Daily Papers

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.

How much autonomy can multi-agent LLM systems sustain -- and what enables it? We present a 25,000-task computational experiment spanning 8 models, 4--256 agents, and 8 coordination protocols ranging from externally imposed hierarchy to emergent self-organization. We observe that autonomous behavior already emerges in current LLM agents: given minimal structural scaffolding (fixed ordering), agents spontaneously invent specialized roles, voluntarily abstain from tasks outside their competence, and form shallow hierarchies -- without any pre-assigned roles or external design. A hybrid protocol (Sequential) that enables this autonomy outperforms centralized coordination by 14% (p<0.001), with a 44% quality spread between protocols (Cohen's d=1.86, p<0.0001). The degree of emergent autonomy scales with model capability: strong models self-organize effectively, while models below a capability threshold still benefit from rigid structure -- suggesting that as foundation models improve, the scope for autonomous coordination will expand. The system scales sub-linearly to 256 agents without quality degradation (p=0.61), producing 5,006 unique roles from just 8 agents. Results replicate across closed- and open-source models, with open-source achieving 95% of closed-source quality at 24x lower cost. The practical implication: give agents a mission, a protocol, and a capable model -- not a pre-assigned role.

Generating long-range, geometrically consistent video presents a fundamental dilemma: while consistency demands strict adherence to 3D geometry in pixel space, state-of-the-art generative models operate most effectively in a camera-conditioned latent space. This disconnect causes current methods to struggle with occluded areas and complex camera trajectories. To bridge this gap, we propose WorldWarp, a framework that couples a 3D structural anchor with a 2D generative refiner. To establish geometric grounding, WorldWarp maintains an online 3D geometric cache built via Gaussian Splatting (3DGS). By explicitly warping historical content into novel views, this cache acts as a structural scaffold, ensuring each new frame respects prior geometry. However, static warping inevitably leaves holes and artifacts due to occlusions. We address this using a Spatio-Temporal Diffusion (ST-Diff) model designed for a "fill-and-revise" objective. Our key innovation is a spatio-temporal varying noise schedule: blank regions receive full noise to trigger generation, while warped regions receive partial noise to enable refinement. By dynamically updating the 3D cache at every step, WorldWarp maintains consistency across video chunks. Consequently, it achieves state-of-the-art fidelity by ensuring that 3D logic guides structure while diffusion logic perfects texture. Project page: https://hyokong.github.io/worldwarp-page/{https://hyokong.github.io/worldwarp-page/}.

Animatable 3D assets, defined as geometry equipped with an articulated skeleton and skinning weights, are fundamental to interactive graphics, embodied agents, and animation production. While recent 3D generative models can synthesize visually plausible shapes from images, the results are typically static. Obtaining usable rigs via post-hoc auto-rigging is brittle and often produces skeletons that are topologically inconsistent with the generated geometry. We present AniGen, a unified framework that directly generates animate-ready 3D assets conditioned on a single image. Our key insight is to represent shape, skeleton, and skinning as mutually consistent S^3 Fields (Shape, Skeleton, Skin) defined over a shared spatial domain. To enable the robust learning of these fields, we introduce two technical innovations: (i) a confidence-decaying skeleton field that explicitly handles the geometric ambiguity of bone prediction at Voronoi boundaries, and (ii) a dual skin feature field that decouples skinning weights from specific joint counts, allowing a fixed-architecture network to predict rigs of arbitrary complexity. Built upon a two-stage flow-matching pipeline, AniGen first synthesizes a sparse structural scaffold and then generates dense geometry and articulation in a structured latent space. Extensive experiments demonstrate that AniGen substantially outperforms state-of-the-art sequential baselines in rig validity and animation quality, generalizing effectively to in-the-wild images across diverse categories including animals, humanoids, and machinery. Homepage: https://yihua7.github.io/AniGen-web/

While Multimodal Large Language Models (MLLMs) excel in semantic tasks, they frequently lack the "spatial sense" essential for sophisticated geometric reasoning. Current models typically suffer from exorbitant modality-alignment costs and deficiency in fine-grained structural modeling precision.We introduce SSR, a framework designed for Structured Scene Reasoning that seamlessly integrates 2D and 3D representations via a lightweight alignment mechanism. To minimize training overhead, our framework anchors 3D geometric features to the large language model's pre-aligned 2D visual semantics through cross-modal addition and token interleaving, effectively obviating the necessity for large-scale alignment pre-training. To underpin complex spatial reasoning, we propose a novel scene graph generation pipeline that represents global layouts as a chain of independent local triplets defined by relative coordinates. This is complemented by an incremental generation algorithm, enabling the model to construct "language-model-friendly" structural scaffolds for complex environments. Furthermore, we extend these capabilities to global-scale 3D global grounding task, achieving absolute metric precision across heterogeneous data sources. At a 7B parameter scale, SSR achieves state-of-the-art performance on multiple spatial intelligence benchmarks, notably scoring 73.9 on VSI-Bench. Our approach significantly outperforms much larger models, demonstrating that efficient feature alignment and structured scene reasoning are the cornerstones of authentic spatial intelligence.

Autoregressive mesh generation has gained attention by tokenizing meshes into sequences and training models in a language-modeling fashion. However, existing approaches suffer from two fundamental limitations: (i) low tokenization efficiency, which yields long token sequences and prevents scaling to high-poly meshes, and (ii) absence of geometry-aware guidance, as generation is conditioned only on global shape embeddings rather than local surface cues. We introduce MeshWeaver, an autoregressive framework that treats mesh generation as a surface weaving process by directly predicting the next vertex instead of independent coordinates. At its core is a multi-level sparse-voxel encoder that injects geometric context into the generative process in three complementary ways: providing voxel features as vertex representations, guiding token prediction via cross-attention to voxel features, and serving as a structural scaffold that constrains generation around the input surface. Our hierarchical design enables coarse-to-fine vertex prediction in a single decoding step, while tightly coupling the generative model with 3D geometry. Extensive experiments demonstrate that MeshWeaver achieves a state-of-the-art compression ratio of 18%, can generate meshes with up to 16K faces, and significantly improves geometric fidelity over prior approaches.

Multi-LLM revision pipelines, in which a second model reviews and improves a draft produced by a first, are widely assumed to derive their gains from genuine error correction. We question this assumption with a controlled decomposition experiment that uses four matched conditions to separate second-pass gains into three additive components: re-solving, scaffold, and content. We evaluate this design across two model pairs on three benchmarks spanning knowledge-intensive MCQ and competitive programming. Our results show that the gains of multi-LLM revision are not monolithic, but depend on task structure, draft quality, and the type of draft information. On MCQ tasks, where the answer space is constrained and drafts provide little structural guidance, most gains are consistent with stronger-model re-solving, and directly routing queries to the stronger model can be more effective than revising a weak draft. On code generation tasks, however, two-stage prompting remains useful because even semantically null drafts can provide substantial structural scaffolding, while weak draft content can be harmful. Finally, role-reversed experiments show that strong drafts clearly benefit weak reviewers. Ultimately, our findings demonstrate that the utility of multi-LLM revision is dynamically bottlenecked by task structure and draft quality, necessitating more targeted pipeline designs rather than blanket revision strategies.

