arXiv subjects

Xiao-yong Wei

Publications and source records attributed to Xiao-yong Wei.

5 recordsLinked to original sources

arXiv2026

Do LLMs Truly Generalize in the Molecular Domain? A Perturbation-Based Analysis

Large Language Models (LLMs) have recently shown promise in molecular discovery, yet a gap remains between their probabilistic nature over discrete sequential tokens and the rigid topological constraints of chemical space. This raises the question of whether molecular LLMs can generalize beyond the local neighborhoods induced by their sequence-based representations. To systematically investigate this question, we introduce a Molecular Perturbation framework that generates syntax-valid structural variants of training molecules under controlled Graph Edit Distance (GED) to probe the manifold regularity of molecular LLMs. Our analysis shows that even a single edit can cause substantial performance drops on common molecular tasks, revealing a narrow local trust region and fragile sensitivity to structural changes. Since similar molecules tend to exhibit similar properties, In-Context Tuning (ICT), which anchors predictions on structurally similar molecules, offers a natural way to mitigate such fragility. Our experiments also examine whether ICT confers robustness under controlled structural perturbations, and the results suggest that it can partially expand the local trust region and offer a promising direction for stabilizing molecular LLMs against structural variation.

cs.LG↗

arXiv2026

Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation

Recently, Large Language Models (LLMs) have demonstrated great potential in natural language-driven molecule discovery. However, existing datasets and benchmarks for molecule-text alignment are predominantly built on one-to-one mappings, measuring LLMs' ability to retrieve a single, pre-defined answer, rather than their creative potential to generate diverse, yet equally valid, molecular candidates. To address this critical gap, we propose Speak-to-Structure (S^2-Bench), the first benchmark to evaluate LLMs in open-domain natural language-driven molecule generation. S^2-Bench is specifically designed for one-to-many relationships, challenging LLMs to exhibit genuine molecular understanding and open-ended generation capabilities. Our benchmark includes three key tasks: molecule editing (MolEdit), molecule optimization (MolOpt), and customized molecule generation (MolCustom), each probing a different aspect of molecule discovery. We also introduce OpenMolIns, a large-scale instruction tuning dataset that enables Llama3.1-8B to surpass the most powerful LLMs like GPT-4o and Claude-3.5 on S^2-Bench. Our comprehensive evaluation of 31 LLMs shifts the focus from simple pattern recall to realistic molecular design, paving the way for more capable LLMs in natural language-driven molecule discovery. Our codes and datasets are fully accessible through the Github Repository: https://github.com/phenixace/S2-TOMG-Bench and Huggingface Datasets: https://huggingface.co/datasets/phenixace/S2-TOMG-Bench.

cs.CL↗

arXiv2026

MolViBench: Evaluating LLMs on Molecular Vibe Coding

Molecular Vibe Coding, a paradigm where chemists interact with LLMs to generate executable programs for molecular tasks, has emerged as a flexible alternative to chemical agents with predefined tools, enabling chemists to express arbitrarily complex, customized workflows. Unlike general coding tasks, molecular coding imposes a distinctive challenge that LLMs should jointly equip programming, molecular understanding, and domain-specific reasoning capabilities. However, existing benchmarks remain disconnected. General code generation benchmarks such as HumanEval and SWE-bench require no chemistry knowledge, while chemistry-focused benchmarks such as S^2-Bench and ChemCoTBench evaluate knowledge recall or property prediction rather than executable code generation. To bridge this gap, we introduce MolViBench, the first benchmark tailored for Molecular Vibe Coding. MolViBench comprises 358 curated tasks across five cognitive levels, ranging from single-API recall to end-to-end virtual screening pipeline design, spanning 12 real-world drug discovery workflows. To rigorously assess generated code, we also propose a multi-layered evaluation framework that combines type-aware output comparison and AST-based API-semantic fallback analysis, which jointly measures executability and chemical correctness. We systematically evaluate 9 frontier coding LLMs and compare three real-world Molecular Vibe Coding paradigms, providing a practical and fine-grained testbed for diagnosing LLMs' coding capabilities in AI-accelerated molecular discovery.

cs.CL↗

arXiv2025

A Survey of WebAgents: Towards Next-Generation AI Agents for Web Automation with Large Foundation Models

With the advancement of web techniques, they have significantly revolutionized various aspects of people's lives. Despite the importance of the web, many tasks performed on it are repetitive and time-consuming, negatively impacting overall quality of life. To efficiently handle these tedious daily tasks, one of the most promising approaches is to advance autonomous agents based on Artificial Intelligence (AI) techniques, referred to as AI Agents, as they can operate continuously without fatigue or performance degradation. In the context of the web, leveraging AI Agents -- termed WebAgents -- to automatically assist people in handling tedious daily tasks can dramatically enhance productivity and efficiency. Recently, Large Foundation Models (LFMs) containing billions of parameters have exhibited human-like language understanding and reasoning capabilities, showing proficiency in performing various complex tasks. This naturally raises the question: `Can LFMs be utilized to develop powerful AI Agents that automatically handle web tasks, providing significant convenience to users?' To fully explore the potential of LFMs, extensive research has emerged on WebAgents designed to complete daily web tasks according to user instructions, significantly enhancing the convenience of daily human life. In this survey, we comprehensively review existing research studies on WebAgents across three key aspects: architectures, training, and trustworthiness. Additionally, several promising directions for future research are explored to provide deeper insights.

cs.AI↗

arXiv2024

Multi-agent Attacks for Black-box Social Recommendations

The rise of online social networks has facilitated the evolution of social recommender systems, which incorporate social relations to enhance users' decision-making process. With the great success of Graph Neural Networks (GNNs) in learning node representations, GNN-based social recommendations have been widely studied to model user-item interactions and user-user social relations simultaneously. Despite their great successes, recent studies have shown that these advanced recommender systems are highly vulnerable to adversarial attacks, in which attackers can inject well-designed fake user profiles to disrupt recommendation performances. While most existing studies mainly focus on argeted attacks to promote target items on vanilla recommender systems, untargeted attacks to degrade the overall prediction performance are less explored on social recommendations under a black-box scenario. To perform untargeted attacks on social recommender systems, attackers can construct malicious social relationships for fake users to enhance the attack performance. However, the coordination of social relations and item profiles is challenging for attacking black-box social recommendations. To address this limitation, we first conduct several preliminary studies to demonstrate the effectiveness of cross-community connections and cold-start items in degrading recommendations performance. Specifically, we propose a novel framework MultiAttack based on multi-agent reinforcement learning to coordinate the generation of cold-start item profiles and cross-community social relations for conducting untargeted attacks on black-box social recommendations. Comprehensive experiments on various real-world datasets demonstrate the effectiveness of our proposed attacking framework under the black-box setting.

cs.SI↗