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He Cao

Publications and source records attributed to He Cao.

At least 19 recordsLinked to original sources
arXiv2026

Insurance as AI Risk Infrastructure: A Generative-Agent Simulation of AI Adoption

The rapid evolution of artificial intelligence (AI) tools has demonstrated immense potential to enhance societal well-being and operational efficiency. However, the inherent unreliability and uncertain operational consequences of modern AI systems, typified by large language models (LLMs), have created a significant barrier to enterprise adoption. Many enterprises remain hesitant to integrate these tools deeply into their workflows due to concerns about unpredictable losses and liability exposure. While existing technical safeguards primarily seek to reduce the likelihood or severity of AI-enabled workflow failures, they do not by themselves provide ex post financial protection when residual pecuniary tail losses materialize. In this paper, we introduce a socio-economic framework that complements these safeguards by transferring and absorbing the residual financial consequences of AI adoption through insurance. To evaluate this framework, we develop an LLM-driven agent-based social simulation (LABSS) system. We assess the behavioral validity of the simulation using established economic and sociological theories. Our analysis demonstrates that the proposed insurance framework reduces firm-level financial exposure, thereby accelerating the aggregate adoption of AI tools and improving firm solvency and aggregate capital.

cs.MA↗
arXiv2026

History-informed Lagrangian Neural Networks

Forecasting the long-horizon evolution of mechanical systems from position-only observations is a pivotal yet difficult task, as hidden velocities and trajectory-specific physical properties must be inferred simultaneously. Although physics-guided neural networks like Lagrangian Neural Networks (LNNs) guarantee physical plausibility, they generally require complete state inputs and lack adaptability to changing system parameters. To break these limitations, we introduce History-informed Lagrangian Neural Networks (HiLNN). Grounded in the insight that temporal position sequences implicitly encode underlying dynamics, HiLNN employs a recurrent encoder to extract a latent context from history. This context not only reconstructs the unobserved initial velocity but also adaptively modulates the mass matrix, potential energy, and damping coefficients of a structured Lagrangian system. By leveraging a differentiable RK4 rollout scheme, the entire pipeline is optimized end-to-end under multi-step trajectory supervision and energy-consistency regularization. Empirical evaluations across conservative, dissipative, and heterogeneous variable-parameter systems show that HiLNN delivers superior long-term prediction accuracy and maintains precise energy profiles compared to state-of-the-art baselines. The source code is publicly available at https://github.com/yingtian22/History-informed-LNN.

cs.LG↗
arXiv2026

Divergence Decoding: Training-Free Capability Fusion

While large language models excel in reasoning, these generalists often lack knowledge for specialized scientific domains. Conversely, domain models~(specialists), while knowledgeable, suffer from specialization side-effects including diminished logic and reduced robustness.To address this dilemma, we introduce Divergence Decoding, a training-free framework for capability fusion. It reconstructs the "draft-and-verify" skeleton of speculative decoding into an adaptive routing mechanism. The core is using Jensen-Shannon divergence to monitor the distributional disagreement between the two models at each token. When the specialist exhibits significant divergence, our method identifies it as a potential reasoning risk and instantaneously routes control to the generalist. This allows the dynamic injection of general reasoning while preserving domain expertise, achieving inference-time policy composition of the generalist and the specialist.We evaluate Divergence Decoding across diverse model families (Qwen and Llama series) on challenging scientific benchmarks (GPQA, ChemBench, and ChemCoTBench). Experimental results demonstrate that Divergence Decoding outperforms both the domain-specialized and general-purpose models, effectively surpassing the performance of most single-model baseline. This suggests that Divergence Decoding provides a general, training-free paradigm for fusing diverse LLM capabilities through adaptive inference-time collaboration.

cs.AI↗
arXiv2026

Harnessing agent memory to build lifelong AI partners for materials scientists

Materials research advances through accumulated experience - scripts that work, protocols that are trusted, warnings attached to failed calculations or experiments, and judgement that links a new question to an old result. This experience is essential for reproducibility and knowledge transfer, yet it is usually fragmented across notebooks, repositories, job logs and individual memory, and it is rarely portable across artificial-intelligence agents. Here we argue that a lifelong AI partner for materials science can be designed around persistent memory rather than around a particular agent implementation. We introduce a self-evolving memory framework that stores scientific experience as inspectable facts and executable skills, so that observations, failure boundaries, protocols and validation checks can be retrieved, revised and migrated across models. We evaluate the idea in three computational settings that expose different layers of materials-research competence. In 49 real-world materials-tool-use questions comprising 138 executable subtasks, memory nearly doubles GPT-5.2 task success without model-parameter updates. In elemental-solid equation-of-state calculations, memory converts a wavefunction-initialization failure into a pre-execution guardrail, improving outcomes from 22/1/4 to 25/2/0 Correct/Partial/Error and avoiding 92% of repeated errors. In 13 practical material simulation workflows, remembered skills and failure facts halve the aggregate trace burden (tokens) and reduce tool calls by over a factor of two by the third round, while preserving physically meaningful outputs in band-gap, phonon, vacancy and work-function analyses. These results show that agent memory can serve as a durable scientific asset; a portable, self-improving record of materials-research experience that outlives any single model or agent stack.

