven method to replace linear modal analysis. An architecture that support a random component is necessary for the construction of the stochastic model of the physical system for non-parametric uncertainties, since the goal is to learn the underlying probabilistic distribution of uncertainty in the data. Generative Adversarial Networks (GANs) are suited for such applications, where the Wasserstein-GAN with gradient penalty variant offers improved convergence results for our problem. The objective of our approach is to train a GAN on data from a finite element method code (Fenics) so as to extract stochastic boundary conditions for faster finite element predictions on a submodel. The submodel and the training data have both the same geometrical support. It is a zone of interest for uncertainty quantification and relevant to engineering purposes. In the exploitation phase, the framework can be viewed as a randomized and parametrized simulation generator on the submodel, which can be used as a Monte Carlo estimator.

Automatic analysis of the enormous sets of images is a critical task in life sciences. This faces many challenges such as: algorithms are highly parameterized, significant human input is intertwined, and lacking a standard meta-visualization approach. This paper proposes an alternative iterative approach for optimizing input parameters, saving time by minimizing the user involvement, and allowing for understanding the workflow of algorithms and discovering new ones. The main focus is on developing an interactive visualization technique that enables users to analyze the relationships between sampled input parameters and corresponding output. This technique is implemented as a prototype called Veni Vidi Vici, or "I came, I saw, I conquered." This strategy is inspired by the mathematical formulas of numbering computable functions and is developed atop ImageJ, a scientific image processing program. A case study is presented to investigate the proposed framework. Finally, the paper explores some potential future issues in the application of the proposed approach in parameter space analysis in visualization.

In quality control, microstructures are investigated rigorously to ensure structural integrity, exclude the presence of critical volume defects, and validate the formation of the target microstructure. For quenched, hierarchically-structured steels, the morphology of the bainitic and martensitic microstructures are of major concern to guarantee the reliability of the material under service conditions. Therefore, industries conduct small sample-size inspections of materials cross-sections through metallographers to validate the needle morphology of such microstructures. We demonstrate round-robin test results revealing that this visual grading is afflicted by pronounced subjectivity despite the thorough training of personnel. Instead, we propose a deep learning image classification approach that distinguishes steels based on their microstructure type and classifies their needle length alluding to the ISO 643 grain size assessment standard. This classification approach facilitates the reliable, objective, and automated classification of hierarchically structured steels. Specifically, an accuracy of 96% and roughly 91% is attained for the distinction of martensite/bainite subtypes and needle length, respectively. This is achieved on an image dataset that contains significant variance and labeling noise as it is acquired over more than ten years from multiple plants, alloys, etchant applications, and light optical microscopes by many metallographers (raters). Interpretability analysis gives insights into the decision-making of these models and allows for estimating their generalization capability.

We propose a novel interpretation technique to explain the behavior of structured output models, which learn mappings between an input vector to a set of output variables simultaneously. Because of the complex relationship between the computational path of output variables in structured models, a feature can affect the value of output through other ones. We focus on one of the outputs as the target and try to find the most important features utilized by the structured model to decide on the target in each locality of the input space. In this paper, we assume an arbitrary structured output model is available as a black box and argue how considering the correlations between output variables can improve the explanation performance. The goal is to train a function as an interpreter for the target output variable over the input space. We introduce an energy-based training process for the interpreter function, which effectively considers the structural information incorporated into the model to be explained. The effectiveness of the proposed method is confirmed using a variety of simulated and real data sets.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

One method for obtaining generalizable solutions to machine learning tasks when presented with diverse training environments is to find invariant representations of the data. These are representations of the covariates such that the best model on top of the representation is invariant across training environments. In the context of linear Structural Equation Models (SEMs), invariant representations might allow us to learn models with out-of-distribution guarantees, i.e., models that are robust to interventions in the SEM. To address the invariant representation problem in a {\em finite sample} setting, we consider the notion of epsilon-approximate invariance. We study the following question: If a representation is approximately invariant with respect to a given number of training interventions, will it continue to be approximately invariant on a larger collection of unseen SEMs? This larger collection of SEMs is generated through a parameterized family of interventions. Inspired by PAC learning, we obtain finite-sample out-of-distribution generalization guarantees for approximate invariance that holds probabilistically over a family of linear SEMs without faithfulness assumptions. Our results show bounds that do not scale in ambient dimension when intervention sites are restricted to lie in a constant size subset of in-degree bounded nodes. We also show how to extend our results to a linear indirect observation model that incorporates latent variables.

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

This document serves as an overview of the different mechanisms and areas of governance in the BigCode project. It aims to support transparency by providing relevant information about choices that were made during the project to the broader public, and to serve as an example of intentional governance of an open research project that future endeavors can leverage to shape their own approach. The first section, Project Structure, covers the project organization, its stated goals and values, its internal decision processes, and its funding and resources. The second section, Data and Model Governance, covers decisions relating to the questions of data subject consent, privacy, and model release.

