I am an Tenure-Track Assistant Professor in the Global Institute of Future Technology (GIFT), Shanghai Jiao Tong University. Prior to that, I finished my Ph.D. in Computer Science at Sun Yat-Sen University, supervised by Yuedong Yang.

My research interests lie in deep learning, drug discovery, synthetic biology and computational biology. Check out our GENTEL Lab Website for a full list of research projects and publications.

I am currently seeking Postdocs, Ph.D. students, master students and undergraduates who share our passion in ML & AI for biomedicine.

Github / Google Scholar / Linkedin

• Molecular Attributes Transfer from Non-Parallel Data S. Zheng*, Y. Song*, Z. Pan, C. Li, L. Song, Y. Yang. Under Review 2022 arxiv
• MolRep: A Deep Representation Learning Library for Molecular Property Prediction J. Rao, S. Zheng^*†, Y. Song, J. Chen, Z. Xie, C. Li, H. Cheng, Y. Yang. Under Review 2021 biorxiv | code

Publication

• Cross-modal Graph Contrastive Learning with Cellular Images S. Zheng^†, J. Rao*, J. Zhang, L. Zhou, E. Cohen, W. Lu, Y. Yang^† Advanced Science 2024 Adv. Sci. | code
• A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions J Rao, J Xie, Q Yuan, D Liu, Z Wang, Y Lu, S. Zheng^†, Y Yang^† Nature Communications 2024 Nat. Commun. | code
• Causal Subgraph Learning for Generalizable Inductive Relation Prediction M. Li, X. Liu, H. Ji, S. Zheng^† SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) 2024
• DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model W. Lu*, J. Zhang*, W. Huang, Z. Zhang, X. Jia, Z. Wang, L. Shi, C. Li, S. Zheng^† Nature Communications 2024 Nat. Commu. | code
• TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction W. Lu, Q. Wu, J. Zhang, J. Rao, C. Li, S. Zheng^*† Advances in Neural Information Processing Systems (NeurIPS) 2022 NeurIPS | code
• Accelerated rational PROTAC design via deep learning and molecular simulations S. Zheng, Y. Tan, Z. Wang, C. Li, Z. Zhang, X. Sang, H. Chen, Y. Yang Nature Machine Intelligence 2022 Nat. Mach. Intell | code
• Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction J. Rao*, S. Zheng*, Y. Lu, Y. Yang Patterns (Just accepted) 2022 Patterns / ICML XAI workshop | code
• Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP S. Zheng*, T. Zeng*, C. Li, B. Chen, C. W. Coley, Y. Yang, R. Wu Nature Communications 2022 Nat. Commun. | code
• Subgraph-aware Few Shot Inductive Link Prediction via Meta Learning S. Zheng, S. Mai, Y Sun, H. Hu, Y. Yang IEEE Transactions on Knowledge and Data Engineering (TKDE) 2022 arxiv
• Communicative Knowledge Graph Attention Network for Inductive Drug-Gene Interaction Prediction J. Rao*, S. Zheng*, Z. Xie, S. Mai, Y. Yang. IJCAI-2022 2022 IJCAI | code
• Structure-Aware Multimodal Deep Learning for Drug–Protein Interaction Prediction P. Wang*, S. Zheng*, Y. Jiang, C. Li, J. Liu, C. Wen, A. Patronov, D. Qian, H. Chen, Y. Yang J. Chem. Inf. Model. 2022 JCIM | code
• Amelioration of Alzheimer’s disease pathology by mitophagy inducers identified via machine learning and a cross-species workflow C. Xie, X. Zhuang, Z. Niu, R. Ai, S. Lautrup, S. Zheng, Y. Jiang,..., F. Fang Nature Biomedical Engineering 2022 Nat. Biomed. Eng.
• Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method J. Gao, S. Zheng, M. Yao, P. Wu Bioinformatics 2022 Bioinfo.
• AlphaFold2-aware protein–DNA binding site prediction using graph transformer Q Yuan, S Chen, J Rao, S. Zheng, H Zhao, Y Yang Briefings in Bioinformatics 2022 BIB | code
• Deep Scaffold Hopping with Multi-modal Transformer Neural Networks S. Zheng, Z. Lei, H Ai, H. Chen, D Deng, Y. Yang Journal of cheminformatics 2021 J. Cheminfo | code
