Daily Papers

Generative Adversarial Networks (GANs) struggle to generate structured objects like molecules and game maps. The issue is that structured objects must satisfy hard requirements (e.g., molecules must be chemically valid) that are difficult to acquire from examples alone. As a remedy, we propose Constrained Adversarial Networks (CANs), an extension of GANs in which the constraints are embedded into the model during training. This is achieved by penalizing the generator proportionally to the mass it allocates to invalid structures. In contrast to other generative models, CANs support efficient inference of valid structures (with high probability) and allows to turn on and off the learned constraints at inference time. CANs handle arbitrary logical constraints and leverage knowledge compilation techniques to efficiently evaluate the disagreement between the model and the constraints. Our setup is further extended to hybrid logical-neural constraints for capturing very complex constraints, like graph reachability. An extensive empirical analysis shows that CANs efficiently generate valid structures that are both high-quality and novel.

LLM-based LEGO assembly generation requires both semantic grounding and physical feasibility. We identify a data-induced failure mode, PhysHack, in which the assemblies satisfy physical-validity constraints while producing structures that are geometrically misaligned, semantically inconsistent, or poorly calibrated. To address this challenge, we propose a model-based data selection approach that uses only a small fraction of the training data while improving physically grounded LEGO assembly generation. Building on the selected trajectories, we introduce PVPO, a sample-efficient reinforcement learning method that couples physical feasibility with voxel-space geometric rewards. Our results show that physical validity alone is an insufficient proxy for reliable physical reasoning: models can learn to generate valid structures without preserving semantic or geometric fidelity. Experiments across model backbones and test-time scaling settings demonstrate that PVPO improves structural and semantic alignment, physical validity, structural stability, and calibration, while reducing reliance on extensive post-hoc rejection sampling. In particular, results on calibration show that PVPO mitigates PhysHack by making test-time selection more predictive of semantic and structural quality.

We introduce Image2Struct, a benchmark to evaluate vision-language models (VLMs) on extracting structure from images. Our benchmark 1) captures real-world use cases, 2) is fully automatic and does not require human judgment, and 3) is based on a renewable stream of fresh data. In Image2Struct, VLMs are prompted to generate the underlying structure (e.g., LaTeX code or HTML) from an input image (e.g., webpage screenshot). The structure is then rendered to produce an output image (e.g., rendered webpage), which is compared against the input image to produce a similarity score. This round-trip evaluation allows us to quantitatively evaluate VLMs on tasks with multiple valid structures. We create a pipeline that downloads fresh data from active online communities upon execution and evaluates the VLMs without human intervention. We introduce three domains (Webpages, LaTeX, and Musical Scores) and use five image metrics (pixel similarity, cosine similarity between the Inception vectors, learned perceptual image patch similarity, structural similarity index measure, and earth mover similarity) that allow efficient and automatic comparison between pairs of images. We evaluate Image2Struct on 14 prominent VLMs and find that scores vary widely, indicating that Image2Struct can differentiate between the performances of different VLMs. Additionally, the best score varies considerably across domains (e.g., 0.402 on sheet music vs. 0.830 on LaTeX equations), indicating that Image2Struct contains tasks of varying difficulty. For transparency, we release the full results at https://crfm.stanford.edu/helm/image2struct/v1.0.1/.

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep learning-based approaches leading to improvements in blind docking efficiency, these methods have encountered notable challenges, such as limited generalization performance on unseen proteins, the inability to concurrently address the settings of blind docking and site-specific docking, and the frequent occurrence of physical implausibilities such as inter-molecular steric clash. In this study, we introduce DeltaDock, a robust and versatile framework designed for efficient molecular docking to overcome these challenges. DeltaDock operates in a two-step process: rapid initial complex structures sampling followed by multi-scale iterative refinement of the initial structures. In the initial stage, to sample accurate structures with high efficiency, we develop a ligand-dependent binding site prediction model founded on large protein models and graph neural networks. This model is then paired with GPU-accelerated sampling algorithms. The sampled structures are updated using a multi-scale iterative refinement module that captures both protein-ligand atom-atom interactions and residue-atom interactions in the following stage. Distinct from previous geometric deep learning methods that are conditioned on the blind docking setting, DeltaDock demonstrates superior performance in both blind docking and site-specific docking settings. Comprehensive experimental results reveal that DeltaDock consistently surpasses baseline methods in terms of docking accuracy. Furthermore, it displays remarkable generalization capabilities and proficiency for predicting physically valid structures, thereby attesting to its robustness and reliability in various scenarios.

Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool for exploring the organic chemical space in search of potentially electro-active compounds, we present "LLamol", a single novel generative transformer model based on the LLama 2 architecture, which was trained on a 13M superset of organic compounds drawn from diverse public sources. To allow for a maximum flexibility in usage and robustness in view of potentially incomplete data, we introduce "Stochastic Context Learning" as a new training procedure. We demonstrate that the resulting model adeptly handles single- and multi-conditional organic molecule generation with up to four conditions, yet more are possible. The model generates valid molecular structures in SMILES notation while flexibly incorporating three numerical and/or one token sequence into the generative process, just as requested. The generated compounds are very satisfactory in all scenarios tested. In detail, we showcase the model's capability to utilize token sequences for conditioning, either individually or in combination with numerical properties, making LLamol a potent tool for de novo molecule design, easily expandable with new properties.

Generative models have shown remarkable performance in speech enhancement (SE), achieving superior perceptual quality over traditional discriminative approaches. However, existing generative SE approaches often overlook the risk of hallucination under severe noise, leading to incorrect spoken content or inconsistent speaker characteristics, which we term linguistic and acoustic hallucinations, respectively. We argue that linguistic hallucination stems from models' failure to constrain valid phonological structures and it is a more fundamental challenge. While language models (LMs) are well-suited for capturing the underlying speech structure through modeling the distribution of discrete tokens, existing approaches are limited in learning from noise-corrupted representations, which can lead to contaminated priors and hallucinations. To overcome these limitations, we propose the Phonologically Anchored Speech Enhancer (PASE), a generative SE framework that leverages the robust phonological prior embedded in the pre-trained WavLM model to mitigate hallucinations. First, we adapt WavLM into a denoising expert via representation distillation to clean its final-layer features. Guided by the model's intrinsic phonological prior, this process enables robust denoising while minimizing linguistic hallucinations. To further reduce acoustic hallucinations, we train the vocoder with a dual-stream representation: the high-level phonetic representation provides clean linguistic content, while a low-level acoustic representation retains speaker identity and prosody. Experimental results demonstrate that PASE not only surpasses state-of-the-art discriminative models in perceptual quality, but also significantly outperforms prior generative models with substantially lower linguistic and acoustic hallucinations.

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with state-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity inherent to discrete spaces. Using PepTune, we generate diverse, chemically-modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling characteristics on various disease-relevant targets. In total, our results demonstrate that MCTS-guided discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces.

