Searcharxiv⌕ Search

arXiv subjects

Wenbin Hu

Publications and source records attributed to Wenbin Hu.

At least 37 records · Page 2Linked to original sources
arXiv2026

When Molecular Similarity Works: Property Cliffs Reveal Hidden Errors

Accurate prediction of molecular properties underpins drug discovery and material design, yet even state-of-the-art models remain vulnerable to localized failure modes that aggregate metrics cannot detect. The places where molecular similarity should be most helpful are also places where standard evaluation can be most misleading. Property cliffs expose this gap: structurally similar molecules can still differ sharply in target property, so models with competitive overall performance may fail in high-risk local neighborhoods. To expose and mitigate this failure mode, CliffSplit, a cliff-aware evaluation protocol that constructs locally supported, cliff-exposed test cases, and CliffLoss, a model-agnostic train-only mitigation mechanism for cliff-sensitive errors, are introduced. Experiments on three QM9 targets and three MoleculeNet tasks across five backbones show that CliffSplit reveals at least 15% higher error in cliff-heavy QM9 regions, while CliffLoss reduces the cliff-to-smooth error gap by up to 30% on Lipophilicity and improves overall MAE by 9.7%. Together, these results turn molecular similarity failure from a descriptive anomaly into a benchmarked evaluation problem for molecular machine learning. The code is available at https://anonymous.4open.science/r/Cliff_Loss.

cs.LG↗
arXiv2026

From Single-Step Edit Response to Multi-Step Molecular Optimization

Conditional molecular optimization aims to edit a molecule to realize a specified property shift. In practice, structurally similar molecule data is scarce, while decisions are inherently action-level: at each step, the system must select one local structural edit from a candidate set that is strictly filtered by chemical feasibility rules. This level mismatch between supervision and decision makes oracle-in-the-loop search unstable in molecular optimization. Regressing on property differences between molecule pairs improves data efficiency but relies on oracle-in-the-loop search, entangling transformation effects with global context and providing limited guidance for selecting the next feasible edit, often resorting to oracle-in-the-loop search. For this reason, we propose a response-oriented discrete edit optimization approach comprising two tightly coupled components: a single-step molecular edit response predictor (SMER) and a multi-step planner that composes local predictions into optimization trajectories via guided tree search (SMER-Opt). The approach learns a directional evaluation model over edit actions to support constraint-aware planning. It mines weakly related molecule pairs and decomposes their structural differences into minimal edit units, turning endpoint property annotations into process-level supervision and yielding reusable, transferable action primitives. A directional edit evaluator then scores feasible candidate edits by their likelihood of moving the molecule toward the desired property change, substantially reducing dependence on external evaluator queries at decision time. Code is available at https://anonymous.4open.science/r/SMER.

cs.AI↗
arXiv2026

GraphSculptor: Sculpting Pre-training Coreset for Graph Self-supervised Learning

Graph self-supervised learning typically relies on large-scale unlabeled datasets, heavily inflating computational costs. However, empirical evidence suggests that these datasets contain substantial redundancy-our analysis reveals that uniformly subsampling 50% of graphs retains over 96% of downstream performance. To exploit this redundancy, we introduce GraphSculptor for pre-training coreset construction. Unlike methods dependent on additional training-time signals or limited solely to topological statistics, GraphSculptor provides a label-free solution that constructs coresets via two complementary perspectives: intrinsic structure and contextual semantics. Concretely, structural diversity is quantified using intrinsic graph statistics, yielding a structural feature vector for each graph, while semantic diversity is captured by utilizing a pre-trained language model to encode descriptions generated via graph-to-text. GraphSculptor integrates these signals into a unified metric space and performs cluster-aware selection to preserve joint structural-semantic diversity. We further derive a theoretical bound on the loss gap between coreset and full-data pre-training, offering theoretical motivation for our selection formulation. Extensive experiments demonstrate that GraphSculptor effectively sculpts the dataset: a 10% coreset achieves 99.6% of full-data performance while reducing pre-training time by nearly 90%, offering a scalable solution for data-efficient graph pre-training.