cs.AI↗
arXiv2026

Improving Cross-Format Robustness in Language Models with Multi-Format Training

Large language models often remain sensitive to answer format: a question solved correctly in one form may fail in another semantically equivalent form. To study this gap, we define cross-format robustness as the extent to which a model answers the same underlying question consistently across formats. We then compare full-format training with FormatMix, which expands only a subset of training items into multiple equivalent formats using either random or targeted selection. Across GLM4 and Llama-3.1, multi-format supervision consistently improves both task performance and cross-format robustness, whereas Multiple-choice question (MCQ)-only supervision alone brings little benefit and can even reduce robustness. We further find that expanding only about 30% of the training set into multiple formats often recovers most of the gain from full-format training, and this effect appears across the model families and sizes we study. These results suggest that format diversity, rather than additional supervision alone, is the key driver of robustness. That lightweight multi-format augmentation is a practical way to make LLMs less sensitive to answer format without changing the base model.

cs.CL↗
arXiv2026

Augmenting Molecular Language Models with Local $n$-gram Memory

Transformer-based language models for SMILES strings suffer from a locality gap: standard character-level tokenization fragments chemically meaningful motifs, forcing models to repeatedly learn local syntax at the expense of long-range dependencies. To address this without disrupting standard tokenizers, we propose MolGram, which integrates a conditional $n$-gram memory module into molecular language models. MolGram maps local string patterns to learned embeddings via scalable hash lookups and dynamically injects this regional context into hidden states. Evaluations across three tasks, including unconditional molecule generation, forward reaction prediction, and single-step retrosynthesis, show that MolGram consistently improves performance. Crucially, our analyses demonstrate that MolGram outperforms baselines with 3$\times$ more parameters, establishing explicit local pattern memory as a highly efficient inductive bias.

cs.CL↗
arXiv2026

From Answers to States: Verifiable Process-Level Evaluation of Chemical Reasoning in Large Language Models

Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers. This masks a critical failure mode: a model may output the correct molecule, product, or option while its reasoning violates chemical logic. Existing process-level evaluators are hard to scale because LLM judges and human step-level process annotation are costly, inconsistent, and vulnerable to hallucination. We introduce ChemCoTBench-V2, a rule-verifiable diagnostic benchmark for low-cost, auditable evaluation of structured, verifier-addressable chemical reasoning traces. It spans molecular understanding, molecule editing, molecular optimization, and reaction prediction, with 5,620 evaluation samples across 18 reporting tasks. Models must expose key intermediate steps in expert-designed templates, and those steps are checked with deterministic chemistry rules and, for closed-answer tasks, reference traces rather than another LLM judge. Open-ended molecular optimization is evaluated with oracle-verifiable state constraints rather than strict trace matching. The benchmark reports three separate signals: final-answer correctness, template adherence, and step-wise verifier correctness over expert-refined intermediate commitments. Experiments on frontier models reveal a persistent gap between final-answer success and structured-reasoning-state consistency: models often follow the requested format while failing chemical-step checks, or answer correctly with weak supporting reasoning. ChemCoTBench-V2 enables fine-grained model comparison and identifies the concrete step at which the trace first violates the verifier.

cs.AI↗
arXiv2026

ProteinOPD: Towards Effective and Efficient Preference Alignment for Protein Design

Designing proteins with desired functions or properties represents a core goal in synthetic biology and drug discovery. Recent advances in protein language models (PLMs) have enabled the generation of highly designable protein sequences, while preference alignment provides a promising way to steer designs toward desired functions and properties. Nevertheless, they often trigger catastrophic forgetting of pretrained knowledge, degrading basic designability and failing to balance multiple competing objectives. To address these issues, we draw inspiration from On-Policy Distillation (OPD), an advanced post-training method renowned for mitigating catastrophic forgetting through its mode-seeking nature. In this work, we propose ProteinOPD, a multi-objective preference alignment framework that can effectively balance multiple preference objectives while maintaining the inherent designability of PLMs. ProteinOPD adapts a pretrained PLM into preference-specific teachers and distills their knowledge into a shared student via token-level OPD on the student's own trajectories. During this process, the student is aligned to a unique normalized geometric consensus of weighted teachers while ensuring bounded optimization under conflicts. This bridges the gap for OPD in multi-objective/teacher alignment. Extensive experiments show that ProteinOPD achieves substantial gains on target preference objectives without compromising the designability, with an 8x training speedup over RL-based alignment competitors.

