Publications

Multimodal Out-of-Distribution Individual Uncertainty Quantification Enhances Binding Affinity Prediction for Polypharmacology
Amitesh Badkul, Li Xie, Shuo Zhang, Lei Xie

Nature Machine Intelligence, 2025 (Accepted in principle).

TrustAffinity: Accurate, Reliable, and Scalable Out-of-Distribution Protein–Ligand Binding Affinity Prediction Using Trustworthy Deep Learning
Amitesh Badkul, Li Xie, Shuo Zhang, Lei Xie

Neural Information Processing Systems (NeurIPS) New Frontiers of AI for Drug Discovery and Development (AI4D3) Workshop, 2023.

Learning Point Cloud Representations with Pose Continuity for Depth-Based Category-Level 6D Object Pose Estimation
Zhujun Li, Shuo Zhang, Ioannis Stamos

International Conference on Computer Vision (ICCV) Recovering 6D Object Pose (R6D) Workshop, 2025.

Sequence-based Drug-Target Binding Site Pre-training Tackles Crypticity and Enhances Protein-Ligand Binding Process Predictions
Shuo Zhang, Li Xie, Daniel Tiourine, Lei Xie

Preprint, under review, 2025.

Protein Language Model-Powered 3D Ligand Binding Site Prediction from Protein Sequence
Shuo Zhang, Lei Xie

Neural Information Processing Systems (NeurIPS) AI for Science Workshop, 2023.

MolGene-E: Inverse Molecular Design to Modulate Single Cell Transcriptomics
Rahul Ohlan, Raswanth Murugan, Li Xie, Mohammadsadeq Mottaqi, Shuo Zhang†, Lei Xie

International Conference on Machine Learning (ICML) AI4Science Workshop, 2024.

A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems
Shuo Zhang, Yang Liu, Lei Xie

Scientific Reports, 2023.

Physics-aware Graph Neural Network for Accurate RNA 3D Structure Prediction
Shuo Zhang, Yang Liu, Lei Xie

Neural Information Processing Systems (NeurIPS) Machine Learning for Structural Biology (MLSB) Workshop, 2022.

Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures
Shuo Zhang, Yang Liu, Lei Xie

Neural Information Processing Systems (NeurIPS) Machine Learning for Structural Biology (MLSB) Workshop, 2020.

End-to-End Sequence-Structure-Function Meta-Learning Predicts Genome-Wide Chemical-Protein Interactions for Dark Proteins
Tian Cai, Li Xie, Shuo Zhang, Muge Chen, Di He, Amitesh Badkul, Yang Liu, Hari Krishna Namballa, Michael Dorogan, Wayne W. Harding, Cameron Mura, Philip E. Bourne, Lei Xie

PLOS Computational Biology, 2023.

Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation
Shuo Zhang, Lei Xie

International Joint Conference on Artificial Intelligence (IJCAI), 2020.

Acceptance rate: 592/4717=12.6%.

Enhancing Attention-based Graph Neural Networks via Cardinality Preservation
Shuo Zhang, Lei Xie

AAAI Conference on Artificial Intelligence (AAAI) Deep Learning on Graphs (DLG) Workshop, 2020.

Heterogeneous Multi-Layered Network Model for Omics Data Integration and Analysis
Bohyun Lee, Shuo Zhang, Aleksandar Poleksic, Lei Xie

Frontiers in Genetics, 2020.

Theoretical Study of Adsorption and Dehydrogenation of C2H4 on Cu(410)
Yangyunli Sun*, Shuo Zhang*, Wenhua Zhang, Zhenyu Li

Chinese Journal of Chemical Physics, 2018.