cs.LG↗
arXiv2026

OmniCompliance-100K: A Multi-Domain, Rule-Grounded, Real-World Safety Compliance Dataset

Ensuring the safety and compliance of large language models (LLMs) is of paramount importance. However, existing LLM safety datasets often rely on ad-hoc taxonomies for data generation and suffer from a significant shortage of rule-grounded, real-world cases that are essential for robustly protecting LLMs. In this work, we address this critical gap by constructing a comprehensive safety dataset from a compliance perspective. Using a powerful web-searching agent, we collect a rule-grounded, real-world case dataset OmniCompliance-100K, sourced from multi-domain authoritative references. The dataset spans 74 regulations and policies across a wide range of domains, including security and privacy regulations, content safety and user data privacy policies from leading AI companies and social media platforms, financial security requirements, medical device risk management standards, educational integrity guidelines, and protections of fundamental human rights. In total, our dataset contains 12,985 distinct rules and 106,009 associated real-world compliance cases. Our analysis confirms a strong alignment between the rules and their corresponding cases. We further conduct extensive benchmarking experiments to evaluate the safety and compliance capabilities of advanced LLMs across different model scales. Our experiments reveal several interesting findings that have great potential to offer valuable insights for future LLM safety research.

cs.CL↗
arXiv2026

ContextLens: Modeling Imperfect Privacy and Safety Context for Legal Compliance

Individuals' concerns about data privacy and AI safety are highly contextualized and extend beyond sensitive patterns. Addressing these issues requires reasoning about the context to identify and mitigate potential risks. Though researchers have widely explored using large language models (LLMs) as evaluators for contextualized safety and privacy assessments, these efforts typically assume the availability of complete and clear context, whereas real-world contexts tend to be ambiguous and incomplete. In this paper, we propose ContextLens, a semi-rule-based framework that leverages LLMs to ground the input context in the legal domain and explicitly identify both known and unknown factors for legal compliance. Instead of directly assessing safety outcomes, our ContextLens instructs LLMs to answer a set of crafted questions that span over applicability, general principles and detailed provisions to assess compliance with pre-defined priorities and rules. We conduct extensive experiments on existing compliance benchmarks that cover the General Data Protection Regulation (GDPR) and the EU AI Act. The results suggest that our ContextLens can significantly improve LLMs' compliance assessment and surpass existing baselines without any training. Additionally, our ContextLens can further identify the ambiguous and missing factors.

cs.CL↗
arXiv2026

GrandGuard: Taxonomy, Benchmark, and Safeguards for Elderly-Chatbot Interaction Safety

As older adults increasingly use LLM-based chatbots for companionship and assistance, a safety gap is emerging. Older adults may face vulnerabilities from social isolation, limited digital literacy, and cognitive decline, yet existing safety benchmarks largely target general harms and overlook elderly-specific risks. For example, a prompt such as "how to repair a ceiling light alone in the dark" may be benign for most users but poses a serious fall risk for older adults with mobility limitations. We introduce GrandGuard, the first comprehensive framework for assessing and mitigating elderly-specific contextual risks in LLM interactions. We develop a three-level taxonomy with 50 fine-grained risk types across mental well-being, financial, medical, toxicity, and privacy domains, grounded in real-world incidents, community discussions, and analysis of stakeholder studies. Using this taxonomy, we construct a benchmark of 10,404 labeled prompts and responses, showing that several leading LLMs mishandle elderly-specific contextual risks in over 50% of cases. We mitigate these failures with two safeguards: a fine-tuned Llama-Guard-3 and a policy-enhanced gpt-oss-safeguard-20b, achieving up to 96.2% and 90.9% unsafe-prompt detection accuracy, respectively. GrandGuard lays the groundwork for AI systems that move beyond general safety to support aging populations.