cs.LG↗
arXiv2026

FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization

Molecular optimization seeks to improve a molecule through small structural edits while preserving similarity to the starting compound. Recent language-model approaches typically treat this task as prompt-conditioned sequence generation. However, relying on natural language introduces an inherent data-scaling bottleneck, often leads to chemical hallucinations, and ignores the strong context dependence of fragment effects. We present FORGE, a two-stage framework that reformulates molecular optimization as context-aware local editing. By utilizing automatically mined, verified low-to-high edit pairs instead of expensive human text annotations, Stage 1 ranks candidate fragments by their property contribution under the full molecular context to inject chemical prior, and Stage 2 generates explicit fragment replacements. Built on a compact 0.6B language model, FORGE further adapts to unseen black-box objectives through in-context demonstrations. Across Prompt-MolOpt, PMO-1k and ChemCoTBench, FORGE consistently outperforms prior methods, including substantially larger language models and graph methods. These results highlight the value of explicit fragment-level supervision as a more easily obtainable, scalable, and hallucination-less alternative to natural language training.

cs.LG↗
arXiv2026

Pushing Biomolecular Utility-Diversity Frontiers with Supergroup Relative Policy Optimization

Biomolecular generators are often adapted with reward feedback to improve task-specific utility, but pushing utility alone can concentrate generation on a narrow family of candidates. Maintaining diversity is difficult because sample diversity is a set-level property. We introduce Supergroup Relative Policy Optimization (SGRPO), a flexible GRPO-style framework that directly constructs rewards from set-level diversity. For each condition, SGRPO samples a supergroup of candidate sets, compares their diversity under the same condition, and redistributes the group diversity reward to individual rollouts through leave-one-out diversity contributions before combining it with rollout-level utility. This design decouples SGRPO from a particular generator, utility reward, or diversity metric, and allows instantiation with different GRPO-style approaches. We evaluate SGRPO on de novo small-molecule design, pocket-based small-molecule design, and de novo protein design, instantiating it with both GRPO and Coupled-GRPO across autoregressive and discrete diffusion generators. Across decoding sweeps, SGRPO expands the utility-diversity Pareto frontier and achieves the best frontier-level metrics relative to pretrained generators, GRPO, and memory-assisted GRPO when applicable. Our analyses further show that direct set-level diversity rewards remain effective with small groups and help preserve broader generation-distribution coverage during post-training. The code is available at https://github.com/IDEA-XL/SGRPO.

cs.CE↗
arXiv2026

ReactBench: A Benchmark for Topological Reasoning in MLLMs on Chemical Reaction Diagrams

Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and cyclic dependencies, their reasoning capabilities degrade sharply, even on tasks as basic as counting endpoints. Existing benchmarks fail to probe this gap, focusing on semantic comprehension rather than structural reasoning. We introduce ReactBench, a benchmark that reveals fundamental limitations in structural reasoning through chemical reaction diagrams. These real-world scientific diagrams offer an ideal testbed because they naturally span diverse structures from linear chains to cyclic graphs, while requiring both precise local recognition and coherent global reasoning. Our benchmark comprises 1,618 expert-annotated QA pairs across four hierarchical task dimensions. Extensive evaluation across 24 MLLMs reveals a significant performance gap exceeding 30% between anchor-based tasks and holistic structural reasoning tasks. Controlled ablations confirm this bottleneck lies in reasoning, not perception. These findings expose a fundamental deficit in structural understanding and establish directions for advancing visual reasoning.

cs.AI↗
arXiv2026

Mozi: Governed Autonomy for Drug Discovery LLM Agents

Tool-augmented large language model (LLM) agents promise to unify scientific reasoning with computation, yet their deployment in high-stakes domains like drug discovery is bottlenecked by two critical barriers: unconstrained tool-use governance and poor long-horizon reliability. In dependency-heavy pharmaceutical pipelines, autonomous agents often drift into irreproducible trajectories, where early-stage hallucinations multiplicatively compound into downstream failures. To overcome this, we present Mozi, a dual-layer architecture that bridges the flexibility of generative AI with the deterministic rigor of computational biology. Layer A (Control Plane) establishes a governed supervisor--worker hierarchy that enforces role-based tool isolation, limits execution to constrained action spaces, and drives reflection-based replanning. Layer B (Workflow Plane) operationalizes canonical drug discovery stages -- from Target Identification to Lead Optimization -- as stateful, composable skill graphs. This layer integrates strict data contracts and strategic human-in-the-loop (HITL) checkpoints to safeguard scientific validity at high-uncertainty decision boundaries. Operating on the design principle of ``free-form reasoning for safe tasks, structured execution for long-horizon pipelines,'' Mozi provides built-in robustness mechanisms and trace-level audibility to completely mitigate error accumulation. We evaluate Mozi on PharmaBench, a curated benchmark for biomedical agents, demonstrating superior orchestration accuracy over existing baselines. Furthermore, through end-to-end therapeutic case studies, we demonstrate Mozi's ability to navigate massive chemical spaces, enforce stringent toxicity filters, and generate highly competitive in silico candidates, effectively transforming the LLM from a fragile conversationalist into a reliable, governed co-scientist.

