Document Type
Article
Publication Date
2023
DOI
10.1093/bioinformatics/btad514
Publication Title
Bioinformatics
Volume
39
Issue
9
Pages
btad514 (1-9)
Abstract
Motivation: Cancer heterogeneity drastically affects cancer therapeutic outcomes. Predicting drug response in vitro is expected to help formulate personalized therapy regimens. In recent years, several computational models based on machine learning and deep learning have been proposed to predict drug response in vitro. However, most of these methods capture drug features based on a single drug description (e.g. drug structure), without considering the relationships between drugs and biological entities (e.g. target, diseases, and side effects). Moreover, most of these methods collect features separately for drugs and cell lines but fail to consider the pairwise interactions between drugs and cell lines.
Results: In this paper, we propose a deep learning framework, named MSDRP for drug response prediction. MSDRP uses an interaction module to capture interactions between drugs and cell lines, and integrates multiple associations/interactions between drugs and biological entities through similarity network fusion algorithms, outperforming some state-of-the-art models in all performance measures for all experiments. The experimental results of de novo test and independent test demonstrate the excellent performance of our model for new drugs. Furthermore, several case studies illustrate the rationality for using feature vectors derived from drug similarity matrices from multisource data to represent drugs and the interpretability of our model.
Rights
© The Authors 2023
This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Data Availability
Article states: The codes of MSDRP are available at: https://github.com/xyzhang-10/MSDRP.
Original Publication Citation
Zhao, H., Zhang, X., Zhao, Q., Li, Y., & Wang, J. (2023). MSDRP: A deep learning model based on multi-source data for predicting drug response. Bioinformatics, 39(9), 1-9, Article btad514. https://doi.org/10.1093/bioinformatics/btad514
Repository Citation
Zhao, H., Zhang, X., Zhao, Q., Li, Y., & Wang, J. (2023). MSDRP: A deep learning model based on multi-source data for predicting drug response. Bioinformatics, 39(9), 1-9, Article btad514. https://doi.org/10.1093/bioinformatics/btad514
Supplementary Data
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