cs.HC↗
arXiv2026

Hi-GMAE: Hierarchical Graph Masked Autoencoders

Graph Masked Autoencoders (GMAEs) have emerged as a notable self-supervised learning approach for graph-structured data. Existing GMAE models primarily focus on reconstructing node-level information, categorizing them as single-scale GMAEs. This methodology, while effective in certain contexts, tends to overlook the complex hierarchical structures inherent in many real-world graphs. For instance, molecular graphs exhibit a clear hierarchical organization in the form of the atoms-functional groups-molecules structure. Therefore, the inability of single-scale GMAE models to incorporate these hierarchical relationships often results in an inadequate capture of crucial high-level graph information, leading to a noticeable decline in performance. To address this limitation, we propose Hierarchical Graph Masked AutoEncoders (Hi-GMAE), a novel multi-scale GMAE framework designed to handle the hierarchical structures within graphs. First, Hi-GMAE constructs a multi-scale graph hierarchy through graph pooling, enabling the exploration of graph structures across different granularity levels. To ensure masking uniformity of subgraphs across these scales, we propose a novel coarse-to-fine strategy that initiates masking at the coarsest scale and progressively back-projects the mask to finer scales. Furthermore, we integrate a gradual recovery strategy with the masking process to mitigate the learning challenges posed by completely masked subgraphs. Our experiments on 17 graph datasets, covering two graph learning tasks, consistently demonstrate that Hi-GMAE outperforms 29 state-of-the-art self-supervised competitors in capturing comprehensive graph information.

cs.LG↗
arXiv2026

PCEvo: Path-Consistent Molecular Representation via Virtual Evolutionary

Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific applications. In many AI for science tasks, labeled data are expensive to obtain and therefore limited in availability. Under the few-shot setting, models trained with scarce supervision often learn brittle structure-property relationships, resulting in substantially higher prediction errors and reduced generalization to unseen molecules. To address this limitation, we propose PCEvo, a path-consistent representation method that learns from virtual paths through dynamic structural evolution. PCEvo enumerates multiple chemically feasible edit paths between retrieved similar molecular pairs under topological dependency constraints. It transforms the labels of the two molecules into stepwise supervision along each virtual evolutionary path. It introduces a path-consistency objective that enforces prediction invariance across alternative paths connecting the same two molecules. Comprehensive experiments on the QM9 and MoleculeNet datasets demonstrate that PCEvo substantially improves the few-shot generalization performance of baseline methods. The code is available at https://anonymous.4open.science/r/PCEvo-4BF2.

q-bio.BM↗
arXiv2025

Text-guided multi-property molecular optimization with a diffusion language model

Molecular optimization (MO) is a crucial stage in drug discovery in which task-oriented generated molecules are optimized to meet practical industrial requirements. Existing mainstream MO approaches primarily utilize external property predictors to guide iterative property optimization. However, learning all molecular samples in the vast chemical space is unrealistic for predictors. As a result, errors and noise are inevitably introduced during property prediction due to the nature of approximation. This leads to discrepancy accumulation, generalization reduction and suboptimal molecular candidates. In this paper, we propose a text-guided multi-property molecular optimization method utilizing transformer-based diffusion language model (TransDLM). TransDLM leverages standardized chemical nomenclature as semantic representations of molecules and implicitly embeds property requirements into textual descriptions, thereby mitigating error propagation during diffusion process. By fusing physically and chemically detailed textual semantics with specialized molecular representations, TransDLM effectively integrates diverse information sources to guide precise optimization, which enhances the model's ability to balance structural retention and property enhancement. Additionally, the success of a case study further demonstrates TransDLM's ability to solve practical problems. Experimentally, our approach surpasses state-of-the-art methods in maintaining molecular structural similarity and enhancing chemical properties on the benchmark dataset.

