Pinned Repositories
CLEIT
Cross-LEvel Information Transmission network (CLEIT) aims to represent the asymmetrical multi-level organization of the biological system by integrating multiple incoherent omics data. It first learns the latent representation of the high-level domain then uses it as ground-truth embedding to improve the representation learning of the low-level domain in the form of contrastive loss.
CODE-AE
Coherent Deconfounding Autoencoder (CODE-AE) can extract both common biological signals shared by incoherent samples and private representations unique to each data set, transfer knowledge learned from cell line data to tissue data, and separate confounding factors from them
DeepREAL
DeepREAL: A Deep Learning Powered Multi-scale Modeling Framework Towards Predicting Out-of-distribution Receptor Activity of Ligand Binding
DISAE
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization
drug_combine
MolGNN_fewshot
MultiDCP
Physics-aware-Multiplex-GNN
Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"
PortalLearning
PrePROTAC
PrePROTAC project
XieResearchGroup's Repositories
XieResearchGroup/Physics-aware-Multiplex-GNN
Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"
XieResearchGroup/CODE-AE
Coherent Deconfounding Autoencoder (CODE-AE) can extract both common biological signals shared by incoherent samples and private representations unique to each data set, transfer knowledge learned from cell line data to tissue data, and separate confounding factors from them
XieResearchGroup/DISAE
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization
XieResearchGroup/DeepREAL
DeepREAL: A Deep Learning Powered Multi-scale Modeling Framework Towards Predicting Out-of-distribution Receptor Activity of Ligand Binding
XieResearchGroup/MolGNN_fewshot
XieResearchGroup/PortalLearning
XieResearchGroup/CLEIT
Cross-LEvel Information Transmission network (CLEIT) aims to represent the asymmetrical multi-level organization of the biological system by integrating multiple incoherent omics data. It first learns the latent representation of the high-level domain then uses it as ground-truth embedding to improve the representation learning of the low-level domain in the form of contrastive loss.
XieResearchGroup/MultiDCP
XieResearchGroup/PrePROTAC
PrePROTAC project
XieResearchGroup/drug_combine
XieResearchGroup/JDINAC
Joint density-based Differential Interaction Network Analysis and Classification
XieResearchGroup/Lab-wiki-Gitbook
XieResearchGroup/seqCrispr
XieResearchGroup/TransPro
XieResearchGroup/PLANS
Self Training Drug Side Effects Detector
XieResearchGroup/WINTF
weighted, imputed, neighbor-regularized matrix tri-factorization algorithm
XieResearchGroup/AttnToCrispr
XieResearchGroup/CPA
Source code for our paper "Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation" (IJCAI 2020)
XieResearchGroup/Interesting-DL-Materials
List of Interesting Deep Learning Materials
XieResearchGroup/L1000-bayesian
L1000 peak deconvolution based on Bayesian analysis
XieResearchGroup/L1000-repurposing
Drug repurposing with L1000 data
XieResearchGroup/Lab-wiki
Wiki of Xie's Lab
XieResearchGroup/MMAPLE
XieResearchGroup/MXMNet
Source code for our paper "Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures"
XieResearchGroup/pathway_repurposing