This paper introduces M^{3}-20M, a large-scale Multi-Modal Molecular dataset that contains over 20 million molecules. Designed to support AI-driven drug design and discovery, M^{3}-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit training or fine-tuning large (language) models with superior performance for drug design and discovery. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated by using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M^{3}-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, and GPT-4. Our experimental results show that M^{3}-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than the existing single-modal datasets, which validates the value and potential of M^{3}-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.

The rapid evolution of 3D content creation, encompassing both AI-powered methods and traditional workflows, is driving an unprecedented demand for automated rigging solutions that can keep pace with the increasing complexity and diversity of 3D models. We introduce UniRig, a novel, unified framework for automatic skeletal rigging that leverages the power of large autoregressive models and a bone-point cross-attention mechanism to generate both high-quality skeletons and skinning weights. Unlike previous methods that struggle with complex or non-standard topologies, UniRig accurately predicts topologically valid skeleton structures thanks to a new Skeleton Tree Tokenization method that efficiently encodes hierarchical relationships within the skeleton. To train and evaluate UniRig, we present Rig-XL, a new large-scale dataset of over 14,000 rigged 3D models spanning a wide range of categories. UniRig significantly outperforms state-of-the-art academic and commercial methods, achieving a 215% improvement in rigging accuracy and a 194% improvement in motion accuracy on challenging datasets. Our method works seamlessly across diverse object categories, from detailed anime characters to complex organic and inorganic structures, demonstrating its versatility and robustness. By automating the tedious and time-consuming rigging process, UniRig has the potential to speed up animation pipelines with unprecedented ease and efficiency. Project Page: https://zjp-shadow.github.io/works/UniRig/

Generalization to novel compound tasks under distribution shift is important for deploying transformer-based language models (LMs). This work investigates Chain-of-Thought (CoT) reasoning as a means to enhance OOD generalization. Through controlled experiments across several compound tasks, we reveal three key insights: (1) While QA-trained models achieve near-perfect in-distribution accuracy, their OOD performance degrades catastrophically, even with 10000k+ training examples; (2) the granularity of CoT data strongly correlates with generalization performance; finer-grained CoT data leads to better generalization; (3) CoT exhibits remarkable sample efficiency, matching QA performance with much less (even 80%) data. Theoretically, we demonstrate that compound tasks inherently permit shortcuts in Q-A data that misalign with true reasoning principles, while CoT forces internalization of valid dependency structures, and thus can achieve better generalization. Further, we show that transformer positional embeddings can amplify generalization by emphasizing subtask condition recurrence in long CoT sequences. Our combined theoretical and empirical analysis provides compelling evidence for CoT reasoning as a crucial training paradigm for enabling LM generalization under real-world distributional shifts for compound tasks.

Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential solutions to these challenges. One promising algorithm is DrugGPT, a transformer-based model, that generates small molecules for input protein sequences. Although promising, it generates both chemically valid and invalid structures and does not incorporate the features of approved drugs, resulting in time-consuming and inefficient drug discovery. To address these issues, we introduce DrugGen, an enhanced model based on the DrugGPT structure. DrugGen is fine-tuned on approved drug-target interactions and optimized with proximal policy optimization. By giving reward feedback from protein-ligand binding affinity prediction using pre-trained transformers (PLAPT) and a customized invalid structure assessor, DrugGen significantly improves performance. Evaluation across multiple targets demonstrated that DrugGen achieves 100% valid structure generation compared to 95.5% with DrugGPT and produced molecules with higher predicted binding affinities (7.22 [6.30-8.07]) compared to DrugGPT (5.81 [4.97-6.63]) while maintaining diversity and novelty. Docking simulations further validate its ability to generate molecules targeting binding sites effectively. For example, in the case of fatty acid-binding protein 5 (FABP5), DrugGen generated molecules with superior docking scores (FABP5/11, -9.537 and FABP5/5, -8.399) compared to the reference molecule (Palmitic acid, -6.177). Beyond lead compound generation, DrugGen also shows potential for drug repositioning and creating novel pharmacophores for existing targets. By producing high-quality small molecules, DrugGen provides a high-performance medium for advancing pharmaceutical research and drug discovery.

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

Articulated objects are central to interactive 3D applications, including embodied AI, robotics, and VR/AR, where functional part decomposition and kinematic motion are essential. Yet producing high-fidelity articulated assets remains difficult to scale because it requires reliable part decomposition and kinematic rigging. Existing approaches largely fall into two paradigms: optimization-based reconstruction or distillation, which can be accurate but often takes tens of minutes to hours per instance, and inference-time methods that rely on template or part retrieval, producing plausible results that may not match the specific structure and appearance in the input observation. We introduce a part-centric generative framework for articulated object creation that synthesizes part geometry, composition, and articulation under explicit part-aware conditioning. Our representation models an object as a set of movable parts, each encoded by latent tokens augmented with part identity and articulation cues. Conditioned on a single image, the model generates articulated 3D assets that preserve instance-level correspondence while maintaining valid part structure and motion. The resulting approach avoids per-instance optimization, enables fast feed-forward inference, and supports controllable assembly and articulation, which are important for embodied interaction. Experiments on common articulated categories (e.g., drawers and doors) show improved input consistency, part accuracy, and articulation plausibility over optimization-based and retrieval-driven baselines, while substantially reducing inference time.

Deep generative models have shown significant promise in generating valid 3D molecular structures, with the GEOM-Drugs dataset serving as a key benchmark. However, current evaluation protocols suffer from critical flaws, including incorrect valency definitions, bugs in bond order calculations, and reliance on force fields inconsistent with the reference data. In this work, we revisit GEOM-Drugs and propose a corrected evaluation framework: we identify and fix issues in data preprocessing, construct chemically accurate valency tables, and introduce a GFN2-xTB-based geometry and energy benchmark. We retrain and re-evaluate several leading models under this framework, providing updated performance metrics and practical recommendations for future benchmarking. Our results underscore the need for chemically rigorous evaluation practices in 3D molecular generation. Our recommended evaluation methods and GEOM-Drugs processing scripts are available at https://github.com/isayevlab/geom-drugs-3dgen-evaluation.

