Research Interests
Our research focuses on AI for Science, with an emphasis on interdisciplinary studies that integrate cutting-edge machine learning and large language models into biology, chemistry, materials science, and medicine. By developing AI-driven methodologies, we aim to transcend conventional research boundaries and accelerate the pace of scientific discovery and knowledge generation.
We warmly welcome outstanding students and scholars with backgrounds in computer science, data science, life sciences, chemistry, and related fields to join us in exploring and shaping the new frontiers of AI-powered scientific research.
Research Topics
- Intelligent Molecular Design: Leveraging generative models to design and synthesize novel functional molecules, including small molecules with tailored properties and peptides or RNAs with specific binding targets.
- Deciphering Molecular Chirality: Algorithm design and representation learning to decode and predict the stereochemical configurations and properties of chiral molecules.
- Biomedical Image Processing: Development of deep learning methods for automated pattern recognition and analysis of biomedical imaging data to enable intelligent healthcare.
News
2025
| Date | News |
|---|---|
| Sep 2-4 | Lab members attended the Computational Structural Immunology Symposium 2025 (CSI2025) at Nijmegen, Netherlands. Prof. Yang presented an invited talk "Multi-objective Guided Diffusion for Epitope Design in TCR-pMHC Complexes". |
| Aug 21-23 | Lab members attended the Conference on Bioinformatics and Intelligent Information Processing 2025 (BIIP2025). Prof. Yang presented an invited talk "Breakthroughs and Prospects of Molecular Large Models in Compound Design and Synthesis". |
| Aug 8-10 | Prof. Yang attended the 10th CCF Bioinformatics Conference (CBC2025). |
| Jul 26 | Congratulations to the "307 Chemists" team—Letian, Runhan, and Runzhe—for winning 2nd place in the Materials Design Track at the World AI4S Prize 2025. |
| Jul 16 | Our collaborative paper "BatGPT-Chem: A Foundation Large Model for Chemical Engineering" is accepted by Research. Congratulations to all co-authors! |
| Jul 10 | Prof. Yang hosted the 3rd Cutting-Edge Lectures in AI4S at SJTU. |
| Jun 13 | Yichuan and Gufeng's proposed chiral molecular classification model, ChiralCat, is accepted by Artificial Intelligence Chemistry. Congratulations! |
| Jun 8 | Prof. Yang hosted the 'AI-Empowered Biomedical Innovation Forum' at SJTU. |
| May 9 | Our proposed workshop, "Large Foundation Models for Multi-Modal Learning in Bioinformatics and Biomedicine Informatics," has been officially accepted for inclusion in BIBM'2025. We warmly invite researchers, academics, and industry professionals to contribution original works to our workshop! |
| Apr 26 | Prof. Yang attended the CCF BIO-3New Conference and delivered an invited talk "From Knowledge Mining to Generative Design: AI-Driven Customized Molecular Generation." |
| Apr 12 | Prof. Yang attended the 4th Chinees Intelligence Health & Bioinformatics Conference (IHB 2025) and chaired Session III: AI-driven Innovative Drug R&D. |
| Mar 20 | Gufeng's work on an open-source database containing chiral ligands and catalysts of various chiral types is accepted by Journal of Cheminformatics. Congratulations! |
| Mar 4 | Runhan's work on reaction yield prediction via cross-modal pretraining is accepted by Artificial Intelligence Chemistry. Congratulations! |
| Feb 13 | Yichong's work on RNA design using reinforcement learning is accepted by Briefings in Bioinformatics. Congratulations! |
| Jan 24 | Yujia's work on lncRNA subcellular localization is accepted by Quantitative Biology. Congratulations! |
| Jan 23 | Our collaborative work "Chain-of-Focus Prompting: Leveraging Sequential Visual Cues to Prompt Large Autoregressive Vision Models" is accepted by ICLR 2025. Congratulations! |
