Publications — AIDDPM Lab

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.*

Nature Communications, 17, 9376, 2026

Figure 1 · Activity-cliff-aware graph learning

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.*

Nature Medicine, 32, 3010–3022, 2026

Figure 1a–c · COMPASS: biological concepts, pretraining and treatment prediction

2026 ChemRxiv Preprint (June 2026)

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.*

ChemRxiv (Preprint), 2026

MusicMol framework: bidirectional molecule-to-music generation and music-to-molecule decoding

2026 ChemRxiv Preprint (March 2026)

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.*

ChemRxiv (Preprint), 2026

FPPool framework: fingerprint matching and hierarchical molecular graph pooling

2026 bioRxiv

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.*

bioRxiv, 2026

Medea · Research planning, analysis and literature reasoning

2026 Journal of Chemical Information and Modeling

TradePool: A Novel Interpretable Framework for Quantifying Atomic Attribution Values in Molecular Property Prediction

Ni B, Shen W., Ye Z*

Journal of Chemical Information and Modeling, 2026

TradePool workflow: subgraph pooling and atomic attribution mapping

2024 Nature Machine Intelligence

Efficient Generation of Protein Pockets with PocketGen

Zhang Z.; Shen W.; Liu Q.*; Zitnik M.*

Nature Machine Intelligence, 6(11), 1382–1395, 2024

Figure 1 · Protein pocket generation with PocketGen

2024 PNAS Nexus

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, 3(8), pgae268, 2024

Raman spectra · Signal aggregation and structured representations

2024 Nature Biomedical Engineering

Bidirectional Linkage of DNA Barcodes for the Multiplexed Mapping of Higher-Order Protein Interactions in Cells

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, 8(7), 909–923, 2024

Figure 1 · Mapping higher-order protein interactions with DNA barcodes

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*.

Cell Press Patterns, 4(1), 100658, 2023

MEGMA · From microbial abundance profiles to structured feature maps

2023 Cell Press Patterns 🏆 People of Data Feature

Toward Ordered-Omics Data Science: Researchers on the Magic of Turning Metagenomic Chaos into Image-Like Patterns

Shen W.*; Chen Y. Z.*

Cell Press Patterns, People of Data Special Issue, 4(1), 100673, 2023

Professor Chen and Dr. Shen · The researchers behind ordered-omics data science

2023 Computers in Biology and Medicine

Deep Learning of 2D-Restructured Gene Expression Representations for Improved Low-Sample Therapeutic Response Prediction

Cheng K.#; Shen W.#; Jiang Y.; Chen Y.; Chen Y. Z.*; Tan Y.*

Computers in Biology and Medicine, 164, 107245, 2023

Gene expression representations for therapeutic response prediction

2023 Brain, Behavior, & Immunity – Health

Chronic Treatment with Baicalein Alleviates Behavioural Disorders and Improves Cerebral Blood Flow via Reverting Metabolic Abnormalities in a J20 Transgenic Mouse Model of Alzheimer's Disease

Zhang L.; Wong L. R.; Wong P.; Shen W.; Yang S.; Huang L.; Lim Y. A.; Ho P. C. L.*

Brain, Behavior, & Immunity – Health, 28, 100599, 2023

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.*

Nucleic Acids Research, 50(8), e45, 2022

Figure 1A–B · Feature aggregation and the AggMapNet architecture

2022 ACS Sensors

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, 7(5), 1524–1532, 2022

Exosome sensing and deep learning for breast cancer diagnosis

2021 Nature Machine Intelligence

Out-of-the-Box Deep Learning Prediction of Pharmaceutical Properties by Broadly Learned Knowledge-Based Molecular Representations (MolMap)

Shen W.; Zeng X.; Zhu F.; Wang Y.; Qin C.; Tan Y.; Jiang Y. Y.*; Chen Y. Z.*

Nature Machine Intelligence, 3(4), 334–343, 2021

Figure 1 · From molecular features to structured MolMap representations

2021 ACS Chemical Biology

High-Content Phenotypic Screen of a Focused TCAMS Drug Library Identifies Novel Disruptors of the Malaria Parasite Calcium Dynamics

Chia W.; Gomez-Lorenzo M. G.; Castellote I.; Tong J. X.; Chandramohanadas R.; Thu Chu T. T.; Shen W.; … Tan K. S.*

ACS Chemical Biology, 16(11), 2348–2372, 2021

Chemical structures and molecular interactions

2021 Life Sciences

Functional Effects of Berberine in Modulating Mitochondrial Dysfunction and Inflammatory Response in the Respective Amyloidogenic Cells and Activated Microglial Cells – In Vitro Models Simulating Alzheimer's Disease Pathology

Wong L. R.; Tan E. A.; Lim M. E. J.; Shen W.; Lian X. L.; Wang Y.; Chen L.; Ho P. C. L.*

Life Sciences, 282, 119824, 2021

Experimental profiles and molecular interaction analysis

2021 Nucleic Acids Research

MASI: Microbiota–Active Substance Interactions Database

Zeng X.; Yang X.; Fan J.; Tan Y.; Ju L.; Shen W.; Cui C.; Zhu F.; Chen Y. Z.*

Nucleic Acids Research, 49(D1), D776–D782, 2021

Figure 1 · The MASI microbiota–active substance search interface

2017 Molecular Informatics

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, 36(11), 2017

Model performance for enzymatic hydrolysis prediction

2017 Oncotarget

Arctigenin Inhibits STAT3 and Exhibits Anticancer Potential in Human Triple-Negative Breast Cancer Therapy

Feng T. T.#; Cao W.#; Shen W.; … [et al.]

Oncotarget, 8(1), 329–344, 2017

Arctigenin · Cell viability and anticancer activity

2015 Open Life Sciences

Mutation of the Conserved GRG Motif and Decreasing Activity of Human RNase H2

Li L.; Shen W.; Zheng J.; [et al.]

Open Life Sciences, 10(1), 2015