Large language models (LLMs) are increasingly deployed as interactive agents, yet their capacity for social and strategic reasoning over extended interaction remains poorly understood. Existing evaluations rely on static vignettes or single-game benchmarks that cannot capture the sustained, multi-faceted reasoning that real-world multi-agent settings demand. We introduce Mindgames, a multi-game arena and evaluation platform for LLM agents that operationalizes complementary reasoning demands relevant to ``theory of mind'': belief attribution under hidden information, opponent modeling through repeated strategic interaction, cooperative inference under knowledge asymmetries, and sustained deception in social deduction. Built on TextArena, Mindgames provides a unified interaction interface, TrueSkill-based rating, and full trajectory logging across four game environments. We instantiate Mindgames through a 2025 competition cycle hosted at a major AI conference, which assessed 944 submitted agents from 76 teams across four games: Colonel Blotto, Iterated Prisoner's Dilemma, Codenames, and Secret Mafia. Our analysis surfaces both agent-level and evaluation-level limitations: brittle rule adherence remains a major bottleneck, top-performing systems repeatedly rely on explicit structural scaffolding, and leaderboard validity differs sharply across environments. In particular, failure-heavy environments can reward robustness to opponent errors as much as strategic ability, with Secret Mafia exhibiting a pronounced error-survival confound in this cycle. We release a dataset of 29,571 multi-agent games with turn-level observations, actions, and rewards, together with MG-Ref, a deterministic offline tournament protocol that scores new agents against a frozen reference pool of top-ranked, low-error Stage~II submissions under the same error-attribution lens used in this analysis.

Direct Preference Optimization is an offline post-SFT method for aligning language models from preference pairs, with strong results in instruction following and summarization. However, DPO's sequence-level implicit reward can be brittle for token-critical structured prediction settings such as medical annotation, which often exhibit (i) low-separation preference pairs, where chosen and rejected completions differ by minimal edit distance (often 1-3 tokens), and (ii) token-importance skew, where sparse semantic tokens (hierarchical labels and evidence Spans) carry disproportionate task importance relative to high-frequency structural tokens (JSON scaffolding). In this regime, standard DPO suffers from margin collapse (insufficient log-probability separation between near-identical preferences), likelihood squeezing (the margin objective shifts the absolute likelihoods of both completions together), and gradient dilution, where uniform sequence-level weighting diffuses learning signal across shared scaffolding while rare, confusable label tokens receive weak, noisy updates. We introduce Token-Adaptive Barrier Preference Optimization (TAB-PO), which augments DPO with token-weighted, reference-adjusted advantages that prioritize high-value semantic tokens, and a conditional token-level barrier that regularizes under-confident tokens balancing SFT-anchored likelihood and preference-driven separation in low-separation, importance-skewed regimes. We evaluate TAB-PO on medical communication annotation, a task requiring joint prediction of hierarchical labels and evidence Spans from patient-provider messages. TAB-PO achieves a ~ 4% relative improvement in micro-F1 over SFT and consistently outperforms recent preference-optimization baselines.

Protein diffusion models have emerged as a promising approach for protein design. One such pioneering model is Genie, a method that asymmetrically represents protein structures during the forward and backward processes, using simple Gaussian noising for the former and expressive SE(3)-equivariant attention for the latter. In this work we introduce Genie 2, extending Genie to capture a larger and more diverse protein structure space through architectural innovations and massive data augmentation. Genie 2 adds motif scaffolding capabilities via a novel multi-motif framework that designs co-occurring motifs with unspecified inter-motif positions and orientations. This makes possible complex protein designs that engage multiple interaction partners and perform multiple functions. On both unconditional and conditional generation, Genie 2 achieves state-of-the-art performance, outperforming all known methods on key design metrics including designability, diversity, and novelty. Genie 2 also solves more motif scaffolding problems than other methods and does so with more unique and varied solutions. Taken together, these advances set a new standard for structure-based protein design. Genie 2 inference and training code, as well as model weights, are freely available at: https://github.com/aqlaboratory/genie2.

Generating scientific manuscripts requires maintaining alignment between narrative reasoning, experimental evidence, and visual artifacts across the document lifecycle. Existing language-model generation pipelines rely on unconstrained text synthesis with validation applied only after generation, often producing structural drift, missing figures or tables, and cross-section inconsistencies. We introduce Story2Proposal, a contract-governed multi-agent framework that converts a research story into a structured manuscript through coordinated agents operating under a persistent shared visual contract. The system organizes architect, writer, refiner, and renderer agents around a contract state that tracks section structure and registered visual elements, while evaluation agents supply feedback in a generate evaluate adapt loop that updates the contract during generation. Experiments on tasks derived from the Jericho research corpus show that Story2Proposal achieved an expert evaluation score of 6.145 versus 3.963 for DirectChat (+2.182) across GPT, Claude, Gemini, and Qwen backbones. Compared with the structured generation baseline Fars, Story2Proposal obtained an average score of 5.705 versus 5.197, indicating improved structural consistency and visual alignment.

CLI-based software-engineering agents have matured rapidly, yet the open ecosystem has converged on a single training environment: trajectory datasets used to fine-tune open models are collected almost exclusively under OpenHands. Models fine-tuned on this data score well under OpenHands but degrade substantially when deployed under any non-training scaffold. Untrained base models do not show this divergence, indicating the gap is fine-tuning-induced and tied to the conventions of the training scaffold. We argue that a load-bearing scaffold-specific behavior is planning structure, in two senses this paper distinguishes: explicit planning, a pre-execution plan produced as a first-class artifact, and implicit planning, the structural conventions that shape execution throughout the agent loop. Under this hypothesis, closing the gap requires moving planning from a fixed scaffold artifact to a learned model capability. We introduce Decoupling CLI Agent Scaffolding (DCAS), a backend-substitution interception layer that routes API traffic between any CLI scaffold and any backend model without modifying the scaffold, enabling cross-scaffold evaluation and planning-aware trajectory collection. Using DCAS, a controlled plan-source intervention confirms planning quality is a high-leverage component, with gains exceeding the cross-scaffold drops we observe. A model fine-tuned on a small set of DCAS-collected planning-aware trajectories under a single scaffold gains consistently across non-training scaffolds, and the two senses of planning are empirically separable in training data.

