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Graph Feature Autoencoder

A repo for implementation of Graph features autoencoder for prediction of expression values paper.

Requirement

Please install the requirement.txt file before use.

  • torch==1.4.0
  • torch-cluster==1.5.4
  • torch-geometric==1.5.0
  • torch-scatter==2.0.4
  • torch-sparse==0.6.0
  • scikit-learn==0.21.3
  • numpy==1.16.4
  • networkx==2.3
  • magic-impute==2.0.3

You can also download the required libraries using:

pip install -r requirements.txt

Dataset

Dataset is available for both Ecoli and Mouse in:

https://drive.google.com/drive/folders/1wQCwjwkkfmzydWW3DPgvj-JEOv05_shj?usp=sharing

Download the datasets and put them in a proper location.

Experiments

You can run the experiments using the run.py file.

Different options for different experiments are available in the options.py.

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A repo for implementation of Graph features autoencoder for expression values prediction and imputation

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