multiclassPairs: An R package to train multiclass pair-based classifier
(2021) In Bioinformatics 37(18). p.3043-3044- Abstract
- Motivation
k–Top Scoring Pairs (kTSP) algorithms utilize in-sample gene expression feature pair rules for class prediction, and have demonstrated excellent performance and robustness. The available packages and tools primarily focus on binary prediction (i.e. two classes). However, many real-world classification problems e.g., tumor subtype prediction, are multiclass tasks.
Results
Here, we present multiclassPairs, an R package to train pair-based single sample classifiers for multiclass problems. multiclassPairs offers two main methods to build multiclass prediction models, either using a one-vs-rest kTSP scheme or through a novel pair-based Random Forest approach. The package also provides options for dealing with class... (More) - Motivation
k–Top Scoring Pairs (kTSP) algorithms utilize in-sample gene expression feature pair rules for class prediction, and have demonstrated excellent performance and robustness. The available packages and tools primarily focus on binary prediction (i.e. two classes). However, many real-world classification problems e.g., tumor subtype prediction, are multiclass tasks.
Results
Here, we present multiclassPairs, an R package to train pair-based single sample classifiers for multiclass problems. multiclassPairs offers two main methods to build multiclass prediction models, either using a one-vs-rest kTSP scheme or through a novel pair-based Random Forest approach. The package also provides options for dealing with class imbalances, multiplatform training, missing features in test data, and visualization of training and test results.
Availability
‘multiclassPairs’ package is available on CRAN servers and GitHub: https://github.com/NourMarzouka/multiclassPairs
Supplementary information
Supplementary data are available at Bioinformatics online. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/046f029e-97c1-423e-aee5-77c9ec34cbfd
- author
- Marzouka, Nour-Al-Dain LU and Eriksson, Pontus LU
- organization
- publishing date
- 2021-02-05
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Bioinformatics
- volume
- 37
- issue
- 18
- article number
- btab088
- pages
- 3043 - 3044
- publisher
- Oxford University Press
- external identifiers
-
- pmid:33543757
- scopus:85119084997
- ISSN
- 1367-4803
- DOI
- 10.1093/bioinformatics/btab088
- language
- English
- LU publication?
- yes
- id
- 046f029e-97c1-423e-aee5-77c9ec34cbfd
- date added to LUP
- 2021-02-08 13:34:49
- date last changed
- 2023-05-17 10:33:45
@misc{046f029e-97c1-423e-aee5-77c9ec34cbfd, abstract = {{Motivation<br/>k–Top Scoring Pairs (kTSP) algorithms utilize in-sample gene expression feature pair rules for class prediction, and have demonstrated excellent performance and robustness. The available packages and tools primarily focus on binary prediction (i.e. two classes). However, many real-world classification problems e.g., tumor subtype prediction, are multiclass tasks.<br/>Results<br/>Here, we present multiclassPairs, an R package to train pair-based single sample classifiers for multiclass problems. multiclassPairs offers two main methods to build multiclass prediction models, either using a one-vs-rest kTSP scheme or through a novel pair-based Random Forest approach. The package also provides options for dealing with class imbalances, multiplatform training, missing features in test data, and visualization of training and test results.<br/>Availability<br/>‘multiclassPairs’ package is available on CRAN servers and GitHub: https://github.com/NourMarzouka/multiclassPairs<br/>Supplementary information<br/>Supplementary data are available at Bioinformatics online.}}, author = {{Marzouka, Nour-Al-Dain and Eriksson, Pontus}}, issn = {{1367-4803}}, language = {{eng}}, month = {{02}}, number = {{18}}, pages = {{3043--3044}}, publisher = {{Oxford University Press}}, series = {{Bioinformatics}}, title = {{multiclassPairs: An R package to train multiclass pair-based classifier}}, url = {{http://dx.doi.org/10.1093/bioinformatics/btab088}}, doi = {{10.1093/bioinformatics/btab088}}, volume = {{37}}, year = {{2021}}, }