Exhaustive Exploitation of Nature-Inspired Computation for Cancer Screening in an Ensemble Manner

Xubin Wang, Yunhe Wang*, Zhiqiang Ma, Ka-Chun Wong, Xiangtao Li*

*Corresponding author for this work

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

1 Citation (Scopus)

Abstract

Accurate screening of cancer types is crucial for effective cancer detection and precise treatment selection. However, the association between gene expression profiles and tumors is often limited to a small number of biomarker genes. While computational methods using nature-inspired algorithms have shown promise in selecting predictive genes, existing techniques are limited by inefficient search and poor generalization across diverse datasets. This study presents a framework termed Evolutionary Optimized Diverse Ensemble Learning (EODE) to improve ensemble learning for cancer classification from gene expression data. The EODE methodology combines an intelligent grey wolf optimization algorithm for selective feature space reduction, guided random injection modeling for ensemble diversity enhancement, and subset model optimization for synergistic classifier combinations. Extensive experiments were conducted across 35 gene expression benchmark datasets encompassing varied cancer types. Results demonstrated that EODE obtained significantly improved screening accuracy over individual and conventionally aggregated models. The integrated optimization of advanced feature selection, directed specialized modeling, and cooperative classifier ensembles helps address key challenges in current nature-inspired approaches. This provides an effective framework for robust and generalized ensemble learning with gene expression biomarkers. Specifically, we have opened EODE source code on Github at <uri>https://github.com/wangxb96/EODE</uri>. IEEE
Original languageEnglish
Pages (from-to)1366-1379
Number of pages14
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume21
Issue number5
Online published5 Apr 2024
DOIs
Publication statusPublished - Sept 2024

Funding

The work described in this paper was substantially supported by the National Natural Science Foundation of China under Grant No. 62076109, and funded by the Natural Science Foundation of Jilin Province under Grant No. 20190103006JH, the Natural Science Funds of Jilin Province under Grant No.20200201158JC. The work described in this paper was supported by the grant from the Health and Medical Research Fund, the Food and Health Bureau, The Government of the Hong Kong Special Administrative Region [07181426], and the funding from Hong Kong Institute for Data Science (HKIDS) at City University of Hong Kong. The work described in this paper was partially supported by two grants from City University of Hong Kong (CityU 11202219, CityU 11203520). This research is also supported by the National Natural Science Foundation of China under Grant No. 32000464.

Research Keywords

  • Cancer
  • Classification
  • Classification algorithms
  • clustering
  • ensemble learning
  • Ensemble learning
  • Feature extraction
  • feature selection
  • Gene expression
  • grey wolf optimizer
  • Optimization
  • Training

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