In diffraction-based crystal structure analysis, thermal ellipsoids, quantified via Anisotropic Displacement Parameters (ADPs), are critical yet challenging to determine. ADPs capture atomic vibrations, reflecting thermal and structural properties, but traditional computation is often expensive. This paper introduces CartNet, a novel graph neural network (GNN) for efficiently predicting crystal properties by encoding atomic geometry into Cartesian coordinates alongside the crystal temperature. CartNet integrates a neighbour equalization technique to emphasize covalent and contact interactions, and a Cholesky-based head to ensure valid ADP predictions. We also propose a rotational SO(3) data augmentation strategy during training to handle unseen orientations. An ADP dataset with over 200,000 experimental crystal structures from the Cambridge Structural Database (CSD) was curated to validate the approach. CartNet significantly reduces computational costs and outperforms existing methods in ADP prediction by 10.87%, while delivering a 34.77% improvement over theoretical approaches. We further evaluated CartNet on other datasets covering formation energy, band gap, total energy, energy above the convex hull, bulk moduli, and shear moduli, achieving 7.71% better results on the Jarvis Dataset and 13.16% on the Materials Project Dataset. These gains establish CartNet as a state-of-the-art solution for diverse crystal property predictions. Project website and online demo: https://www.ee.ub.edu/cartnet

The last few years have seen the development of numerous deep learning-based protein-ligand docking methods. They offer huge promise in terms of speed and accuracy. However, despite claims of state-of-the-art performance in terms of crystallographic root-mean-square deviation (RMSD), upon closer inspection, it has become apparent that they often produce physically implausible molecular structures. It is therefore not sufficient to evaluate these methods solely by RMSD to a native binding mode. It is vital, particularly for deep learning-based methods, that they are also evaluated on steric and energetic criteria. We present PoseBusters, a Python package that performs a series of standard quality checks using the well-established cheminformatics toolkit RDKit. Only methods that both pass these checks and predict native-like binding modes should be classed as having "state-of-the-art" performance. We use PoseBusters to compare five deep learning-based docking methods (DeepDock, DiffDock, EquiBind, TankBind, and Uni-Mol) and two well-established standard docking methods (AutoDock Vina and CCDC Gold) with and without an additional post-prediction energy minimisation step using a molecular mechanics force field. We show that both in terms of physical plausibility and the ability to generalise to examples that are distinct from the training data, no deep learning-based method yet outperforms classical docking tools. In addition, we find that molecular mechanics force fields contain docking-relevant physics missing from deep-learning methods. PoseBusters allows practitioners to assess docking and molecular generation methods and may inspire new inductive biases still required to improve deep learning-based methods, which will help drive the development of more accurate and more realistic predictions.

Generative modeling has emerged as a promising approach for crystal structure discovery. However, existing LLM-based generative models struggle with low-level atomic precision, while diffusion-based methods fall short in integrating high-level scientific knowledge. As a result, generated structures are often invalid, unstable, or do not possess desirable properties. To address this gap, we propose CrystalReasoner (\method), an end-to-end LLM framework that generates crystal structures from natural language instructions through reasoning and alignment. \method introduces physical priors as thinking tokens, which include crystallographic symmetry, local coordination environments and predicted physical properties before generating atomic coordinates. This bridges the gap between natural language and 3D structures. \method then employs reinforcement learning (RL) with a multi-objective, dense reward function to align generation with physical validity, chemical consistency, and thermodynamic stability. For property-conditioned tasks, we design task-specific reward functions and train specialized models for discrete constraints (e.g., space group) and continuous properties (e.g., elasticity, thermal expansion). Empirical results demonstrate that compared to prior works and baselines without thinking traces or RL, \method obtains better performance on diverse metrics, triples S.U.N. ratio, and achieves better performance for property conditioned generation. \method also exhibits adaptive reasoning, increasing reasoning lengths as the number of atoms increases. Our work demonstrates the potential of leveraging thinking traces and RL for generating valid, stable, and property-conditioned crystal structures. Please see our work at https://crystalreasoner.github.io/ .

Metal-organic frameworks (MOFs) are of immense interest in applications such as gas storage and carbon capture due to their exceptional porosity and tunable chemistry. Their modular nature has enabled the use of template-based methods to generate hypothetical MOFs by combining molecular building blocks in accordance with known network topologies. However, the ability of these methods to identify top-performing MOFs is often hindered by the limited diversity of the resulting chemical space. In this work, we propose MOFDiff: a coarse-grained (CG) diffusion model that generates CG MOF structures through a denoising diffusion process over the coordinates and identities of the building blocks. The all-atom MOF structure is then determined through a novel assembly algorithm. Equivariant graph neural networks are used for the diffusion model to respect the permutational and roto-translational symmetries. We comprehensively evaluate our model's capability to generate valid and novel MOF structures and its effectiveness in designing outstanding MOF materials for carbon capture applications with molecular simulations.

Interpretability research on large language models (LLMs) has yielded important insights into model behaviour, yet recurring pitfalls persist: findings that do not generalise, and causal interpretations that outrun the evidence. Our position is that causal inference specifies what constitutes a valid mapping from model activations to invariant high-level structures, the data or assumptions needed to achieve it, and the inferences it can support. Specifically, Pearl's causal hierarchy clarifies what an interpretability study can justify. Observations establish associations between model behaviour and internal components. Interventions (e.g., ablations or activation patching) support claims how these edits affect a behavioural metric (e.g., average change in token probabilities) over a set of prompts. However, counterfactual claims -- i.e., asking what the model output would have been for the same prompt under an unobserved intervention -- remain largely unverifiable without controlled supervision. We show how causal representation learning (CRL) operationalises this hierarchy, specifying which variables are recoverable from activations and under what assumptions. Together, these motivate a diagnostic framework that helps practitioners select methods and evaluations matching claims to evidence such that findings generalise.

We present CAGE (Continuity-Aware edGE) network, a robust framework for reconstructing vector floorplans directly from point-cloud density maps. Traditional corner-based polygon representations are highly sensitive to noise and incomplete observations, often resulting in fragmented or implausible layouts.Recent line grouping methods leverage structural cues to improve robustness but still struggle to recover fine geometric details. To address these limitations,we propose a native edge-centric formulation, modeling each wall segment as a directed, geometrically continuous edge. This representation enables inference of coherent floorplan structures, ensuring watertight, topologically valid room boundaries while improving robustness and reducing artifacts. Towards this design, we develop a dual-query transformer decoder that integrates perturbed and latent queries within a denoising framework, which not only stabilizes optimization but also accelerates convergence. Extensive experiments on Structured3D and SceneCAD show that CAGE achieves state-of-the-art performance, with F1 scores of 99.1% (rooms), 91.7% (corners), and 89.3% (angles). The method also demonstrates strong cross-dataset generalization, underscoring the efficacy of our architectural innovations. Code and pretrained models are available on our project page: https://github.com/ee-Liu/CAGE.git.

Language models are widely used in chemistry for molecular property prediction and small-molecule generation, yet Natural Products (NPs) remain underexplored despite their importance in drug discovery. To address this gap, we develop NP-specific chemical language models (NPCLMs) by pre-training state-space models (Mamba and Mamba-2) and comparing them with transformer baselines (GPT). Using a dataset of about 1M NPs, we present the first systematic comparison of selective state-space models and transformers for NP-focused tasks, together with eight tokenization strategies including character-level, Atom-in-SMILES (AIS), byte-pair encoding (BPE), and NP-specific BPE. We evaluate molecule generation (validity, uniqueness, novelty) and property prediction (membrane permeability, taste, anti-cancer activity) using MCC and AUC-ROC. Mamba generates 1-2 percent more valid and unique molecules than Mamba-2 and GPT, with fewer long-range dependency errors, while GPT yields slightly more novel structures. For property prediction, Mamba variants outperform GPT by 0.02-0.04 MCC under random splits, while scaffold splits show comparable performance. Results demonstrate that domain-specific pre-training on about 1M NPs can match models trained on datasets over 100 times larger.