Document chunking is a critical task in natural language processing (NLP) that involves dividing a document into meaningful segments. Traditional methods often rely solely on semantic analysis, ignoring the spatial layout of elements, which is crucial for understanding relationships in complex documents. This paper introduces a novel hybrid approach that combines layout structure, semantic analysis, and spatial relationships to enhance the cohesion and accuracy of document chunks. By leveraging bounding box information (bbox) and text embeddings, our method constructs a weighted graph representation of document elements, which is then clustered using spectral clustering. Experimental results demonstrate that this approach outperforms traditional methods, particularly in documents with diverse layouts such as reports, articles, and multi-column designs. The proposed method also ensures that no chunk exceeds a specified token length, making it suitable for use cases where token limits are critical (e.g., language models with input size limitations)

We explore local vs. global evolution of knowledge systems through the framework of socio-epistemic networks (SEN), applying two complementary methods to a corpus of scientific texts. The framework comprises three interconnected layers-social, semiotic (material), and semantic-proposing a multilayered approach to understanding structural developments of knowledge. To analyse diachronic changes on the semantic layer, we first use information-theoretic measures based on relative entropy to detect semantic shifts, assess their significance, and identify key driving features. Second, variations in document embedding densities reveal changes in semantic neighbourhoods, tracking how concentration of similar documents increase, remain stable, or disperse. This enables us to trace document trajectories based on content (topics) or metadata (authorship, institution). Case studies of Joseph Silk and Hans-J\"urgen Treder illustrate how individual scholar's work aligns with broader disciplinary shifts in general relativity and gravitation research, demonstrating the applications, limitations, and further potential of this approach.

We describe HypotheSAEs, a general method to hypothesize interpretable relationships between text data (e.g., headlines) and a target variable (e.g., clicks). HypotheSAEs has three steps: (1) train a sparse autoencoder on text embeddings to produce interpretable features describing the data distribution, (2) select features that predict the target variable, and (3) generate a natural language interpretation of each feature (e.g., "mentions being surprised or shocked") using an LLM. Each interpretation serves as a hypothesis about what predicts the target variable. Compared to baselines, our method better identifies reference hypotheses on synthetic datasets (at least +0.06 in F1) and produces more predictive hypotheses on real datasets (~twice as many significant findings), despite requiring 1-2 orders of magnitude less compute than recent LLM-based methods. HypotheSAEs also produces novel discoveries on two well-studied tasks: explaining partisan differences in Congressional speeches and identifying drivers of engagement with online headlines.

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and others parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

Recent advancements in large language models and their multi-modal extensions have demonstrated the effectiveness of unifying generation and understanding through autoregressive next-token prediction. However, despite the critical role of 3D structural generation and understanding ({3D GU}) in AI for science, these tasks have largely evolved independently, with autoregressive methods remaining underexplored. To bridge this gap, we introduce Uni-3DAR, a unified framework that seamlessly integrates {3D GU} tasks via autoregressive prediction. At its core, Uni-3DAR employs a novel hierarchical tokenization that compresses 3D space using an octree, leveraging the inherent sparsity of 3D structures. It then applies an additional tokenization for fine-grained structural details, capturing key attributes such as atom types and precise spatial coordinates in microscopic 3D structures. We further propose two optimizations to enhance efficiency and effectiveness. The first is a two-level subtree compression strategy, which reduces the octree token sequence by up to 8x. The second is a masked next-token prediction mechanism tailored for dynamically varying token positions, significantly boosting model performance. By combining these strategies, Uni-3DAR successfully unifies diverse {3D GU} tasks within a single autoregressive framework. Extensive experiments across multiple microscopic {3D GU} tasks, including molecules, proteins, polymers, and crystals, validate its effectiveness and versatility. Notably, Uni-3DAR surpasses previous state-of-the-art diffusion models by a substantial margin, achieving up to 256\% relative improvement while delivering inference speeds up to 21.8x faster. The code is publicly available at https://github.com/dptech-corp/Uni-3DAR.

