10 papers
MolWorld: Molecule World Models for Actionable Molecular Optimization
Yang Qiao, Bo Pan, Hao-Wei Pang +3
Molecular optimization in drug discovery aims to discover molecules with improved target properties, but practical lead optimization often requires more than high predicted scores.…
Retrieval-Augmented Foundation Models for Matched Molecular Pair Transformations to Recapitulate Medicinal Chemistry Intuition
Bo Pan, Peter Zhiping Zhang, Hao-Wei Pang +4
Matched molecular pairs (MMPs) capture the local chemical edits that medicinal chemists routinely use to design analogs, but existing ML approaches either operate at the whole-mole…
Bi-Level Prompt Optimization for Multimodal LLM-as-a-Judge
Bo Pan, Xuan Kan, Kaitai Zhang +6
Large language models (LLMs) have become widely adopted as automated judges for evaluating AI-generated content. Despite their success, aligning LLM-based evaluations with human ju…
Transformer-Based Approach for Automated Functional Group Replacement in Chemical Compounds
Bo Pan, Zhiping Zhang, Kevin Spiekermann +4
Functional group replacement is a pivotal approach in cheminformatics to enable the design of novel chemical compounds with tailored properties. Traditional methods for functional…
Structural Disentanglement of Causal and Correlated Concepts
Qilong Zhao, Shiyu Wang, Zeeshan Memon +5
Controllable data generation aims to synthesize data by specifying values for target concepts. Achieving this reliably requires modeling the underlying generative factors and their…
GRAG: Graph Retrieval-Augmented Generation
Yuntong Hu, Zhihan Lei, Zheng Zhang +3
Naive Retrieval-Augmented Generation (RAG) focuses on individual documents during retrieval and, as a result, falls short in handling networked documents which are very popular in…