Literature DB >> 33558580

A machine learning method based on the genetic and world competitive contests algorithms for selecting genes or features in biological applications.

Yosef Masoudi-Sobhanzadeh1, Habib Motieghader2,3, Yadollah Omidi4, Ali Masoudi-Nejad5.   

Abstract

Gene/feature selection is an essential preprocessing step for creating models using machine learning techniques. It also plays a critical role in different biological applications such as the identification of biomarkers. Although many feature/gene selection algorithms and methods have been introduced, they may suffer from problems such as parameter tuning or low level of performance. To tackle such limitations, in this study, a universal wrapper approach is introduced based on our introduced optimization algorithm and the genetic algorithm (GA). In the proposed approach, candidate solutions have variable lengths, and a support vector machine scores them. To show the usefulness of the method, thirteen classification and regression-based datasets with different properties were chosen from various biological scopes, including drug discovery, cancer diagnostics, clinical applications, etc. Our findings confirmed that the proposed method outperforms most of the other currently used approaches and can also free the users from difficulties related to the tuning of various parameters. As a result, users may optimize their biological applications such as obtaining a biomarker diagnostic kit with the minimum number of genes and maximum separability power.

Entities:  

Year:  2021        PMID: 33558580     DOI: 10.1038/s41598-021-82796-y

Source DB:  PubMed          Journal:  Sci Rep        ISSN: 2045-2322            Impact factor:   4.379


  18 in total

1.  mRNA and microRNA selection for breast cancer molecular subtype stratification using meta-heuristic based algorithms.

Authors:  Habib MotieGhader; Yosef Masoudi-Sobhanzadeh; Saman Hosseini Ashtiani; Ali Masoudi-Nejad
Journal:  Genomics       Date:  2020-06-09       Impact factor: 5.736

2.  DrugR+: A comprehensive relational database for drug repurposing, combination therapy, and replacement therapy.

Authors:  Yosef Masoudi-Sobhanzadeh; Yadollah Omidi; Massoud Amanlou; Ali Masoudi-Nejad
Journal:  Comput Biol Med       Date:  2019-05-08       Impact factor: 4.589

3.  Logistic Regression Confined by Cardinality-Constrained Sample and Feature Selection.

Authors:  Ehsan Adeli; Xiaorui Li; Dongjin Kwon; Yong Zhang; Kilian M Pohl
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  2019-02-26       Impact factor: 6.226

4.  Microvesicle Proteomic Profiling of Uterine Liquid Biopsy for Ovarian Cancer Early Detection.

Authors:  Georgina D Barnabas; Keren Bahar-Shany; Stav Sapoznik; Limor Helpman; Yfat Kadan; Mario Beiner; Omer Weitzner; Nissim Arbib; Jacob Korach; Tamar Perri; Guy Katz; Anna Blecher; Benny Brandt; Eitan Friedman; David Stockheim; Ariella Jakobson-Setton; Ram Eitan; Shunit Armon; Hadar Brand; Oranit Zadok; Sarit Aviel-Ronen; Michal Harel; Tamar Geiger; Keren Levanon
Journal:  Mol Cell Proteomics       Date:  2019-02-13       Impact factor: 5.911

Review 5.  Glyoxalase I: mechanism-based inhibitors.

Authors:  F Jordan; J F Cohen; C T Wang; J M Wilmott; S S Hall; D L Foxall
Journal:  Drug Metab Rev       Date:  1983       Impact factor: 4.518

6.  Gene selection using hybrid binary black hole algorithm and modified binary particle swarm optimization.

Authors:  Elnaz Pashaei; Elham Pashaei; Nizamettin Aydin
Journal:  Genomics       Date:  2018-04-14       Impact factor: 5.736

7.  Automated feature selection of predictors in electronic medical records data.

Authors:  Jessica Gronsbell; Jessica Minnier; Sheng Yu; Katherine Liao; Tianxi Cai
Journal:  Biometrics       Date:  2019-04-02       Impact factor: 2.571

8.  Random forest feature selection, fusion and ensemble strategy: Combining multiple morphological MRI measures to discriminate among healhy elderly, MCI, cMCI and alzheimer's disease patients: From the alzheimer's disease neuroimaging initiative (ADNI) database.

Authors:  S I Dimitriadis; Dimitris Liparas; Magda N Tsolaki
Journal:  J Neurosci Methods       Date:  2017-12-18       Impact factor: 2.390

9.  Metabolite and transcript markers for the prediction of potato drought tolerance.

Authors:  Heike Sprenger; Alexander Erban; Sylvia Seddig; Katharina Rudack; Anja Thalhammer; Mai Q Le; Dirk Walther; Ellen Zuther; Karin I Köhl; Joachim Kopka; Dirk K Hincha
Journal:  Plant Biotechnol J       Date:  2017-10-17       Impact factor: 9.803

10.  The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic.

Authors:  Alexander M Frankell; SriGanesh Jammula; Xiaodun Li; Gianmarco Contino; Sarah Killcoyne; Sujath Abbas; Juliane Perner; Lawrence Bower; Ginny Devonshire; Emma Ococks; Nicola Grehan; James Mok; Maria O'Donovan; Shona MacRae; Matthew D Eldridge; Simon Tavaré; Rebecca C Fitzgerald
Journal:  Nat Genet       Date:  2019-02-04       Impact factor: 38.330

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  2 in total

1.  Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries.

Authors:  Yosef Masoudi-Sobhanzadeh; Aysan Salemi; Mohammad M Pourseif; Behzad Jafari; Yadollah Omidi; Ali Masoudi-Nejad
Journal:  Brief Bioinform       Date:  2021-11-05       Impact factor: 11.622

2.  Risk Stratification for Breast Cancer Patient by Simultaneous Learning of Molecular Subtype and Survival Outcome Using Genetic Algorithm-Based Gene Set Selection.

Authors:  Bonil Koo; Dohoon Lee; Sangseon Lee; Inyoung Sung; Sun Kim; Sunho Lee
Journal:  Cancers (Basel)       Date:  2022-08-25       Impact factor: 6.575

  2 in total

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