This paper presents a pioneering methodology, termed StructTuning, to efficiently transform foundation Large Language Models (LLMs) into domain specialists. It significantly minimizes the training corpus requirement to a mere 0.3% while achieving an impressive 50% of traditional knowledge injection performance. Our method is inspired by the educational processes for human students, particularly how structured domain knowledge from textbooks is absorbed and then applied to tackle real-world challenges through specific exercises. Based on this, we propose a novel two-stage knowledge injection strategy: Structure-aware Continual Pre-Training (SCPT) and Structure-aware Supervised Fine-Tuning (SSFT). In the SCPT phase, we organize the training data into an auto-generated taxonomy of domain knowledge, enabling LLMs to effectively memorize textual segments linked to specific expertise within the taxonomy's architecture. Subsequently, in the SSFT phase, we explicitly prompt models to reveal the underlying knowledge structure in their outputs, leveraging this structured domain insight to address practical problems adeptly. Our ultimate method has undergone extensive evaluations across model architectures and scales, using closed-book question-answering tasks on LongBench and MMedBench datasets. Remarkably, our method matches 50% of the improvement displayed by the state-of-the-art MMedLM2 on MMedBench, but with only 0.3% quantity of the training corpus. This breakthrough showcases the potential to scale up our StructTuning for stronger domain-specific LLMs. Code will be made public soon.

Engineered timber is pivotal to low-carbon construction, but moisture uptake during its service life can compromise structural reliability and impede reuse within a circular economy model. Despite growing interest, quantitative standards for classifying the reusability of moisture-exposed timber are still lacking. This study develops a probabilistic framework to determine the post-exposure reusability of engineered timber. Laminated specimens were soaked to full saturation, dried to 25% moisture content, and subjected to destructive three-point flexural testing. Structural integrity was quantified by a residual-performance metric that assigns 80% weight to the retained flexural modulus and 20% to the retained maximum load, benchmarked against unexposed controls. A hierarchical Bayesian multinomial logistic model with horseshoe priors, calibrated through Markov-Chain Monte-Carlo sampling, jointly infers the decision threshold separating three Modern Methods of Construction (MMC) reuse levels and predicts those levels from five field-measurable features: density, moisture content, specimen size, grain orientation, and surface hardness. Results indicate that a single wet-dry cycle preserves 70% of specimens above the 0.90 residual-performance threshold (Level 1), whereas repeated cycling lowers the mean residual to 0.78 and reallocates many specimens to Levels 2-3. The proposed framework yields quantified decision boundaries and a streamlined on-site testing protocol, providing a foundation for robust quality assurance standards.

A major step toward Artificial General Intelligence (AGI) and Super Intelligence is AI's ability to autonomously conduct research - what we term Artificial Research Intelligence (ARI). If machines could generate hypotheses, conduct experiments, and write research papers without human intervention, it would transform science. Sakana recently introduced the 'AI Scientist', claiming to conduct research autonomously, i.e. they imply to have achieved what we term Artificial Research Intelligence (ARI). The AI Scientist gained much attention, but a thorough independent evaluation has yet to be conducted. Our evaluation of the AI Scientist reveals critical shortcomings. The system's literature reviews produced poor novelty assessments, often misclassifying established concepts (e.g., micro-batching for stochastic gradient descent) as novel. It also struggles with experiment execution: 42% of experiments failed due to coding errors, while others produced flawed or misleading results. Code modifications were minimal, averaging 8% more characters per iteration, suggesting limited adaptability. Generated manuscripts were poorly substantiated, with a median of five citations, most outdated (only five of 34 from 2020 or later). Structural errors were frequent, including missing figures, repeated sections, and placeholder text like 'Conclusions Here'. Some papers contained hallucinated numerical results. Despite these flaws, the AI Scientist represents a leap forward in research automation. It generates full research manuscripts with minimal human input, challenging expectations of AI-driven science. Many reviewers might struggle to distinguish its work from human researchers. While its quality resembles a rushed undergraduate paper, its speed and cost efficiency are unprecedented, producing a full paper for USD 6 to 15 with 3.5 hours of human involvement, far outpacing traditional researchers.

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is {\em persistent homology}, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. In particular, a central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on {\em decompositions} of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and nonidentifiability of the parameters due to rotation invariance properties of the likelihood. We address these concerns by proposing a fast correlation thresholding (CT) algorithm that simultaneously learns the number of latent factors and a rotationally identifiable model structure. Our novel approach translates this structure learning problem into the search for so-called independent maximal cliques in a thresholded correlation graph that can be easily constructed from the observed data. Our clique analysis technique scales well up to thousands of variables, while competing methods are not applicable in a reasonable amount of running time. We establish a finite-sample error bound and high-dimensional consistency for the structure learning of our method. Through a series of simulation studies and a real data example, we show that the CT algorithm is an accurate method for learning the structure of factor analysis models and is robust to violations of its assumptions.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

Narrative frames are a powerful way of conceptualizing and communicating complex, controversial ideas, however automated frame analysis to date has mostly overlooked this framing device. In this paper, we connect elements of narrativity with fundamental aspects of framing, and present a framework which formalizes and operationalizes such aspects. We annotate and release a data set of news articles in the climate change domain, analyze the dominance of narrative frame components across political leanings, and test LLMs in their ability to predict narrative frames and their components. Finally, we apply our framework in an unsupervised way to elicit components of narrative framing in a second domain, the COVID-19 crisis, where our predictions are congruent with prior theoretical work showing the generalizability of our approach.