While vision-language models excel at general multimodal understanding, they still struggle with visual spatial planning. We attribute this to a perception-reasoning modality gap: visual planning requires models to infer latent state structures from pixels and then reason over the recovered structure to produce valid actions, whereas symbolic planning directly leverages explicit objects and constraints. This creates dual bottlenecks in visual state recovery and multi-step planning. To address this, we propose MGSD, a two-stage modality-gap-aware self-distillation framework. First, a cold-start grounding stage equips the visual student with reliable state representations, minimizing early perception noise. Second, a privileged teacher transfers planning capabilities via on-policy distillation, using explicit symbolic states to supervise the student's own visual rollout prefixes. Crucially, symbolic data is used strictly during training, leaving inference purely visual. Experiments on visual planning benchmarks show that MGSD consistently improves visual planning across both 4B and 8B backbones, raising the macro average by 19.3% and 18.4%, respectively. The resulting models narrow the gap to symbolic-input upper bounds, while ablations and diagnostics confirm that the improvement comes from both visual state recovery and optimal-path reasoning. These results suggest that modality-gap-aware self-distillation improves not only how models perceive actionable states, but also how they plan over the inferred structure. Code is available at https://github.com/Oranger-l/MGSD.

Many complicated network problems can be easily understood on small networks. Difficulties arise when small networks are combined into larger ones. Fortunately, the mathematical theory of sheaves was constructed to address just this kind of situation; it extends locally-defined structures to globally valid inferences by way of consistency relations. This paper exhibits examples in network monitoring and filter hardware where sheaves have useful descriptive power.

Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reaction and retrosynthesis. While drug editing, a critical task in the drug discovery pipeline, remains largely unexplored. To bridge this gap, we propose ChatDrug, a framework to facilitate the systematic investigation of drug editing using LLMs. ChatDrug jointly leverages a prompt module, a retrieval and domain feedback (ReDF) module, and a conversation module to streamline effective drug editing. We empirically show that ChatDrug reaches the best performance on 33 out of 39 drug editing tasks, encompassing small molecules, peptides, and proteins. We further demonstrate, through 10 case studies, that ChatDrug can successfully identify the key substructures (e.g., the molecule functional groups, peptide motifs, and protein structures) for manipulation, generating diverse and valid suggestions for drug editing. Promisingly, we also show that ChatDrug can offer insightful explanations from a domain-specific perspective, enhancing interpretability and enabling informed decision-making. This research sheds light on the potential of ChatGPT and conversational LLMs for drug editing. It paves the way for a more efficient and collaborative drug discovery pipeline, contributing to the advancement of pharmaceutical research and development.

The Abstraction and Reasoning Corpus (ARC) is a general artificial intelligence benchmark that poses difficulties for pure machine learning methods due to its requirement for fluid intelligence with a focus on reasoning and abstraction. In this work, we introduce an ARC solver, Generalized Planning for Abstract Reasoning (GPAR). It casts an ARC problem as a generalized planning (GP) problem, where a solution is formalized as a planning program with pointers. We express each ARC problem using the standard Planning Domain Definition Language (PDDL) coupled with external functions representing object-centric abstractions. We show how to scale up GP solvers via domain knowledge specific to ARC in the form of restrictions over the actions model, predicates, arguments and valid structure of planning programs. Our experiments demonstrate that GPAR outperforms the state-of-the-art solvers on the object-centric tasks of the ARC, showing the effectiveness of GP and the expressiveness of PDDL to model ARC problems. The challenges provided by the ARC benchmark motivate research to advance existing GP solvers and understand new relations with other planning computational models. Code is available at github.com/you68681/GPAR.

Deployed language models must produce outputs that are both correct and format-compliant. We study this structured-output reliability gap using two mathematical benchmarks -- GSM8K and MATH -- as a controlled testbed: ground truth is unambiguous and the output contract is strict (JSON with required fields). We evaluate three 7-9B models under five prompting strategies and report output accuracy -- the joint event of mathematical correctness and valid JSON structure -- as the primary metric. A systematic format failure emerges: NAIVE prompting (no system prompt) achieves up to 85% task accuracy on GSM8K but 0% output accuracy across all models and datasets. REFERENCE prompting (a minimal hand-written JSON format prompt) fares little better, yielding 0% output accuracy for two of four models tested. Constrained decoding enforces syntactic validity but incurs 3.6x-8.2x latency overhead and in several settings degrades task performance substantially. To overcome this limitation, we developed AloLab, an iterative system-prompt optimizer (meta-agent: Claude Sonnet 4.5) requiring only black-box API access to the target model; it reaches 84-87% output accuracy on GSM8K and 34-40% on MATH across five independent runs per model, with 29/30 paired McNemar comparisons against the best static prompt significant at p < 0.05, at near-NAIVE inference latency and without model fine-tuning. The same format failure extends to GPT-4o (OpenAI, 2024), a proprietary closed-source model: REFERENCE achieves 0% output accuracy due to systematic markdown-fence wrapping, while AloLab reaches 95.2% [94.8, 95.6]. An ablation replacing the Sonnet 4.5 meta-agent with Claude 3 Haiku reduces mean output accuracy to 61.0% and increases run-to-run standard deviation from <1 pp to 21.8 pp, confirming that meta-agent capability is a primary driver of optimization quality.

We give a conceptual treatment of the notion of joints, marginals, and independence in the setting of categorical probability. This is achieved by endowing the usual probability monads (like the Giry monad) with a monoidal and an opmonoidal structure, mutually compatible (i.e. a bimonoidal structure). If the underlying monoidal category is cartesian monoidal, a bimonoidal structure is given uniquely by a commutative strength. However, if the underlying monoidal category is not cartesian monoidal, a strength is not enough to guarantee all the desired properties of joints and marginals. A bimonoidal structure is then the correct requirement for the more general case. We explain the theory and the operational interpretation, with the help of the graphical calculus for monoidal categories. We give a definition of stochastic independence based on the bimonoidal structure, compatible with the intuition and with other approaches in the literature for cartesian monoidal categories. We then show as an example that the Kantorovich monad on the category of complete metric spaces is a bimonoidal monad for a non-cartesian monoidal structure.

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.

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

Structural modeling is a fundamental component of computational engineering science, in which even minor physical inconsistencies or specification violations may invalidate downstream simulations. The potential of large language models (LLMs) for automatic generation of modeling code has been demonstrated. However, non-executable or physically inconsistent outputs remain prevalent under stringent engineering constraints. A framework for physics-consistent automatic building modeling is therefore proposed, integrating domain knowledge construction, constraint-oriented model alignment, and verification-driven evaluation. CivilInstruct is introduced as a domain-specific dataset that formalizes structural engineering knowledge and constraint reasoning to enable simulation-ready model generation. A two-stage fine-tuning strategy is further employed to enforce constraint satisfaction and application programming interface compliance, substantially reducing hallucinated and non-conforming outputs. MBEval is presented as a verification-driven benchmark that evaluates executability and structural dynamics consistency through closed-loop validation. Experimental results show consistent improvements over baselines across rigorous verification metrics. Our code is available at https://github.com/Jovanqing/AutoBM.

