Shen Lab at Texas A&M University

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

DeepAffinity. Protein-compound affinity prediction through unified RNN-CNN

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

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

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

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

gcWGAN. Guided Conditional Wasserstein GAN for De Novo Protein Design

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

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

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

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

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

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

EGCN. Energy-based Graph Convolutional Networks for Scoring Protein Docking Models

JointDiff. Jupyter Notebook

ncVarPred-1D3D. Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

EBD. Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation (Park and Shen, NeurIPS 2024)

Signals-and-Systems. Signals and Systems Honors Projects

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

cNMA. Encounter Complex-based Normal Mode Analysis for Proteins

Fold2Seq-icml2021. [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

Shen-Lab.github.io. HTML

MultimodalVEP. Protein variant effect prediction by multimodal representations

MultiModalMutation. Python

AbLM. Python

Rev_scripts_MutEffect.