Structure information is critical for understanding the semantics of text-rich images, such as documents, tables, and charts. Existing Multimodal Large Language Models (MLLMs) for Visual Document Understanding are equipped with text recognition ability but lack general structure understanding abilities for text-rich document images. In this work, we emphasize the importance of structure information in Visual Document Understanding and propose the Unified Structure Learning to boost the performance of MLLMs. Our Unified Structure Learning comprises structure-aware parsing tasks and multi-grained text localization tasks across 5 domains: document, webpage, table, chart, and natural image. To better encode structure information, we design a simple and effective vision-to-text module H-Reducer, which can not only maintain the layout information but also reduce the length of visual features by merging horizontal adjacent patches through convolution, enabling the LLM to understand high-resolution images more efficiently. Furthermore, by constructing structure-aware text sequences and multi-grained pairs of texts and bounding boxes for publicly available text-rich images, we build a comprehensive training set DocStruct4M to support structure learning. Finally, we construct a small but high-quality reasoning tuning dataset DocReason25K to trigger the detailed explanation ability in the document domain. Our model DocOwl 1.5 achieves state-of-the-art performance on 10 visual document understanding benchmarks, improving the SOTA performance of MLLMs with a 7B LLM by more than 10 points in 5/10 benchmarks. Our codes, models, and datasets are publicly available at https://github.com/X-PLUG/mPLUG-DocOwl/tree/main/DocOwl1.5.

Important information that relates to a specific topic in a document is often organized in tabular format to assist readers with information retrieval and comparison, which may be difficult to provide in natural language. However, tabular data in unstructured digital documents, e.g., Portable Document Format (PDF) and images, are difficult to parse into structured machine-readable format, due to complexity and diversity in their structure and style. To facilitate image-based table recognition with deep learning, we develop the largest publicly available table recognition dataset PubTabNet (https://github.com/ibm-aur-nlp/PubTabNet), containing 568k table images with corresponding structured HTML representation. PubTabNet is automatically generated by matching the XML and PDF representations of the scientific articles in PubMed Central Open Access Subset (PMCOA). We also propose a novel attention-based encoder-dual-decoder (EDD) architecture that converts images of tables into HTML code. The model has a structure decoder which reconstructs the table structure and helps the cell decoder to recognize cell content. In addition, we propose a new Tree-Edit-Distance-based Similarity (TEDS) metric for table recognition, which more appropriately captures multi-hop cell misalignment and OCR errors than the pre-established metric. The experiments demonstrate that the EDD model can accurately recognize complex tables solely relying on the image representation, outperforming the state-of-the-art by 9.7% absolute TEDS score.

In many scenarios, the interpretability of machine learning models is a highly required but difficult task. To explain the individual predictions of such models, local model-agnostic approaches have been proposed. However, the process generating the explanations can be, for a user, as mysterious as the prediction to be explained. Furthermore, interpretability methods frequently lack theoretical guarantees, and their behavior on simple models is frequently unknown. While it is difficult, if not impossible, to ensure that an explainer behaves as expected on a cutting-edge model, we can at least ensure that everything works on simple, already interpretable models. In this paper, we present a theoretical analysis of Anchors (Ribeiro et al., 2018): a popular rule-based interpretability method that highlights a small set of words to explain a text classifier's decision. After formalizing its algorithm and providing useful insights, we demonstrate mathematically that Anchors produces meaningful results when used with linear text classifiers on top of a TF-IDF vectorization. We believe that our analysis framework can aid in the development of new explainability methods based on solid theoretical foundations.

Table structure recognition is an essential part for making machines understand tables. Its main task is to recognize the internal structure of a table. However, due to the complexity and diversity in their structure and style, it is very difficult to parse the tabular data into the structured format which machines can understand easily, especially for complex tables. In this paper, we introduce Split, Embed and Merge (SEM), an accurate table structure recognizer. Our model takes table images as input and can correctly recognize the structure of tables, whether they are simple or a complex tables. SEM is mainly composed of three parts, splitter, embedder and merger. In the first stage, we apply the splitter to predict the potential regions of the table row (column) separators, and obtain the fine grid structure of the table. In the second stage, by taking a full consideration of the textual information in the table, we fuse the output features for each table grid from both vision and language modalities. Moreover, we achieve a higher precision in our experiments through adding additional semantic features. Finally, we process the merging of these basic table grids in a self-regression manner. The correspondent merging results is learned through the attention mechanism. In our experiments, SEM achieves an average F1-Measure of 97.11% on the SciTSR dataset which outperforms other methods by a large margin. We also won the first place in the complex table and third place in all tables in ICDAR 2021 Competition on Scientific Literature Parsing, Task-B. Extensive experiments on other publicly available datasets demonstrate that our model achieves state-of-the-art.

