RCE-IFE: recursive cluster elimination with intra-cluster feature elimination
The computational and interpretational difficulties caused by the ever-increasing dimensionality of biological data generated by new technologies pose a significant challenge. Feature selection (FS) methods aim to reduce the dimension, and feature grouping has emerged as a foundation for FS techniqu...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2025-02-01
|
| Series: | PeerJ Computer Science |
| Subjects: | |
| Online Access: | https://peerj.com/articles/cs-2528.pdf |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1823861396024066048 |
|---|---|
| author | Cihan Kuzudisli Burcu Bakir-Gungor Bahjat Qaqish Malik Yousef |
| author_facet | Cihan Kuzudisli Burcu Bakir-Gungor Bahjat Qaqish Malik Yousef |
| author_sort | Cihan Kuzudisli |
| collection | DOAJ |
| description | The computational and interpretational difficulties caused by the ever-increasing dimensionality of biological data generated by new technologies pose a significant challenge. Feature selection (FS) methods aim to reduce the dimension, and feature grouping has emerged as a foundation for FS techniques that seek to detect strong correlations among features and identify irrelevant features. In this work, we propose the Recursive Cluster Elimination with Intra-Cluster Feature Elimination (RCE-IFE) method that utilizes feature grouping and iterates grouping and elimination steps in a supervised context. We assess dimensionality reduction and discriminatory capabilities of RCE-IFE on various high-dimensional datasets from different biological domains. For a set of gene expression, microRNA (miRNA) expression, and methylation datasets, the performance of RCE-IFE is comparatively evaluated with RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE. On average, RCE-IFE attains an area under the curve (AUC) of 0.85 among tested expression datasets with the fewest features and the shortest running time, while RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE achieve similar AUCs of 0.84 and 0.83, respectively. RCE-IFE and SVM-RCE yield AUCs of 0.79 and 0.68, respectively when averaged over seven different metagenomics datasets, with RCE-IFE significantly reducing feature subsets. Furthermore, RCE-IFE surpasses several state-of-the-art FS methods, such as Minimum Redundancy Maximum Relevance (MRMR), Fast Correlation-Based Filter (FCBF), Information Gain (IG), Conditional Mutual Information Maximization (CMIM), SelectKBest (SKB), and eXtreme Gradient Boosting (XGBoost), obtaining an average AUC of 0.76 on five gene expression datasets. Compared with a similar tool, Multi-stage, RCE-IFE gives a similar average accuracy rate of 89.27% using fewer features on four cancer-related datasets. The comparability of RCE-IFE is also verified with other biological domain knowledge-based Grouping-Scoring-Modeling (G-S-M) tools, including mirGediNET, 3Mint, and miRcorrNet. Additionally, the biological relevance of the selected features by RCE-IFE is evaluated. The proposed method also exhibits high consistency in terms of the selected features across multiple runs. Our experimental findings imply that RCE-IFE provides robust classifier performance and significantly reduces feature size while maintaining feature relevance and consistency. |
| format | Article |
| id | doaj-art-195fecf2a2e1414a90ed593da280c82e |
| institution | Kabale University |
| issn | 2376-5992 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ Computer Science |
| spelling | doaj-art-195fecf2a2e1414a90ed593da280c82e2025-02-09T15:05:14ZengPeerJ Inc.PeerJ Computer Science2376-59922025-02-0111e252810.7717/peerj-cs.2528RCE-IFE: recursive cluster elimination with intra-cluster feature eliminationCihan Kuzudisli0Burcu Bakir-Gungor1Bahjat Qaqish2Malik Yousef3Department of Computer Engineering, Faculty of Engineering, Hasan Kalyoncu University, Gaziantep, TurkeyDepartment of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, TurkeyDepartment of Biostatistics, University of North Carolina at Chapel Hill, North Carolina, Chapel Hill, United StatesDepartment of Information Systems, Zefat Academic College, Zefat, IsraelThe computational and interpretational difficulties caused by the ever-increasing dimensionality of biological data generated by new technologies pose a significant challenge. Feature selection (FS) methods aim to reduce the dimension, and feature grouping has emerged as a foundation for FS techniques that seek to detect strong correlations among features and identify irrelevant features. In this work, we propose the Recursive Cluster Elimination with Intra-Cluster Feature Elimination (RCE-IFE) method that utilizes feature grouping and iterates grouping and elimination steps in a supervised context. We assess dimensionality reduction and discriminatory capabilities of RCE-IFE on various high-dimensional datasets from different biological domains. For a set of gene expression, microRNA (miRNA) expression, and methylation datasets, the performance of RCE-IFE is comparatively evaluated with RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE. On average, RCE-IFE attains an area under the curve (AUC) of 0.85 among tested expression datasets with the fewest features and the shortest running time, while RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE achieve similar AUCs of 0.84 and 0.83, respectively. RCE-IFE and SVM-RCE yield AUCs of 0.79 and 0.68, respectively when averaged over seven different metagenomics datasets, with RCE-IFE significantly reducing feature subsets. Furthermore, RCE-IFE surpasses several state-of-the-art FS methods, such as Minimum Redundancy Maximum Relevance (MRMR), Fast Correlation-Based Filter (FCBF), Information Gain (IG), Conditional Mutual Information Maximization (CMIM), SelectKBest (SKB), and eXtreme Gradient Boosting (XGBoost), obtaining an average AUC of 0.76 on five gene expression datasets. Compared with a similar tool, Multi-stage, RCE-IFE gives a similar average accuracy rate of 89.27% using fewer features on four cancer-related datasets. The comparability of RCE-IFE is also verified with other biological domain knowledge-based Grouping-Scoring-Modeling (G-S-M) tools, including mirGediNET, 3Mint, and miRcorrNet. Additionally, the biological relevance of the selected features by RCE-IFE is evaluated. The proposed method also exhibits high consistency in terms of the selected features across multiple runs. Our experimental findings imply that RCE-IFE provides robust classifier performance and significantly reduces feature size while maintaining feature relevance and consistency.https://peerj.com/articles/cs-2528.pdfFeature groupingFeature selectionRecursive cluster eliminationIntra-cluster feature eliminationDisease |
| spellingShingle | Cihan Kuzudisli Burcu Bakir-Gungor Bahjat Qaqish Malik Yousef RCE-IFE: recursive cluster elimination with intra-cluster feature elimination PeerJ Computer Science Feature grouping Feature selection Recursive cluster elimination Intra-cluster feature elimination Disease |
| title | RCE-IFE: recursive cluster elimination with intra-cluster feature elimination |
| title_full | RCE-IFE: recursive cluster elimination with intra-cluster feature elimination |
| title_fullStr | RCE-IFE: recursive cluster elimination with intra-cluster feature elimination |
| title_full_unstemmed | RCE-IFE: recursive cluster elimination with intra-cluster feature elimination |
| title_short | RCE-IFE: recursive cluster elimination with intra-cluster feature elimination |
| title_sort | rce ife recursive cluster elimination with intra cluster feature elimination |
| topic | Feature grouping Feature selection Recursive cluster elimination Intra-cluster feature elimination Disease |
| url | https://peerj.com/articles/cs-2528.pdf |
| work_keys_str_mv | AT cihankuzudisli rceiferecursiveclustereliminationwithintraclusterfeatureelimination AT burcubakirgungor rceiferecursiveclustereliminationwithintraclusterfeatureelimination AT bahjatqaqish rceiferecursiveclustereliminationwithintraclusterfeatureelimination AT malikyousef rceiferecursiveclustereliminationwithintraclusterfeatureelimination |