Repositories list

• ECLARE

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

• scGraphETM

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

• SpaTM

  Public
  Topic Models for Spatially Informed Transcriptomic Analyses

  C++

  •

  MIT License

  •0•0•1•0•Updated Feb 1, 2025Feb 1, 2025

• penprs

  Public
  Penalized Regression for Inference of Polygenic Risk Scores

  Python

  •

  MIT License

  •1•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• TimelyGPT

  Public
  Public code for ACM-BCB 2024 paper TimelyGPT

  Python

  •0•1•0•0•Updated Nov 11, 2024Nov 11, 2024

• BiTimelyGPT

  Public
  Code for the paper "Bidirectional Generative Pre-training for Improving Healthcare Time-series Representation Learning"

  Python

  •1•8•0•0•Updated Aug 12, 2024Aug 12, 2024

• MixEHR-Nest

  Public
  Python

  •0•0•0•0•Updated Jul 16, 2024Jul 16, 2024

• MixEHR_Seed_Tutorial

  Public
  This tutorial is provided for the UK Biobank Data Training Workshop, Tokyo, Japan

  Jupyter Notebook

  •1•3•0•0•Updated Apr 29, 2024Apr 29, 2024

• MixEHR-SurG

  Public
  Code for MixEHR-SurG: a joint proportional hazard and guided topic model for inferring mortality-associated topics from electronic health records

  Python

  •0•0•0•0•Updated Dec 9, 2023Dec 9, 2023

• TSFpaper

  Public
  This repository contains a reading list of papers on Time Series Forecasting/Prediction (TSF) and Spatio-Temporal Forecasting/Prediction (STF). These papers are mainly categorized according to the type of model.

  203•0•0•0•Updated Nov 22, 2023Nov 22, 2023

• hART-heart-failure-Attentive-Risk-Trajectory

  Public
  Jupyter Notebook

  •2•1•0•0•Updated Sep 1, 2023Sep 1, 2023

• gtm-decon

  Public
  Python

  •

  GNU General Public License v3.0

  •4•7•3•1•Updated Aug 2, 2023Aug 2, 2023

• iGEM

  Public
  Python

  •0•0•0•0•Updated Apr 27, 2023Apr 27, 2023

• getm

  Public
  Jupyter Notebook

  •0•3•0•0•Updated Mar 29, 2023Mar 29, 2023

• GAT-ETM

  Public
  "Modeling electronic health record data using an end-to-end knowledge-graph-informed topic model" paper on Sci Rep (2022)

  topic-modelingehrneural-topic-models+ 2graph-attention-networksbiomedical-knowledge-graph

  Python

  •0•9•2•0•Updated Mar 16, 2023Mar 16, 2023

• MixEHR-Seed

  Public
  Public code for KDD 2022 paper Automatic Phenotyping by a Seed-guided Topic Model

  Python

  •1•3•0•0•Updated Jul 7, 2022Jul 7, 2022

• MixEHR-Guided

  Public
  C++

  •0•1•0•0•Updated Jun 17, 2022Jun 17, 2022

• covid-npi

  Public
  Python

  •0•0•0•0•Updated Mar 24, 2022Mar 24, 2022

• scETM-1

  Public
  A generative topic model that facilitates integrative analysis of large-scale single-cell RNA sequencing data.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •8•0•0•0•Updated Jan 17, 2022Jan 17, 2022

• mixehrS

  Public
  Python

  •0•3•0•0•Updated Sep 1, 2021Sep 1, 2021

• heterogeneous_ehr

  Public
  Jupyter Notebook

  •

  MIT License

  •0•6•0•0•Updated Dec 1, 2020Dec 1, 2020

• recurrent-disease-progression-networks

  Public
  Python

  •0•1•0•0•Updated Nov 30, 2020Nov 30, 2020

• covid19_media

  Public
  Python

  •2•6•3•0•Updated Oct 21, 2020Oct 21, 2020

• mixehr

  Public
  C++

  •2•16•2•0•Updated Aug 28, 2020Aug 28, 2020

• singlecell-deepfeature

  Public
  Single Cell Generative Adversarial Network (scGAN)

  Jupyter Notebook

  •5•13•3•0•Updated May 29, 2020May 29, 2020

• BEHRT

  Public
  Code for BEHRT: Transformer for Electronic Health Records

  Jupyter Notebook

  •32•0•0•0•Updated May 11, 2020May 11, 2020

• examples

  Public
  A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •9.6k•0•0•0•Updated May 3, 2020May 3, 2020

• GSR

  Public
  Python

  •0•0•0•0•Updated Mar 17, 2020Mar 17, 2020

• vGraph

  Public
  Code for NeurIPS paper "vGraph: A Generative Model for Joint CommunityDetection and Node Representation Learning"

  Python

  •17•0•0•0•Updated Dec 20, 2019Dec 20, 2019