18 papers
Augmenting Molecular Language Models with Local -gram Memory
Xinni Zhang, Zijing Liu, He Cao +2
Transformer-based language models for SMILES strings suffer from a locality gap: standard character-level tokenization fragments chemically meaningful motifs, forcing models to rep…
Pushing Biomolecular Utility-Diversity Frontiers with Supergroup Relative Policy Optimization
Xinwu Ye, He Cao, Hao Li +5
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 candidat…
Learning the Interaction Prior for Protein-Protein Interaction Prediction: A Model-Agnostic Approach
Ziqi Gao, Chenyi Zi, Zijing Liu +3
Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representa…
ProteinOPD: Towards Effective and Efficient Preference Alignment for Protein Design
Yulin Zhang, He Cao, Zihao Jiang +6
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 enabl…
ReactBench: A Benchmark for Topological Reasoning in MLLMs on Chemical Reaction Diagrams
Qiang Xu, Shengyuan Bai, Yu Wang +6
Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological str…
Mozi: Governed Autonomy for Drug Discovery LLM Agents
He Cao, Siyu Liu, Fan Zhang +7
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 bottlene…