Tables condense key transactional and administrative information into compact layouts, but practical extraction requires more than text recognition: systems must also recover structure (rows, columns, merged cells, headers) and interpret roles such as line items, subtotals, and totals under common capture artifacts. Many existing resources for table structure recognition and TableVQA are built from clean digital-born sources or rendered tables, and therefore only partially reflect noisy administrative conditions. We introduce DenTab, a dataset of 2{,}000 cropped table images from dental estimates with high-quality HTML annotations, enabling evaluation of table recognition (TR) and table visual question answering (TableVQA) on the same inputs. DenTab includes 2{,}208 questions across eleven categories spanning retrieval, aggregation, and logic/consistency checks. We benchmark 16 systems, including 14 vision--language models (VLMs) and two OCR baselines. Across models, strong structure recovery does not consistently translate into reliable performance on multi-step arithmetic and consistency questions, and these reasoning failures persist even when using ground-truth HTML table inputs. To improve arithmetic reliability without training, we propose the Table Router Pipeline, which routes arithmetic questions to deterministic execution. The pipeline combines (i) a VLM that produces a baseline answer, a structured table representation, and a constrained table program with (ii) a rule-based executor that performs exact computation over the parsed table. The source code and dataset will be made publicly available at https://github.com/hamdilaziz/DenTab.

JSON Schema is an important, evolving standard schema language for families of JSON documents. It is based on a complex combination of structural and Boolean assertions, and features negation and recursion. The static analysis of JSON Schema documents comprises practically relevant problems, including schema satisfiability, inclusion, and equivalence. These three problems can be reduced to witness generation: given a schema, generate an element of the schema, if it exists, and report failure otherwise. Schema satisfiability, inclusion, and equivalence have been shown to be decidable, by reduction to reachability in alternating tree automata. However, no witness generation algorithm has yet been formally described. We contribute a first, direct algorithm for JSON Schema witness generation. We study its effectiveness and efficiency, in experiments over several schema collections, including thousands of real-world schemas. Our focus is on the completeness of the language, where we only exclude the uniqueItems operator, and on the ability of the algorithm to run in a reasonable time on a large set of real-world examples, despite the exponential complexity of the underlying problem.

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally matter engineering -- generally denoted as inverse design -- was based massively on human intuition and high-throughput virtual screening. The last few years have seen the emergence of significant interest in computer-inspired designs based on evolutionary or deep learning methods. The major challenge here is that the standard strings molecular representation SMILES shows substantial weaknesses in that task because large fractions of strings do not correspond to valid molecules. Here, we solve this problem at a fundamental level and introduce SELFIES (SELF-referencIng Embedded Strings), a string-based representation of molecules which is 100\% robust. Every SELFIES string corresponds to a valid molecule, and SELFIES can represent every molecule. SELFIES can be directly applied in arbitrary machine learning models without the adaptation of the models; each of the generated molecule candidates is valid. In our experiments, the model's internal memory stores two orders of magnitude more diverse molecules than a similar test with SMILES. Furthermore, as all molecules are valid, it allows for explanation and interpretation of the internal working of the generative models.

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.

We show how to "compile" human-readable programs into standard decoder-only transformer models. Our compiler, Tracr, generates models with known structure. This structure can be used to design experiments. For example, we use it to study "superposition" in transformers that execute multi-step algorithms. Additionally, the known structure of Tracr-compiled models can serve as ground-truth for evaluating interpretability methods. Commonly, because the "programs" learned by transformers are unknown it is unclear whether an interpretation succeeded. We demonstrate our approach by implementing and examining programs including computing token frequencies, sorting, and parenthesis checking. We provide an open-source implementation of Tracr at https://github.com/google-deepmind/tracr.

Many deployments must compare candidate language models for safety before a labeled benchmark exists for the relevant language, sector, or regulatory regime. We formalize this setting as benchmarkless comparative safety scoring and specify the contract under which a scenario-based audit can be interpreted as deployment evidence. Scores are valid only under a fixed scenario pack, rubric, auditor, judge, sampling configuration, and rerun budget. Because no labels are available, we replace ground-truth agreement with an instrumental-validity chain: responsiveness to a controlled safe-versus-abliterated contrast, dominance of target-driven variance over auditor and judge artifacts, and stability across reruns. We instantiate the chain in SimpleAudit, a local-first scoring instrument, and validate it on a Norwegian safety pack. Safe and abliterated targets separate with AUROC values between 0.89 and 1.00, target identity is the dominant variance component (η^2 approx 0.52), and severity profiles stabilize by ten reruns. Applying the same chain to Petri shows that it admits both tools. The substantial differences arise upstream of the chain, in claim-contract enforcement and deployment fit. A Norwegian public-sector procurement case comparing Borealis and Gemma 3 demonstrates the resulting evidence in practice: the safer model depends on scenario category and risk measure. Consequently, scores, matched deltas, critical rates, uncertainty, and the auditor and judge used must be reported together rather than collapsed into a single ranking.

In industrial procurement, an LLM answer is useful only if it survives a standards check: recommended material must match operating condition, every parameter must respect a regulated threshold, and no procedure may contradict a safety clause. Partial correctness can mask safety-critical contradictions that aggregate LLM benchmarks rarely capture. We introduce IndustryBench, a 2,049-item benchmark for industrial procurement QA in Chinese, grounded in Chinese national standards (GB/T) and structured industrial product records, organized by seven capability dimensions, ten industry categories, and panel-derived difficulty tiers, with item-aligned English, Russian, and Vietnamese renderings. Our construction pipeline rejects 70.3% of LLM-generated candidates at a search-based external-verification stage, calibrating how unreliable industrial QA remains after LLM-only filtering.Our evaluation decouples raw correctness, scored by a Qwen3-Max judge validated at κ_w = 0.798 against a domain expert, from a separate safety-violation (SV) check against source texts. Across 17 models in Chinese and an 8-model intersection over four languages, we find: (i) the best system reaches only 2.083 on the 0--3 rubric, leaving substantial headroom; (ii) Standards & Terminology is the most persistent capability weakness and survives item-aligned translation; (iii) extended reasoning lowers safety-adjusted scores for 12 of 13 models, primarily by introducing unsupported safety-critical details into longer final answers; and (iv) safety-violation rates reshuffle the leaderboard -- GPT-5.4 climbs from rank 6 to rank 3 after SV adjustment, while Kimi-k2.5-1T-A32B drops seven positions.Industrial LLM evaluation therefore requires source-grounded, safety-aware diagnosis rather than aggregate accuracy. We release IndustryBench with all prompts, scoring scripts, and dataset documentation.

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.