T\"urkiye is located on a fault line; earthquakes often occur on a large and small scale. There is a need for effective solutions for gathering current information during disasters. We can use social media to get insight into public opinion. This insight can be used in public relations and disaster management. In this study, Twitter posts on Izmir Earthquake that took place on October 2020 are analyzed. We question if this analysis can be used to make social inferences on time. Data mining and natural language processing (NLP) methods are used for this analysis. NLP is used for sentiment analysis and topic modelling. The latent Dirichlet Allocation (LDA) algorithm is used for topic modelling. We used the Bidirectional Encoder Representations from Transformers (BERT) model working with Transformers architecture for sentiment analysis. It is shown that the users shared their goodwill wishes and aimed to contribute to the initiated aid activities after the earthquake. The users desired to make their voices heard by competent institutions and organizations. The proposed methods work effectively. Future studies are also discussed.

Background. The development of empirical studies in software engineering mainly relies on the data available on code hosting platforms, being GitHub the most representative. Nevertheless, in the last years, the emergence of Machine Learning (ML) has led to the development of platforms specifically designed for developing ML-based projects, being Hugging Face Hub (HFH) the most popular one. With over 250k repositories, and growing fast, HFH is becoming a promising ecosystem of ML artifacts and therefore a potential source of data for empirical studies. However, so far there have been no studies evaluating the potential of HFH for such studies. Objective. In this proposal for a registered report, we aim at performing an exploratory study of the current state of HFH in order to investigate its suitability to be used as a source platform for empirical studies. Method. We conduct a qualitative and quantitative analysis of HFH for empirical studies. The former will be performed by comparing the features of HFH with those of other code hosting platforms, such as GitHub and GitLab. The latter will be performed by analyzing the data available in HFH.

Many production processes are characterized by numerous and complex cause-and-effect relationships. Since they are only partially known they pose a challenge to effective process control. In this work we present how Structural Equation Models can be used for deriving cause-and-effect relationships from the combination of prior knowledge and process data in the manufacturing domain. Compared to existing applications, we do not assume linear relationships leading to more informative results.

Gait disorders are commonly observed in older adults, who frequently experience various issues related to walking. Additionally, researchers and clinicians extensively investigate mobility related to gait in typically and atypically developing children, athletes, and individuals with orthopedic and neurological disorders. Effective gait analysis enables the understanding of the causal mechanisms of mobility and balance control of patients, the development of tailored treatment plans to improve mobility, the reduction of fall risk, and the tracking of rehabilitation progress. However, analyzing gait data is a complex task due to the multivariate nature of the data, the large volume of information to be interpreted, and the technical skills required. Existing tools for gait analysis are often limited to specific patient groups (e.g., cerebral palsy), only handle a specific subset of tasks in the entire workflow, and are not openly accessible. To address these shortcomings, we conducted a requirements assessment with gait practitioners (e.g., researchers, clinicians) via surveys and identified key components of the workflow, including (1) data processing and (2) data analysis and visualization. Based on the findings, we designed VIGMA, an open-access visual analytics framework integrated with computational notebooks and a Python library, to meet the identified requirements. Notably, the framework supports analytical capabilities for assessing disease progression and for comparing multiple patient groups. We validated the framework through usage scenarios with experts specializing in gait and mobility rehabilitation. VIGMA is available at https://github.com/komar41/VIGMA.

As Large Language Models (LLMs) become integral to software development workflows, their ability to generate structured outputs has become critically important. We introduce StructEval, a comprehensive benchmark for evaluating LLMs' capabilities in producing both non-renderable (JSON, YAML, CSV) and renderable (HTML, React, SVG) structured formats. Unlike prior benchmarks, StructEval systematically evaluates structural fidelity across diverse formats through two paradigms: 1) generation tasks, producing structured output from natural language prompts, and 2) conversion tasks, translating between structured formats. Our benchmark encompasses 18 formats and 44 types of task, with novel metrics for format adherence and structural correctness. Results reveal significant performance gaps, even state-of-the-art models like o1-mini achieve only 75.58 average score, with open-source alternatives lagging approximately 10 points behind. We find generation tasks more challenging than conversion tasks, and producing correct visual content more difficult than generating text-only structures.

