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glit_pf's Introduction

GLIT: A Graph Neural Network for Drug-induced Liver Injury Prediction using Transcriptome Data

  • Overview & GNN achitecture of GLIT

figure1

Overall architecture of GLIT

figure2

Graph neural network architecture of GLIT

Required modules are:

python==3.6
torch==1.0.1
torch-scatter==1.1.2
torch-sparse==0.2.4
torch-cluster==1.2.4
torch-geometric==1.1.2
networkx==2.3
rdkit

  1. Download required data/models from https://drive.google.com/drive/folders/1_NLeSBIdQO2Gbh6n97is5tKfUi_zSsH5?usp=sharing

  2. run 'run_main4.sh' for gpu users, or run 'run_main4_cpu.sh' for cpu users

You can also download docker images to run models.

For cpu users:

# for cpu users
docker pull doxxitxxyoung/glit_cpu

docker run -i -t doxxitxxyoung/glit_cpu /bin/bash
cd GLIT
./run_main4_cpu.sh

# for gpu users
docker pull doxxitxxyoung/glit_gpu

docker run -i -t --runtime=nvidia doxxitxxyoung/glit_gpu /bin/bash
cd GLIT
./run_main4.sh

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