Automated analysis for engineering structures offers considerable potential for boosting efficiency by minimizing repetitive tasks. Although AI-driven methods are increasingly common, no systematic framework yet leverages Large Language Models (LLMs) for automatic structural analysis. To address this gap, we propose a novel framework that integrates LLMs with structural analysis software. LLMs serve as the core engine: they parse structural descriptions from text and translate them into executable Python scripts. Moreover, the framework integrates the generative capabilities of LLMs with code-based finite element (FE) tools like OpenSeesPy. It employs domain-specific prompt design and in-context learning strategies to enhance the LLM's problem-solving capabilities and generative stability, enabling fully automated structural analysis from descriptive text to model outputs. In our experiments, we introduce a well-curated small-scale benchmark dataset of 20 structural analysis word problems (SAWPs) with ground-truth solutions and evaluate the performance of different LLMs within our framework in solving these SAWPs. The role of system instructions, crafted by structural engineers, is also investigated to understand their impact on LLM-driven structural analysis. Additionally, the generative stability of our framework is examined. Through multiple validation experiments on the benchmark, our results demonstrate that the proposed framework can substantially increase the level of automation in solving SAWPs compared to traditional methods. Quantitatively, the framework, built on GPT-4o, achieved 100% accuracy, surpassing GPT-4 (85%), Gemini 1.5 Pro (80%), and Llama-3.3 (30%) on the test examples. Furthermore, integrating domain-specific instructions enhanced performance by 30% on problems with asymmetrical structural configurations.

In order to properly train a machine learning model, data must be properly collected. To guarantee a proper data collection, verifying that the collected data set holds certain properties is a possible solution. For example, guaranteeing that the data set contains samples across the whole input space, or that the data set is balanced w.r.t. different classes. We present a formal approach for verifying a set of arbitrarily stated properties over a data set. The proposed approach relies on the transformation of the data set into a first order logic formula, which can be later verified w.r.t. the different properties also stated in the same logic. A prototype tool, which uses the z3 solver, has been developed; the prototype can take as an input a set of properties stated in a formal language and formally verify a given data set w.r.t. to the given set of properties. Preliminary experimental results show the feasibility and performance of the proposed approach, and furthermore the flexibility for expressing properties of interest.

The effective utilization of structured data, integral to corporate data strategies, has been challenged by the rise of large language models (LLMs) capable of processing unstructured information. This shift prompts the question: can LLMs interpret structured data directly in its unstructured form? We propose an automatic evaluation data generation method for assessing LLMs' reasoning capabilities on structure-rich text to explore this. Our approach supports 8 structured languages and 29 tasks, generating data with adjustable complexity through controllable nesting and structural width. We introduce StrucText-Eval, a benchmark containing 5,800 pre-generated and annotated samples designed to evaluate how well LLMs understand and reason through structured text. StrucText-Eval is divided into two suites: a regular Test suite (3,712 samples) and a Test-Hard suite (2,088 samples), the latter emphasizing the gap between human and model performance on more complex tasks. Experimental results show that while open-source LLMs achieve a maximum accuracy of 74.9\% on the standard dataset, their performance drops significantly to 45.8\% on the harder dataset. In contrast, human participants reach an accuracy of 92.6\% on StrucText-Eval-Hard, highlighting LLMs' current limitations in handling intricate structural information. The benchmark and generation codes are open sourced in https://github.com/MikeGu721/StrucText-Eval

Large Language Models (LLMs) have demonstrated remarkable capabilities in natural language generation and reasoning. However, their integration into automated software ecosystems is often hindered by the "Structure Gap" - the inherent tension between the probabilistic nature of token generation and the deterministic requirements of structured data formats (e.g., JSON, XML). Traditional Supervised Fine-Tuning (SFT) often fails to enforce strict syntactic constraints, leading to "hallucinated" keys or malformed structures, while constrained decoding methods impose significant inference latency. In this paper, we propose a lightweight, efficient Reinforcement Learning (RL) framework to bridge this gap. We introduce a novel Multi-dimensional Reward Function that decomposes the structured output task into a hierarchy of constraints: structural integrity, format correctness, content accuracy, and validity. Leveraging Gradient Regularized Policy Optimization (GRPO), we enable the model to internalize these constraints without the need for a separate critic network, reducing peak VRAM usage by 40% compared to PPO. We validate our approach on multiple tasks, including complex recipe generation and structured math reasoning (GSM8K-JSON). Experimental results demonstrate that our method achieves 89.7% structural accuracy and 92.1% JSON validity, significantly outperforming both zero-shot baselines (e.g., GPT-3.5) and SFT on larger models like LLaMA-3-8B. Furthermore, we provide a detailed analysis of training dynamics, revealing a distinct self-paced curriculum where the model sequentially acquires syntactic proficiency before semantic accuracy. Our model is publicly available at https://huggingface.co/Freakz3z/Qwen-JSON.

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

In this paper, we introduce fundamental notions of homotopy theory, including homotopy excision and the Freudenthal suspension theorem. We then explore framed cobordism and its connection to stable homotopy groups of spheres through the Pontryagin-Thom construction. Using this framework, we compute the stable stems in dimensions 0, 1, and 2. This work is primarily expository, revisiting proofs from Pont1 with slight modifications incorporating modern notation. Furthermore, in the final section, we discuss 2-dimensional framed manifolds with Arf invariant one and examine why the result of Pont2 regarding π_2^S is incorrect.

A formal system called cologic is proposed for the study of compacta. A counterpart of countable model theory is developed for this system, and it is applied to model theory of the pseudo-arc.

The ideal LLM content moderation system would be both structurally interpretable (so its decisions can be explained to users) and steerable (to reflect a community's values or align to safety standards). However, current systems fall short on both of these dimensions. To address this gap, we present SafetyAnalyst, a novel LLM safety moderation framework. Given a prompt, SafetyAnalyst creates a structured "harm-benefit tree," which identifies 1) the actions that could be taken if a compliant response were provided, 2) the harmful and beneficial effects of those actions (along with their likelihood, severity, and immediacy), and 3) the stakeholders that would be impacted by those effects. It then aggregates this structured representation into a harmfulness score based on a parameterized set of safety preferences, which can be transparently aligned to particular values. Using extensive harm-benefit features generated by SOTA LLMs on 19k prompts, we fine-tuned an open-weight LM to specialize in generating harm-benefit trees through symbolic knowledge distillation. On a comprehensive set of prompt safety benchmarks, we show that our system (average F1=0.75) outperforms existing LLM safety moderation systems (average F1<0.72) on prompt harmfulness classification, while offering the additional advantages of interpretability and steerability.

Recent works on structured text translation remain limited to the sentence level, as they struggle to effectively handle the complex document-level XML or HTML structures. To address this, we propose Format Reinforcement Learning (FormatRL), which employs Group Relative Policy Optimization on top of a supervised fine-tuning model to directly optimize novel structure-aware rewards: 1) TreeSim, which measures structural similarity between predicted and reference XML trees and 2) Node-chrF, which measures translation quality at the level of XML nodes. Additionally, we apply StrucAUC, a fine-grained metric distinguishing between minor errors and major structural failures. Experiments on the SAP software-documentation benchmark demonstrate improvements across six metrics and an analysis further shows how different reward functions contribute to improvements in both structural and translation quality.

