Received a Bachelor's degree in Computer Science and Technology from Shanghai Jiao Tong University (SJTU). Subsequently, pursued a successive Master-Ph.D. program in the Department of Computer Science at SJTU, during which time was selected for the joint Ph.D. program between SJTU and the University of California, USA, ultimately earning a Ph.D. in Computer Software and Theory.

Served as a Visiting Scholar in the Department of Computer Science and Engineering at the University of California, Riverside. Following this, joined the faculty at Shanghai Jiao Tong University, successively holding the positions of Lecturer and Associate Professor in the Department of Computer Science. Currently serves as a Professor in the School of Computer Science at Shanghai Jiao Tong University.

• Artificial Intelligence (CS3317) | Undergraduate Course | Fall Semesters 2021~2023, Spring Semesters 2025–Present

• Intelligent Algorithms for Sciences (CS7357) | Graduate Course | Fall Semesters 2024–Present

• Machine Learning (CS7336) | Graduate Course | Spring Semesters 2015~2024

• Machine Learning (CS385) | Zhiyuan Honors Course | Spring Semesters 2016~2020

Recent Representative Publications

1. Y Huang, G Yu, L Chen, H Luan, Y Yang*, EPIC: Multi-objective Guided Diffusion for Epitope Design in TCR-pMHC Complexes, Bioinformatics, Vol 42(6), June 2026.

2. W Lu, Y Hong*, Y Yang*, Harmonizing Generalization and Specialization: Uncertainty-Informed Collaborative Learning for Semi-supervised Medical Image Segmentation, IEEE Transactions on Medical Imaging, 2026.

3. R Shi#, C Zhang#, G Yu, X Huo, Y Yang*, A unifying geometric framework for computational representation of stereoisomers based on mixed product, Cell Reports Physical Science, Vol 7(1), 2026, 103065.

4. H Luan, G Yu, L Chen, Z Xiao, Y Huang, J Guo, Y Yang*, EpiCoCo: De Novo Epitope Generation via MHC-Context Co-Modeling and Contrastive Affinity Guidance, Forty-Third International Conference on Machine Learning (ICML 2026).

5. R Shi, Z Zhang, L Chen, G Yu, Y Yang*, Learning Molecular Chirality via Chiral Determinant Kernels, The Fourteenth International Conference on Learning Representations (ICLR 2026).

6. L Chen#, R Shi#, G Yu, Y Yang*. RTMol: Rethinking Molecule-text Alignment in a Round-trip View, The 40th Annual AAAI Conference on Artificial Intelligence (AAAI 2026).

7. R Shi, L Chen, G Yu, Y Yang*. Reaction Prediction via Interaction Modeling of Symmetric Difference Shingle Sets, The Thirty-ninth Annual Conference on Neural Information Processing Systems (NeurIPS 2025).

8. H Li#, Z Han#, …, H Chen*, Y Yang*, X Bo*. CGMega: Explainable Graph Neural Network Framework with Attention Mechanisms for Cancer Gene Module Dissection. Nature Communications (2024), 15:5997

9. Y Yang#, R Shi#, Z Li, S Jiang, B-L Lu, Y Yang*, H Zhao*. BatGPT-Chem: A Foundation Large Model For Chemical Engineering, Research 2025.

10. Y Li, X Pan*, H Shen, Y Yang*. DRAG: design RNAs as hierarchical graphs with reinforcement learning, Briefings in Bioinformatics vol. 26(2), 13 March 2025.

For more publications, please visit: https://compbio.sjtu.edu.cn/publications_cn.html

NSFC and MOST Projects Led in the Last Five Years:

• National Natural Science Foundation of China (NSFC), General Program: Research on RNA Molecular Representation Learning Based on Self-Supervised Learning. 2023.01 - 2026.12. (PI)

• National Natural Science Foundation of China (NSFC), General Program: Non-coding RNA Subcellular Localization Prediction Based on Multimodal Machine Learning. 2020.01 - 2023.12. (PI)

• National Key R&D Program of China, Ministry of Science and Technology: In-situ Rapid Intelligent Sensing Technology for Deep-Sea Animals. 2024.01 - 2026.12. (PI)

• Second Prize, The 3rd World AI for Science Competition (Materials Design Track), 2025 (Advisor)

• Gold Medal & Best Software Project Nomination, International Genetically Engineered Machine Competition (iGEM), 2021 (Advisor)

• First Prize, China Computer Federation (CCF) CBC2023 Data Challenge, 2023 (Advisor)

• Super AI Leader (SAIL) Award Nomination at WAIC, for "Artificial Intelligence Basic Analysis Algorithm and Online Prediction Application System for Biomedical Big Data", 2018 (Ranked 3rd)

• March 8th Red Banner Pacesetter (Sanba Hongqishou), Shanghai Jiao Tong University, 2025

• Second Prize, SJTU Teaching Achievement Award for "Innovation and Practice of AI-Driven Interdisciplinary Graduate Training Model", 2025 (Ranked 1st)

• First Prize, SJTU Teaching and Educating Award (as a member of the "Computer Basic Course Teaching Team"), 2023

• Director, Shanghai Municipal Key Course for Universities ("Artificial Intelligence"), 2024

• Huawei Cloud and Computing Pioneer Teacher (2020-2025)

• Editorial Board Member, Neural Networks and Frontiers in Genetics

• Member, Technical Committee on Bioinformatics, China Computer Federation (CCF)

• Standing Committee Member, Technical Committee on Bioinformatics and Artificial Life, Chinese Association for Artificial Intelligence (CAAI)

• Organizing Chair, The Conference on Bioinformatics and Intelligent Information Processing (BIIP)