{"title":"MMCL-CDR: Enhancing Cancer Drug Response Prediction with Multi-Omics and Morphology Images Contrastive Representation Learning","authors":"Yang Li, Zihou Guo, Xin Gao, Guohua Wang","doi":"10.1093/bioinformatics/btad734","DOIUrl":null,"url":null,"abstract":"Motivation Cancer is a complex disease that results in a significant number of global fatalities. Treatment strategies can vary among patients, even if they have the same type of cancer. The application of precision medicine in cancer shows promise for treating different types of cancer, reducing healthcare expenses, and improving recovery rates. To achieve personalized cancer treatment, machine learning models have been developed to predict drug responses based on tumor and drug characteristics. However, current studies either focus on constructing homogeneous networks from single data source or heterogeneous networks from multi-omics data. While multi-omics data have shown potential in predicting drug responses in cancer cell lines, there is still a lack of research that effectively utilizes insights from different modalities. Furthermore, effectively utilizing the multi-modal knowledge of cancer cell lines poses a challenge due to the heterogeneity inherent in these modalities. Results To address these challenges, we introduce MMCL-CDR, a multi-modal approach for cancer drug response prediction that integrates copy number variation, gene expression, morphology images of cell lines and chemical structure of drugs. The objective of MMCL-CDR is to align cancer cell lines across different data modalities by learning cell line representations from omic and image data, and combined with structural drug representations to enhance the prediction of Cancer Drug Responses (CDR). We have carried out comprehensive experiments and show that our model significantly outperforms other state-of-the-art methods in CDR prediction. The experimental results also prove that the model can learn more accurate cell line representation by integrating multi-omics and morphological data from cell lines, thereby improving the accuracy of CDR prediction. In addition, the ablation study and qualitative analysis also confirm the effectiveness of each part of our proposed model. Last but not least, MMCL-CDR opens up a new dimension for cancer drug response prediction through multimodal contrastive learning, pioneering a novel approach that integrates multi-omics and multi-modal drug and cell line modeling. Availability and Implementation MMCL-CDR is available at https://github.com/catly/MMCL-CDR","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":null,"pages":null},"PeriodicalIF":4.4000,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btad734","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
Motivation Cancer is a complex disease that results in a significant number of global fatalities. Treatment strategies can vary among patients, even if they have the same type of cancer. The application of precision medicine in cancer shows promise for treating different types of cancer, reducing healthcare expenses, and improving recovery rates. To achieve personalized cancer treatment, machine learning models have been developed to predict drug responses based on tumor and drug characteristics. However, current studies either focus on constructing homogeneous networks from single data source or heterogeneous networks from multi-omics data. While multi-omics data have shown potential in predicting drug responses in cancer cell lines, there is still a lack of research that effectively utilizes insights from different modalities. Furthermore, effectively utilizing the multi-modal knowledge of cancer cell lines poses a challenge due to the heterogeneity inherent in these modalities. Results To address these challenges, we introduce MMCL-CDR, a multi-modal approach for cancer drug response prediction that integrates copy number variation, gene expression, morphology images of cell lines and chemical structure of drugs. The objective of MMCL-CDR is to align cancer cell lines across different data modalities by learning cell line representations from omic and image data, and combined with structural drug representations to enhance the prediction of Cancer Drug Responses (CDR). We have carried out comprehensive experiments and show that our model significantly outperforms other state-of-the-art methods in CDR prediction. The experimental results also prove that the model can learn more accurate cell line representation by integrating multi-omics and morphological data from cell lines, thereby improving the accuracy of CDR prediction. In addition, the ablation study and qualitative analysis also confirm the effectiveness of each part of our proposed model. Last but not least, MMCL-CDR opens up a new dimension for cancer drug response prediction through multimodal contrastive learning, pioneering a novel approach that integrates multi-omics and multi-modal drug and cell line modeling. Availability and Implementation MMCL-CDR is available at https://github.com/catly/MMCL-CDR
期刊介绍:
The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.