2026 Nature Medicine Generalizable AI predicts immunotherapy outcomes across cancers and treatments Shen W., Moon I., Nguyen T. H., Li M. M., Huang Y., Nair N., Marbach D.*, and Zitnik M.*
2026 Nature Communications Activity-cliff awareness enables robust graph learning for molecular property prediction Cui C., Shi X. C., Su X., Zhang Z., Arce A. V., Wang J., Zhang Y., Wu J., Chen Y. Z.*, Zitnik M.*, and Shen W.*
2026 ChemRxiv MusicMol: Bidirectional Molecule–Music Translation via Neighborhood-Aligned Generation and Transformer Decoding Tang J., Zhu Z., Cui C., Ke N., Song C., Li Y., Zhou Y., Yu C., Jing P., Zhu C., Yang Z., Shen W.*
2026 ChemRxiv Bridging Molecular Fingerprints and Graph Neural Networks through Knowledge-Guided Pooling (FPPool) Cui C., Feng S., Song C., Yu S., Lu S., Chen Y. Z.*, Shen W.*
2023 Cell Press Patterns Enhanced Metagenomic Deep Learning for Disease Prediction and Consistent Signature Recognition by Restructured Microbiome 2D Representations Shen W., Liang S. R., Jiang Y. Y.*, Chen Y. Z*.
2022 Nucleic Acids Research AggMapNet: Enhanced and Explainable Low-Sample Omics Deep Learning with Feature-Aggregated Multi-Channel Networks Shen W., Liu Y., Chen Y., Zeng X., Tan Y., Jiang Y. Y.*, Chen Y. Z.*