cs.LG↗
arXiv2025

FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation

Computational antibody design holds immense promise for therapeutic discovery, yet existing generative models are fundamentally limited by two core challenges: (i) a lack of dynamical consistency, which yields physically implausible structures, and (ii) poor generalization due to data scarcity and structural bias. We introduce FP-AbDiff, the first antibody generator to enforce Fokker-Planck Equation (FPE) physics along the entire generative trajectory. Our method minimizes a novel FPE residual loss over the mixed manifold of CDR geometries (R^3 x SO(3)), compelling locally-learned denoising scores to assemble into a globally coherent probability flow. This physics-informed regularizer is synergistically integrated with deep biological priors within a state-of-the-art SE(3)-equivariant diffusion framework. Rigorous evaluation on the RAbD benchmark confirms that FP-AbDiff establishes a new state-of-the-art. In de novo CDR-H3 design, it achieves a mean Root Mean Square Deviation of 0.99 Å when superposing on the variable region, a 25% improvement over the previous state-of-the-art model, AbX, and the highest reported Contact Amino Acid Recovery of 39.91%. This superiority is underscored in the more challenging six-CDR co-design task, where our model delivers consistently superior geometric precision, cutting the average full-chain Root Mean Square Deviation by ~15%, and crucially, achieves the highest full-chain Amino Acid Recovery on the functionally dominant CDR-H3 loop (45.67%). By aligning generative dynamics with physical laws, FP-AbDiff enhances robustness and generalizability, establishing a principled approach for physically faithful and functionally viable antibody design.

cs.LG↗
arXiv2025

MASLegalBench: Benchmarking Multi-Agent Systems in Deductive Legal Reasoning

Multi-agent systems (MAS), leveraging the remarkable capabilities of Large Language Models (LLMs), show great potential in addressing complex tasks. In this context, integrating MAS with legal tasks is a crucial step. While previous studies have developed legal benchmarks for LLM agents, none are specifically designed to consider the unique advantages of MAS, such as task decomposition, agent specialization, and flexible training. In fact, the lack of evaluation methods limits the potential of MAS in the legal domain. To address this gap, we propose MASLegalBench, a legal benchmark tailored for MAS and designed with a deductive reasoning approach. Our benchmark uses GDPR as the application scenario, encompassing extensive background knowledge and covering complex reasoning processes that effectively reflect the intricacies of real-world legal situations. Furthermore, we manually design various role-based MAS and conduct extensive experiments using different state-of-the-art LLMs. Our results highlight the strengths, limitations, and potential areas for improvement of existing models and MAS architectures.

cs.AI↗
arXiv2025

MCIP: Protecting MCP Safety via Model Contextual Integrity Protocol

As Model Context Protocol (MCP) introduces an easy-to-use ecosystem for users and developers, it also brings underexplored safety risks. Its decentralized architecture, which separates clients and servers, poses unique challenges for systematic safety analysis. This paper proposes a novel framework to enhance MCP safety. Guided by the MAESTRO framework, we first analyze the missing safety mechanisms in MCP, and based on this analysis, we propose the Model Contextual Integrity Protocol (MCIP), a refined version of MCP that addresses these gaps. Next, we develop a fine-grained taxonomy that captures a diverse range of unsafe behaviors observed in MCP scenarios. Building on this taxonomy, we develop benchmark and training data that support the evaluation and improvement of LLMs' capabilities in identifying safety risks within MCP interactions. Leveraging the proposed benchmark and training data, we conduct extensive experiments on state-of-the-art LLMs. The results highlight LLMs' vulnerabilities in MCP interactions and demonstrate that our approach substantially improves their safety performance.

cs.CL↗
arXiv2025

Safety Compliance: Rethinking LLM Safety Reasoning through the Lens of Compliance

