Publications

You can find a full list of works at Google Scholar profile.

• Ziqi Chen, Bo Peng, Srinivasan Parthasarathy, Xia Ning, Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models, NeurIPS 2023 Generative AI and Biology (GenBio) Workshop, 2023. paper

• Ziqi Chen, Oluwatosin R Ayinde, James R Fuchs, Huan Sun, Xia Ning, G$^2$Retro as a two-step graph generative models for retrosynthesis prediction, Communications Chemistry 6.1 (2023): 102. [Paper][Code]

• Ziqi Chen, Martin Renqiang Min, Hongyu Guo, Chao Cheng, Trevor Clancy, Xia Ning, T-Cell Receptor Optimization with Reinforcement Learning and Mutation Polices for Precision Immunotherapy, in Proceedings of the 27th Annual International Conference on Research in Computational Molecular Biology, (RECOMB 2023), Istanbul, Turkey, April 16–19, 2023. [Paper][Code]

• Ziqi Chen*, Baoyi Zhang*, Hongyu Guo, Prashant Emani, Trevor Clancy, Chongming Jiang, Mark Gerstein, Xia Ning, Chao Cheng, Martin Renqiang Min, Binding peptide generation for MHC Class I proteins with deep reinforcement learning, Bioinformatics 39.2 (2023): btad055. [Paper][Code]

• Ziqi Chen*, Bo Peng*, Vassilis N Ioannidis, Mufei Li, George Karypis, Xia Ning, A knowledge graph of clinical trials (CTKG), Scientific reports 12.1 (2022): 4724. [Paper][Code]

• Ziqi Chen, Martin Renqiang Min, Srinivasan Parthasarathy, Xia Ning, A deep generative model for molecule optimization via one fragment modification, Nature machine intelligence 3.12 (2021): 1040-1049. [Paper][Code][Previous code]

• Ziqi Chen, Martin Renqiang Min, Xia Ning, Ranking-based convolutional neural network models for peptide-MHC class I binding prediction, Frontiers in Molecular Biosciences 8 (2021): 634836. [Paper][Code]