Shen-Lab
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TALE Public
Transformer-based protein function Annotation with joint feature-Label Embedding
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EBD Public
Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation (Park and Shen, NeurIPS 2024)
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GraphCL_Automated Public
[ICML 2021] "Graph Contrastive Learning Automated" by Yuning You, Tianlong Chen, Yang Shen, Zhangyang Wang; [WSDM 2022] "Bringing Your Own View: Graph Contrastive Learning without Prefabricated Dat…
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DeepAffinity Public
Protein-compound affinity prediction through unified RNN-CNN
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GraphCL Public
[NeurIPS 2020] "Graph Contrastive Learning with Augmentations" by Yuning You, Tianlong Chen, Yongduo Sui, Ting Chen, Zhangyang Wang, Yang Shen
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LDM-3DG Public
[ICLR 2024] "Latent 3D Graph Diffusion" by Yuning You, Ruida Zhou, Jiwoong Park, Haotian Xu, Chao Tian, Zhangyang Wang, Yang Shen
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CPAC Public
[Bioinformatics 2022] Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction
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Structure-informed_PLM Public
Forked from Stephen2526/Structure-informed_PLMProtein language modeling with information from structures
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ncVarPred-1D3D Public
Multimodal learning of noncoding variant effects using genome sequence and chromatin structure
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Drug-Combo-Generator Public
Deep Generative Models for Drug Combination (Graph Set) Generation given Hierarchical Disease Network Embedding
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GDA-SpecReg Public
[ICLR 2023] "Graph Domain Adaptation via Theory-Grounded Spectral Regularization" by Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen
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HyperGCL Public
Forked from weitianxin/HyperGCL[NeurIPS 2022] "Augmentations in Hypergraph Contrastive Learning: Fabricated and Generative" by Tianxin Wei, Yuning You, Tianlong Chen, Yang Shen, Jingrui He, Zhangyang Wang
Python UpdatedOct 23, 2022 -
Bayesian-L2O Public
[ICLR 2022] "Bayesian Modeling and Uncertainty Quantification for Learning to Optimize: What, Why, and How" by Yuning You, Yue Cao, Tianlong Chen, Zhangyang Wang, Yang Shen
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Fold2Seq-icml2021 Public
Forked from IBM/fold2seq[ICML 2021] "Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design" by Yue Cao, Payel Das, Vijil Chenthamarakshan, Pin-Yu Chen, Igor Melnyk, Yang Shen
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Signals-and-Systems Public
Signals and Systems Honors Projects
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EGCN Public
Energy-based Graph Convolutional Networks for Scoring Protein Docking Models
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LOIS Public
[NeurIPS 2019] LOIS: Learning to Optimize In Swarms, guided by posterior estimation
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SS-GCNs Public
[ICML 2020] "When Does Self-Supervision Help Graph Convolutional Networks?" by Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen
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BAL Public
Bayesian Active Learning for Optimization and Uncertainty Quantification with Applications to Protein Docking
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gcWGAN Public
Guided Conditional Wasserstein GAN for De Novo Protein Design
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WSR-PredictPofPathogenicity Public
A weakly supervised regression approach to directly predict the probability of pathogenicity based on categorized pathogenicity classes
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cNMA Public
Encounter Complex-based Normal Mode Analysis for Proteins