The proliferation of Large Language Models (LLMs) has demonstrated remarkable capabilities, elevating the critical importance of LLM safety. However, existing safety methods rely on ad-hoc taxonomy and lack a rigorous, systematic protection, failing to ensure safety for the nuanced and complex behaviors of modern LLM systems. To address this problem, we solve LLM safety from legal compliance perspectives, named safety compliance. In this work, we posit relevant established legal frameworks as safety standards for defining and measuring safety compliance, including the EU AI Act and GDPR, which serve as core legal frameworks for AI safety and data security in Europe. To bridge the gap between LLM safety and legal compliance, we first develop a new benchmark for safety compliance by generating realistic LLM safety scenarios seeded with legal statutes. Subsequently, we align Qwen3-8B using Group Policy Optimization (GRPO) to construct a safety reasoner, Compliance Reasoner, which effectively aligns LLMs with legal standards to mitigate safety risks. Our comprehensive experiments demonstrate that the Compliance Reasoner achieves superior performance on the new benchmark, with average improvements of +10.45% for the EU AI Act and +11.85% for GDPR.

cs.CL↗
arXiv2025

Context Reasoner: Incentivizing Reasoning Capability for Contextualized Privacy and Safety Compliance via Reinforcement Learning

While Large Language Models (LLMs) exhibit remarkable capabilities, they also introduce significant safety and privacy risks. Current mitigation strategies often fail to preserve contextual reasoning capabilities in risky scenarios. Instead, they rely heavily on sensitive pattern matching to protect LLMs, which limits the scope. Furthermore, they overlook established safety and privacy standards, leading to systemic risks for legal compliance. To address these gaps, we formulate safety and privacy issues into contextualized compliance problems following the Contextual Integrity (CI) theory. Under the CI framework, we align our model with three critical regulatory standards: GDPR, EU AI Act, and HIPAA. Specifically, we employ reinforcement learning (RL) with a rule-based reward to incentivize contextual reasoning capabilities while enhancing compliance with safety and privacy norms. Through extensive experiments, we demonstrate that our method not only significantly enhances legal compliance (achieving a +8.58% accuracy improvement in safety/privacy benchmarks) but also further improves general reasoning capability. For OpenThinker-7B, a strong reasoning model that significantly outperforms its base model Qwen2.5-7B-Instruct across diverse subjects, our method enhances its general reasoning capabilities, with +2.05% and +8.98% accuracy improvement on the MMLU and LegalBench benchmark, respectively.

cs.CL↗
arXiv2025

BSL: A Unified and Generalizable Multitask Learning Platform for Virtual Drug Discovery from Design to Synthesis

Drug discovery is of great social significance in safeguarding human health, prolonging life, and addressing the challenges of major diseases. In recent years, artificial intelligence has demonstrated remarkable advantages in key tasks across bioinformatics and pharmacology, owing to its efficient data processing and data representation capabilities. However, most existing computational platforms cover only a subset of core tasks, leading to fragmented workflows and low efficiency. In addition, they often lack algorithmic innovation and show poor generalization to out-of-distribution (OOD) data, which greatly hinders the progress of drug discovery. To address these limitations, we propose Baishenglai (BSL), a deep learning-enhanced, open-access platform designed for virtual drug discovery. BSL integrates seven core tasks within a unified and modular framework, incorporating advanced technologies such as generative models and graph neural networks. In addition to achieving state-of-the-art (SOTA) performance on multiple benchmark datasets, the platform emphasizes evaluation mechanisms that focus on generalization to OOD molecular structures. Comparative experiments with existing platforms and baseline methods demonstrate that BSL provides a comprehensive, scalable, and effective solution for virtual drug discovery, offering both algorithmic innovation and high-precision prediction for real-world pharmaceutical research. In addition, BSL demonstrated its practical utility by discovering novel modulators of the GluN1/GluN3A NMDA receptor, successfully identifying three compounds with clear bioactivity in in-vitro electrophysiological assays. These results highlight BSL as a promising and comprehensive platform for accelerating biomedical research and drug discovery. The platform is accessible at https://www.baishenglai.net.