cs.AI↗
arXiv2026

Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesis

Language models are revolutionizing the biochemistry domain, assisting scientists in drug design and chemical synthesis with high efficiency. Yet current approaches struggle between small language models prone to hallucination and limited knowledge retention, and large cloud-based language models plagued by privacy risks and high inference costs. To bridge this gap, we introduce ChemCRAFT, a novel framework leveraging agentic reinforcement learning to decouple chemical reasoning from knowledge storage. Instead of forcing the model to memorize vast chemical data, our approach empowers the language model to interact with a sandbox for precise information retrieval. This externalization of knowledge allows a locally deployable small model to achieve superior performance with minimal inference costs. To enable small language models for agent-calling ability, we build an agentic trajectory construction pipeline and a comprehensive chemical-agent sandbox. Based on sandbox interactions, we constructed ChemToolDataset, the first large-scale chemical tool trajectory dataset. Simultaneously, we propose SMILES-GRPO to build a dense chemical reward function, promoting the model's ability to call chemical agents. Evaluations across diverse aspects of drug design show that ChemCRAFT outperforms current cloud-based LLMs in molecular structure analysis, molecular optimization, and synthesis pathway prediction, demonstrating that scientific reasoning is not solely an emergent ability of model scale, but a learnable policy of tool orchestration. This work establishes a cost-effective and privacy-preserving paradigm for AI-aided chemistry, opening new avenues for accelerating molecular discovery with locally deployable agents. Code available at https://github.com/HowardLi1984/ChemCraft.

cs.LG↗
arXiv2025

From Static Structures to Ensembles: Studying and Harnessing Protein Structure Tokenization

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

cs.LG↗
arXiv2025

Floating-Body Hydrodynamic Neural Networks

Fluid-structure interaction is common in engineering and natural systems, where floating-body motion is governed by added mass, drag, and background flows. Modeling these dissipative dynamics is difficult: black-box neural models regress state derivatives with limited interpretability and unstable long-horizon predictions. We propose Floating-Body Hydrodynamic Neural Networks (FHNN), a physics-structured framework that predicts interpretable hydrodynamic parameters such as directional added masses, drag coefficients, and a streamfunction-based flow, and couples them with analytic equations of motion. This design constrains the hypothesis space, enhances interpretability, and stabilizes integration. On synthetic vortex datasets, FHNN achieves up to an order-of-magnitude lower error than Neural ODEs, recovers physically consistent flow fields. Compared with Hamiltonian and Lagrangian neural networks, FHNN more effectively handles dissipative dynamics while preserving interpretability, which bridges the gap between black-box learning and transparent system identification.

cs.LG↗
arXiv2025

Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations

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

cs.AI↗
arXiv2025

Rethinking Text-based Protein Understanding: Retrieval or LLM?

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

cs.CL↗
arXiv2025

How to Detect and Defeat Molecular Mirage: A Metric-Driven Benchmark for Hallucination in LLM-based Molecular Comprehension

Large language models are increasingly used in scientific domains, especially for molecular understanding and analysis. However, existing models are affected by hallucination issues, resulting in errors in drug design and utilization. In this paper, we first analyze the sources of hallucination in LLMs for molecular comprehension tasks, specifically the knowledge shortcut phenomenon observed in the PubChem dataset. To evaluate hallucination in molecular comprehension tasks with computational efficiency, we introduce \textbf{Mol-Hallu}, a novel free-form evaluation metric that quantifies the degree of hallucination based on the scientific entailment relationship between generated text and actual molecular properties. Utilizing the Mol-Hallu metric, we reassess and analyze the extent of hallucination in various LLMs performing molecular comprehension tasks. Furthermore, the Hallucination Reduction Post-processing stage~(HRPP) is proposed to alleviate molecular hallucinations, Experiments show the effectiveness of HRPP on decoder-only and encoder-decoder molecular LLMs. Our findings provide critical insights into mitigating hallucination and improving the reliability of LLMs in scientific applications.

cs.CL↗