Precise prediction of multiple anticancer drug efficacy using multi target regression and support vector regression analysis. (September 2022)

• Record Type: Journal Article
• Authors: Brindha, G.R.; Rishiikeshwer, B.S.; Santhi, B.; Nakendraprasath, K.; Manikandan, R.; Gandomi, Amir H.
• Is Part Of: Computer methods and programs in biomedicine. Volume 224(2022)
• Publication Date: 2022-09
• Subjects: Oral squamous cell carcinoma -- Support vector regression -- Precision medicine -- Computational models -- Multi target drug efficacy prediction; Medicine -- Computer programs -- Periodicals; Biology -- Computer programs -- Periodicals; Computers -- Periodicals; Medicine -- Periodicals; Médecine -- Logiciels -- Périodiques; Biologie -- Logiciels -- Périodiques; Biology -- Computer programs; Medicine -- Computer programs; Periodicals; Electronic journals; 610.28
• DOI: 10.1016/j.cmpb.2022.107027
• Languages: English
• ISSNs: 0169-2607

Abstract

Highlights: The enhanced multi target regression and support vector regression was found to be the most effective and accurate method for the selection of anticancer drugs based on tumor features of the patients in a personalized manner. Increasing the training samples and statistical feature engineering improve the robustness of the model. EL_MTR is the best to predict multiple anticancer drug efficacies and improve the accuracy of ranking drugs, irrespective of sample size. ELM_SVR performs better than other MTR models with a large sample size and precise ranking process. Abstract: Background and objectives: The prediction of multiple drug efficacies using machine learning prediction techniques based on clinical and molecular attributes of tumors is a new approach in the field of precision medicine of oncology. The selection of suitable and effective therapeutic drugs among the potential drugs is performed computationally considering the tumor features. In this study, we developed and validated machine learning models to predict the efficacy of five anti-cancer drugs according to the clinical and molecular attributes of 30 oral squamous cell carcinoma (OSCC) cohorts. This sounds a bit odd – consider: Ranking of the drugs was achieved using their apoptotic priming. Methods: We developed multiple drug efficacy prediction models based on three types of tumor characteristics by applying machine learning methods, including multi-target regression (MTR) and support vector regression (SVR). The prediction accuracy of existing machine learning methods was enhanced by introducing novel pre-processing techniques to develop Enhanced MTR (E_MTR), Enhanced Log-based MTR (EL_MTR), Enhanced Multi-target SVR (EM_SVR), and Enhanced Log-based Multi-target SVR (ELM_SVR). As a unique capability, ELM_SVR and EL_MTR rank the drugs based on their predicted efficacy. All the drug efficacy prediction models were built using OSCC real samples and theoretical samples. The best model was selected was based on dataset size and evaluation metrics, such as error terms, residuals and parameter tuning, and cross-validated (CV) using 30 real samples and 340 theoretical samples. Results: When 30 real tumor samples were used for the train-test and CV methods, MTR models predicted the efficacy with less error than SVR models. Comparatively, using 340 theoretical samples for the train-test and CV methods, though MTR improved the performance, SVR predicted the efficacy with zero error. We found that, for small samples, the proposed MTR provided a 0.01 difference between actual apoptotic priming and predicted priming of five drugs. For large samples, the predicted values by the proposed SVR had a difference of 0.00001. The error terms (Actual vs. Predicted) also reveal that the enhanced log model is suitable when MTR is applied. Meanwhile, the enhanced model is suitable for SVR learning for multiple drug efficacy prediction. It was found that the predicted ranks of the drugs based on the multi-targeted efficacy prediction exactly match the actual rankings. Conclusion: We developed efficient statistical and machine learning models using MTR and SVR analysis for anticancer drug efficacy, which will be useful in the field of precision medicine to choose the most suitable drugs in personalized manner. The performance results of the proposed enhanced ranking techniques are described as follows: i) EL_MTR is the best to predict multiple anticancer drug efficacies and improve the accuracy of ranking drugs, irrespective of sample size; and ii) ELM_SVR performs better than other MTR models with a large sample size and precise ranking process.