Pre-training of Graph Augmented Transformers for Medication Recommendation

Related tags

Deep LearningG-Bert
Overview

G-Bert

Pre-training of Graph Augmented Transformers for Medication Recommendation

Intro

G-Bert combined the power of Graph Neural Networks and BERT (Bidirectional Encoder Representations from Transformers) for medical code representation and medication recommendation. We use the graph neural networks (GNNs) to represent the structure information of medical codes from a medical ontology. Then we integrate the GNN representation into a transformer-based visit encoder and pre-train it on single-visit EHR data. The pre-trained visit encoder and representation can be fine-tuned for downstream medical prediction tasks. Our model is the first to bring the language model pre-training schema into the healthcare domain and it achieved state-of-the-art performance on the medication recommendation task.

Requirements

  • pytorch>=0.4
  • python>=3.5
  • torch_geometric==1.0.3

Guide

We list the structure of this repo as follows:

.
├── [4.0K]  code/
│   ├── [ 13K]  bert_models.py % transformer models
│   ├── [5.9K]  build_tree.py % build ontology
│   ├── [4.3K]  config.py % hyperparameters for G-Bert
│   ├── [ 11K]  graph_models.py % GAT models
│   ├── [   0]  __init__.py
│   ├── [9.8K]  predictive_models.py % G-Bert models
│   ├── [ 721]  run_alternative.sh % script to train G-Bert
│   ├── [ 19K]  run_gbert.py % fine tune G-Bert
│   ├── [ 19K]  run_gbert_side.py
│   ├── [ 18K]  run_pretraining.py % pre-train G-Bert
│   ├── [4.4K]  run_tsne.py # output % save embedding for tsne visualization
│   └── [4.7K]  utils.py
├── [4.0K]  data/
│   ├── [4.9M]  data-multi-side.pkl 
│   ├── [3.6M]  data-multi-visit.pkl % patients data with multi-visit
│   ├── [4.3M]  data-single-visit.pkl % patients data with singe-visit
│   ├── [ 11K]  dx-vocab-multi.txt % diagnosis codes vocabulary in multi-visit data
│   ├── [ 11K]  dx-vocab.txt % diagnosis codes vocabulary in all data
│   ├── [ 29K]  EDA.ipynb % jupyter version to preprocess data
│   ├── [ 18K]  EDA.py % python version to preprocess data
│   ├── [6.2K]  eval-id.txt % validation data ids
│   ├── [6.9K]  px-vocab-multi.txt % procedure codes vocabulary in multi-visit data
│   ├── [ 725]  rx-vocab-multi.txt % medication codes vocabulary in multi-visit data
│   ├── [2.6K]  rx-vocab.txt % medication codes vocabulary in all data
│   ├── [6.2K]  test-id.txt % test data ids
│   └── [ 23K]  train-id.txt % train data ids
└── [4.0K]  saved/
    └── [4.0K]  GBert-predict/ % model files to reproduce our result
        ├── [ 371]  bert_config.json 
        └── [ 12M]  pytorch_model.bin

Preprocessing Data

We have released the preprocessing codes named data/EDA.ipynb to process data using raw files from MIMIC-III dataset. You can download data files from MIMIC and get necessary mapping files from GAMENet.

Quick Test

To validate the performance of G-Bert, you can run the following script since we have provided the trained model binary file and well-preprocessed data.

cd code/
python run_gbert.py --model_name GBert-predict --use_pretrain --pretrain_dir ../saved/GBert-predict --graph

Cite

Please cite our paper if you find this code helpful:

@article{shang2019pre,
  title={Pre-training of Graph Augmented Transformers for Medication Recommendation},
  author={Shang, Junyuan and Ma, Tengfei and Xiao, Cao and Sun, Jimeng},
  journal={arXiv preprint arXiv:1906.00346},
  year={2019}
}

Acknowledgement

Many thanks to the open source repositories and libraries to speed up our coding progress.

Owner
GitHub Repository
Jremesh-tools - Blender addon for quad remeshing

JRemesh Tools Blender 2.8 - 3.x addon for quad remeshing. Currently it is a wrap

Jayanam 89 Dec 30, 2022
Unofficial implementation of MLP-Mixer: An all-MLP Architecture for Vision

MLP-Mixer: An all-MLP Architecture for Vision This repo contains PyTorch implementation of MLP-Mixer: An all-MLP Architecture for Vision. Usage : impo

Rishikesh (ऋषिकेश) 175 Dec 23, 2022
This is an official implementation for "PlaneRecNet".