| Jan 17 | Yifei's work "ZeRPI: A Graph Neural Network Model for Zero-Shot Prediction of RNA-Protein Interactions" is accepted by Methods. Congratulations! |
| Jan 14 | Yuyang and Yifei successfully passed their master's degree thesis defense. Congratulations to them! |
2024
| Date | News |
|---|---|
| Dec 30 | Prof. Yang hosted the Forum on AI4S Frontiers at SJTU and delivered a talk titled "AI Empowers Chemical Science Studies." |
| Dec 19 | Gufeng's work for Reaction Performance Prediction is accepted by Journal of Chemial Information and Modeling. Congratulations! |
| Dec 8-9 | Prof. Yang attended BMDMC 2024 and gave an invited talk "Uncertainty-aware Semi-supervised Medical Image Segmentation". |
| Dec 2-7 | Lab members attended BIBM 2024. Prof. Yang and Wenjing delivered oral presentations. Prof. Yang and Prof. Hong hosted the workshop. |
| Dec 1 | Letian, Runhan, and Gufeng won the third prize in the "Material Science Track" of the 2nd World AI4S Prize. Congratulations! |
| Oct 26-27 | Lab members attended 2024 International Conference on Biomedicine and AI (ICBAI). Prof. Yang chaired the Medical Image Processing Session. |
| Aug 19-22 | Lab members attended ICPOC 2024. Gufeng and Letian presented their posters on LLM for retrosynthesis and molecular chiral representation, respectively. |
| Aug 6-7 | Prof. Yang attended the 2nd RIKEN AIP-SJTU CS Joint Workshop on Machine Learning and Brain-like Intelligence (Agenda) at RIKEN AIP, delivering a talk on Uncertainty-based Semi-supervised Learning in Medical Image Segmentation. |
| July 19-21 | Lab members attended ISBRA 2024. Yifei and Yujia delivered oral presentations on their works on RNA-protein binding and RNA localization prediction, respectively. |
| July 5 | Lab members attended ACM TURC 2024, where Prof. Yang gave an invited talk "Deep Learning Revolutionizes Chemical Informatics: Model Evolution and Applications". |
| June 16 | Lab members attended the 2024 Bioinformatics and Intelligent Information Processing Conference (BIIP2024), where Prof. Yang and Runhan presented on "LLM in Chemistry" and "Chemical Reaction Prediction via Multi-view Learning," respectively. |
| May 30 | Our database CLC-DB containing 1800+ chiral ligands/catalysts of different chiral types is online! |
| May 30 | Yichong and Wenjing passed their PhD proposal defense. Congratulations! |
| May 24 | Prof. Yang gave a talk "Medical Image Analysis Driven by Large Models: From Single-Modality to Multi-Modal Learning" at the 13th Shanghai Jiao Tong University Vascular Disease Forum. |
| May 16 | Our collaborative work "Measuring Bargaining Abilities of LLMs: A Benchmark and A Buyer-Enhancement Method" is accepted accepted to the ACL Findings. Congratulations! |
| May 7 | Our proposed workshop, "Large Foundation Models for Multi-Modal Learning in Bioinformatics and Biomedicine Informatics," has been officially accepted for inclusion in BIBM'2024. We warmly invite researchers, academics, and industry professionals to contribution original works to our workshop! |
| Apr 17 | Yuyang's work ClusterDrop for addressing over-smoothing issue in GNNs is accepted by IJCAI 2024. Congratulations! |
| Apr 15 | Our GaCaMML paper is accepted by Artificial Intelligence in Medicine. Congratulations, Yuzhang and Guoshuai! |
| Mar 29 | Zebei, Guoshuai, Kuo, and Jingyao completed their Computer Science MS degree. Congratulations! |
| Feb 25 | Runhan's work RMVP for large-scale prepretraining of chemical reactions is published in Journal of Cheminformatics. Congratulations! |
| Feb 23 | Our CGMega paper is accepted by Nature Communications. Congratulations, Zebei! |
| Feb 22 | Our collaborative work CircSite on predicting circRNA-protein binding is published in Computers in Biology and Medicine. Congratulations! |
| Feb 10 | Guoshuai's work for designing new Al-Zn-Mg-Cu-Zr-Hf alloy is published in Materials Today Communications. Congratulations! |