Research Interests

Interdisciplinary studies of artificial intelligence and science (AI for Science), including bioinformatics, medical image analysis, cheminformatics, and the design of new materials.

Research Topics

  • Molecular Representation Learning: Developing deep learning, self-supervised learning, and large language models to decipher the properties, functions, and interactions of compound molecules and biological macromolecules. Our methods are further extended to predict chemical reaction outcomes and facilitate retrosynthesis, aiming to speed up drug discovery and materials design.
  • Biomedical image understanding: Designing semi-supervised and multi-modal learning approaches for pattern recognition and segmentation of biomedical images, with applications to biomarker identification and disease outcome prediction.

News

2025

DateNews
Jan 24Yujia's work on lncRNA subcellular localization is accepted by Quantitative Biology. Congratulations!
Jan 23Our collaborative work "Chain-of-Focus Prompting: Leveraging Sequential Visual Cues to Prompt Large Autoregressive Vision Models" is accepted by ICLR 2025. Congratulations!
Jan 17Yifei's work "ZeRPI: A Graph Neural Network Model for Zero-Shot Prediction of RNA-Protein Interactions" is accepted by Methods. Congratulations!
Jan 14Yuyang and Yifei successfully passed their master's degree thesis defense. Congratulations to them!

2024

DateNews
Dec 30Prof. Yang hosted the Forum on AI4S Frontiers at SJTU and delivered a talk titled "AI Empowers Chemical Science Studies."
Dec 19Gufeng's work for Reaction Performance Prediction is accepted by Journal of Chemial Information and Modeling. Congratulations!
Dec 8-9Prof. Yang attended BMDMC 2024 and gave an invited talk "Uncertainty-aware Semi-supervised Medical Image Segmentation".
Dec 2-7Lab members attended BIBM 2024. Prof. Yang and Wenjing delivered oral presentations. Prof. Yang and Prof. Hong hosted the workshop.
Dec 1Letian, Runhan, and Gufeng won the third prize in the "Material Science Track" of the 2nd World AI4S Prize. Congratulations!
Oct 26-27Lab members attended 2024 International Conference on Biomedicine and AI (ICBAI). Prof. Yang chaired the Medical Image Processing Session.
Aug 19-22Lab members attended ICPOC 2024. Gufeng and Letian presented their posters on LLM for retrosynthesis and molecular chiral representation, respectively.
Aug 6-7Prof. 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 19-21Lab members attended ISBRA 2024. Yifei and Yujia delivered oral presentations on their works on RNA-protein binding and RNA localization prediction, respectively.
July 5Lab members attended ACM TURC 2024, where Prof. Yang gave an invited talk "Deep Learning Revolutionizes Chemical Informatics: Model Evolution and Applications".
June 16Lab 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 30Our database CLC-DB containing 1800+ chiral ligands/catalysts of different chiral types is online!
May 30Yichong and Wenjing passed their PhD proposal defense. Congratulations!
May 24Prof. 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 16Our collaborative work "Measuring Bargaining Abilities of LLMs: A Benchmark and A Buyer-Enhancement Method" is accepted accepted to the ACL Findings. Congratulations!
May 7Our 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 17Yuyang's work ClusterDrop for addressing over-smoothing issue in GNNs is accepted by IJCAI 2024. Congratulations!
Apr 15Our GaCaMML paper is accepted by Artificial Intelligence in Medicine. Congratulations, Yuzhang and Guoshuai!
Mar 29Zebei, Guoshuai, Kuo, and Jingyao completed their Computer Science MS degree. Congratulations!
Feb 25Runhan's work RMVP for large-scale prepretraining of chemical reactions is published in Journal of Cheminformatics. Congratulations!
Feb 23Our CGMega paper is accepted by Nature Communications. Congratulations, Zebei!
Feb 22Our collaborative work CircSite on predicting circRNA-protein binding is published in Computers in Biology and Medicine. Congratulations!
Feb 10Guoshuai's work for designing new Al-Zn-Mg-Cu-Zr-Hf alloy is published in Materials Today Communications. Congratulations!