Literature DB >> 21532969

Testing and Validating Machine Learning Classifiers by Metamorphic Testing.

Xiaoyuan Xie1, Joshua W K Ho, Christian Murphy, Gail Kaiser, Baowen Xu, Tsong Yueh Chen.   

Abstract

Machine Learning algorithms have provided core functionality to many application domains - such as bioinformatics, computational linguistics, etc. However, it is difficult to detect faults in such applications because often there is no "test oracle" to verify the correctness of the computed outputs. To help address the software quality, in this paper we present a technique for testing the implementations of machine learning classification algorithms which support such applications. Our approach is based on the technique "metamorphic testing", which has been shown to be effective to alleviate the oracle problem. Also presented include a case study on a real-world machine learning application framework, and a discussion of how programmers implementing machine learning algorithms can avoid the common pitfalls discovered in our study. We also conduct mutation analysis and cross-validation, which reveal that our method has high effectiveness in killing mutants, and that observing expected cross-validation result alone is not sufficiently effective to detect faults in a supervised classification program. The effectiveness of metamorphic testing is further confirmed by the detection of real faults in a popular open-source classification program.

Entities:  

Year:  2011        PMID: 21532969      PMCID: PMC3082144          DOI: 10.1016/j.jss.2010.11.920

Source DB:  PubMed          Journal:  J Syst Softw        ISSN: 0164-1212            Impact factor:   2.829


  5 in total

1.  BioWeka--extending the Weka framework for bioinformatics.

Authors:  Jan E Gewehr; Martin Szugat; Ralf Zimmer
Journal:  Bioinformatics       Date:  2007-01-19       Impact factor: 6.937

Review 2.  Customising an antibody leukocyte capture microarray for systemic lupus erythematosus: beyond biomarker discovery.

Authors:  Joshua W K Ho; Ming-Wei Lin; Filip Braet; Ying Ying Su; Stephen Adelstein; Cristobal G dos Remedios
Journal:  Proteomics Clin Appl       Date:  2009-12-02       Impact factor: 3.494

3.  Application of Metamorphic Testing to Supervised Classifiers.

Authors:  Xiaoyuan Xie; Joshua Ho; Christian Murphy; Gail Kaiser; Baowen Xu; Tsong Yueh Chen
Journal:  Proc Int Conf Qual Softw       Date:  2010-01-15

4.  An innovative approach for testing bioinformatics programs using metamorphic testing.

Authors:  Tsong Yueh Chen; Joshua W K Ho; Huai Liu; Xiaoyuan Xie
Journal:  BMC Bioinformatics       Date:  2009-01-19       Impact factor: 3.169

5.  Differential variability analysis of gene expression and its application to human diseases.

Authors:  Joshua W K Ho; Maurizio Stefani; Cristobal G dos Remedios; Michael A Charleston
Journal:  Bioinformatics       Date:  2008-07-01       Impact factor: 6.937

  5 in total
  9 in total

Review 1.  Application of a systems approach to study developmental gene regulation.

Authors:  Joshua W K Ho
Journal:  Biophys Rev       Date:  2012-09-01

Review 2.  How to test bioinformatics software?

Authors:  Amir Hossein Kamali; Eleni Giannoulatou; Tsong Yueh Chen; Michael A Charleston; Alistair L McEwan; Joshua W K Ho
Journal:  Biophys Rev       Date:  2015-08-13

3.  Testing Scientific Software: A Systematic Literature Review.

Authors:  Upulee Kanewala; James M Bieman
Journal:  Inf Softw Technol       Date:  2014-10-01       Impact factor: 2.730

4.  Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE.

Authors:  K Bretonnel Cohen; Jingbo Xia; Christophe Roeder; Lawrence E Hunter
Journal:  LREC Int Conf Lang Resour Eval       Date:  2016-05

5.  Technology readiness levels for machine learning systems.

Authors:  Alexander Lavin; Ciarán M Gilligan-Lee; Alessya Visnjic; Siddha Ganju; Dava Newman; Sujoy Ganguly; Danny Lange; Atílím Güneş Baydin; Amit Sharma; Adam Gibson; Stephan Zheng; Eric P Xing; Chris Mattmann; James Parr; Yarin Gal
Journal:  Nat Commun       Date:  2022-10-20       Impact factor: 17.694

6.  Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie.

Authors:  Eleni Giannoulatou; Shin-Ho Park; David T Humphreys; Joshua W K Ho
Journal:  BMC Bioinformatics       Date:  2014-12-08       Impact factor: 3.169

Review 7.  Scalability and Validation of Big Data Bioinformatics Software.

Authors:  Andrian Yang; Michael Troup; Joshua W K Ho
Journal:  Comput Struct Biotechnol J       Date:  2017-07-20       Impact factor: 7.271

8.  A metamorphic testing approach for event sequences.

Authors:  Jing Chen; Yinglong Wang; Ying Guo; Mingyue Jiang
Journal:  PLoS One       Date:  2019-02-19       Impact factor: 3.240

9.  Machine learning to predict effective reaction rates in 3D porous media from pore structural features.

Authors:  Min Liu; Beomjin Kwon; Peter K Kang
Journal:  Sci Rep       Date:  2022-03-31       Impact factor: 4.379

  9 in total

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