Xuefeng Liu

Assistant Professor, College of Medicine and AI for Health Institute, University of Florida
Postdoc, School of Medicine, Stanford University
Ph.D., Department of Computer Science, University of Chicago
xuefeng.liu@ufl.edu (primary), xfl@stanford.edu, xuefeng@uchicago.edu

prof_pic2.jpg

1889 Museum Road, #2407

Gainesville, FL 32611

Research: My research spans two complementary directions.

  • Machine Learning Foundations: I develop practically driven, theoretically grounded methods in reinforcement learning, Agentic AI,and generative modeling.

  • AI for Biomedical Discovery: My research primarily focuses on building   Agentic Reinforcement Learning Systems for Automated Biomedical Discovery, encompassing scientific reasoning and hypothesis generation, adaptive experimental design, lab automation, multimodal feedback learning, and self-evolution. A central goal is to advance these systems in terms of efficiency, trustworthiness, autonomy, cost-effectiveness, adaptability, and reliability in achieving scientific discoveries.

In parallel, I develop novel generative AI models as core components of these systems, with the ultimate goal of accelerating disease diagnosis and therapeutic discovery. My research interests include, but are not limited to:

  • Reinforcement Learning
    • RL in pretraining, post-training, decoding optimization
    • Reasoning, planning, decision-making under uncertainty and sequential experiment design
  • Agentic AI Systems
    • Agentic reinforcement learning, self-distillation, and self-evolution
    • Autonomous scientific discovery, auto-research, and lab automation
  • Generative AI and Foundation Models
    • Generative modeling for biomedicine and beyond
  • Human-AI co-scientist
    • Human–AI collaboration for scientific reasoning, hypothesis generation, and discovery
  • AI for Biomedicine
    • Biomolecular design, drug discovery, biomarker discovery, lead optimization
    • Physics- and Biology-informed machine learning

About Me: Before joining UF, I was a Postdoctoral Fellow at School of Medicine, Stanford University, working with Prof. Le Cong and Prof. Mengdi Wang (Princeton University). Prior to Stanford, I received my Ph.D. in Computer Science from University of Chicago, where I was advised by Prof. Rick L. Stevens, with co-advisors Prof. Yuxin Chen and Prof. Jinbo Xu, and mentorship from Prof. Tobin R. Sosnick. I also served as a AI Researcher at Argonne National Laboratory, where my work focuses on AI for Biomedicine.


Open Opportunities:

  • [Recruiting] My lab is actively recruiting motivated PhD students and Postdoc researchers. If you are interested in our research, please send your CV, a brief summary of your research experience, and a description of your research interests to xuefeng.liu@ufl.edu.

  • [Research Students] I have open research opportunities, including on-site visiting student positions. Feel free to email me if you are interested! Candidates are expected to have earned an A- or A in Deep Learning or a related course.


Teaching:

  • [CAI 6734] Applied Generative AI in Medicine — Fall 2026

Team:

I am fortunate to work with the following talented and motivated students and researchers: (* Visiting, in person/remote)

  • Postdoctoral Researchers:
    • Yisel Martinez Noa, Ph.D., University of Florida
    • Xiao Luo, Ph.D., University of Chicago *
    • Xiaotian Duan, Ph.D., Argonne National Laboratory *
  • Ph.D. Students:
    • Mingxuan Cao, University of Chicago *
    • Zhenya Liu, University of Chicago *
    • Luna Lyu, Stanford University *
    • Minghao Guo, MIT *
    • Jingtian Ji, Toyota Technological Institute at Chicago *
  • Master Students:
    • Weiyi Tian, University of Chicago *
  • Undergraduate Students:
    • Tianyi Chen, University of Wisconsin–Madison *
    • Meitong Chen, University of North Carolina at Chapel Hill *
    • Lilah Chen, Barnard College, Columbia University *
    • Siyuan Jiang, Tsinghua University *