• Meta Learning for Low Resource Molecular Optimization J Wang*, S Zheng*, J Chen, Y Yang J. Chem. Inf. Model. 2021 JCIM | code
• Learning Attributed Graph Representation with Communicative Message Passing Transformer J. Chen*, S. Zheng*, Y. Song, J. Rao, Y. Yang IJCAI 2021 IJCAI | code
• MTDsites: simultaneously predicting protein binding residues with multi-task deep neural network Z. Sun*, S. Zheng*, H. Zhao, Z. Niu, Y. Lu, Y. Yang. IEEE-ACM Transactions on Computational Biology and Bioinformatics 2021 TCBB
• DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks P. Zhang, S Zheng*, J. Chen, Y. Zhou, Y. Yang IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2021 BIBM | code
• Deep learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) with CT images Y.Song*, S. Zheng*, L. Li, X. Zhang, X. Zhang, Z. Huang, J. Shen, Y. Zha, Y. Yang IEEE-ACM Transactions on Computational Biology and Bioinformatics 2021 TCBB | code
• Structure-aware Protein Solubility Prediction From Sequence Through Graph Convolutional Network And Predicted Contact Map J Chen*, S Zheng*, H Zhao, Y Yang Journal of Cheminformatics 2021 J.Cheminfo | code
• Communicative Message Passing for Inductive Relation Reasoning S. Mai*, S. Zheng*, Y. Yang, H. Hu Association for the Advancement of Artificial Intelligence (AAAI) 2021 arxiv | code
• Predicting Drug Protein Interaction using Quasi-Visual Question Answering Systems S. Zheng, Y Li, S. Chen, J. Xu, Y. Yang Nature Machine Intelligence 2020 NMI | code
• PharmKG: A Dedicated Knowledge Graph Benchmark for Biomedical Data Mining S. Zheng, J. Rao, Y. Song, J. Zhang, X. Xiao, F. Fang, Y. Yang, Z. Niu Briefings in Bioinformatics 2020 Brief Bioinfo | code
• Biomedical Knowledge Graph of COVID-19: Construction and Applications S. Zheng, J. Zhang, J. Rao, X. Xiao, S. Wade, C. Jake, Y. Yang, Z. Niu Data Mining in Bioinformatics Workshop at KDD (spotlight) 2020 BioKDD
• Deep learning enables discovery of highly potent anti-osteoporosis natural products Z. Liu*, D. Huang*, S. Zheng*, Y. Song, B. Liu, J. Sun, Z. Niu, Q. Gu, J. Xu, L. Xie Eur. J. Med. Chem. 2020 EJMC
• RetroXpert: Decompose Retrosynthesis Prediction like A Chemist C Yan, Q Ding, P Zhao, S Zheng, J Yang, Y Yu, J Huang Advances in Neural Information Processing Systems (NeurIPS) 2020 NeurIPS | code
• Biomedical Knowledge Graph of COVID-19: Construction and Applications S. Zheng, J. Zhang, J. Rao, X. Xiao, S. Wade, C. Jake, Y. Yang, Z. Niu Data Mining in Bioinformatics Workshop at KDD (spotlight) 2020 BioKDD
• SyntaLinker: Automatic Fragment Linking with Deep Conditional Transformer Neural Networks Y Yang*, S Zheng*, S Su, J Xu, H Chen Chemical Science 2020 Chem. Sci | code
• Communicative Representation Learning on Attributed Molecular Graphs Y.Song*, S. Zheng*, Z. Niu, Z. Fu, Y. Lu, Y. Yang. IJCAI-PRICAI 2020 2020 IJCAI (Oral) | code
• Predicting the Feasibility of Copper (I)-catalyzed Alkyne-AzideCycloaddition Reactions Using Recurrent Neural Network with Self-Attention Mechanism S. Shu, Y. Yang, H. Gan, S. Zheng, J. Xu J. Chem. Inf. Model. 2020 JCIM | code
• Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks S. Zheng*, J. Rao*, Z. Zhang, J. Xu, Y. Yang J. Chem. Inf. Model. 2019 JCIM | code
• Predicting Drug Protein Interaction using Quasi-Visual Question Answering Systems S. Zheng, Y Li, S. Chen, J. Xu, Y. Yang ML4H NeurIPS Workshop at NeurIPS-2019 2019
• Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism S. Zheng, X. Yan, Y. Yang, J. Xu J. Chem. Inf. Model. 2019 JCIM |
• QBMG: quasi-biogenic molecule generator with deep recurrent neural network S. Zheng, X. Yan, Q. Gu, Y. Yang, Y. Du, Y. Lu, J. Xu J. Cheminfo. 2019 JC | code
† denotes co-corresponding author. * denotes equal contribution.