Optimizing embedding systems for production recommendation pipelines demands systematic exploration that consumes disproportionate engineering effort at scale. We apply Andrej Karpathy's AutoResearch paradigm -- a large language model that iteratively edits a training script and retains modifications that improve a held-out scalar metric -- to automate this exploration. We report on twelve weeks of running this paradigm at production scale, where iterations consume hours of multi-GPU compute, evaluation involves competing criteria, and campaigns span weeks across many training jobs. Across two independently developed representation-learning systems for a book recommendation pipeline, we ran 220+ experiments and observed five recurring failure modes absent from the original setting: infrastructure fragility, agent memory decay, search-direction stagnation, iteration-cost asymmetry, and metric fixation. We contribute a three-principle scaffolding design -- prevent, persist, redirect -- that maps each failure mode to a structural remedy and whose instantiation scales with iteration cost. The framework produced a 1.82x Recall@6 lift and a 2.1x coherence lift over hand-tuned baselines, and the agent autonomously designed a text-only fallback that expanded catalog coverage by 5.8x. The two systems span nearly three orders of magnitude in per-iteration cost yet exhibit the same failure modes, suggesting these are structural properties of production-scale autonomous research rather than artifacts of either application.

Reasoning in Large Language Models incurs significant inference-time compute, yet the token-level information structure of reasoning traces remains underexplored. We observe that reasoning tokens split into two functional types: low-entropy structural tokens (recurring phrases that scaffold the reasoning process) and higher-entropy organic tokens (problem-specific content that drives toward a solution). This asymmetry motivates a simple, model-agnostic compression pipeline: apply cross-word BPE merges on a model's own reasoning traces to derive supertokens that capture frequent structural patterns, then teach the model to adopt them via supervised fine-tuning. Across three model families and five mathematical reasoning benchmarks, our approach shortens reasoning traces by 8.1% on average; under a TOST equivalence analysis at a +/- 2pp margin, accuracy is equivalent or inconclusive on 13/15 model -- benchmark cells (2 pass equivalence, 11 inconclusive, predominantly AIME at N=30, with non-equivalent degradation on 2/15 cells (DeepSeek-R1-Distill-Llama-70B on MATH-500 and OlympiadBench). Beyond compression, learned supertokens often align with interpretable reasoning moves such as backtracking, verification, and strategy shifts. This enables a compact structural analysis of reasoning traces: correct traces show more recovery and verification patterns, while incorrect traces show more repeated hedging and unresolved counterarguments. We release the full pipeline as open-source code.

Reparameterized diffusion models (RDMs) have recently matched autoregressive methods in protein generation, motivating their use for challenging tasks such as designing membrane proteins, which possess interleaved soluble and transmembrane (TM) regions. We introduce the Membrane Diffusion Language Model (MemDLM), a fine-tuned RDM-based protein language model that enables controllable membrane protein sequence design. MemDLM-generated sequences recapitulate the TM residue density and structural features of natural membrane proteins, achieving comparable biological plausibility and outperforming state-of-the-art diffusion baselines in motif scaffolding tasks by producing lower perplexity, higher BLOSUM-62 scores, and improved pLDDT confidence. To enhance controllability, we develop Per-Token Guidance (PET), a novel classifier-guided sampling strategy that selectively solubilizes residues while preserving conserved TM domains, yielding sequences with reduced TM density but intact functional cores. Importantly, MemDLM designs validated in TOXCAT beta-lactamase growth assays demonstrate successful TM insertion, distinguishing high-quality generated sequences from poor ones. Together, our framework establishes the first experimentally-validated diffusion-based model for rational membrane protein generation, integrating de novo design, motif scaffolding, and targeted property optimization.

Domain models are central to software engineering, as they enable a shared understanding, guide implementation, and support automated analyses and model-driven development. Yet, despite these benefits, practitioners often skip modeling because it is time-consuming and demands scarce expertise. We address this barrier by investigating whether open-weight large language models, adapted via instruction tuning, can generate high-quality BPMN process models directly from natural language descriptions in a cost-effective and privacy-preserving way. We introduce InstruBPM, a reproducible approach that prepares paired text-diagram data and instruction tunes an open source large language model with parameter-efficient fine-tuning and quantization for on-prem deployment. We evaluate the tuned model through complementary perspectives: (i) text/code similarity using BLEU, ROUGE-L, and METEOR, (ii) structural fidelity using Relative Graph Edit Distance, (iii) guidelines conformance using external tool checks, and (iv) a small expert review. Using a curated subset of a multi-domain BPMN dataset, we compare the tuned model with untuned open-weight baselines and strong proprietary models under consistent prompting regimes. Our compact tuned model outperforms all baselines across sequence and structural metrics while requiring substantially fewer resources; guideline analysis and expert feedback further indicate that the generated diagrams largely follow BPMN best practices and are useful starting points that reduce modeling effort. Overall, instruction tuning improves structural accuracy and robustness compared to untuned baselines and reduces reliance on heavy prompt scaffolding. We publicly share the trained models and scripts to support reproducibility and further research.

End-to-end autonomous driving via Vision-Language-Action (VLA) models demands a precarious balance between high-fidelity trajectory planning and efficient inference. Existing paradigms typically fall short: autoregressive (AR) VLAs are memory-bandwidth-bound on edge hardware and prone to exposure-bias drift, while full-sequence diffusion models preclude KV-cache reuse and suffer from "logical leakage" that violates the fundamental perceive-then-plan causality. We present Fast-dDrive, a block-diffusion VLA that performs bidirectional refinement within semantic units while enforcing strict causal ordering across them. Leveraging the observation that driving VLAs often emit structured JSON-like outputs, Fast-dDrive freezes structural tokens into a section scaffold and employs a section-aware training recipe that prioritizes safety-critical planning. We further introduce Scaffold Speculative Decoding to achieve AR-equivalent quality at significantly higher throughput. Finally, we propose a low-overhead test-time scaling scheme: by forking N stochastic trajectory rollouts from a single shared-prefix KV cache and averaging them, we effectively suppress prediction variance at a fractional computational cost. Empirical results demonstrate that Fast-dDrive redefines the speed-accuracy frontier for driving agents. On the WOD-E2E test set, Fast-dDrive achieves SOTA ADE@3s and ADE@5s, alongside the highest RFS among diffusion-based VLAs; on nuScenes, it reduces average L2 error to 0.32m (a 22% improvement). When integrated with SGLang, our framework delivers 12times throughput speedup over the AR baseline, narrowing the gap between high-capacity VLAs and the efficiency demands of real-time on-vehicle deployment.

