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Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms
BACKGROUND: With modern methods in biotechnology, the search for biomarkers has advanced to a challenging statistical task exploring high dimensional data sets. Feature selection is a widely researched preprocessing step to handle huge numbers of biomarker candidates and has special importance for t...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986087/ https://www.ncbi.nlm.nih.gov/pubmed/31992203 http://dx.doi.org/10.1186/s12859-020-3361-9 |
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author | Jagdhuber, Rudolf Lang, Michel Stenzl, Arnulf Neuhaus, Jochen Rahnenführer, Jörg |
author_facet | Jagdhuber, Rudolf Lang, Michel Stenzl, Arnulf Neuhaus, Jochen Rahnenführer, Jörg |
author_sort | Jagdhuber, Rudolf |
collection | PubMed |
description | BACKGROUND: With modern methods in biotechnology, the search for biomarkers has advanced to a challenging statistical task exploring high dimensional data sets. Feature selection is a widely researched preprocessing step to handle huge numbers of biomarker candidates and has special importance for the analysis of biomedical data. Such data sets often include many input features not related to the diagnostic or therapeutic target variable. A less researched, but also relevant aspect for medical applications are costs of different biomarker candidates. These costs are often financial costs, but can also refer to other aspects, for example the decision between a painful biopsy marker and a simple urine test. In this paper, we propose extensions to two feature selection methods to control the total amount of such costs: greedy forward selection and genetic algorithms. In comprehensive simulation studies of binary classification tasks, we compare the predictive performance, the run-time and the detection rate of relevant features for the new proposed methods and five baseline alternatives to handle budget constraints. RESULTS: In simulations with a predefined budget constraint, our proposed methods outperform the baseline alternatives, with just minor differences between them. Only in the scenario without an actual budget constraint, our adapted greedy forward selection approach showed a clear drop in performance compared to the other methods. However, introducing a hyperparameter to adapt the benefit-cost trade-off in this method could overcome this weakness. CONCLUSIONS: In feature cost scenarios, where a total budget has to be met, common feature selection algorithms are often not suitable to identify well performing subsets for a modelling task. Adaptations of these algorithms such as the ones proposed in this paper can help to tackle this problem. |
format | Online Article Text |
id | pubmed-6986087 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-69860872020-01-30 Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms Jagdhuber, Rudolf Lang, Michel Stenzl, Arnulf Neuhaus, Jochen Rahnenführer, Jörg BMC Bioinformatics Methodology Article BACKGROUND: With modern methods in biotechnology, the search for biomarkers has advanced to a challenging statistical task exploring high dimensional data sets. Feature selection is a widely researched preprocessing step to handle huge numbers of biomarker candidates and has special importance for the analysis of biomedical data. Such data sets often include many input features not related to the diagnostic or therapeutic target variable. A less researched, but also relevant aspect for medical applications are costs of different biomarker candidates. These costs are often financial costs, but can also refer to other aspects, for example the decision between a painful biopsy marker and a simple urine test. In this paper, we propose extensions to two feature selection methods to control the total amount of such costs: greedy forward selection and genetic algorithms. In comprehensive simulation studies of binary classification tasks, we compare the predictive performance, the run-time and the detection rate of relevant features for the new proposed methods and five baseline alternatives to handle budget constraints. RESULTS: In simulations with a predefined budget constraint, our proposed methods outperform the baseline alternatives, with just minor differences between them. Only in the scenario without an actual budget constraint, our adapted greedy forward selection approach showed a clear drop in performance compared to the other methods. However, introducing a hyperparameter to adapt the benefit-cost trade-off in this method could overcome this weakness. CONCLUSIONS: In feature cost scenarios, where a total budget has to be met, common feature selection algorithms are often not suitable to identify well performing subsets for a modelling task. Adaptations of these algorithms such as the ones proposed in this paper can help to tackle this problem. BioMed Central 2020-01-28 /pmc/articles/PMC6986087/ /pubmed/31992203 http://dx.doi.org/10.1186/s12859-020-3361-9 Text en © The Author(s) 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Methodology Article Jagdhuber, Rudolf Lang, Michel Stenzl, Arnulf Neuhaus, Jochen Rahnenführer, Jörg Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms |
title | Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms |
title_full | Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms |
title_fullStr | Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms |
title_full_unstemmed | Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms |
title_short | Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms |
title_sort | cost-constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986087/ https://www.ncbi.nlm.nih.gov/pubmed/31992203 http://dx.doi.org/10.1186/s12859-020-3361-9 |
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