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DeepPheno: Predicting single gene loss of function phenotypes

DeepPheno is a method for predicting gene-phenotype (HPO classes) associations from gene functional annotations (GO classes) and gene expression values.

This repository contains script which were used to build and train the DeepPheno model together with the scripts for evaluating the model's performance.

Dependencies

Installation

Data

Running the prediction model

deeppheno --data-root <path to data folder> --in-file <input-file>

Scripts

The scripts require GeneOntology and Human Phenotype Ontology in OBO Format.

Training

Citation

If you use DeepPheno for your research, or incorporate our learning algorithms in your work, please cite:

Maxat Kulmanov and Robert Hoehndorf. DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PLoS Computational Biology, 2020. https://doi.org/10.1371/journal.pcbi.1008453