The success of generative molecular design hinges on a model's steerability toward high-reward samples. Because many molecular properties are intrinsically linked to molecular size, accurately capturing the joint distribution of properties and the number of atoms is essential. However, current diffusion and flow-based models fix the number of atoms, which ultimately limits their ability to navigate this complex relationship. To address this, we introduce Morph, a flexible-size generative model for conditional and unconditional 3D molecular design based on geometric graphs. By dynamically adapting size, Morph can seamlessly integrate existing structural priors, like scaffolds, and significantly enhances property steering. We show that Morph matches current fixed-size state-of-the-art models while offering the benefit of unparalleled sampling flexibility. We demonstrate out-of-distribution generation in regimes where previous models fail, paving the way for enhanced generative modeling for molecular design.

High-quality singing annotations are fundamental to modern Singing Voice Synthesis (SVS) systems. However, obtaining these annotations at scale through manual labeling is unrealistic due to the substantial labor and musical expertise required, making automatic annotation highly necessary. Despite their utility, current automatic transcription systems face significant challenges: they often rely on complex multi-stage pipelines, struggle to recover text-note alignments, and exhibit poor generalization to out-of-distribution (OOD) singing data. To alleviate these issues, we present VocalParse, a unified singing voice transcription (SVT) model built upon a Large Audio Language Model (LALM). Specifically, our novel contribution is to introduce an interleaved prompting formulation that jointly models lyrics, melody, and word-note correspondence, yielding a generated sequence that directly maps to a structured musical score. Furthermore, we propose a Chain-of-Thought (CoT) style prompting strategy, which decodes lyrics first as a semantic scaffold, significantly mitigating the context disruption problem while preserving the structural benefits of interleaved generation. Experiments demonstrate that VocalParse achieves state-of-the-art SVT performance on multiple singing datasets. The source code and checkpoint are available at https://github.com/pymaster17/VocalParse.

Designing antibody sequences to better resemble those observed in natural human repertoires is a key challenge in biologics development. We introduce IgCraft: a multi-purpose model for paired human antibody sequence generation, built on Bayesian Flow Networks. IgCraft presents one of the first unified generative modeling frameworks capable of addressing multiple antibody sequence design tasks with a single model, including unconditional sampling, sequence inpainting, inverse folding, and CDR motif scaffolding. Our approach achieves competitive results across the full spectrum of these tasks while constraining generation to the space of human antibody sequences, exhibiting particular strengths in CDR motif scaffolding (grafting) where we achieve state-of-the-art performance in terms of humanness and preservation of structural properties. By integrating previously separate tasks into a single scalable generative model, IgCraft provides a versatile platform for sampling human antibody sequences under a variety of contexts relevant to antibody discovery and engineering. Model code and weights are publicly available at github.com/mgreenig/IgCraft.

We present Connection-Aware Motif Sequencing (CamS), a graph-to-sequence representation that enables decoder-only Transformers to learn molecular graphs via standard next-token prediction (NTP). For molecular property prediction, SMILES-based NTP scales well but lacks explicit topology, whereas graph-native masked modeling captures connectivity but risks disrupting the pivotal chemical details (e.g., activity cliffs). CamS bridges this gap by serializing molecular graphs into structure-rich causal sequences. CamS first mines data-driven connection-aware motifs. It then serializes motifs via scaffold-rooted breadth-first search (BFS) to establish a stable core-to-periphery order. Crucially, CamS enables hierarchical modeling by concatenating sequences from fine to coarse motif scales, allowing the model to condition global scaffolds on dense, uncorrupted local structural evidence. We instantiate CamS-LLaMA by pre-training a vanilla LLaMA backbone on CamS sequences. It achieves state-of-the-art performance on MoleculeNet and the activity-cliff benchmark MoleculeACE, outperforming both SMILES-based language models and strong graph baselines. Interpretability analysis confirms that our multi-scale causal serialization effectively drives attention toward cliff-determining differences.

Computer science papers rely heavily on diagrams: architecture drawings, system flowcharts, and pipeline schematics that often carry more information than the text around them. There is currently no public dataset that pairs this specific kind of figure with captions, context, questions, answers, and step-by-step reasoning, which is exactly what is needed to train a vision-language model to understand them. We present SCAFFOLDhttps://github.com/theranjitraut/scaffold, a large-scale structured dataset of computer science research figures with diagram QA and Chain-of-Thought reasoning traces. This dataset consists of (image, caption, context, question-answer, chain-of-thought) tuples from arXiv computer science papers prepared using layout detection and PDF parsing, with an AI-assisted question-generation step. The resulting large-sized SCAFFOLD-157K dataset spans 3,058 papers with 29,887 figures (157,387 pairs), a medium-sized SCAFFOLD-37K dataset (36,797 pairs), and a small-sized SCAFFOLD-12K dataset (12,000 pairs). We used SCAFFOLD-12K for baseline experiments on Qwen2.5-VL-3B-Instruct.

Addressing a structural-engineering request requires more than a single answer; it requires a chain of interdependent artifacts: interpreted requirements, a computable model, validation records, solver outputs, code-check records, and a final report. Evaluations centered on question answering or script generation rarely verify this complete evidence chain and may therefore reward fluent outputs even when the underlying engineering workflow is incomplete, internally inconsistent, or non-executable. To address this limitation, we present StructureClaw, an artifact-centered workbench in which LLM agents operate through governed engineering skills, typed tools, shared artifact state, and local analysis backends. We also introduce StructureClaw-Bench, an executable benchmark of 150 controlled scenarios spanning standard workflow execution, interactive robustness, and multimodal structural-model reconstruction. A scenario succeeds only when all required artifact- and execution-level assertions pass in a single run. Across ten agent-model configurations, each evaluated on the same 50 standard cases, the average Success Rate rises from 56.8% with the generic-skill baseline to 88.6% with the full automatic workflow. The interactive and multimodal evaluations identify two prominent remaining challenges: safe handling of invalid numerical inputs and fixture-consistent reconstruction of structural models. These findings show that artifact-centered evaluation can expose workflow-level failures that are difficult to identify from final responses alone, providing a more rigorous basis for evaluating and improving structural-engineering agents. The code and benchmark are available at https://github.com/structureclaw/structureclaw.