cs.LG↗
arXiv2025

DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery

Large language models (LLMs) integrated with autonomous agents hold significant potential for advancing scientific discovery through automated reasoning and task execution. However, applying LLM agents to drug discovery is still constrained by challenges such as large-scale multimodal data processing, limited task automation, and poor support for domain-specific tools. To overcome these limitations, we introduce DrugPilot, a LLM-based agent system with a parameterized reasoning architecture designed for end-to-end scientific workflows in drug discovery. DrugPilot enables multi-stage research processes by integrating structured tool use with a novel parameterized memory pool. The memory pool converts heterogeneous data from both public sources and user-defined inputs into standardized representations. This design supports efficient multi-turn dialogue, reduces information loss during data exchange, and enhances complex scientific decision-making. To support training and benchmarking, we construct a drug instruction dataset covering eight core drug discovery tasks. Under the Berkeley function-calling benchmark, DrugPilot significantly outperforms state-of-the-art agents such as ReAct and LoT, achieving task completion rates of 98.0%, 93.5%, and 64.0% for simple, multi-tool, and multi-turn scenarios, respectively. These results highlight DrugPilot's potential as a versatile agent framework for computational science domains requiring automated, interactive, and data-integrated reasoning.

cs.AI↗
arXiv2025

Zero-Shot Learning with Subsequence Reordering Pretraining for Compound-Protein Interaction

Given the vastness of chemical space and the ongoing emergence of previously uncharacterized proteins, zero-shot compound-protein interaction (CPI) prediction better reflects the practical challenges and requirements of real-world drug development. Although existing methods perform adequately during certain CPI tasks, they still face the following challenges: (1) Representation learning from local or complete protein sequences often overlooks the complex interdependencies between subsequences, which are essential for predicting spatial structures and binding properties. (2) Dependence on large-scale or scarce multimodal protein datasets demands significant training data and computational resources, limiting scalability and efficiency. To address these challenges, we propose a novel approach that pretrains protein representations for CPI prediction tasks using subsequence reordering, explicitly capturing the dependencies between protein subsequences. Furthermore, we apply length-variable protein augmentation to ensure excellent pretraining performance on small training datasets. To evaluate the model's effectiveness and zero-shot learning ability, we combine it with various baseline methods. The results demonstrate that our approach can improve the baseline model's performance on the CPI task, especially in the challenging zero-shot scenario. Compared to existing pre-training models, our model demonstrates superior performance, particularly in data-scarce scenarios where training samples are limited. Our implementation is available at https://github.com/Hoch-Zhang/PSRP-CPI.

cs.LG↗
arXiv2025

Antibody Design and Optimization with Multi-scale Equivariant Graph Diffusion Models for Accurate Complex Antigen Binding

Antibody design remains a critical challenge in therapeutic and diagnostic development, particularly for complex antigens with diverse binding interfaces. Current computational methods face two main limitations: (1) capturing geometric features while preserving symmetries, and (2) generalizing novel antigen interfaces. Despite recent advancements, these methods often fail to accurately capture molecular interactions and maintain structural integrity. To address these challenges, we propose \textbf{AbMEGD}, an end-to-end framework integrating \textbf{M}ulti-scale \textbf{E}quivariant \textbf{G}raph \textbf{D}iffusion for antibody sequence and structure co-design. Leveraging advanced geometric deep learning, AbMEGD combines atomic-level geometric features with residue-level embeddings, capturing local atomic details and global sequence-structure interactions. Its E(3)-equivariant diffusion method ensures geometric precision, computational efficiency, and robust generalizability for complex antigens. Furthermore, experiments using the SAbDab database demonstrate a 10.13\% increase in amino acid recovery, 3.32\% rise in improvement percentage, and a 0.062~Å reduction in root mean square deviation within the critical CDR-H3 region compared to DiffAb, a leading antibody design model. These results highlight AbMEGD's ability to balance structural integrity with improved functionality, establishing a new benchmark for sequence-structure co-design and affinity optimization. The code is available at: https://github.com/Patrick221215/AbMEGD.

cs.LG↗