Meta-analysis is a systematic research methodology that synthesizes data from multiple existing studies to derive comprehensive conclusions. This approach not only mitigates limitations inherent in individual studies but also facilitates novel discoveries through integrated data analysis. Traditional meta-analysis involves a complex multi-stage pipeline including literature retrieval, paper screening, and data extraction, which demands substantial human effort and time. However, while LLM-based methods can accelerate certain stages, they still face significant challenges, such as hallucinations in paper screening and data extraction. In this paper, we propose a multi-agent system, Manalyzer, which achieves end-to-end automated meta-analysis through tool calls. The hybrid review, hierarchical extraction, self-proving, and feedback checking strategies implemented in Manalyzer significantly alleviate these two hallucinations. To comprehensively evaluate the performance of meta-analysis, we construct a new benchmark comprising 729 papers across 3 domains, encompassing text, image, and table modalities, with over 10,000 data points. Extensive experiments demonstrate that Manalyzer achieves significant performance improvements over the LLM baseline in multi meta-analysis tasks. Project page: https://black-yt.github.io/meta-analysis-page/ .

In many real-world applications, graph-structured data used for training and testing have differences in distribution, such as in high energy physics (HEP) where simulation data used for training may not match real experiments. Graph domain adaptation (GDA) is a method used to address these differences. However, current GDA primarily works by aligning the distributions of node representations output by a single graph neural network encoder shared across the training and testing domains, which may often yield sub-optimal solutions. This work examines different impacts of distribution shifts caused by either graph structure or node attributes and identifies a new type of shift, named conditional structure shift (CSS), which current GDA approaches are provably sub-optimal to deal with. A novel approach, called structural reweighting (StruRW), is proposed to address this issue and is tested on synthetic graphs, four benchmark datasets, and a new application in HEP. StruRW has shown significant performance improvement over the baselines in the settings with large graph structure shifts, and reasonable performance improvement when node attribute shift dominates.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Literature review requires researchers to synthesize a large amount of information and is increasingly challenging as the scientific literature expands. In this work, we investigate the potential of LLMs for producing hierarchical organizations of scientific studies to assist researchers with literature review. We define hierarchical organizations as tree structures where nodes refer to topical categories and every node is linked to the studies assigned to that category. Our naive LLM-based pipeline for hierarchy generation from a set of studies produces promising yet imperfect hierarchies, motivating us to collect CHIME, an expert-curated dataset for this task focused on biomedicine. Given the challenging and time-consuming nature of building hierarchies from scratch, we use a human-in-the-loop process in which experts correct errors (both links between categories and study assignment) in LLM-generated hierarchies. CHIME contains 2,174 LLM-generated hierarchies covering 472 topics, and expert-corrected hierarchies for a subset of 100 topics. Expert corrections allow us to quantify LLM performance, and we find that while they are quite good at generating and organizing categories, their assignment of studies to categories could be improved. We attempt to train a corrector model with human feedback which improves study assignment by 12.6 F1 points. We release our dataset and models to encourage research on developing better assistive tools for literature review.

Linear structural equation models are multivariate statistical models encoded by mixed graphs. In particular, the set of covariance matrices for distributions belonging to a linear structural equation model for a fixed mixed graph G=(V, D,B) is parameterized by a rational function with parameters for each vertex and edge in G. This rational parametrization naturally allows for the study of these models from an algebraic and combinatorial point of view. Indeed, this point of view has led to a collection of results in the literature, mainly focusing on questions related to identifiability and determining relationships between covariances (i.e., finding polynomials in the Gaussian vanishing ideal). So far, a large proportion of these results has focused on the case when D, the directed part of the mixed graph G, is acyclic. This is due to the fact that in the acyclic case, the parametrization becomes polynomial and there is a description of the entries of the covariance matrices in terms of a finite sum. We move beyond the acyclic case and give a closed form expression for the entries of the covariance matrices in terms of the one-connections in a graph obtained from D through some small operations. This closed form expression then allows us to show that if G is simple, then the parametrization map is generically finite-to-one. Finally, having a closed form expression for the covariance matrices allows for the development of an algorithm for systematically exploring possible polynomials in the Gaussian vanishing ideal.

We study neural network loss landscapes through the lens of mode connectivity, the observation that minimizers of neural networks retrieved via training on a dataset are connected via simple paths of low loss. Specifically, we ask the following question: are minimizers that rely on different mechanisms for making their predictions connected via simple paths of low loss? We provide a definition of mechanistic similarity as shared invariances to input transformations and demonstrate that lack of linear connectivity between two models implies they use dissimilar mechanisms for making their predictions. Relevant to practice, this result helps us demonstrate that naive fine-tuning on a downstream dataset can fail to alter a model's mechanisms, e.g., fine-tuning can fail to eliminate a model's reliance on spurious attributes. Our analysis also motivates a method for targeted alteration of a model's mechanisms, named connectivity-based fine-tuning (CBFT), which we analyze using several synthetic datasets for the task of reducing a model's reliance on spurious attributes.

