Yang Shen - RankMe

43 papers A* 10A 1Journal 29Unranked 3

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	Correlational Lagrangian Schrödinger Bridge: Learning Dynamics with Population-Level Regularization. CoRR Yuning You, Ruida Zhou, Yang Shen
2024	A*	`conf`	Latent 3D Graph Diffusion. ICLR Yuning You, Ruida Zhou, Jiwoong Park, Haotian Xu, Chao Tian, Zhangyang Wang, Yang Shen
2023	J	`jnl`	Graph Contrastive Learning: An Odyssey towards Generalizable, Scalable and Principled Representation Learning on Graphs. IEEE Data Eng. Bull. Yan Han, Yuning You, Wenqing Zheng, Scott Hoang, Tianxin Wei, Majdi Hassan, Tianlong Chen, Ying Ding, Yang Shen, Zhangyang Wang
2023	A*	`conf`	Graph Domain Adaptation via Theory-Grounded Spectral Regularization. ICLR Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen
2023	J	`jnl`	Multimodal learning of noncoding variant effects using genome sequence and chromatin structure. Bioinform. Wuwei Tan, Yang Shen
2022	A*	`conf`	Augmentations in Hypergraph Contrastive Learning: Fabricated and Generative. NeurIPS Tianxin Wei, Yuning You, Tianlong Chen, Yang Shen, Jingrui He, Zhangyang Wang
2022	J	`jnl`	Augmentations in Hypergraph Contrastive Learning: Fabricated and Generative. CoRR Tianxin Wei, Yuning You, Tianlong Chen, Yang Shen, Jingrui He, Zhangyang Wang
2022	A*	`conf`	Bayesian Modeling and Uncertainty Quantification for Learning to Optimize: What, Why, and How. ICLR Yuning You, Yue Cao, Tianlong Chen, Zhangyang Wang, Yang Shen
2022	A	`conf`	Bringing Your Own View: Graph Contrastive Learning without Prefabricated Data Augmentations. WSDM Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen
2022	J	`jnl`	Bringing Your Own View: Graph Contrastive Learning without Prefabricated Data Augmentations. CoRR Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen
2022	J	`jnl`	Cross-modality and self-supervised protein embedding for compound-protein affinity and contact prediction. Bioinform. Yuning You, Yang Shen
2022	J	`jnl`	Guest Editorial Special Section on Learning With Multimodal Data for Biomedical Informatics. IEEE Trans. Circuits Syst. Video Technol. Zhangyang Wang, Vishal Patel, Bing Yao, Steve B. Jiang, Huimin Lu, Yang Shen
2022	J	`jnl`	Predicting protein structure from single sequences. Nat. Comput. Sci. Yang Shen
2021	J	`jnl`	Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. J. Chem. Inf. Model. Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen
2021	A*	`conf`	Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. ICML Yue Cao, Payel Das, Vijil Chenthamarakshan, Pin-Yu Chen, Igor Melnyk, Yang Shen
2021	J	`jnl`	Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. CoRR Yue Cao, Payel Das, Vijil Chenthamarakshan, Pin-Yu Chen, Igor Melnyk, Yang Shen
2021	A*	`conf`	Graph Contrastive Learning Automated. ICML Yuning You, Tianlong Chen, Yang Shen, Zhangyang Wang
2021	J	`jnl`	Graph Contrastive Learning Automated. CoRR Yuning You, Tianlong Chen, Yang Shen, Zhangyang Wang
2021	J	`jnl`	TALE: Transformer-based protein function Annotation with joint sequence-Label Embedding. Bioinform. Yue Cao, Yang Shen
2020	J	`jnl`	Cross-Modality Protein Embedding for Compound-Protein Affinity and Contact Prediction. CoRR Yuning You, Yang Shen
2020	J	`jnl`	De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks. J. Chem. Inf. Model. Mostafa Karimi, Shaowen Zhu, Yue Cao, Yang Shen
2020	A*	`conf`	Graph Contrastive Learning with Augmentations. NeurIPS Yuning You, Tianlong Chen, Yongduo Sui, Ting Chen, Zhangyang Wang, Yang Shen
2020	J	`jnl`	Graph Contrastive Learning with Augmentations. CoRR Yuning You, Tianlong Chen, Yongduo Sui, Ting Chen, Zhangyang Wang, Yang Shen
2020	A*	`conf`	L2-GCN: Layer-Wise and Learned Efficient Training of Graph Convolutional Networks. CVPR Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen
2020	J	`jnl`	L^2-GCN: Layer-Wise and Learned Efficient Training of Graph Convolutional Networks. CoRR Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen
2020	J	`jnl`	Network-principled deep generative models for designing drug combinations as graph sets. Bioinform. Mostafa Karimi, Arman Hasanzadeh, Yang Shen
2020	J	`jnl`	Network-principled deep generative models for designing drug combinations as graph sets. CoRR Mostafa Karimi, Arman Hasanzadeh, Yang Shen
2020	A*	`conf`	When Does Self-Supervision Help Graph Convolutional Networks? ICML Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen
2020	J	`jnl`	When Does Self-Supervision Help Graph Convolutional Networks? CoRR Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen
2019	J	`jnl`	Bayesian active learning for optimization and uncertainty quantification in protein docking. CoRR Yue Cao, Yang Shen
2019	J	`jnl`	DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. Bioinform. Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen
2019	J	`jnl`	Energy-based Graph Convolutional Networks for Scoring Protein Docking Models. CoRR Yue Cao, Yang Shen
2019	J	`jnl`	Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. CoRR Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen
2019	A*	`conf`	Learning to Optimize in Swarms. NeurIPS Yue Cao, Tianlong Chen, Zhangyang Wang, Yang Shen
2019	J	`jnl`	Learning to Optimize in Swarms. CoRR Yue Cao, Tianlong Chen, Zhangyang Wang, Yang Shen
2018	J	`jnl`	DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks. CoRR Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen
2018	J	`jnl`	iCFN: an efficient exact algorithm for multistate protein design. Bioinform. Mostafa Karimi, Yang Shen
2017	J	`jnl`	Biomedical informatics with optimization and machine learning. EURASIP J. Bioinform. Syst. Biol. Thomas S. Huang, Jiayu Zhou, Zhangyang Wang, Qing Ling, Yang Shen
2008	J	`jnl`	Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. PLoS Comput. Biol. Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda
2007	—	`conf`	Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking. CDC Yang Shen, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis
2007	J	`jnl`	SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Trans. Autom. Control. Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda
2006	—	`conf`	Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. EMBC Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda
2005	—	`conf`	A Semi-Definite programming-based Underestimation method for global optimization in molecular docking. CDC/ECC Ioannis Ch. Paschalidis, Yang Shen, Sandor Vajda, Pirooz Vakili