Native 3D generative models have achieved remarkable fidelity and speed, yet they suffer from a critical limitation: inability to prescribe precise structural articulations, where precise structural control within the native 3D space remains underexplored. This paper proposes SK-Adapter, a simple and yet highly efficient and effective framework that unlocks precise skeletal manipulation for native 3D generation. Moving beyond text or image prompts, which can be ambiguous for precise structure, we treat the 3D skeleton as a first-class control signal. SK-Adapter is a lightweight structural adapter network that encodes joint coordinates and topology into learnable tokens, which are injected into the frozen 3D generation backbone via cross-attention. This smart design allows the model to not only effectively "attend" to specific 3D structural constraints but also preserve its original generative priors. To bridge the data gap, we contribute Objaverse-TMS dataset, a large-scale dataset of 24k text-mesh-skeleton pairs. Extensive experiments confirm that our method achieves robust structural control while preserving the geometry and texture quality of the foundation model, significantly outperforming existing baselines. Furthermore, we extend this capability to local 3D editing, enabling the region specific editing of existing assets with skeletal guidance, which is unattainable by previous methods. Project Page: https://sk-adapter.github.io/

The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures (scaffolds) that include the motif and maintain its geometry. Significant recent progress on motif-scaffolding has been made due to computational evaluation with reliable protein structure prediction and fixed-backbone sequence design methods. However, significant variability in evaluation strategies across publications has hindered comparability of results, challenged reproducibility, and impeded robust progress. In response we introduce MotifBench, comprising (1) a precisely specified pipeline and evaluation metrics, (2) a collection of 30 benchmark problems, and (3) an implementation of this benchmark and leaderboard at github.com/blt2114/MotifBench. The MotifBench test cases are more difficult compared to earlier benchmarks, and include protein design problems for which solutions are known but on which, to the best of our knowledge, state-of-the-art methods fail to identify any solution.

Natural structural materials, such as bone and wood, can autonomously adapt their mechanical properties in response to loading to prevent failure. They smartly control the addition of material in locations of high stress by utilizing locally available resources guided by biological signals. On the contrary, synthetic structural materials have unchanging mechanical properties limiting their mechanical performance and service life. Here, a material system that autonomously adapts its mechanical properties in response to mechanical loading is reported inspired by the mineralization process of bone. It is observed that charges from piezoelectric scaffolds can induce mineralization from media with mineral ions. The material system adapts to mechanical loading by inducing mineral deposition in proportion to the magnitude of the loading and the resulting piezoelectric charges. Moreover, the mechanism allows a simple one-step route for making graded materials by controlling stress distribution along the scaffold. The findings can pave the way for a new class of self-adaptive materials that reinforce the region of high stress or induce deposition of minerals on the damaged areas from the increase in stress to prevent/mitigate failure. They can also contribute to addressing the current challenges of synthetic materials for load-bearing applications from self-adaptive capabilities.

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.

Machine learning (ML) is increasingly used in structural engineering and design, yet its broader adoption is hampered by the lack of openly accessible datasets of structural systems. We introduce BridgeNet, a publicly available graph-based dataset of 20,000 form-found bridge structures aimed at enabling Graph ML and multi-modal learning in the context of conceptual structural design. Each datapoint consists of (i) a pin-jointed equilibrium wireframe model generated with the Combinatorial Equilibrium Modeling (CEM) form-finding method, (ii) a volumetric 3D mesh obtained through force-informed materialization, and (iii) rendered images from two canonical camera angles. The resulting dataset is modality-rich and application-agnostic, supporting tasks such as CEM-specific edge classification and parameter inference, surrogate modeling of form-finding, cross-modal reconstruction between graphs, meshes and images, and generative structural design. BridgeNet addresses a key bottleneck in data-driven applications for structural engineering and design by providing a dataset that facilitates the development of new ML-based approaches for equilibrium bridge structures.

Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.

Speech carries more information than just words: a child's voice, a fearful tone, or a noisy background should all lead a sufficiently competent spoken-dialogue assistant to different replies. Current Speech Language Models (SLMs) can recognize such paralinguistic cues but often ignore them in open-ended dialogue. We observe that a simple paralinguistic instruction scaffold at the inference stage narrows this perception-behavior gap, suggesting that the relevant cues are already latent in the model. Such scaffolds, however, remain brittle under multi-turn context and competing instructions. Therefore, we propose ParaBridge, an on-policy self-distillation method that turns a brittle inference-time scaffold into stable model behavior. During training, the scaffold serves only as a temporary privileged view; the scaffold-free model rolls out its own response, while the scaffolded view supplies dense, full-vocabulary next-token targets along its trajectory. This supervision teaches when non-lexical cues should affect the reply without the need for curated dialogues, human labels, or external reward models. On Qwen3-Omni-thinking, ParaBridge raises scaffold-free VoxSafeBench SAR from 14.6% to 40.3% and improves EchoMind average rating from 3.27 to 3.92. It also preserves general ability, with MMAU-Pro, VoiceBench, and GPQA all within 0.4 points of the original model. Beyond the training distribution, ParaBridge generalizes to unseen paralinguistic cues, transfers from safety-oriented training to empathy-oriented dialogue, and works on a different SLM backbone.

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.

Structural topology optimization (TO) is central to engineering design but remains computationally intensive due to complex physics and hard constraints. Existing deep-learning methods are limited to fixed square grids, a few hand-coded boundary conditions, and post-hoc optimization, preventing general deployment. We introduce Optimize Any Topology (OAT), a foundation-model framework that directly predicts minimum-compliance layouts for arbitrary aspect ratios, resolutions, volume fractions, loads, and fixtures. OAT combines a resolution- and shape-agnostic autoencoder with an implicit neural-field decoder and a conditional latent-diffusion model trained on OpenTO, a new corpus of 2.2 million optimized structures covering 2 million unique boundary-condition configurations. On four public benchmarks and two challenging unseen tests, OAT lowers mean compliance up to 90% relative to the best prior models and delivers sub-1 second inference on a single GPU across resolutions from 64 x 64 to 256 x 256 and aspect ratios as high as 10:1. These results establish OAT as a general, fast, and resolution-free framework for physics-aware topology optimization and provide a large-scale dataset to spur further research in generative modeling for inverse design. Code & data can be found at https://github.com/ahnobari/OptimizeAnyTopology.

Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development of all-atom foundation models for molecular modeling and generation, existing approaches face challenges in generalization due to the multi-modal nature of atomic data and the lack of comprehensive analysis of training and sampling strategies. To address these limitations, we propose PharMolixFM, a unified framework for constructing all-atom foundation models based on multi-modal generative techniques. Our framework includes three variants using state-of-the-art multi-modal generative models. By formulating molecular tasks as a generalized denoising process with task-specific priors, PharMolixFM achieves robust performance across various structural biology applications. Experimental results demonstrate that PharMolixFM-Diff achieves competitive prediction accuracy in protein-small-molecule docking (83.9% vs. 90.2% RMSD < 2Å, given pocket) with significantly improved inference speed. Moreover, we explore the empirical inference scaling law by introducing more sampling repeats or steps. Our code and model are available at https://github.com/PharMolix/OpenBioMed.

Benchmarks are often used as a standard to understand LLM capabilities in different domains. However, aggregate benchmark scores provide limited insight into compositional skill gaps of LLMs and how to improve them. To make these weaknesses visible, we propose Scaffolded Task Design (STaD) framework. STaD generates controlled variations of benchmark tasks based on the concept of scaffolding, which introduces structured, incremental support in a step-by-step manner. Rather than inspecting failures individually, this approach enables systematic and scalable probing of model behavior by identifying the specific reasoning skill compositions they lack. Treating the LLM as a black box, our experiments on six models of varying sizes reveal multiple failure points in three reasoning benchmarks and highlight each model's unique and distinct skill gaps.