Inferring music time structures has a broad range of applications in music production, processing and analysis. Scholars have proposed various methods to analyze different aspects of time structures, such as beat, downbeat, tempo and meter. Many state-of-the-art (SOFA) methods, however, are computationally expensive. This makes them inapplicable in real-world industrial settings where the scale of the music collections can be millions. This paper proposes a new state space and a semi-Markov model for music time structure analysis. The proposed approach turns the commonly used 2D state spaces into a 1D model through a jump-back reward strategy. It reduces the state spaces size drastically. We then utilize the proposed method for causal, joint beat, downbeat, tempo, and meter tracking, and compare it against several previous methods. The proposed method delivers similar performance with the SOFA joint causal models with a much smaller state space and a more than 30 times speedup.

Deep Learning (DL) in neuroimaging has become increasingly relevant for detecting neurological conditions and neurodegenerative disorders. One of the most predominant biomarkers in neuroimaging is represented by brain age, which has been shown to be a good indicator for different conditions, such as Alzheimer's Disease. Using brain age for weakly supervised pre-training of DL models in transfer learning settings has also recently shown promising results, especially when dealing with data scarcity of different conditions. On the other hand, anatomical information of brain MRIs (e.g. cortical thickness) can provide important information for learning good representations that can be transferred to many downstream tasks. In this work, we propose AnatCL, an anatomical foundation model for brain MRIs that i.) leverages anatomical information in a weakly contrastive learning approach, and ii.) achieves state-of-the-art performances across many different downstream tasks. To validate our approach we consider 12 different downstream tasks for the diagnosis of different conditions such as Alzheimer's Disease, autism spectrum disorder, and schizophrenia. Furthermore, we also target the prediction of 10 different clinical assessment scores using structural MRI data. Our findings show that incorporating anatomical information during pre-training leads to more robust and generalizable representations. Pre-trained models can be found at: https://github.com/EIDOSLAB/AnatCL.

In this report, we introduce DocXChain, a powerful open-source toolchain for document parsing, which is designed and developed to automatically convert the rich information embodied in unstructured documents, such as text, tables and charts, into structured representations that are readable and manipulable by machines. Specifically, basic capabilities, including text detection, text recognition, table structure recognition and layout analysis, are provided. Upon these basic capabilities, we also build a set of fully functional pipelines for document parsing, i.e., general text reading, table parsing, and document structurization, to drive various applications related to documents in real-world scenarios. Moreover, DocXChain is concise, modularized and flexible, such that it can be readily integrated with existing tools, libraries or models (such as LangChain and ChatGPT), to construct more powerful systems that can accomplish more complicated and challenging tasks. The code of DocXChain is publicly available at:~https://github.com/AlibabaResearch/AdvancedLiterateMachinery/tree/main/Applications/DocXChain

Evaluation is the baton for the development of large language models. Current evaluations typically employ a single-item assessment paradigm for each atomic test objective, which struggles to discern whether a model genuinely possesses the required capabilities or merely memorizes/guesses the answers to specific questions. To this end, we propose a novel evaluation framework referred to as StructEval. Starting from an atomic test objective, StructEval deepens and broadens the evaluation by conducting a structured assessment across multiple cognitive levels and critical concepts, and therefore offers a comprehensive, robust and consistent evaluation for LLMs. Experiments on three widely-used benchmarks demonstrate that StructEval serves as a reliable tool for resisting the risk of data contamination and reducing the interference of potential biases, thereby providing more reliable and consistent conclusions regarding model capabilities. Our framework also sheds light on the design of future principled and trustworthy LLM evaluation protocols.

Tables are widely used in documents because of their compact and structured representation of information. In particular, in scientific papers, tables can sum up novel discoveries and summarize experimental results, making the research comparable and easily understandable by scholars. Since the layout of tables is highly variable, it would be useful to interpret their content and classify them into categories. This could be helpful to directly extract information from scientific papers, for instance comparing performance of some models given their paper result tables. In this work, we address the classification of tables using a Graph Neural Network, exploiting the table structure for the message passing algorithm in use. We evaluate our model on a subset of the Tab2Know dataset. Since it contains few examples manually annotated, we propose data augmentation techniques directly on the table graph structures. We achieve promising preliminary results, proposing a data augmentation method suitable for graph-based table representation.

