Literature DB >> 33661899

Hands-on training about overfitting.

Janez Demšar1, Blaž Zupan1,2.   

Abstract

Overfitting is one of the critical problems in developing models by machine learning. With machine learning becoming an essential technology in computational biology, we must include training about overfitting in all courses that introduce this technology to students and practitioners. We here propose a hands-on training for overfitting that is suitable for introductory level courses and can be carried out on its own or embedded within any data science course. We use workflow-based design of machine learning pipelines, experimentation-based teaching, and hands-on approach that focuses on concepts rather than underlying mathematics. We here detail the data analysis workflows we use in training and motivate them from the viewpoint of teaching goals. Our proposed approach relies on Orange, an open-source data science toolbox that combines data visualization and machine learning, and that is tailored for education in machine learning and explorative data analysis.

Entities:  

Year:  2021        PMID: 33661899      PMCID: PMC7932115          DOI: 10.1371/journal.pcbi.1008671

Source DB:  PubMed          Journal:  PLoS Comput Biol        ISSN: 1553-734X            Impact factor:   4.475


  10 in total

1.  Knowledge-based analysis of microarray gene expression data by using support vector machines.

Authors:  M P Brown; W N Grundy; D Lin; N Cristianini; C W Sugnet; T S Furey; M Ares; D Haussler
Journal:  Proc Natl Acad Sci U S A       Date:  2000-01-04       Impact factor: 11.205

Review 2.  Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification.

Authors:  Richard Simon; Michael D Radmacher; Kevin Dobbin; Lisa M McShane
Journal:  J Natl Cancer Inst       Date:  2003-01-01       Impact factor: 13.506

3.  Microarray data mining with visual programming.

Authors:  Tomaz Curk; Janez Demsar; Qikai Xu; Gregor Leban; Uros Petrovic; Ivan Bratko; Gad Shaulsky; Blaz Zupan
Journal:  Bioinformatics       Date:  2004-08-12       Impact factor: 6.937

4.  VizRank: finding informative data projections in functional genomics by machine learning.

Authors:  Gregor Leban; Ivan Bratko; Uros Petrovic; Tomaz Curk; Blaz Zupan
Journal:  Bioinformatics       Date:  2004-09-09       Impact factor: 6.937

Review 5.  Machine learning in bioinformatics.

Authors:  Pedro Larrañaga; Borja Calvo; Roberto Santana; Concha Bielza; Josu Galdiano; Iñaki Inza; José A Lozano; Rubén Armañanzas; Guzmán Santafé; Aritz Pérez; Victor Robles
Journal:  Brief Bioinform       Date:  2006-03       Impact factor: 11.622

6.  Patterns of resistance and incomplete response to docetaxel by gene expression profiling in breast cancer patients.

Authors:  Jenny C Chang; Eric C Wooten; Anna Tsimelzon; Susan G Hilsenbeck; M Carolina Gutierrez; Yee-Lu Tham; Mamta Kalidas; Richard Elledge; Syed Mohsin; C Kent Osborne; Gary C Chamness; D Craig Allred; Michael T Lewis; Helen Wong; Peter O'Connell
Journal:  J Clin Oncol       Date:  2005-02-20       Impact factor: 44.544

7.  Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.

Authors:  Marinka Zitnik; Francis Nguyen; Bo Wang; Jure Leskovec; Anna Goldenberg; Michael M Hoffman
Journal:  Inf Fusion       Date:  2018-09-21       Impact factor: 12.975

Review 8.  Ten quick tips for machine learning in computational biology.

Authors:  Davide Chicco
Journal:  BioData Min       Date:  2017-12-08       Impact factor: 2.522

Review 9.  scOrange-a tool for hands-on training of concepts from single-cell data analytics.

Authors:  Martin Stražar; Lan Žagar; Jaka Kokošar; Vesna Tanko; Aleš Erjavec; Pavlin G Poličar; Anže Starič; Janez Demšar; Gad Shaulsky; Vilas Menon; Andrew Lemire; Anup Parikh; Blaž Zupan
Journal:  Bioinformatics       Date:  2019-07-15       Impact factor: 6.937

10.  Democratized image analytics by visual programming through integration of deep models and small-scale machine learning.

Authors:  Primož Godec; Matjaž Pančur; Nejc Ilenič; Andrej Čopar; Martin Stražar; Aleš Erjavec; Ajda Pretnar; Janez Demšar; Anže Starič; Marko Toplak; Lan Žagar; Jan Hartman; Hamilton Wang; Riccardo Bellazzi; Uroš Petrovič; Silvia Garagna; Maurizio Zuccotti; Dongsu Park; Gad Shaulsky; Blaž Zupan
Journal:  Nat Commun       Date:  2019-10-07       Impact factor: 14.919

  10 in total
  4 in total

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Authors:  Tianming Du; Haidong Zhao
Journal:  Biomed Res Int       Date:  2022-05-26       Impact factor: 3.246

2.  Machine learning and bioinformatics approaches for classification and clinical detection of bevacizumab responsive glioblastoma subtypes based on miRNA expression.

Authors:  Jian Shi
Journal:  Sci Rep       Date:  2022-05-23       Impact factor: 4.996

3.  Editorial: Clinical Application of Artificial Intelligence in Emergency and Critical Care Medicine, Volume I.

Authors:  Zhongheng Zhang; Nan Liu; Qinghe Meng; Longxiang Su
Journal:  Front Med (Lausanne)       Date:  2021-12-06

4.  A Novel Computer Vision Model for Medicinal Plant Identification Using Log-Gabor Filters and Deep Learning Algorithms.

Authors:  Stephen Opoku Oppong; Frimpong Twum; James Ben Hayfron-Acquah; Yaw Marfo Missah
Journal:  Comput Intell Neurosci       Date:  2022-09-27
  4 in total

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