Highly accurate biomolecular structure prediction is a key component of developing biomolecular foundation models, and one of the most critical aspects of building foundation models is identifying the recipes for scaling the model. In this work, we present SeedFold, a folding model that successfully scales up the model capacity. Our contributions are threefold: first, we identify an effective width-scaling strategy for the Pairformer to increase representation capacity; second, we introduce a novel linear triangular attention that reduces computational complexity to enable efficient scaling; finally, we construct a large-scale distillation dataset to substantially enlarge the training set. Experiments on FoldBench show that SeedFold outperforms AlphaFold3 on most protein-related tasks.

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration overhead. We present an agentic end-to-end drug design framework that leverages a Large Language Model (LLM) in conjunction with the Model Context Protocol (MCP) to dynamically coordinate access to biochemical databases, modular toolchains, and task-specific AI models. The system integrates four state-of-the-art components: MaSIF (MaSIF-site and MaSIF-seed-search) for geometric deep learning-based identification of protein-protein interaction (PPI) sites, Rosetta for grafting protein fragments onto protein backbones to form mini proteins, ProteinMPNN for amino acid sequences redesign, and AlphaFold3 for near-experimental accuracy in complex structure prediction. Starting from a target structure, the framework supports de novo binder generation via surface analysis, scaffold grafting and pose construction, sequence optimization, and structure prediction. Additionally, by replacing rigid, script-based workflows with a protocol-driven, LLM-coordinated architecture, the framework improves reproducibility, reduces manual overhead, and ensures extensibility, portability, and auditability across the entire drug design process.

We present Muses, the first training-free method for fantastic 3D creature generation in a feed-forward paradigm. Previous methods, which rely on part-aware optimization, manual assembly, or 2D image generation, often produce unrealistic or incoherent 3D assets due to the challenges of intricate part-level manipulation and limited out-of-domain generation. In contrast, Muses leverages the 3D skeleton, a fundamental representation of biological forms, to explicitly and rationally compose diverse elements. This skeletal foundation formalizes 3D content creation as a structure-aware pipeline of design, composition, and generation. Muses begins by constructing a creatively composed 3D skeleton with coherent layout and scale through graph-constrained reasoning. This skeleton then guides a voxel-based assembly process within a structured latent space, integrating regions from different objects. Finally, image-guided appearance modeling under skeletal conditions is applied to generate a style-consistent and harmonious texture for the assembled shape. Extensive experiments establish Muses' state-of-the-art performance in terms of visual fidelity and alignment with textual descriptions, and potential on flexible 3D object editing. Project page: https://luhexiao.github.io/Muses.github.io/.

High-fidelity 3D MRI synthesis requires both globally coherent anatomy and fine-grained voxel-level detail. Although latent diffusion makes volumetric generation tractable, its image autoencoder introduces a reconstruction bottleneck that can limit the fine detail recoverable in the final volume. We present VoxStruct3D, a voxel-space flow-matching framework that directly models full-resolution MRI volumes using a clean-data prediction objective. Its Volumetric Voxel Generator (VVG) combines factorized 3D patch embedding with overlapping upsampling, time-modulated residual refinement, and skip fusion, enabling neighboring tokens to jointly reconstruct shared voxel regions and suppress patch-boundary artifacts. To complement direct voxel-space modeling with an explicit anatomical prior, we further introduce a Structure-First, Image-Follows (SFIF) strategy. A frozen pretrained 3D medical encoder and a StructVAE extract compact structure tokens that preserve dominant anatomy, while a structure-leading schedule keeps their trajectory ahead of the image trajectory. Patch-Aligned RoPE spatially aligns the unequal token grids, and asymmetric attention enforces one-way guidance from structure to image. Experiments on pathological and healthy T1-weighted brain MRI datasets show that VoxStruct3D achieves the strongest overall performance across feature-distribution alignment, sample diversity, and perceptual quality, producing anatomically coherent and visually realistic volumes.

Modern coding scaffolds turn LLMs into capable software agents, but their ability to follow scaffold-specified instructions remains under-examined, especially when constraints are heterogeneous and persist across interactions. To fill this gap, we introduce OctoBench, which benchmarks scaffold-aware instruction following in repository-grounded agentic coding. OctoBench includes 34 environments and 217 tasks instantiated under three scaffold types, and is paired with 7,098 objective checklist items. To disentangle solving the task from following the rules, we provide an automated observation-and-scoring toolkit that captures full trajectories and performs fine-grained checks. Experiments on eight representative models reveal a systematic gap between task-solving and scaffold-aware compliance, underscoring the need for training and evaluation that explicitly targets heterogeneous instruction following. We release the benchmark to support reproducible benchmarking and to accelerate the development of more scaffold-aware coding agents.

Structural pruning enables model acceleration by removing structurally-grouped parameters from neural networks. However, the parameter-grouping patterns vary widely across different models, making architecture-specific pruners, which rely on manually-designed grouping schemes, non-generalizable to new architectures. In this work, we study a highly-challenging yet barely-explored task, any structural pruning, to tackle general structural pruning of arbitrary architecture like CNNs, RNNs, GNNs and Transformers. The most prominent obstacle towards this goal lies in the structural coupling, which not only forces different layers to be pruned simultaneously, but also expects all removed parameters to be consistently unimportant, thereby avoiding structural issues and significant performance degradation after pruning. To address this problem, we propose a general and {fully automatic} method, Dependency Graph (DepGraph), to explicitly model the dependency between layers and comprehensively group coupled parameters for pruning. In this work, we extensively evaluate our method on several architectures and tasks, including ResNe(X)t, DenseNet, MobileNet and Vision transformer for images, GAT for graph, DGCNN for 3D point cloud, alongside LSTM for language, and demonstrate that, even with a simple norm-based criterion, the proposed method consistently yields gratifying performances.

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

LLM-based coding agents can localize bugs, generate patches, and run tests with diminishing human oversight, yet the scaffolding code that surrounds the language model (the control loop, tool definitions, state management, and context strategy) remains poorly understood. Existing surveys classify agents by abstract capabilities (tool use, planning, reflection) that cannot distinguish between architecturally distinct systems, and trajectory studies observe what agents do without examining the scaffold code that determines why. This paper presents a source-code-level architectural taxonomy derived from analysis of 13 open-source coding agent scaffolds at pinned commit hashes. Each agent is characterized across 12 dimensions organized into three layers: control architecture, tool and environment interface, and resource management. The analysis reveals that scaffold architectures resist discrete classification: control strategies range from fixed pipelines to Monte Carlo Tree Search, tool counts range from 0 to 37, and context compaction spans seven distinct strategies. Five loop primitives (ReAct, generate-test-repair, plan-execute, multi-attempt retry, tree search) function as composable building blocks that agents layer in different combinations; 11 of 13 agents compose multiple primitives rather than relying on a single control structure. Dimensions converge where external constraints dominate (tool capability categories, edit formats, execution isolation) and diverge where open design questions remain (context compaction, state management, multi-model routing). All taxonomic claims are grounded in file paths and line numbers, providing a reusable reference for researchers studying agent behavior and practitioners designing new scaffolds.