In this work, we propose a framework that constructs reduced order models for nonlinear structural mechanics in a nonintrusive fashion, and can handle large scale simulations. We identify three steps that are carried out separately in time, and possibly on different devices: (i) the production of high-fidelity solutions by a commercial software, (ii) the offline stage of the model reduction and (iii) the online stage where the reduced order model is exploited. The nonintrusivity assumes that only the displacement field solution is known, and relies on operations on simulation data during the offline phase by using an in-house code. The compatibility with a new commercial code only needs the implementation of a routine converting the mesh and result format into our in-house data format. The nonintrusive capabilities of the framework are demonstrated on numerical experiments using commercial versions of the finite element softwares Zset and Ansys Mechanical. The nonlinear constitutive equations are evaluated by using the same external plugins as for Zset or Ansys Mechanical. The large scale simulations are handled using domain decomposition and parallel computing with distributed memory. The features and performances of the framework are evaluated on two numerical applications involving elastoviscoplastic materials: the second one involves a model of high-pressure blade, where the framework is used to extrapolate cyclic loadings in 6.5 hours, whereas the reference high-fidelity computation would take 9.5 days.

Amid mounting concern about the reliability and credibility of machine learning research, we present a principled framework for making robust and generalizable claims: the multiverse analysis. Our framework builds upon the multiverse analysis (Steegen et al., 2016) introduced in response to psychology's own reproducibility crisis. To efficiently explore high-dimensional and often continuous ML search spaces, we model the multiverse with a Gaussian Process surrogate and apply Bayesian experimental design. Our framework is designed to facilitate drawing robust scientific conclusions about model performance, and thus our approach focuses on exploration rather than conventional optimization. In the first of two case studies, we investigate disputed claims about the relative merit of adaptive optimizers. Second, we synthesize conflicting research on the effect of learning rate on the large batch training generalization gap. For the machine learning community, the multiverse analysis is a simple and effective technique for identifying robust claims, for increasing transparency, and a step toward improved reproducibility.

Document AI aims to automatically analyze documents by leveraging natural language processing and computer vision techniques. One of the major tasks of Document AI is document layout analysis, which structures document pages by interpreting the content and spatial relationships of layout, image, and text. This task can be image-centric, wherein the aim is to identify and label various regions such as authors and paragraphs, or text-centric, where the focus is on classifying individual words in a document. Although there are increasingly sophisticated methods for improving layout analysis, doubts remain about the extent to which their findings can be generalized to a broader context. Specifically, prior work developed systems based on very different architectures, such as transformer-based, graph-based, and CNNs. However, no work has mentioned the effectiveness of these models in a comparative analysis. Moreover, while language-independent Document AI models capable of knowledge transfer have been developed, it remains to be investigated to what degree they can effectively transfer knowledge. In this study, we aim to fill these gaps by conducting a comparative evaluation of state-of-the-art models in document layout analysis and investigating the potential of cross-lingual layout analysis by utilizing machine translation techniques.

Language models and specialized table embedding models have recently demonstrated strong performance on many tasks over tabular data. Researchers and practitioners are keen to leverage these models in many new application contexts; but limited understanding of the strengths and weaknesses of these models, and the table representations they generate, makes the process of finding a suitable model for a given task reliant on trial and error. There is an urgent need to gain a comprehensive understanding of these models to minimize inefficiency and failures in downstream usage. To address this need, we propose Observatory, a formal framework to systematically analyze embedding representations of relational tables. Motivated both by invariants of the relational data model and by statistical considerations regarding data distributions, we define eight primitive properties, and corresponding measures to quantitatively characterize table embeddings for these properties. Based on these properties, we define an extensible framework to evaluate language and table embedding models. We collect and synthesize a suite of datasets and use Observatory to analyze nine such models. Our analysis provides insights into the strengths and weaknesses of learned representations over tables. We find, for example, that some models are sensitive to table structure such as column order, that functional dependencies are rarely reflected in embeddings, and that specialized table embedding models have relatively lower sample fidelity. Such insights help researchers and practitioners better anticipate model behaviors and select appropriate models for their downstream tasks, while guiding researchers in the development of new models.

Currently, high-dimensional data is ubiquitous in data science, which necessitates the development of techniques to decompose and interpret such multidimensional (aka tensor) datasets. Finding a low dimensional representation of the data, that is, its inherent structure, is one of the approaches that can serve to understand the dynamics of low dimensional latent features hidden in the data. Nonnegative RESCAL is one such technique, particularly well suited to analyze self-relational data, such as dynamic networks found in international trade flows. Nonnegative RESCAL computes a low dimensional tensor representation by finding the latent space containing multiple modalities. Estimating the dimensionality of this latent space is crucial for extracting meaningful latent features. Here, to determine the dimensionality of the latent space with nonnegative RESCAL, we propose a latent dimension determination method which is based on clustering of the solutions of multiple realizations of nonnegative RESCAL decompositions. We demonstrate the performance of our model selection method on synthetic data and then we apply our method to decompose a network of international trade flows data from International Monetary Fund and validate the resulting features against empirical facts from economic literature.