Weicai Long

About Me

I am a third-year (Final-year) Ph.D. candidate in Data Science and Analytics at HKUST(GZ), advised by Prof. Yanlin Zhang and Prof. Jiaheng Wei. Before joining HKUST(GZ), I received my M.Eng. in Electronic and Communication Engineering from Tsinghua University in 2023, advised by Prof. Xingjun Wang, and my B.Eng. in Communication Engineering from the University of Science and Technology Beijing in 2020.

My research focuses on BioMedical AI, spanning genome language models (gLMs) and medical large language models (MedLLM). I study domain-specific pretraining and multimodal representation learning for biomedical data, together with post-training, reasoning, evaluation, and agentic systems for healthcare. My work also draws on experience in wearable devices, with the goal of developing reliable AI systems for both patients and healthcare professionals.

I am currently on the job market and open to opportunities in both academia and industry. Please feel free to contact me at longwc819@gmail.com.

Research Interests

  • BioMedical foundation models. Pretraining and representation learning for biological sequences and heterogeneous biomedical data, including genome language models, and multimodal modeling of physiological signals, laboratory tests, and clinical information.
  • Medical LLM post-training. Domain-specific data construction, SFT, RL, and evaluation for improving medical reasoning, factuality, safety, and reliability.
  • Agents for healthcare systems. Tool-augmented and workflow-oriented agents for patient- and clinician-facing healthcare applications, with an emphasis on information gathering, multi-step task execution, long-term interaction, and effective human–AI collaboration.

To Prospective Collaborators

I am always open to collaboration with researchers and students interested in LLMs for biomedicine. I particularly welcome discussions on genome language models (gLMs), Medical LLMs, LLM post-training and AI agents for scientific workflows.

If you are interested in working with me, please feel free to email me at with a brief introduction to your background and research interests.

Talks

  • I give an oral presentation at ISMB/ECCB 2025. Video Link.

News

  • BioMaster is published in Patterns.
  • GenomeQA and PhageBench accepted to ACL 2026.
  • Porcine MutBERT is published in Briefings in Bioinformatics.
  • NyxBind is published in Briefings in Bioinformatics.
  • MutBERT accepted to ISMB 2025.
  • Started my Ph.D. in Data Science and Analytics at HKUST(GZ).
  • Started working full-time at HONOR as a Sport Health Algorithm Engineer.
  • BPNet is published in Biomedical Signal Processing and Control.
  • BP-LKA accepted to ICDIP 2023.
  • Started an internship at HONOR, working on cuffless blood-pressure estimation.

Selected Publications

[Full List]

† Equal contribution.

  1. BioMaster: Multi-agent system for automated bioinformatics analysis workflow

    Houcheng Su, Junning Feng, Yawen Lu, Yucheng Xu, Jinming Yang, Haojie Lu, Jixin Yang, Xu Yang, Sirui Xie, Weicai Long, Chengrui Wang, Yusen Hou, Tingyu Zhu, Yanlin Zhang

    Patterns, 2026.[IF: 10.8 · SCI-Q1]

  2. GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding

    Weicai Long†, Yusen Hou†, Junning Feng, Houcheng Su, Shuo Yang, Donglin Xie, Yanlin Zhang

    ACL 2026 · Main Conference, 2026.[CCF-A]

  3. PhageBench: Can LLMs Understand Raw Bacteriophage Genomes?

    Yusen Hou†, Weicai Long†, Haitao Hu, Houcheng Su, Junning Feng, Yanlin Zhang

    ACL 2026 · Findings, 2026.

  4. GenomeHarness: Harnessing AI Agents for Reliable Adaptation of Genome Language Models [Under review]

    Weicai Long, Yusen Hou, Houcheng Su, Junning Feng, Yanlin Zhang

    Bioinformatics, 2026.[IF: 5.5 · CCF-A]

  5. ContextTAD: Context-aware boundary learning for TAD calling from Hi-C contact maps [Under review]

    Weicai Long†, Yusen Hou†, Yanlin Zhang

    Nucleic Acids Research, 2026.[IF: 15.0]

  6. Porcine MutBERT: A Family of Lightweight Genomic Foundation Models for Functional Element Prediction in Pigs

    Weicai Long†, Rong Zhou†, Wenkang Wei, Xiaoai Zhang, Shanshan Wu, Kui Li, Yanlin Zhang, Zishuai Wang

    Briefings in Bioinformatics, 2026.[IF: 7.3 · SCI-Q2]

  7. NyxBind: enhancing deep neural representations for transcription factor binding site prediction via contrastive learning

    Xu Yang, Qingfa Xiao, Yucheng Xu, Jixin Yang, Yusen Hou, Weicai Long, Miaojun Huang, Yanlin Zhang

    Briefings in Bioinformatics, 2026.[IF: 7.3 · SCI-Q2]

  8. PopGenAgent: An Agent-Mediated Workflow for Population Genetics Analyses

    Houcheng Su, Weicai Long, Junning Feng, Yusen Hou, Yanlin Zhang

    bioRxiv, 2026.

  9. MutBERT: Probabilistic Genome Representation Improves Genomics Foundation Models

    Weicai Long, Houcheng Su, Jiaqi Xiong, Yanlin Zhang

    ISMB 2025 (Published in Bioinformatics), 2025.[IF: 5.5 · CCF-A · ISMB: Top Conference]

  10. Large Language Models for Network Intrusion Detection Systems: Foundations, Implementations, and Future Directions

    Shuo Yang, Xinran Zheng, Xinchen Zhang, Jinfeng Xu, Jinze Li, Donglin Xie, Weicai Long, Edith C. H. Ngai

    arXiv, 2025.

  11. BPNet: A Multi-Modal Fusion Neural Network for Blood Pressure Estimation Using ECG and PPG

    Weicai Long, Xingjun Wang

    Biomedical Signal Processing and Control, 2023.[IF: 5.7 · SCI-Q2]

  12. Blood Pressure Estimation Neural Network Using Large Kernel Convolutional Attention

    Weicai Long, Jingyuan Li, Xingjun Wang

    ICDIP 2023, 2023.

Experience

Sport Health Algorithm Engineer, HONOR

Developed wearable digital-health algorithms for continuous blood-pressure monitoring and sleep analysis using multimodal physiological signals.

Sport Health Algorithm Intern, HONOR

Researched cuffless blood-pressure estimation and developed BPNet and BP-LKA.

Teaching & Service

  • Teaching Assistant, Design and Analysis of Algorithms, HKUST(GZ), 2025 and 2026.
  • Teaching Assistant, Pattern Recognition, Tsinghua University, 2021.

Languages

  • Chinese — Native speaker.
  • English — Fluent (professional working proficiency).

Patent

  • A Blood Pressure Prediction Apparatus and Device, CN115836847B.

Awards

  • Second Prize, Tsinghua Tongfang Cup Sensor Competition, 2017.
  • USTB People’s Scholarships, 2016–2018.