The strive to make AI applications "safe" has led to the development of safety-measures as the main or even sole normative requirement of their permissible use. Similar can be attested to the latest version of chatbots, such as chatGPT. In this view, if they are "safe", they are supposed to be permissible to deploy. This approach, which we call "safety-normativity", is rather limited in solving the emerging issues that chatGPT and other chatbots have caused thus far. In answering this limitation, in this paper we argue for limiting chatbots in the range of topics they can chat about according to the normative concept of appropriateness. We argue that rather than looking for "safety" in a chatbot's utterances to determine what they may and may not say, we ought to assess those utterances according to three forms of appropriateness: technical-discursive, social, and moral. We then spell out what requirements for chatbots follow from these forms of appropriateness to avoid the limits of previous accounts: positionality, acceptability, and value alignment (PAVA). With these in mind, we may be able to determine what a chatbot may and may not say. Lastly, one initial suggestion is to use challenge sets, specifically designed for appropriateness, as a validation method.

Derived datasets can be defined implicitly or explicitly. An implicit definition (of dataset O in terms of datasets I) is a logical specification involving the source data I and the interface data O. It is a valid definition of O in terms of I, if any two models of the specification agreeing on I agree on O. In contrast, an explicit definition is a query that produces O from I. Variants of Beth's theorem state that one can convert implicit definitions to explicit ones. Further, this conversion can be done effectively given a proof witnessing implicit definability in a suitable proof system. We prove the analogous effective implicit-to-explicit result for nested relations: implicit definitions, given in the natural logic for nested relations, can be effectively converted to explicit definitions in the nested relational calculus NRC. As a consequence, we can effectively extract rewritings of NRC queries in terms of NRC views, given a proof witnessing that the query is determined by the views.

Engineering efficient implementations of compact and succinct structures is a time-consuming and challenging task, since there is no standard library of easy-to- use, highly optimized, and composable components. One consequence is that measuring the practical impact of new theoretical proposals is a difficult task, since older base- line implementations may not rely on the same basic components, and reimplementing from scratch can be very time-consuming. In this paper we present a framework for experimentation with succinct data structures, providing a large set of configurable components, together with tests, benchmarks, and tools to analyze resource requirements. We demonstrate the functionality of the framework by recomposing succinct solutions for document retrieval.

Semi-structured tables, widely used in real-world applications (e.g., financial reports, medical records, transactional orders), often involve flexible and complex layouts (e.g., hierarchical headers and merged cells). These tables generally rely on human analysts to interpret table layouts and answer relevant natural language questions, which is costly and inefficient. To automate the procedure, existing methods face significant challenges. First, methods like NL2SQL require converting semi-structured tables into structured ones, which often causes substantial information loss. Second, methods like NL2Code and multi-modal LLM QA struggle to understand the complex layouts of semi-structured tables and cannot accurately answer corresponding questions. To this end, we propose ST-Raptor, a tree-based framework for semi-structured table question answering using large language models. First, we introduce the Hierarchical Orthogonal Tree (HO-Tree), a structural model that captures complex semi-structured table layouts, along with an effective algorithm for constructing the tree. Second, we define a set of basic tree operations to guide LLMs in executing common QA tasks. Given a user question, ST-Raptor decomposes it into simpler sub-questions, generates corresponding tree operation pipelines, and conducts operation-table alignment for accurate pipeline execution. Third, we incorporate a two-stage verification mechanism: forward validation checks the correctness of execution steps, while backward validation evaluates answer reliability by reconstructing queries from predicted answers. To benchmark the performance, we present SSTQA, a dataset of 764 questions over 102 real-world semi-structured tables. Experiments show that ST-Raptor outperforms nine baselines by up to 20% in answer accuracy. The code is available at https://github.com/weAIDB/ST-Raptor.

As AI systems become more advanced, companies and regulators will make difficult decisions about whether it is safe to train and deploy them. To prepare for these decisions, we investigate how developers could make a 'safety case,' which is a structured rationale that AI systems are unlikely to cause a catastrophe. We propose a framework for organizing a safety case and discuss four categories of arguments to justify safety: total inability to cause a catastrophe, sufficiently strong control measures, trustworthiness despite capability to cause harm, and -- if AI systems become much more powerful -- deference to credible AI advisors. We evaluate concrete examples of arguments in each category and outline how arguments could be combined to justify that AI systems are safe to deploy.

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.

Sentence-level human value detection is typically framed as multi-label classification over Schwartz values, but it remains unclear whether Schwartz higher-order (HO) categories provide usable structure. We study this under a strict compute-frugal budget (single 8 GB GPU) on ValueEval'24 / ValuesML (74K English sentences). We compare (i) direct supervised transformers, (ii) HOrightarrowvalues pipelines that enforce the hierarchy with hard masks, and (iii) PresencerightarrowHOrightarrowvalues cascades, alongside low-cost add-ons (lexica, short context, topics), label-wise threshold tuning, small instruction-tuned LLM baselines (le10B), QLoRA, and simple ensembles. HO categories are learnable from single sentences (e.g., the easiest bipolar pair reaches Macro-F_1approx0.58), but hard hierarchical gating is not a reliable win: it often reduces end-task Macro-F_1 via error compounding and recall suppression. In contrast, label-wise threshold tuning is a high-leverage knob (up to +0.05 Macro-F_1), and small transformer ensembles provide the most consistent additional gains (up to +0.02 Macro-F_1). Small LLMs lag behind supervised encoders as stand-alone systems, yet can contribute complementary errors in cross-family ensembles. Overall, HO structure is useful descriptively, but enforcing it with hard gates hurts sentence-level value detection; robust improvements come from calibration and lightweight ensembling.

We provide here a dataset for tasks related to natural language understanding and natural language inference. The dataset contains logical puzzles in natural language from three domains: comparing puzzles, knighs and knaves, and zebra puzzles. Each puzzle is associated with the entire set of atomic questions that can be generated based on the relations and individuals occurring in the text. For each question we provide the correct answer: entailment, contradiction or ambiguity. The answer's correctness is verified against theorem provers. Good puzzles have two properties: (i) each piece of information is necessary and (ii) no unnecessary information is provided. These properties make puzzles interesting candidates for machine comprehension tasks.

Can reinforcement learning with hard, verifiable rewards teach a compact language model to reason about physics, or does it primarily learn to pattern-match toward correct answers? We study this question by training a 1.5B-parameter reasoning model on beam statics, a classic engineering problem, using parameter-efficient RLVR with binary correctness rewards from symbolic solvers, without teacher-generated reasoning traces. The best BeamPERL checkpoint achieves a 66.7% improvement in Pass@1 over the base model. However, the learned competence is anisotropic: the model generalizes compositionally (more loads) but fails under topological shifts (moved supports) that require the same equilibrium equations. Intermediate checkpoints yield the strongest reasoning, while continued optimization degrades robustness while maintaining reward. These findings reveal a key limitation of outcome-level alignment: reinforcement learning with exact physics rewards induces procedural solution templates rather than internalization of governing equations. The precision of the reward signal - even when analytically exact - does not by itself guarantee transferable physical reasoning. Our results suggest that verifiable rewards may need to be paired with structured reasoning scaffolding to move beyond template matching toward robust scientific reasoning.

