---

Education

Shanghai, China East China University of Science and Technology
2018.09-2022.06 B.S in Software Engineering & #1 in major ranking / #1 in overall ranking

Shanghai, China East China University of Science and Technology
2022.09-2025.06 M.S in Computer Science & GPA: 3.79 / 4 & #1 in major ranking

---

Experience

2022.10-2023.06 Shanghai Tianwu Technology Co., Ltd
- Algorithm Intern, AI4Bio
- Protein language model pre-training and zero-shot mutantion prediction.
2023.06-2023.07 Shanghai-Chongqing Artificial Intelligence Research Institute
- Algorithm Intern, Large Languge Model
- Participated in the research and development of the “Zhaoyan” large language model.
2023.08-Now Shanghai Artificial Intelligence Laboratory
- Algorithm Intern, AI4Science
- Protein language model and graph network model for protein engineering.

---

Oral Presentation

2023.07 Shanghai Jiao Tong University AI4SCIENCE Summer School
- Oral report/group report was rated as excellent (3/100)
2023.08 Shanghai “Green Biomanufacturing” Summer School
- Oral report at the Youth Academic Forum and was rated as excellent (6/100)
2024.08 Shanghai Jiao Tong University AI4BioE Summer School
- Oral report/poster was rated as excellent (1/200)

---

Main Awards & Activities

• National Scholarship Master. 2024
• First-Class Scholarship, East China University of Technology, Master. 2023
• Bronze Award, “Challenge Cup” Competition, Master, China. 2023
• Silver Award, “Internet+” Competition, Master, Shanghai. 2022
• College Graduate Excellence Award of Shanghai. 2022
• Arkema Bachelor’s Scholarship (3 in university). 2022
• First-Class Scholarship, East China University of Technology, Undergraduate. 2022
• Special Scholarship, East China University of Technology, Undergraduate. 2021, 2020
• Second/ Third Prize, College Students Computer Design Competition, China. 2021, 2020
• National Undergraduate Innovation Training Program, Project Leader. 2021
• National Scholarship, Undergraduate. 2020
• Lingma Bachelor’s Scholarship (4 in major). 2019
• 4th of the 5th “Hanhong Cup” Shanghai Nine Schools Speech Competition. 2018
• “District Mayor Award for Science and Technology Innovation” in Shapingba, Chongqing, 2018

---

Publications (*equal contribution)

1. Tan Y, Zhang Z, Li M, et al. MedChatZH: A tuning LLM for traditional Chinese medicine consultations. Computers in Biology and Medicine, 2024.
2. Zhou B*, Zheng L*, Wu B*, Tan Y* et al. Protein engineering with lightweight graph denoising neural networks. Journal of Chemical Information and Modeling, 2024.
3. Tan Y, Li M, Tan P, et al. PETA: Evaluating the Impact of Protein Transfer Learning with Sub-word Tokenization on Downstream Applications. Journal of Cheminformatics, 2024.
4. Tan Y, Zhou B, Zheng L, et al. Semantical and Topological Protein Encoding Toward Enhanced Bioactivity and Thermostability. eLife, 2024.
5. Tan Y, Li M, Zhou B, et al. Simple, efficient and scalable structure-aware adapter boosts protein language models. Journal of Chemical Information and Modeling, 2024.
6. Y Hu*, Y Tan*, A Han*, et al. Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion. IEEE BIBM, 2024.
7. Tan Y, Zheng L, Zhong B, et al. Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?. IEEE BIBM, 2024.
8. Tan Y, Zheng J, Hong L, et al. ProtSolM: Protein Solubility Prediction with Multi-modal Features. IEEE BIBM, 2024.
9. Li M*, Tan Y*, Ma X, et al. ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention. NeurIPS, 2024.
10. Li S*, Tan Y*, Ke S, et al. Immunogenicity Prediction with Dual Attention Enables Vaccine Target Selection. ICLR, 2025. (Under review)
11. Tan Y, Wang R, Wu B, et al. Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model. RECOMB, 2025. (Under review)

---

Publications (co-author)

1. Zhou B, Tan Y, Hu Y, et al. Protein Engineering in Deep Learning Era. mLife, 2024.
2. Zheng L, Zhou B, Wu B, Tan Y, et al. Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K. eLife, 2024.
3. Zhou B, Zheng L, Wu B, et al. A conditional protein diffusion model generates artificial programmable endonuclease sequences with enhanced activity. Cell Discovery, 2024
4. Fan J, Li M, Dong J, et al. A general Temperature-Guided Language model to design proteins of enhanced Stability and Activity. Science Advances, 2024.
5. Wu Y, Yi X, Tan Y, et al. A PLMs based protein retrieval framework. Computer Methods and Programs in Biomedicine 2024. (Under review)
6. Gou W, Ge W, Tan Y, et al. CPE-Pro: A Structure-Sensitive Deep Learning Model for Protein Representation and Origin Evaluation. 2024 (Under review)
7. Li M, Zhou B, Tan Y, et al. Unlearning Virus Knowledge Toward Safe and Responsible Mutation Effect Predictions. ICLR. 2025. (Under review)

---