4 papers
Monte Carlo Tree Diffusion with Multiple Experts for Protein Design
Xuefeng Liu, Mingxuan Cao, Songhao Jiang +6
The goal of protein design is to generate amino acid sequences that fold into functional structures with desired properties. Prior methods combining autoregressive language models…
From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?
Hanqun Cao, Hongrui Zhang, Junde Xu +12
Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has…
Bidirectional Hierarchical Protein Multi-Modal Representation Learning
Xuefeng Liu, Songhao Jiang, Chih-chan Tien +2
Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequen…
ScaffoldGPT: A Scaffold-based GPT Model for Drug Optimization
Xuefeng Liu, Songhao Jiang, Ian Foster +2
Drug optimization has become increasingly crucial in light of fast-mutating virus strains and drug-resistant cancer cells. Nevertheless, it remains challenging as it necessitates r…