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.

Neurosymbolic approaches integrating large language models with formal reasoning have recently achieved human-level performance on mathematics competition problems in algebra, geometry and number theory. In comparison, combinatorics remains a challenging domain, characterized by a lack of appropriate benchmarks and theorem libraries. To address this gap, we introduce CombiBench, a comprehensive benchmark comprising 100 combinatorial problems, each formalized in Lean~4 and paired with its corresponding informal statement. The problem set covers a wide spectrum of difficulty levels, ranging from middle school to IMO and university level, and span over ten combinatorial topics. CombiBench is suitable for testing IMO solving capabilities since it includes all IMO combinatorial problems since 2000 (except IMO 2004 P3 as its statement contain an images). Furthermore, we provide a comprehensive and standardized evaluation framework, dubbed Fine-Eval (for Fill-in-the-blank in Lean Evaluation), for formal mathematics. It accommodates not only proof-based problems but also, for the first time, the evaluation of fill-in-the-blank questions. Using Fine-Eval as the evaluation method and Kimina Lean Server as the backend, we benchmark several LLMs on CombiBench and observe that their capabilities for formally solving combinatorial problems remain limited. Among all models tested (none of which has been trained for this particular task), Kimina-Prover attains the best results, solving 7 problems (out of 100) under both ``with solution'' and ``without solution'' scenarios. We open source the benchmark dataset alongside with the code of the proposed evaluation method at https://github.com/MoonshotAI/CombiBench/.

Proof autoformalization, the task of translating natural language theorems and proofs into machine-verifiable code, is a critical step for integrating large language models into rigorous mathematical workflows. Current approaches focus on producing executable code, but they frequently fail to preserve the semantic meaning and logical structure of the original human-written argument. To address this, we introduce ProofFlow, a novel pipeline that treats structural fidelity as a primary objective. ProofFlow first constructs a directed acyclic graph (DAG) to map the logical dependencies between proof steps. Then, it employs a novel lemma-based approach to systematically formalize each step as an intermediate lemma, preserving the logical structure of the original argument. To facilitate evaluation, we present a new benchmark of 184 undergraduate-level problems, manually annotated with step-by-step solutions and logical dependency graphs, and introduce ProofScore, a new composite metric to evaluate syntactic correctness, semantic faithfulness, and structural fidelity. Experimental results show our pipeline sets a new state-of-the-art for autoformalization, achieving a ProofScore of 0.545, substantially exceeding baselines like full-proof formalization (0.123), which processes the entire proof at once, and step-proof formalization (0.072), which handles each step independently. Our pipeline, benchmark, and score metric are open-sourced to encourage further progress at https://github.com/Huawei-AI4Math/ProofFlow.

Directed acyclic graphs (DAGs) encode a lot of information about a particular distribution in their structure. However, compute required to infer these structures is typically super-exponential in the number of variables, as inference requires a sweep of a combinatorially large space of potential structures. That is, until recent advances made it possible to search this space using a differentiable metric, drastically reducing search time. While this technique -- named NOTEARS -- is widely considered a seminal work in DAG-discovery, it concedes an important property in favour of differentiability: transportability. To be transportable, the structures discovered on one dataset must apply to another dataset from the same domain. We introduce D-Struct which recovers transportability in the discovered structures through a novel architecture and loss function while remaining fully differentiable. Because D-Struct remains differentiable, our method can be easily adopted in existing differentiable architectures, as was previously done with NOTEARS. In our experiments, we empirically validate D-Struct with respect to edge accuracy and structural Hamming distance in a variety of settings.

We explain how the simplicial higher-order unstable homotopy operations defined in [BBS2] may be composed and inserted one in another, thus forming a coherent if complicated algebraic structure.

NVIDIA's CUTLASS library provides a robust and expressive set of methods for describing and manipulating multi-dimensional tensor data on the GPU. These methods are conceptually grounded in the abstract notion of a CuTe layout and a rich algebra of such layouts, including operations such as composition, logical product, and logical division. In this paper, we present a categorical framework for understanding this layout algebra by focusing on a naturally occurring class of tractable layouts. To this end, we define two categories Tuple and Nest whose morphisms give rise to layouts. We define a suite of operations on morphisms in these categories and prove their compatibility with the corresponding layout operations. Moreover, we give a complete characterization of the layouts which arise from our construction. Finally, we provide a Python implementation of our categorical constructions, along with tests that demonstrate alignment with CUTLASS behavior. This implementation can be found at our git repository https://github.com/ColfaxResearch/layout-categories.

Reliable verification of proofs remains a bottleneck for training and evaluating AI systems on hard mathematical reasoning. Fully formal proofs, in languages like Lean, are easy to verify because they are unambiguous and modular. Most proofs, particularly those written by AI systems, have neither property, and translating them into formal languages remains challenging in many frontier math settings. We propose Pseudo-Formalization (PF), a proof format that captures the modularity and precision of formal proofs while retaining the flexibility of natural language. A Pseudo-Formal proof is decomposed into self-contained modules, each stating its premises, conclusion, and proof in natural language. To verify the correctness of a regular natural language proof, an LLM translates it to Pseudo-Formal and then verifies each module independently, an algorithm we call Block Verification (BV). We evaluate PF+BV on two benchmarks spanning olympiad and research-level mathematics, where it pareto-dominates LLM-as-judge baselines on error-finding precision and recall. To support future work, we release our research-level proof verification benchmark ArxivMathGradingBench.

Humanity's Last Exam (HLE) has become a widely used benchmark for evaluating frontier large language models on challenging, multi-domain questions. However, community-led analyses have raised concerns that HLE contains a non-trivial number of noisy items, which can bias evaluation results and distort cross-model comparisons. To address this challenge, we introduce HLE-Verified, a verified and revised version of HLE with a transparent verification protocol and fine-grained error taxonomy. Our construction follows a two-stage validation-and-repair workflow resulting in a certified benchmark. In Stage I, each item undergoes binary validation of the problem and final answer through domain-expert review and model-based cross-checks, yielding 641 verified items. In Stage II, flawed but fixable items are revised under strict constraints preserving the original evaluation intent, through dual independent expert repairs, model-assisted auditing, and final adjudication, resulting in 1,170 revised-and-certified items. The remaining 689 items are released as a documented uncertain set with explicit uncertainty sources and expertise tags for future refinement. We evaluate seven state-of-the-art language models on HLE and HLE-Verified, observing an average absolute accuracy gain of 7--10 percentage points on HLE-Verified. The improvement is particularly pronounced on items where the original problem statement and/or reference answer is erroneous, with gains of 30--40 percentage points. Our analyses further reveal a strong association between model confidence and the presence of errors in the problem statement or reference answer, supporting the effectiveness of our revisions. Overall, HLE-Verified improves HLE-style evaluations by reducing annotation noise and enabling more faithful measurement of model capabilities. Data is available at: https://github.com/SKYLENAGE-AI/HLE-Verified