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Developing computational methods to reduce high-dimensional space of features in in vitro, in vivo and clinical data is essential to discover the evolution and mechanisms of the drug responses and drug resistance. In this paper, we have utilized the matrix factorization (MF) as a modality for high dimensionality reduction in systems pharmacology. In this respect, we have proposed three novel feature selection methods using the mathematical conception of a basis for features. We have applied these techniques as well as three other MF methods to analyze eight different gene expression datasets to investigate and compare their performance for feature selection. Our results show that these methods are capable of reducing the feature spaces and find predictive features in terms of phenotype determination. The three proposed techniques outperform the other methods used and can extract a 2-gene signature predictive of a tyrosine kinase inhibitor treatment response in the Cancer Cell Line Encyclopedia.<\/jats:p>","DOI":"10.1093\/bib\/bbab410","type":"journal-article","created":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T15:38:09Z","timestamp":1631115489000},"source":"Crossref","is-referenced-by-count":36,"title":["High dimensionality reduction by matrix factorization for systems pharmacology"],"prefix":"10.1093","volume":"23","author":[{"given":"Adel","family":"Mehrpooya","sequence":"first","affiliation":[{"name":"School of Mathematical Sciences, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Australia"},{"name":"Department of Computer Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran"}]},{"given":"Farid","family":"Saberi-Movahed","sequence":"additional","affiliation":[{"name":"Department of Applied Mathematics, Faculty of Sciences and Modern Technologies, Graduate University of Advanced Technology, Kerman, Iran"}]},{"given":"Najmeh","family":"Azizizadeh","sequence":"additional","affiliation":[{"name":"Department of Applied Mathematics, Faculty of Mathematics and Computer, Shahid Bahonar University of Kerman, Iran"}]},{"given":"Mohammad","family":"Rezaei-Ravari","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran"}]},{"given":"Farshad","family":"Saberi-Movahed","sequence":"additional","affiliation":[{"name":"College of Engineering, North Carolina State University, Raleigh, NC 22606, USA"}]},{"given":"Mahdi","family":"Eftekhari","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, 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