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The analyzed data consist of two gene expression sets obtained in studies of radiosensitive and radioresistant breast cancer patients undergoing radiotherapy. The data sets were similar in principle; however, the treatment dose differed. It is shown that introducing mathematical adjustments in data preprocessing, differentiation and trend testing, and classification, coupled with current biological knowledge, allows efficient data analysis and obtaining accurate results. The tools used to customize the analysis workflow were batch effect filtration with empirical Bayes models, identifying gene trends through the Jonckheere\u2013Terpstra test and linear interpolation adjustment according to specific gene profiles for multiple random validation. The application of non-standard techniques enabled successful sample classification at the rate of 93.5% and the identification of potential biomarkers of radiation response in breast cancer, which were confirmed with an independent Monte Carlo feature selection approach and by literature references. This study shows that using customized analysis workflows is a necessary step towards novel discoveries in complex fields such as personalized individual therapy.<\/jats:p>","DOI":"10.2478\/amcs-2019-0013","type":"journal-article","created":{"date-parts":[[2019,4,1]],"date-time":"2019-04-01T17:30:51Z","timestamp":1554139851000},"page":"169-178","source":"Crossref","is-referenced-by-count":0,"title":["Machine learning techniques combined with dose profiles indicate radiation response biomarkers"],"prefix":"10.61822","volume":"29","author":[{"given":"Anna","family":"Papiez","sequence":"first","affiliation":[{"name":"Data Mining Group, Institute of Automatic Control , Silesian University of Technology , ul. 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