Yuhang Yang
Publications
BioMiner: A Multi-modal System for Automated Mining of Protein-Ligand Bioactivity Data from Literature
Protein-ligand bioactivity data published in the literature are essential for drug discovery, yet manual curation struggles to keep pace with rapidly growing literature. Automated bioactivity extraction remains challenging because it requires not only interpreting biochemical semantics distributed across text, tables, and figures, but also reconstructing chemically exact ligand structures (e.g., Markush structures). To address this bottleneck, we introduce BioMiner, a multi-modal extraction framework that explicitly separates bioactivity semantic interpretation from ligand structure construction. Within BioMiner, bioactivity semantics are inferred through direct reasoning, while chemical structures are resolved via a chemical-structure-grounded visual semantic reasoning paradigm, in which multi-modal large language models operate on chemically grounded visual representations to infer inter-structure relationships, and exact molecular construction is delegated to domain chemistry tools. For rigorous evaluation and method development, we further establish BioVista, a comprehensive benchmark comprising 16,457 bioactivity entries curated from 500 publications. BioMiner validates its extraction ability and provides a quantitative baseline, achieving an F1 score of 0.32 for bioactivity triplets. BioMiner's practical utility is demonstrated via three applications: (1) extracting 82,262 data from 11,683 papers to build a pre-training database that improves downstream models performance by 3.9%; (2) enabling a human-in-the-loop workflow that doubles the number of high-quality NLRP3 bioactivity data, helping 38.6% improvement over 28 QSAR models and identification of 16 hit candidates with novel scaffolds; and (3) accelerating protein-ligand complex bioactivity annotation, achieving a 5.59-fold speed increase and 5.75% accuracy improvement over manual workflows in PoseBusters dataset.
CeProAgents: A Hierarchical Agents System for Automated Chemical Process Development
The development of chemical processes, a cornerstone of chemical engineering, presents formidable challenges due to its multi-faceted nature, integrating specialized knowledge, conceptual design, and parametric simulation. Capitalizing on this, we propose CeProAgents, a hierarchical multi-agent system designed to automate the development of chemical process through collaborative division of labor. Our architecture comprises three specialized agent cohorts focused on knowledge, concept, and parameter respectively. To effectively adapt to the inherent complexity of chemical tasks, each cohort employs a novel hybrid architecture that integrates dynamic agent chatgroups with structured agentic workflows. To rigorously evaluate the system, we establish CeProBench, a multi-dimensional benchmark structured around three core pillars of chemical engineering. We design six distinct types of tasks across these dimensions to holistically assess the comprehensive capabilities of the system in chemical process development. The results not only confirm the effectiveness and superiority of our proposed approach but also reveal the transformative potential as well as the current boundaries of Large Language Models (LLMs) for industrial chemical engineering.