news

Aug 30, 2026
  • Our preprint "Shared Actors Need Not Share Critics: Effects of Value Mismatch in Parallel Reinforcement Learning" is posted on arXiv.
Aug 21, 2026
  • Our paper "Unified Fragment Growing, Linking, and Merging with Energy-Aware Pretraining and Reward-Ranked Alignment" is accepted as finding paper of EMNLP 2026!
Aug 21, 2026
  • Our preprint "Leveraging generative hallucination and biophysics-informed modeling for unified biomolecular sequence-structure co-design" is posted on arXiv.
Aug 16, 2026
  • Honored to be invited to attend the Reinforcement Learning for Healthcare Summit in Asheville, NC, from September 3–5, 2026!
Aug 06, 2026
  • Our preprint "Agentic Laboratories of the Future: Towards World Models for Scientific Discovery" is posted on Preprints.org.
Jul 04, 2026
  • Our paper "DrugImproverGPT: GPT-Driven Drug Optimization with Structured Policy Optimization Post-training" is accepted by Machine Learning for Healthcare (MLHC) 2026 as Spotlight! Thanks to my collaborators Songhao, Siyu, Zhuoran, Yuxin, Ian, and Rick!
Jul 03, 2026
Jul 01, 2026
  • Our preprint "Active-GRPO: Adaptive Imitation and Self-Improving Reasoning for Molecular Optimization" is posted on arXiv.
Jun 20, 2026
  • Our paper "Regime-Adaptive Bayesian Optimization via Dirichlet Process Mixtures of Gaussian Processes" is accepted by ICML 2026.
May 31, 2026
  • Our preprint "Protein Thoughts: Interpretable Reasoning with Tree of Thoughts and Embedding-Space Flow Matching for Protein-Protein Interaction Discovery" is posted on arXiv.
May 15, 2026
  • My Ph.D. thesis "Leveraging Active Reinforcement Learning and Generative Models for Biomolecular Design" is completed at the University of Chicago.
Apr 15, 2026
  • Our paper "CACHE Challenge# 3: Targeting the Nsp3 Macrodomain of SARS-CoV-2" is published in Journal of Chemical Information and Modeling.
Feb 20, 2026
  • Our paper "Multi-Objective Coverage via Constraint Active Search" is accepted by AAMAS 2026 as an oral presentation.
Dec 02, 2025
  • Traveling to San Diego to attend NeurIPS 2025.
    • I am organizing the workshop AI Virtual Cells and Instruments: A New Era in Drug Discovery and Development. In light of the FDA’s recent initiative to phase out animal testing requirements, the workshop aims to foster deeper discussion on AI virtual cells and computational instruments for drug discovery. Looking forward to seeing you on Saturday, December 6.
    • Organizers: Quanquan Gu (UCLA), Michelle M. Li (Harvard), Chong Liu (UAlbany), Xuefeng Liu, Abhishek Pandey (AbbVie), Ji Won Park (Prescient Design, Genentech), Natasa Tagasovska (Prescient Design, Genentech), and Marinka Zitnik (Harvard).
    • Invited speakers: Linda Goodman (FaunaBio), Arvind Ramanathan (Argonne National Laboratory), Mengdi Wang (Princeton), Eric Xing (MBZUAI, GenBio, & CMU), Jinbo Xu (TTIC & Molecule Mind), and Alex Zhavoronkov (Insilico Medicine).
Nov 20, 2025
  • Our paper "FragmentGPT: A Unified GPT Model for Fragment Growing, Linking, and Merging in Molecular Design" is selected as an oral presentation at the NeurIPS 2025 Workshop on AI Virtual Cells and Instruments.
Nov 10, 2025
  • Our paper "Monte Carlo Tree Diffusion with Multiple Experts for Protein Design" is presented at the NeurIPS 2025 Workshop on AI Virtual Cells and Instruments.
Aug 15, 2025
  • Our paper "Bidirectional Hierarchical Protein Multi-Modal Representation Learning" is accepted by MLHC 2025.
Aug 10, 2025
  • Our paper "ScaffoldGPT: A Scaffold-based GPT Model for Drug Optimization" is accepted by MLHC 2025.
Jul 20, 2025
  • Our paper "A Ground-Up Designed Controllable GPT for Molecule Optimization" is presented at the ICML 2025 Generative AI and Biology Workshop.
Jul 15, 2025
  • Our paper "Scaffold-Driven GPT Model for Drug Optimization" is presented at the ICML 2025 Generative AI and Biology Workshop.
Jul 10, 2025
  • Our paper "Active Advantage-Aligned Online Reinforcement Learning with Offline Data" is presented at the ICML 2025 Exploration in AI Today Workshop.
Apr 04, 2025
Feb 15, 2025
  • Our preprint "ControllableGPT: A Ground-Up Designed Controllable GPT for Molecule Optimization" is posted on arXiv.
Nov 25, 2024
  • Our preprint "Reflections from the 2024 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry" is posted on arXiv.
Nov 15, 2024
  • Our paper "Contextual Active Model Selection" is accepted by NeurIPS 2024.
Oct 10, 2024
  • Our preprint "Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches" is posted on arXiv.
May 15, 2024
  • Our paper "Entropy-Reinforced Planning with Large Language Models for Drug Discovery" is accepted by ICML 2024.
May 05, 2024
  • Our paper "Learning from Imperfect Human Feedback: A Tale from Corruption-Robust Dueling" is accepted by ICLR 2024 and received the Best Poster Award at Midwest ML Symposium 2024.
Apr 20, 2024
  • Our paper "Leveraging Protein Large Language Models and Graph Neural Networks for Binding Affinity Prediction" is presented at the ICML 2024 Machine Learning for Life and Material Science Workshop.
Apr 10, 2024
  • Our paper "APO: Advantage-Alignment Policy Optimization for Fine-Tuning Generative Models" is presented at the ICLR 2024 Generative Models for Decision Making Workshop.
Dec 05, 2023
  • Our paper "DRUGIMPROVER: Utilizing Reinforcement Learning for Multi-Objective Alignment in Drug Optimization" is selected as an oral presentation at the NeurIPS 2023 Workshop on New Frontiers of AI for Drug Discovery and Development.
Jul 20, 2023
  • Our paper "Active Policy Improvement from Multiple Black-Box Oracles" is accepted by ICML 2023.
May 10, 2023
  • Our paper "Blending Imitation and Reinforcement Learning for Robust Policy Improvement" is accepted by ICLR 2023 as a spotlight presentation.
Feb 10, 2023
  • Our paper "AI-Accelerated Protein-Ligand Docking for SARS-CoV-2 Is 100-Fold Faster with No Significant Change in Detection" is published in Scientific Reports.