Research Output

Publications

Full publication list. * denotes PI as first or corresponding author. Graphical abstracts are shown as placeholders — replace with actual images in each publications/[slug]/ folder.

2026
Medea: An Omics AI Agent for Therapeutic Discovery
Sui, P.; Li, M. M.; Gao, S.; Shen, W.*; Giunchiglia, V.; Shen, A.; Huang, Y.; Kong, Z.; Zitnik, M.
openRxiv (Preprint), 2026
DOI PDF
Graphical abstract
2025
Generalizable AI Predicts Immunotherapy Outcomes Across Cancers and Treatments bioRxiv
Shen, W.*; Nguyen, T. H.; Li, M. M.; Huang, Y.; Moon, I.; Nair, N.; Marbach, D.; Zitnik, M.
bioRxiv / medRxiv (Preprint), 2025
DOI PDF Web App
Graphical abstract
2024
Activity Cliff-Informed Contrastive Learning for Molecular Property Prediction Under Review
Shen, W.*; Cui, C.; Su, X.; Zhang, Z.; Arce, A. V.; Wang, J.; Shi, X.; Zhang, Y.; Wu, J.; Chen, Y. Z.; Zitnik, M.
Springer Science and Business Media LLC (Under Review), 2024
DOI (Preprint v2) ChemRxiv PDF Code
Graphical abstract
Efficient Generation of Protein Pockets with PocketGen NMI
Zhang, Z.; Shen, W.; Liu, Q.; Zitnik, M.
Nature Machine Intelligence, vol. 6, no. 11, pp. 1382–1395, 2024
DOI PDF Code
Graphical abstract
Raman Spectroscopic Deep Learning with Signal Aggregated Representations for Enhanced Cell Phenotype and Signature Identification
Lu, S.; Huang, Y.; Shen, W.; Cao, Y. L.; Cai, M.; Chen, Y.; Tan, Y.; Jiang, Y. Y.; Chen, Y. Z.
PNAS Nexus, vol. 3, no. 8, 2024
DOI PDF
Graphical abstract
Bidirectional Linkage of DNA Barcodes for the Multiplexed Mapping of Higher-Order Protein Interactions in Cells NBE
Liu, Y.; Sundah, N. R.; Ho, N. R. Y.; Shen, W.; Xu, Y.; Natalia, A.; Yu, Z.; Seet, J. E.; Chan, C. W.; Loh, T. P.; Lim, B. Y.; Shao, H.
Nature Biomedical Engineering, vol. 8, no. 7, pp. 909–923, 2024
DOI PDF
Graphical abstract
2023
Online Triplet Contrastive Learning Enables Efficient Cliff Awareness in Molecular Activity Prediction
Shen, W.*; Cui, C.; Shi, X.; Zhang, Y.; Wu, J.; Chen, Y. Z.
Preprint (Springer / ACS ChemRxiv), 2023
DOI (v1) ChemRxiv PDF
Graphical abstract
2022
AggMapNet: Enhanced and Explainable Low-Sample Omics Deep Learning with Feature-Aggregated Multi-Channel Networks NAR
Shen, W.*; Liu, Y.; Chen, Y.; Zeng, X.; Tan, Y.; Jiang, Y. Y.; Chen, Y. Z.
Nucleic Acids Research, 2022
DOI PDF Code
Graphical abstract
Fluorescence Analysis of Circulating Exosomes for Breast Cancer Diagnosis Using a Sensor Array and Deep Learning
Jin, Y.; Du, N.; Huang, Y.; Shen, W.; Tan, Y.; Chen, Y. Z.; Dou, W.-T.; He, X.-P.; Yang, Z.; Xu, N.; Tan, C.
ACS Sensors, vol. 7, no. 5, pp. 1524–1532, 2022
DOI PDF
Graphical abstract
2021
Out-of-the-Box Deep Learning Prediction of Pharmaceutical Properties by Broadly Learned Knowledge-Based Molecular Representations (MolMap) NMI
Shen, W.*; Zeng, X.; Zhu, F.; Wang, Y.; Qin, C.; Tan, Y.; Jiang, Y. Y.; Chen, Y. Z.
Nature Machine Intelligence, vol. 3, no. 4, pp. 334–343, 2021
DOI PDF Code
Graphical abstract
2017
Predicting the Enzymatic Hydrolysis Half-Lives of New Chemicals Using Support Vector Regression Models Based on Stepwise Feature Elimination
Shen, W.*; Xiao, T.; Chen, S.; Liu, F.; Chen, Y. Z.; Jiang, Y.
Molecular Informatics, vol. 36, no. 11, 2017
DOI PDF
Graphical abstract