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. 2023 Sep 2;39(9):btad514.
doi: 10.1093/bioinformatics/btad514.

MSDRP: a deep learning model based on multisource data for predicting drug response

Haochen Zhao  1   2 , Xiaoyu Zhang  1   2 , Qichang Zhao  1   2 , Yaohang Li  3 , Jianxin Wang  1   2
Affiliations

MSDRP: a deep learning model based on multisource data for predicting drug response

Haochen Zhao et al. Bioinformatics. .

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.

Availability and implementation: The codes of MSDRP are available at https://github.com/xyzhang-10/MSDRP.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1.
Figure 1.
The architecture of MSDRP
Figure 2.
Figure 2.
Association of the 10 drugs with the pathways. For visualization, the top 40 pathways with the highest cross-drug correlations are selected. Negative and positive correlations between pathway activity and drug sensitivity scores are denoted as “sensitive” and “resistant” associations, respectively
Figure 3.
Figure 3.
Heatmap of drug response of 170 drugs on 10 samples
See this image and copyright information in PMC

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