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ablm

bal

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

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

cnma

Encounter Complex-based Normal Mode Analysis for Proteins

covid-ab-lowdataregime

cpac

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

deepaffinity

Protein-compound affinity prediction through unified RNN-CNN

drug-combo-generator

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

egcn

Energy-based Graph Convolutional Networks for Scoring Protein Docking Models

encode-impute

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

gcc

gcwgan

Guided Conditional Wasserstein GAN for De Novo Protein Design

gda-specreg

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

graphcl

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

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

hypergcl

[NeurIPS 2022] "Augmentations in Hypergraph Contrastive Learning: Fabricated and Generative" by Tianxin Wei, Yuning You, Tianlong Chen, Yang Shen, Jingrui He, Zhangyang Wang

ldm-3dg

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

lois

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

ncvarpred-1d3d

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

rev_scripts_muteffect

shen-lab.github.io

signals-and-systems

Signals and Systems Honors Projects

ss-gcns

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

structure-informed_plm

Protein language modeling with information from structures

tale

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

wsr-predictpofpathogenicity

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