Shen-Lab/CPAC

[Bioinformatics 2022] Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction

Language: Python - Size: 134 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 12 - Forks: 1

Shen-Lab/Shen-Lab.github.io

Language: HTML - Size: 15.1 MB - Last synced: 21 days ago - Pushed: 22 days ago - Stars: 2 - Forks: 2

Shen-Lab/LDM-3DG

[ICLR 2024] "Latent 3D Graph Diffusion" by Yuning You, Ruida Zhou, Jiwoong Park, Haotian Xu, Chao Tian, Zhangyang Wang, Yang Shen

Language: Python - Size: 21.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 18 - Forks: 4

Shen-Lab/Rev_scripts_MutEffect

Size: 625 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

Shen-Lab/gcc Fork of gcc-mirror/gcc

Size: 2.81 GB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

Shen-Lab/Fold2Seq-icml2021 Fork of 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

Language: Python - Size: 4.85 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 5 - Forks: 1

Shen-Lab/ENCODE-impute

Language: Python - Size: 39.1 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

Shen-Lab/COVID-Ab-LowDataRegime

Language: Jupyter Notebook - Size: 5.28 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

Shen-Lab/Bayesian-L2O

[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

Language: Python - Size: 3.54 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 10 - Forks: 1

Shen-Lab/BAL

Bayesian Active Learning for Optimization and Uncertainty Quantification with Applications to Protein Docking

Language: C++ - Size: 35.1 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 13 - Forks: 4

Shen-Lab/GraphCL_Automated

[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 Data Augmentations" by Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen

Language: Python - Size: 423 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 106 - Forks: 8

Shen-Lab/GraphCL

[NeurIPS 2020] "Graph Contrastive Learning with Augmentations" by Yuning You, Tianlong Chen, Yongduo Sui, Ting Chen, Zhangyang Wang, Yang Shen

Language: Python - Size: 244 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 525 - Forks: 98

Shen-Lab/Drug-Combo-Generator

Deep Generative Models for Drug Combination (Graph Set) Generation given Hierarchical Disease Network Embedding

Language: Python - Size: 60.1 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 29 - Forks: 14

Shen-Lab/DeepAffinity

Protein-compound affinity prediction through unified RNN-CNN

Language: Python - Size: 307 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 133 - Forks: 30

Shen-Lab/TALE

Transformer-based protein function Annotation with joint feature-Label Embedding

Language: Python - Size: 572 MB - Last synced: about 1 month ago - Pushed: 12 months ago - Stars: 30 - Forks: 9

Shen-Lab/GDA-SpecReg

[ICLR 2023] "Graph Domain Adaptation via Theory-Grounded Spectral Regularization" by Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen

Language: Python - Size: 174 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 21 - Forks: 0

Shen-Lab/SS-GCNs

[ICML 2020] "When Does Self-Supervision Help Graph Convolutional Networks?" by Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen

Language: Python - Size: 12.2 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 105 - Forks: 27

Shen-Lab/EGCN

Energy-based Graph Convolutional Networks for Scoring Protein Docking Models

Language: Python - Size: 34.8 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 11 - Forks: 0

Shen-Lab/LOIS

[NeurIPS 2019] LOIS: Learning to Optimize In Swarms, guided by posterior estimation

Language: C++ - Size: 10 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 16 - Forks: 10

Shen-Lab/WSR-PredictPofPathogenicity

A weakly supervised regression approach to directly predict the probability of pathogenicity based on categorized pathogenicity classes

Language: Python - Size: 856 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 4 - Forks: 5

Shen-Lab/ncVarPred-1D3D

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

Language: Python - Size: 353 KB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 4 - Forks: 1

Shen-Lab/Signals-and-Systems

Signals and Systems Honors Projects

Size: 13.7 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 4 - Forks: 0

Shen-Lab/HyperGCL Fork of 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

Size: 76.4 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

Shen-Lab/gcWGAN

Guided Conditional Wasserstein GAN for De Novo Protein Design

Language: Roff - Size: 334 MB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 36 - Forks: 7

Shen-Lab/cNMA

Encounter Complex-based Normal Mode Analysis for Proteins

Language: Python - Size: 117 MB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 4 - Forks: 3