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ORCIDYang Shen 0001
Person information
- affiliation: Texas A&M University, College Station, TX, USA
Other persons with the same name
- Yang Shen — disambiguation page
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2020 – today
- 2024
[c14]Yuning You, Ruida Zhou, Jiwoong Park, Haotian Xu, Chao Tian, Zhangyang Wang, Yang Shen:
Latent 3D Graph Diffusion. ICLR 2024- [i15]Yuning You, Ruida Zhou, Yang Shen:
Correlational Lagrangian Schrödinger Bridge: Learning Dynamics with Population-Level Regularization. CoRR abs/2402.10227 (2024) - 2023
- [j13]Wuwei Tan, Yang Shen
:
Multimodal learning of noncoding variant effects using genome sequence and chromatin structure. Bioinform. 39(9) (2023) - [j12]Yan Han, Yuning You, Wenqing Zheng, Scott Hoang, Tianxin Wei, Majdi Hassan, Tianlong Chen, Ying Ding, Yang Shen, Zhangyang Wang:
Graph Contrastive Learning: An Odyssey towards Generalizable, Scalable and Principled Representation Learning on Graphs. IEEE Data Eng. Bull. 46(2): 80-95 (2023) - [c13]Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen:
Graph Domain Adaptation via Theory-Grounded Spectral Regularization. ICLR 2023 - 2022
- [j11]Yang Shen:
Predicting protein structure from single sequences. Nat. Comput. Sci. 2(12): 775-776 (2022) - [j10]Zhangyang Wang, Vishal Patel, Bing Yao, Steve B. Jiang, Huimin Lu, Yang Shen:
Guest Editorial Special Section on Learning With Multimodal Data for Biomedical Informatics. IEEE Trans. Circuits Syst. Video Technol. 32(5): 2508-2511 (2022) - [c12]Yuning You, Yue Cao, Tianlong Chen, Zhangyang Wang, Yang Shen:
Bayesian Modeling and Uncertainty Quantification for Learning to Optimize: What, Why, and How. ICLR 2022 - [c11]Tianxin Wei, Yuning You, Tianlong Chen, Yang Shen, Jingrui He, Zhangyang Wang:
Augmentations in Hypergraph Contrastive Learning: Fabricated and Generative. NeurIPS 2022 - [c10]Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen:
Bringing Your Own View: Graph Contrastive Learning without Prefabricated Data Augmentations. WSDM 2022: 1300-1309 - [i14]Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen:
Bringing Your Own View: Graph Contrastive Learning without Prefabricated Data Augmentations. CoRR abs/2201.01702 (2022) - [i13]Tianxin Wei, Yuning You, Tianlong Chen, Yang Shen, Jingrui He, Zhangyang Wang:
Augmentations in Hypergraph Contrastive Learning: Fabricated and Generative. CoRR abs/2210.03801 (2022) - 2021
- [j9]Yue Cao, Yang Shen:
TALE: Transformer-based protein function Annotation with joint sequence-Label Embedding. Bioinform. 37(18): 2825-2833 (2021) - [j8]Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen:
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. J. Chem. Inf. Model. 61(1): 46-66 (2021) - [c9]Yue Cao, Payel Das, Vijil Chenthamarakshan, Pin-Yu Chen, Igor Melnyk, Yang Shen:
Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. ICML 2021: 1261-1271 - [c8]Yuning You, Tianlong Chen, Yang Shen, Zhangyang Wang:
Graph Contrastive Learning Automated. ICML 2021: 12121-12132 - [i12]Yuning You, Tianlong Chen, Yang Shen, Zhangyang Wang:
Graph Contrastive Learning Automated. CoRR abs/2106.07594 (2021) - [i11]Yue Cao, Payel Das, Vijil Chenthamarakshan, Pin-Yu Chen, Igor Melnyk, Yang Shen:
Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. CoRR abs/2106.13058 (2021) - 2020
- [j7]Mostafa Karimi, Arman Hasanzadeh, Yang Shen:
Network-principled deep generative models for designing drug combinations as graph sets. Bioinform. 36(Supplement-1): i445-i454 (2020) - [j6]Mostafa Karimi, Shaowen Zhu, Yue Cao, Yang Shen:
De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks. J. Chem. Inf. Model. 60(12): 5667-5681 (2020) - [c7]Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen:
L2-GCN: Layer-Wise and Learned Efficient Training of Graph Convolutional Networks. CVPR 2020: 2124-2132 - [c6]Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen:
When Does Self-Supervision Help Graph Convolutional Networks? ICML 2020: 10871-10880 - [c5]Yuning You, Tianlong Chen, Yongduo Sui, Ting Chen, Zhangyang Wang, Yang Shen:
Graph Contrastive Learning with Augmentations. NeurIPS 2020 - [i10]Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen:
L^2-GCN: Layer-Wise and Learned Efficient Training of Graph Convolutional Networks. CoRR abs/2003.13606 (2020) - [i9]Mostafa Karimi, Arman Hasanzadeh, Yang Shen:
Network-principled deep generative models for designing drug combinations as graph sets. CoRR abs/2004.07782 (2020) - [i8]Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen:
When Does Self-Supervision Help Graph Convolutional Networks? CoRR abs/2006.09136 (2020) - [i7]Yuning You, Tianlong Chen, Yongduo Sui, Ting Chen, Zhangyang Wang, Yang Shen:
Graph Contrastive Learning with Augmentations. CoRR abs/2010.13902 (2020) - [i6]Yuning You, Yang Shen:
Cross-Modality Protein Embedding for Compound-Protein Affinity and Contact Prediction. CoRR abs/2012.00651 (2020)
2010 – 2019
- 2019
- [j5]Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen:
DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks. Bioinform. 35(18): 3329-3338 (2019) - [c4]Yue Cao, Tianlong Chen, Zhangyang Wang, Yang Shen:
Learning to Optimize in Swarms. NeurIPS 2019: 15018-15028 - [i5]Yue Cao, Yang Shen:
Bayesian active learning for optimization and uncertainty quantification in protein docking. CoRR abs/1902.00067 (2019) - [i4]Yue Cao, Tianlong Chen, Zhangyang Wang, Yang Shen:
Learning to Optimize in Swarms. CoRR abs/1911.03787 (2019) - [i3]Yue Cao, Yang Shen:
Energy-based Graph Convolutional Networks for Scoring Protein Docking Models. CoRR abs/1912.12476 (2019) - [i2]Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen:
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. CoRR abs/1912.12553 (2019) - 2018
- [j4]Mostafa Karimi, Yang Shen:
iCFN: an efficient exact algorithm for multistate protein design. Bioinform. 34(17): i811-i820 (2018) - [i1]Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen:
DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks. CoRR abs/1806.07537 (2018) - 2017
- [j3]Thomas S. Huang, Jiayu Zhou, Zhangyang Wang, Qing Ling, Yang Shen:
Biomedical informatics with optimization and machine learning. EURASIP J. Bioinform. Syst. Biol. 2017: 4 (2017)
2000 – 2009
- 2008
- [j2]Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda:
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. PLoS Comput. Biol. 4(10) (2008) - 2007
- [j1]Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda:
SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Trans. Autom. Control. 52(4): 664-676 (2007) - [c3]Yang Shen, Pirooz Vakili, Sandor Vajda, Ioannis Ch. Paschalidis:
Optimizing noisy funnel-like functions on the euclidean group with applications to protein docking. CDC 2007: 4545-4550 - 2006
- [c2]Ioannis Ch. Paschalidis, Yang Shen, Pirooz Vakili, Sandor Vajda:
Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. EMBC 2006: 5330-5333 - 2005
- [c1]Ioannis Ch. Paschalidis, Yang Shen, Sandor Vajda, Pirooz Vakili:
A Semi-Definite programming-based Underestimation method for global optimization in molecular docking. CDC/ECC 2005: 3675-3680
Coauthor Index
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