GCN-HGT

Prediction of horizontal gene transfer (HGT) using graph convolutional network

This pipeline performs data splitting (train/validation/test) of computed HGT data, and trains a graph convolutional network model to predict HGT events.

• Zhou, Hao, Juan Felipe Beltrán, and Ilana Lauren Brito. "Functions predict horizontal gene transfer and the emergence of antibiotic resistance." Science Advances 7.43 (2021): eabj5056.

Acknowledgement

• Kipf, Thomas N., and Max Welling. "Variational graph auto-encoders." arXiv preprint arXiv:1611.07308 (2016).
• Leskovec, Jure, and Rok Sosič. "Snap: A general-purpose network analysis and graph-mining library." ACM Transactions on Intelligent Systems and Technology (TIST) 8.1 (2016): 1-20.

Requirement

• TensorFlow (1.13.1)
• python 3.5.5
• networkx
• scikit-learn
• scipy
• pandas
• numpy
• tqdm