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@XieResearchGroup Hunter College, The City University of New York

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    26 repositories

    • Physics-aware-Multiplex-GNN

      Public
      Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"
      machine-learningcomputational-biologycomputational-chemistrydockingrna-structure-predictionprotein-ligand-interactionsgeometric-deep-learninggraph-neural-networks
      Python
      •11•53•0•0•Updated Oct 31, 2024Oct 31, 2024

    • MMAPLE

      Public
      Python
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • CODE-AE

      Public
      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
      Jupyter Notebook
      •
      Other
      •8•16•0•0•Updated Oct 1, 2024Oct 1, 2024

    • eMOSAIC

      Public
      Python
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • PrePROTAC

      Public
      PrePROTAC project
      Python
      •0•2•0•0•Updated Jul 24, 2023Jul 24, 2023

    • MultiDCP

      Public
      Python
      •
      Other
      •2•2•1•0•Updated Apr 24, 2023Apr 24, 2023

    • TransPro

      Public
      Python
      •1•1•0•0•Updated Mar 13, 2023Mar 13, 2023

    • PortalLearning

      Public
      Python
      •
      Other
      •0•4•0•0•Updated Feb 20, 2023Feb 20, 2023

    • DISAE

      Public
      MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization
      orphan-proteins
      Python
      •
      Other
      •4•11•10•0•Updated Oct 16, 2022Oct 16, 2022

    • PLANS

      Public
      Self Training Drug Side Effects Detector
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Apr 25, 2022Apr 25, 2022

    • drug_combine

      Public
      Roff
      •
      Other
      •0•1•1•0•Updated Apr 25, 2022Apr 25, 2022

    • pathway_repurposing

      Public
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated Apr 25, 2022Apr 25, 2022

    • DeepREAL

      Public
      DeepREAL: A Deep Learning Powered Multi-scale Modeling Framework Towards Predicting Out-of-distribution Receptor Activity of Ligand Binding
      Python
      •
      Other
      •1•10•2•0•Updated Apr 23, 2022Apr 23, 2022

    • L1000-repurposing

      Public
      Drug repurposing with L1000 data
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Feb 14, 2022Feb 14, 2022

    • L1000-bayesian

      Public
      L1000 peak deconvolution based on Bayesian analysis
      Mathematica
      •
      Apache License 2.0
      •7•0•0•0•Updated Oct 10, 2021Oct 10, 2021

    • AttnToCrispr

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 25, 2021Aug 25, 2021

    • MXMNet

      Public
      Source code for our paper "Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures"
      Python
      •
      MIT License
      •16•0•0•0•Updated Jun 14, 2021Jun 14, 2021

    • MolGNN_fewshot

      Public
      Python
      •
      MIT License
      •3•5•0•0•Updated Jun 11, 2021Jun 11, 2021

    • CPA

      Public
      Source code for our paper "Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation" (IJCAI 2020)
      Python
      •
      MIT License
      •5•0•0•0•Updated Jun 5, 2021Jun 5, 2021

    • WINTF

      Public
      weighted, imputed, neighbor-regularized matrix tri-factorization algorithm
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Jun 5, 2021Jun 5, 2021

    • JDINAC

      Public
      Joint density-based Differential Interaction Network Analysis and Classification
      R
      •
      MIT License
      •6•1•0•0•Updated Jun 5, 2021Jun 5, 2021

    • CLEIT

      Public
      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 …
      Python
      •
      MIT License
      •1•2•0•0•Updated Jun 5, 2021Jun 5, 2021

    • Lab-wiki-Gitbook

      Public
      3•1•0•0•Updated Nov 9, 2020Nov 9, 2020

    • Lab-wiki

      Public archive
      Wiki of Xie's Lab
      Python
      •1•0•1•0•Updated May 19, 2020May 19, 2020

    • Interesting-DL-Materials

      Public
      List of Interesting Deep Learning Materials
      1•0•0•0•Updated Feb 3, 2019Feb 3, 2019

    • seqCrispr

      Public
      Python
      •5•1•1•0•Updated Jan 11, 2019Jan 11, 2019