DNN-PNN: A parallel deep neural network model to improve anticancer drug sensitivity

• Published in: Methods (San Diego, Calif.) Calif.), 2023-01, Vol.209, p.1-9
• Main Authors: Chen, Siqi, Yang, Yang, Zhou, Haoran, Sun, Qisong, Su, Ran
• Format: Article
• Language: English
• Subjects: Antineoplastic Agents - pharmacology; Antineoplastic Agents - therapeutic use; Deep learning; Drug sensitivity; Machine Learning; Neural Networks, Computer; Prediction
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1016/j.ymeth.2022.11.002

•A parallel deep neural network model is proposed to makes full use of the heterogeneous information.•It solves two challenges when using high-dimensional sparse binary feature representation for deep learning.•It provides a novel and more effective data representation strategy of pharmaceutical chemical structure. With the rapid development of deep learning techniques and large-scale genomics database, it is of great potential to apply deep learning to the prediction task of anticancer drug sensitivity, which can effectively improve the identification efficiency and accuracy of therapeutic biomarkers. In this study, we propose a parallel deep learning framework DNN-PNN, which integrates rich and heterogeneous information from gene expression and pharmaceutical chemical structure data. With the proposal of DNN-PNN, a new and more effective drug data representation strategy is introduced, that is, the correlation between features is represented by product, which alleviates the limitations of high-dimensional discrete data in deep learning. Furthermore, the framework is optimized to reduce the time complexity of the model. We conducted extensive experiments on the CCLE datasets to compare DNN-PNN with its variant DNN-FM representing the traditional feature correlation model, the component DNN or PNN alone, and the common machine learning models. It is found that DNN-PNN not only has high prediction accuracy, but also has significant advantages in stability and convergence speed.