mgokhanbakal / nmf-repodb-benchmarking

Benchmarking Files Used in NMF Experiments with repoDB Dataset

This repository contains the validation and test set splits of repoDB drug–disease pairs used in the study of "Non-Negative Matrix Factorization for Drug Repositioning: Experiments with the repoDB Dataset" published at AMIA 2019 Annual Symposium.

For the test set, there are two files under the benchmark/test/ directory:

• Approved_treatments_test.txt - Each line represents an approved treatment CUI pair from repoDB in the format of (<subject_CUI> <object_CUI>).

• Failed_indications_test.txt - Each line similarly indicates a failed indication CUI pair from repoDB in the format of (<subject_CUI> <object_CUI>).

For the validation set, there are two files under the benchmark/validation/ directory:

• Approved_treatments_validation.txt - Each line implies an approved treatment CUI pair from repoDB in the format of (<subject_CUI> <object_CUI>).

• Failed_indications_validation.txt - Each line similarly shows a failed indication CUI pair from repoDB in the format of (<subject_CUI> <object_CUI>).