Yang Tan

Yang Tan (谭扬)

ECUST -> SJTU & SII

Yang Tan (谭扬) — PhD student at SJTU & SII, AI for Biology, protein language models, and TCM LLMs

My name is Yang Tan (谭扬). I am now a PhD student in Shanghai Jiao Tong University & Shanghai Innovation Institute, supervised by Prof. Liang Hong and co-advised by Prof. Nanqing Dong. I receive my M.S. degree of Computer Science (GPA 3.8/4.0, #1 ranking) from East China University of Science and Technology in 2025, supervised by Prof. Guisheng Fan and Prof. Huiqun Yu, and B.S. degree of Software Engineering (GPA 3.8/4.0, #1 ranking) from East China University of Science and Technology in 2022.

My research interests lie at the intersection of Artificial Intelligence and Biology.

  • AI research: Large Language Models, Graph Neural Networks, and Agent Workflow.
  • Biology research: Directed Evolution, Function Prediction, and Protein Design.

I have published over 20 papers in the field of AI4Bio such as NeurIPS, ICLR, and eLife. I also serve as a reviewer for NMI, JCTC, and ICLR. I also maintain the TCM LLM hub (Awesome-TCM-LLM), which continuously tracks Traditional Chinese Medicine large language models, papers, benchmarks, and open datasets.

🔥 News

📝 Selected Publications

* denotes equal contribution.

✈️ Conference

ICLR 2026
VenusX: fine-grained protein functional understanding benchmark

VenusX: Unlocking Fine-Grained Functional Understanding of Proteins

Yang Tan, Wenrui Gou, Bozitao Zhong, Huiqun Yu, Liang Hong, Bingxin Zhou

ACL Demo 2025
VenusFactory: integrated protein engineering system

VenusFactory: An Integrated System for Protein Engineering with Data Retrieval and Language Model Fine-Tuning

Yang Tan, Chen Liu, Jingyuan Gao, Banghao Wu, Mingchen Li, Ruilin Wang, Lingrong Zhang, Huiqun Yu, Guisheng Fan, Liang Hong, Bingxin Zhou

ISMB/ECCB 2025
VenusREM: retrieval-enhanced mutation effect prediction

From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model

Yang Tan, Ruilin Wang, Banghao Wu, Liang Hong, Bingxin Zhou

ICLR 2025
VenusVaccine: immunogenicity prediction for vaccine targets

Immunogenicity Prediction with Dual Attention Enables Vaccine Target Selection

Song Li*, Yang Tan*, Song Ke, Liang Hong, Bingxin Zhou

NeurIPS 2024
ProSST: protein language modeling with quantized structure

ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention

Mingchen Li*, Yang Tan*, Xinzhu Ma, Bozitao Zhong, Huiqun Yu, Ziyi Zhou, Wanli Ouyang, Bingxin Zhou, Pan Tan, Liang Hong

📚 Journal

eLife 2025
ProtSSN: semantical and geometrical protein encoding

Semantical and geometrical protein encoding toward enhanced bioactivity and thermostability

Yang Tan, Bingxin Zhou, Lirong Zheng, Guisheng Fan, Liang Hong

Comput. Biol. Med. 2024
MedChatZH: TCM consultation large language model

MedChatZH: A tuning LLM for traditional Chinese medicine consultations

Yang Tan, Zhixing Zhang, Mingchen Li, Fei Pan, Hao Duan, Zijie Huang, Hua Deng, Zhuohang Yu, Chen Yang, Guoyang Shen, Peng Qi, Chengyuan Yue, Yuxian Liu, Liang Hong, Huiqun Yu, Guisheng Fan, Yun Tang

J. Chem. Inf. Model. 2024
SES-Adapter: structure-aware adapters for protein language models

Simple, efficient, and scalable structure-aware adapter boosts protein language models

Yang Tan, Mingchen Li, Bingxin Zhou, Bozitao Zhong, Lirong Zheng, Pan Tan, Ziyi Zhou, Huiqun Yu, Guisheng Fan, Liang Hong

J. Cheminformatics 2024
PETA: protein transfer learning with sub-word tokenization

PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications

Yang Tan, Mingchen Li, Ziyi Zhou, Pan Tan, Huiqun Yu, Guisheng Fan, Liang Hong

🏆 Honors

  • 2026, WAIC 2026 National Treasure, MatwingsVenus (晓鹜), Project Leader, Ph.D.
  • 2026, Shanghai Innovation Institute Student Project (1,250,000 RMB), Project Leader, Ph.D.
  • 2025, Young Science and Technology Talent Development Program (40,000 RMB), CAST, Ph.D.
  • 2025, College Graduate Excellence Award of Shanghai, M.S.
  • 2025, Huanchuang Scholarship (10 in university), M.S.
  • 2024, Annual Student, East China University of Science and Technology.
  • 2024, National Scholarship, M.S.
  • 2023, Bronze Award, National “Challenge Cup” Competition.
  • 2022, Silver Award, Shanghai “Internet+” Competition.
  • 2022, College Graduate Excellence Award of Shanghai, B.S.
  • 2022, Arkema Scholarship (3 in university), B.S.
  • 2021/2020, Second/Third Prize, National College Students Computer Design Competition.
  • 2021/2020, Special Scholarship, East China University of Science and Technology.
  • 2021, National Undergraduate Innovation Training Program, Project Leader.
  • 2020, National Scholarship, B.S.
  • 2019, Lingma Scholarship (4 in major), B.S.
  • 2018, District Mayor Award for Science and Technology Innovation of Shapingba, Chongqing.
  • 2017, Third Prize at World Championship, American Houston FIRST Tech Challenge, Team Leader.
  • 2017, Outstanding Project, Chongqing Youth Innovation Talent Training Eaglet Program, Project Leader.
  • 2017/2016, First/Second Prize, China FIRST Tech Challenge, Team Leader.

🎤 Talks

📰 Media

📖 Educations

  • 2025.09 - Now, Shanghai Jiao Tong University & Shanghai Innovation Institute. Ph.D. in Computer Science.
  • 2022.06 - 2025.06, East China University of Science and Technology. M.S. in Computer Science & GPA: 3.8 / 4.0 & #1 ranking.
  • 2018.09 - 2022.06, East China University of Science and Technology. B.S. in Software Engineering & GPA 3.8/4.0 & #1 ranking.