NDLI: Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies

Content Provider	ACM Digital Library
Author	Alpaydin, Ethem Irsoy, Ozan Yildiz, Olcay Taner
Abstract	In many bioinformatics applications, it is important to assess and compare the performances of algorithms trained from data, to be able to draw conclusions unaffected by chance and are therefore significant. Both the design of such experiments and the analysis of the resulting data using statistical tests should be done carefully for the results to carry significance. In this paper, we first review the performance measures used in classification, the basics of experiment design and statistical tests. We then give the results of our survey over 1,500 papers published in the last two years in three bioinformatics journals (including this one). Although the basics of experiment design are well understood, such as resampling instead of using a single training set and the use of different performance metrics instead of error, only 21 percent of the papers use any statistical test for comparison. In the third part, we analyze four different scenarios which we encounter frequently in the bioinformatics literature, discussing the proper statistical methodology as well as showing an example case study for each. With the supplementary software, we hope that the guidelines we discuss will play an important role in future studies.
Starting Page	1663
Ending Page	1675
Page Count	13
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2012.117
Volume Number	9
Issue Number	6
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2012-11-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Training,Bioinformatics,Algorithm design and analysis,Measurement,Testing,Approximation algorithms,Computational biology,model selection,Statistical tests,classification
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies

Design and analysis of classifier learning experiments in bioinformatics: survey and case.

Ensemble Learning with Active Example Selection for Imbalanced Biomedical Data Classification

Online Feature Selection and Its Applications

1Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies

A fast algorithm for the nearest-neighbor classifier

Ordering and finding the best of K > 2 supervised learning algorithms

Adaptive Manifold Learning

A New Measure of Classifier Performance for Gene Expression Data

Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies

Similar Documents

Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies

Design and analysis of classifier learning experiments in bioinformatics: survey and case.

Ensemble Learning with Active Example Selection for Imbalanced Biomedical Data Classification

Online Feature Selection and Its Applications

1Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies

A fast algorithm for the nearest-neighbor classifier

Ordering and finding the best of K > 2 supervised learning algorithms

Adaptive Manifold Learning

A New Measure of Classifier Performance for Gene Expression Data

Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies