DeepGOA

A deep learning framework for gene ontology annotation with sequence- and network-based information.

Requirements

torch (0.4.0)

pandas (0.23.1)

numpy (1.15.0)

fire (0.1.3)

torchvision (0.2.1)

pickle

Usage

• download dataset and our trained model

  You first need to download the source code and dataset. Then you should extract the dataset to the DeepGOA directory. If you want to run our saved model, you should download saved_model and save to the DeepGOA directory.

• train model

  You can run the DeepGOA.py file to train DeepGOA and the model will be saved in checkpoints path. Before you run the Predict_DeepGOA.py file, you should move the model to the saved_model path or change the load path. If you want to tune some hyper-parameters, you can change some values of hyper-parameters in config.py in utils folder.

  The other details can see the paper and the codes.

Citation

License

This project is licensed under the MIT License - see the LICENSE.txt file for details