Simple Matrix Factorization Collaborative Filtering for Drug Repositioning on Cell Lines

Iván Carrera, Iván Carrera, Eduardo Tejera, Inês Dutra

2021

Abstract

The discovery of new biological interactions, such as interactions between drugs and cell lines, can improve the way drugs are developed. Recently, there has been important interest for predicting interactions between drugs and targets using recommender systems; and more specifically, using recommender systems to predict drug activity on cellular lines. In this work, we present a simple and straightforward approach for the discovery of interactions between drugs and cellular lines using collaborative filtering. We represent cellular lines by their drug affinity profile, and correspondingly, represent drugs by their cell line affinity profile in a single interaction matrix. Using simple matrix factorization, we predicted previously unknown values, minimizing the regularized squared error. We build a comprehensive dataset with information from the ChEMBL database. Our dataset comprises 300,000+ molecules, 1,200+ cellular lines, and 3,000,000+ reported activities. We have been able to successfully predict drug activity, and evaluate the performance of our model via utility, achieving an Area Under ROC Curve (AUROC) of near 0.9.

Paper Citation

in Harvard Style

Carrera I., Tejera E. and Dutra I. (2021). Simple Matrix Factorization Collaborative Filtering for Drug Repositioning on Cell Lines. In Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - Volume 5: HEALTHINF; ISBN 978-989-758-490-9, SciTePress, pages 768-775. DOI: 10.5220/0010394007680775

in Bibtex Style

@conference{healthinf21,
author={Iván Carrera and Eduardo Tejera and Inês Dutra},
title={Simple Matrix Factorization Collaborative Filtering for Drug Repositioning on Cell Lines},
booktitle={Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - Volume 5: HEALTHINF},
year={2021},
pages={768-775},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0010394007680775},
isbn={978-989-758-490-9},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - Volume 5: HEALTHINF
TI - Simple Matrix Factorization Collaborative Filtering for Drug Repositioning on Cell Lines
SN - 978-989-758-490-9
AU - Carrera I.
AU - Tejera E.
AU - Dutra I.
PY - 2021
SP - 768
EP - 775
DO - 10.5220/0010394007680775
PB - SciTePress