PlaneRecNet This is an official implementation for PlaneRecNet: A multi-task convolutional neural network provides instance segmentation for piece-wis

yaxu 50 Nov 17, 2022
A PyTorch-based Semi-Supervised Learning (SSL) Codebase for Pixel-wise (Pixel) Vision Tasks

PixelSSL is a PyTorch-based semi-supervised learning (SSL) codebase for pixel-wise (Pixel) vision tasks. The purpose of this project is to promote the

Zhanghan Ke 255 Dec 11, 2022
Code for ACM MM 2020 paper "NOH-NMS: Improving Pedestrian Detection by Nearby Objects Hallucination"

NOH-NMS: Improving Pedestrian Detection by Nearby Objects Hallucination The offical implementation for the "NOH-NMS: Improving Pedestrian Detection by

Tencent YouTu Research 64 Nov 11, 2022
These are the materials for the paper "Few-Shot Out-of-Domain Transfer Learning of Natural Language Explanations"

Few-shot-NLEs These are the materials for the paper "Few-Shot Out-of-Domain Transfer Learning of Natural Language Explanations". You can find the smal

Yordan Yordanov 0 Oct 21, 2022
MILK: Machine Learning Toolkit

MILK: MACHINE LEARNING TOOLKIT Machine Learning in Python Milk is a machine learning toolkit in Python. Its focus is on supervised classification with

Luis Pedro Coelho 610 Dec 14, 2022
Repository for the "Gotta Go Fast When Generating Data with Score-Based Models" paper

Gotta Go Fast When Generating Data with Score-Based Models This repo contains the official implementation for the paper Gotta Go Fast When Generating

Alexia Jolicoeur-Martineau 89 Nov 09, 2022
Isaac Gym Reinforcement Learning Environments

Isaac Gym Reinforcement Learning Environments

NVIDIA Omniverse 714 Jan 08, 2023
A collection of models for image<->text generation in ACM MM 2021.

Bi-directional Image and Text Generation UMT-BITG (image & text generator) Unifying Multimodal Transformer for Bi-directional Image and Text Generatio

Multimedia Research 63 Oct 30, 2022
An imperfect information game is a type of game with asymmetric information

DecisionHoldem An imperfect information game is a type of game with asymmetric information. Compared with perfect information game, imperfect informat

Decision AI 25 Dec 23, 2022
PyTorch for Semantic Segmentation

PyTorch for Semantic Segmentation This repository contains some models for semantic segmentation and the pipeline of training and testing models, impl

Zijun Deng 1.7k Jan 06, 2023
A library for hidden semi-Markov models with explicit durations

hsmmlearn hsmmlearn is a library for unsupervised learning of hidden semi-Markov models with explicit durations. It is a port of the hsmm package for

Joris Vankerschaver 69 Dec 20, 2022
OMAMO: orthology-based model organism selection

OMAMO: orthology-based model organism selection OMAMO is a tool that suggests the best model organism to study a biological process based on orthologo

Dessimoz Lab 5 Apr 22, 2022
🙄 Difficult algorithm, Simple code.

🎉TensorFlow2.0-Examples🎉! "Talk is cheap, show me the code." ----- Linus Torvalds Created by YunYang1994 This tutorial was designed for easily divin

1.7k Dec 25, 2022
NATS-Bench: Benchmarking NAS Algorithms for Architecture Topology and Size

NATS-Bench: Benchmarking NAS Algorithms for Architecture Topology and Size Xuanyi Dong, Lu Liu, Katarzyna Musial, Bogdan Gabrys in IEEE Transactions o

D-X-Y 137 Dec 20, 2022
Selective Wavelet Attention Learning for Single Image Deraining

SWAL Code for Paper "Selective Wavelet Attention Learning for Single Image Deraining" Prerequisites Python 3 PyTorch Models We provide the models trai

Bobo 9 Jun 17, 2022
Unified Instance and Knowledge Alignment Pretraining for Aspect-based Sentiment Analysis

Unified Instance and Knowledge Alignment Pretraining for Aspect-based Sentiment Analysis Requirements python 3.7 pytorch-gpu 1.7 numpy 1.19.4 pytorch_

12 Oct 29, 2022
Code for the paper "Adversarially Regularized Autoencoders (ICML 2018)" by Zhao, Kim, Zhang, Rush and LeCun

ARAE Code for the paper "Adversarially Regularized Autoencoders (ICML 2018)" by Zhao, Kim, Zhang, Rush and LeCun https://arxiv.org/abs/1706.04223 Disc

Junbo (Jake) Zhao 399 Jan 02, 2023
Deep Learning for Human Part Discovery in Images - Chainer implementation

Deep Learning for Human Part Discovery in Images - Chainer implementation NOTE: This is not official implementation. Original paper is Deep Learning f

Shintaro Shiba 63 Sep 25, 2022