A Semi-Definite programming-based Underestimation method for global optimization in molecular docking. - Ioannis Ch. Paschalidis; Yang Shen 001; Sandor Vajda; Pirooz Vakili (CDC/ECC, 2005)

Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. - Ioannis Ch. Paschalidis; Yang Shen 001; Pirooz Vakili; Sandor Vajda (EMBC, 2006)

Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking. - Yang Shen 001; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2007)

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. - Ioannis Ch. Paschalidis; Yang Shen 001; Pirooz Vakili; Sandor Vajda (IEEE Trans. Autom. Control., 2007)

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. - Yang Shen 001; Ioannis Ch. Paschalidis; Pirooz Vakili; Sandor Vajda (PLoS Comput. Biol., 2008)

Biomedical informatics with optimization and machine learning. - Thomas S. Huang; Jiayu Zhou; Zhangyang Wang; Qing Ling 001; Yang Shen 001 (EURASIP J. Bioinform. Syst. Biol., 2017)

iCFN: an efficient exact algorithm for multistate protein design. - Mostafa Karimi; Yang Shen 001 (Bioinform., 2018)

Learning to Optimize in Swarms. - Yue Cao 010; Tianlong Chen 001; Zhangyang Wang; Yang Shen 001 (NeurIPS, 2019)

DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. - Mostafa Karimi; Di Wu 017; Zhangyang Wang; Yang Shen 001 (Bioinform., 2019)

Bayesian active learning for optimization and uncertainty quantification in protein docking. - Yue Cao 010; Yang Shen 001 (CoRR, 2019)

Energy-based Graph Convolutional Networks for Scoring Protein Docking Models. - Yue Cao 010; Yang Shen 001 (CoRR, 2019)

L2-GCN: Layer-Wise and Learned Efficient Training of Graph Convolutional Networks. - Yuning You; Tianlong Chen 001; Zhangyang Wang; Yang Shen 001 (CVPR, 2020)

When Does Self-Supervision Help Graph Convolutional Networks? - Yuning You; Tianlong Chen 001; Zhangyang Wang; Yang Shen 001 (ICML, 2020)

Graph Contrastive Learning with Augmentations. - Yuning You; Tianlong Chen 001; Yongduo Sui; Ting Chen; Zhangyang Wang; Yang Shen 001 (NeurIPS, 2020)

Network-principled deep generative models for designing drug combinations as graph sets. - Mostafa Karimi; Arman Hasanzadeh; Yang Shen 001 (Bioinform., 2020)

L^2-GCN: Layer-Wise and Learned Efficient Training of Graph Convolutional Networks. - Yuning You; Tianlong Chen 001; Zhangyang Wang; Yang Shen 001 (CoRR, 2020)

Cross-Modality Protein Embedding for Compound-Protein Affinity and Contact Prediction. - Yuning You; Yang Shen 001 (CoRR, 2020)

De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks. - Mostafa Karimi; Shaowen Zhu; Yue Cao 010; Yang Shen 001 (J. Chem. Inf. Model., 2020)

Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. - Yue Cao 010; Payel Das; Vijil Chenthamarakshan; Pin-Yu Chen; Igor Melnyk; Yang Shen 001 (ICML, 2021)

Graph Contrastive Learning Automated. - Yuning You; Tianlong Chen 001; Yang Shen 001; Zhangyang Wang (ICML, 2021)

TALE: Transformer-based protein function Annotation with joint sequence-Label Embedding. - Yue Cao 010; Yang Shen 001 (Bioinform., 2021)

Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. - Mostafa Karimi; Di Wu 017; Zhangyang Wang; Yang Shen 001 (J. Chem. Inf. Model., 2021)

Bayesian Modeling and Uncertainty Quantification for Learning to Optimize: What, Why, and How. - Yuning You; Yue Cao 010; Tianlong Chen 001; Zhangyang Wang; Yang Shen 001 (ICLR, 2022)

Augmentations in Hypergraph Contrastive Learning: Fabricated and Generative. - Tianxin Wei; Yuning You; Tianlong Chen 001; Yang Shen 001; Jingrui He; Zhangyang Wang (NeurIPS, 2022)

Bringing Your Own View: Graph Contrastive Learning without Prefabricated Data Augmentations. - Yuning You; Tianlong Chen 001; Zhangyang Wang; Yang Shen 001 (WSDM, 2022)

Cross-modality and self-supervised protein embedding for compound-protein affinity and contact prediction. - Yuning You; Yang Shen 001 (Bioinform., 2022)

Predicting protein structure from single sequences. - Yang Shen 001 (Nat. Comput. Sci., 2022)

Guest Editorial Special Section on Learning With Multimodal Data for Biomedical Informatics. - Zhangyang Wang; Vishal Patel 001; Bing Yao; Steve B. Jiang; Huimin Lu 001; Yang Shen 001 (IEEE Trans. Circuits Syst. Video Technol., 2022)

Graph Domain Adaptation via Theory-Grounded Spectral Regularization. - Yuning You; Tianlong Chen 001; Zhangyang Wang; Yang Shen 001 (ICLR, 2023)

Graph Contrastive Learning: An Odyssey towards Generalizable, Scalable and Principled Representation Learning on Graphs. - Yan Han 001; Yuning You; Wenqing Zheng; Scott Hoang; Tianxin Wei; Majdi Hassan; Tianlong Chen 001; Ying Ding 001; Yang Shen 001; Zhangyang Wang (IEEE Data Eng. Bull., 2023)

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure. - Wuwei Tan; Yang Shen 001 (Bioinform., 2023)

Latent 3D Graph Diffusion. - Yuning You; Ruida Zhou; Jiwoong Park; Haotian Xu 004; Chao Tian 002; Zhangyang Wang; Yang Shen 001 (ICLR, 2024)

Correlational Lagrangian Schrödinger Bridge: Learning Dynamics with Population-Level Regularization. - Yuning You; Ruida Zhou; Yang Shen 001 (CoRR, 2024)