Garment folding is a common yet challenging task in robotic manipulation. The deformability of garments leads to a vast state space and complex dynamics, which complicates precise and fine-grained manipulation. Previous approaches often rely on predefined key points or demonstrations, limiting their generalization across diverse garment categories. This paper presents a framework, MetaFold, that disentangles task planning from action prediction, learning each independently to enhance model generalization. It employs language-guided point cloud trajectory generation for task planning and a low-level foundation model for action prediction. This structure facilitates multi-category learning, enabling the model to adapt flexibly to various user instructions and folding tasks. Experimental results demonstrate the superiority of our proposed framework. Supplementary materials are available on our website: https://meta-fold.github.io/.

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce StructTokenBench, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop AminoAseed, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83% and 124.03%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench

Anatomical structure labels for chest radiographs are essential for medical image segmentation and a broad range of downstream diagnostic tasks. However, annotating anatomy directly on 2D chest radiographs is labor-intensive and intrinsically ambiguous, as 3D anatomical structures are projected onto a single 2D plane where boundaries may overlap, be occluded, or appear only partially visible. Consequently, existing anatomy-labeled chest radiograph datasets remain limited in scale, anatomy coverage, and label reliability. To address these limitations, we introduce RadGenome-Anatomy, the largest anatomy-labeled chest radiograph dataset, containing over 10 million segmentation masks across 210 anatomical structures in 25,692 studies. It is constructed by projecting large-scale 3D anatomical masks from CT volumes into 2D radiographic space through canonical radiographic geometry. This shifts annotation from directly tracing uncertain 2D boundaries to defining anatomy in volumetric space, where structures that overlap or become partially invisible in radiographs remain spatially separable. As a result, each 2D mask represents the physically grounded projected footprint of a volumetrically defined structure. The scale and broad anatomical coverage of RadGenome-Anatomy, including structures that are overlapping, partially visible, or difficult to delineate directly, enable research on geometric measurements as explicit evidence for chest radiograph interpretation. We demonstrate this by training XAnatomy to predict structure-specific masks and derive clinically relevant measurements, achieving diagnostic accuracies of 96.4%, 95.6%, and 89.2% for cardiomegaly, kyphosis, and scoliosis, respectively.

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.

Reconstructing complex structures from planar cross-sections is a challenging problem, with wide-reaching applications in medical imaging, manufacturing, and topography. Out-of-the-box point cloud reconstruction methods can often fail due to the data sparsity between slicing planes, while current bespoke methods struggle to reconstruct thin geometric structures and preserve topological continuity. This is important for medical applications where thin vessel structures are present in CT and MRI scans. This paper introduces CrossSDF, a novel approach for extracting a 3D signed distance field from 2D signed distances generated from planar contours. Our approach makes the training of neural SDFs contour-aware by using losses designed for the case where geometry is known within 2D slices. Our results demonstrate a significant improvement over existing methods, effectively reconstructing thin structures and producing accurate 3D models without the interpolation artifacts or over-smoothing of prior approaches.

Construction-safety models must handle concrete deployment risks, such as a worker standing near a scaffold edge without guardrails, rather than only recognize common objects in curated images. Yet real inspection archives are redundant, long-tailed, and collected across changing sites and months. We introduce SafeBuild-Bench, a metadata-driven benchmark for evaluating multimodal large language models on construction safety under realistic temporal and site variation. It is mined from 100K+ industrial image-text records and contains 3,314 task instances from over 3,000 expert-verified images, covering multiple-choice hazard identification and free-form hazard description. To make expert verification scalable, we develop GEMS, a graph-enhanced multimodal selection pipeline that combines a proxy-model confusion signal with graph-based diversity to identify informative candidates from redundant streams. On public instruction-tuning data, GEMS-selected subsets preserve robustness-oriented performance under small data budgets. On SafeBuild-Bench, current MLLMs remain far from reliable construction-safety understanding, with the best overall score near 60. We release the benchmark, evaluation scripts, and GEMS codebase at https://github.com/safebuild/gems.

We present a method for estimating neural scenes representations of objects given only a single image. The core of our method is the estimation of a geometric scaffold for the object and its use as a guide for the reconstruction of the underlying radiance field. Our formulation is based on a generative process that first maps a latent code to a voxelized shape, and then renders it to an image, with the object appearance being controlled by a second latent code. During inference, we optimize both the latent codes and the networks to fit a test image of a new object. The explicit disentanglement of shape and appearance allows our model to be fine-tuned given a single image. We can then render new views in a geometrically consistent manner and they represent faithfully the input object. Additionally, our method is able to generalize to images outside of the training domain (more realistic renderings and even real photographs). Finally, the inferred geometric scaffold is itself an accurate estimate of the object's 3D shape. We demonstrate in several experiments the effectiveness of our approach in both synthetic and real images.

Hyperelastic models have been widely used to model polymers and soft tissues. However, most hyperelastic models are phenomenological material models. Based on statistical mechanics and molecular chain configuration, 8 chain model or Arruda-Boyce model is a physical model which can be used to understand how microstructures of chains affect macroscopic mechanical properties of polymers and soft tissues. Mechanical properties of many polymers and soft tissues are directional dependent. Polymer matrix can be reinforced by fibers. For soft tissues, ligaments and tendons will lead to anisotropic properties. Since matrix and reinforcements are composed of similar microstructural molecular chains, they can be modeled by using the same mathematical model. In this paper, a series of 8 chain models is used to understand composite properties. That is, an isotropic 8 chain model will be used to model matrix and anisotropic 8 chain models will be used to model fibers. Replacing I_1 in isotropic 8 chain model with I_4 in anisotropic 8 chain model is physically corresponding to changing representative 8 chain cubic cell to 8 chain slender cell. This treatment not only simplifies exist anisotropic mathematical structures but also keeps microscopic physics of 8 chain model unchanged.

Virtual Screening (VS) of vast compound libraries guided by Artificial Intelligence (AI) models is a highly productive approach to early drug discovery. Data splitting is crucial for better benchmarking of such AI models. Traditional random data splits produce similar molecules between training and test sets, conflicting with the reality of VS libraries which mostly contain structurally distinct compounds. Scaffold split, grouping molecules by shared core structure, is widely considered to reflect this real-world scenario. However, here we show that the scaffold split also overestimates VS performance. The reason is that molecules with different chemical scaffolds are often similar, which hence introduces unrealistically high similarities between training molecules and test molecules following a scaffold split. Our study examined three representative AI models on 60 NCI-60 datasets, each with approximately 30,000 to 50,000 molecules tested on a different cancer cell line. Each dataset was split with three methods: scaffold, Butina clustering and the more accurate Uniform Manifold Approximation and Projection (UMAP) clustering. Regardless of the model, model performance is much worse with UMAP splits from the results of the 2100 models trained and evaluated for each algorithm and split. These robust results demonstrate the need for more realistic data splits to tune, compare, and select models for VS. For the same reason, avoiding the scaffold split is also recommended for other molecular property prediction problems. The code to reproduce these results is available at https://github.com/ScaffoldSplitsOverestimateVS

The recovery of damaged or resected ribcage structures requires precise, custom-designed implants to restore the integrity and functionality of the thoracic cavity. Traditional implant design methods rely mainly on manual processes, making them time-consuming and susceptible to variability. In this work, we explore the feasibility of automated ribcage implant generation using deep learning. We present a framework based on 3D U-Net architecture that processes CT scans to generate patient-specific implant designs. To the best of our knowledge, this is the first investigation into automated thoracic implant generation using deep learning approaches. Our preliminary results, while moderate, highlight both the potential and the significant challenges in this complex domain. These findings establish a foundation for future research in automated ribcage reconstruction and identify key technical challenges that need to be addressed for practical implementation.

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.

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing F_{max} from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

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.

3D fragment reassembly aims to recover the rigid poses of unordered fragment point clouds or meshes in a common object coordinate system to reconstruct the complete shape. The problem becomes particularly challenging as the number of fragments grows, since the target shape is unknown and fragments provide weak semantic cues. Existing end-to-end approaches are prone to cascading failures due to unreliable contact reasoning, most notably inaccurate fragment adjacencies. To address this, we propose Structure-Aware Reassembly (SARe), a generative framework with SARe-Gen for Euclidean-space assembly generation and SARe-Refine for inference-time refinement, with explicit contact modeling. SARe-Gen jointly predicts fracture-surface token probabilities and an inter-fragment contact graph to localize contact regions and infer candidate adjacencies. It adopts a query-point-based conditioning scheme and extracts aligned local geometric tokens at query locations from a frozen geometry encoder, yielding queryable structural representations without additional structural pretraining. We further introduce an inference-time refinement stage, SARe-Refine. By verifying candidate contact edges with geometric-consistency checks, it selects reliable substructures and resamples the remaining uncertain regions while keeping verified parts fixed, leading to more stable and consistent assemblies in the many-fragment regime. We evaluate SARe across three settings, including synthetic fractures, simulated fractures from scanned real objects, and real physically fractured scans. The results demonstrate state-of-the-art performance, with more graceful degradation and higher success rates as the fragment count increases in challenging large-scale reassembly.

The recently proposed term "heterostructured (HS) materials" serves as an umbrella classification encompassing a wide range of materials that hold great promise for enhanced mechanical properties. Most HS materials exhibit back-stress strengthening, as is typical for all plastically non-homogeneous materials. To better embody the distinctiveness of materials crafted via innovative heterostructuring, here we introduce the concept of "structural gradient hardening" (SGH), which captures an essential feature of HS materials and complements traditional strengthening mechanisms. SGH refers to the extra strengthening that arises from a characteristic gradient structure introduced by heterostructuring, beyond what is predicted by the rule of mixtures. This distinction is useful, as the overall back stress can in fact be partitioned into Type I and Type II components, with the latter specifically quantifying the extra hardening originating from the structural and strain gradients established by heterostructuring, as articulated in this Viewpoint article.

Diatoms have been described as nanometer-born lithographers because of their ability to create sophisticated three-dimensional amorphous silica exoskeletons. The hierarchical architecture of these structures provides diatoms with mechanical protection and the ability to filter, float, and manipulate light. Therefore, they emerge as an extraordinary model of multifunctional materials from which to draw inspiration. In this paper, we use numerical simulations, analytical models, and experimental tests to unveil the structural and fluid dynamic efficiency of the Coscinodiscus species diatom. Then we propose a novel 3D printable multifunctional biomimetic material for applications such as porous filters, heat exchangers, drug delivery systems, lightweight structures, and robotics. Our results demonstrate the role of Nature as a material designer for efficient and tunable systems and highlight the potential of diatoms for engineering materials innovation. Additionally, the results reported in this paper lay the foundation to extend the structure-property characterization of diatoms.

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.

We consider the matrix composite materials (CM) of either random (statistically homogeneous or inhomogeneous), periodic, or deterministic (neither random nor periodic) structures. CMs exhibit linear or nonlinear behavior, coupled or uncoupled multi-physical phenomena, locally elastic, weakly nonlocal (strain gradient and stress gradient), or strongly nonlocal (strain-type and displacement-type, peridynamics) phase properties. A modified Computational Analytical Micromechanics (CAM) approach introduces an exact Additive General Integral Equation (AGIE) for CMs of any structure and phase properties mentioned above. The unified iteration solution of static AGIEs is adapted to the body force with compact support serving as a fundamentally new universal training parameter. The approach also establishes a critical threshold for filtering out unsuitable sub-datasets of effective parameters through a novel Representative Volume Element (RVE) concept, which extends Hill's classical framework. This RVE concept eliminates sample size, boundary layer, and edge effects, making it applicable to CMs of any structure and phase properties, regardless of local or nonlocal, linear or nonlinear. Incorporating this new RVE concept into machine learning and neural network techniques enables the construction of any unpredefined surrogate nonlocal operators. The methodology is structured as a modular, block-based framework, allowing independent development and refinement of software components. This flexible, robust AGIE-CAM framework integrates data-driven, multi-scale, and multi-physics modeling, accelerating research in CM of any microtopology and phase properties considered. The AGIE-CAM framework represents a groundbreaking paradigm shift in the micromechanics of composites, redefining the very philosophy that underpins our understanding of their behavior at the microscopic level.

The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have not been observed in nature. However, there exists no principled methodological framework for diffusion on SE(3), the space of orientation preserving rigid motions in R3, that operates on frames and confers the group invariance. We address these shortcomings by developing theoretical foundations of SE(3) invariant diffusion models on multiple frames followed by a novel framework, FrameDiff, for learning the SE(3) equivariant score over multiple frames. We apply FrameDiff on monomer backbone generation and find it can generate designable monomers up to 500 amino acids without relying on a pretrained protein structure prediction network that has been integral to previous methods. We find our samples are capable of generalizing beyond any known protein structure.