Abstract
Today, with the increase of data dimensions, many challenges are faced in many contexts including machine learning, informatics, and medicine. However, reducing data dimension can be considered as a basic method in handling high-dimensional data, because by reducing dimensions, applying many of the existing operations on data is facilitated.
Microarray data are derived from tissues and cells considering differences in the gene, which can be useful for diagnosing disease and tumors. Due to the large number of features (genes) and small number of samples in microarray datasets, selecting the most salient genes is a difficult task. Among the many techniques of machine learning, feature selection and data classification play a very important and widespread role in enhancing human life, from detecting voice emotion to detecting illness in the body. In medicine, an effective gene selection can greatly enhance the process of prediction and diagnosis of cancer. After selecting effective genes, the duty of a specific classifier is usually to discriminate healthy people from patients that are suffering from cancer based on their expression of the selected genes.
A vast body of feature selection methods has been proposed for high-dimensional microarray data. Traditionally, these methods fall into three categories including filter, wrapper, and hybrid approaches. Furthermore, new techniques such as ensemble methods have recently been developed to improve the process of feature selection and classification.
This chapter presents an overview of the most popular feature selection methods to deal with high-dimensional data and analyze their performance under different conditions. The chapter starts with a global overview of the high-dimensional data and feature selection (Sects. 5.2 and 5.3). Then, in Sect. 5.4 we review the state-of-the-art methods on filter algorithms. In the next three Sects. (5.5, 5.6 and 5.7) we describe the wrapper, hybrid, and embedded methods and in each section, an overview of several works performed on these methods is discussed. Sect. 5.8 describes the ensemble techniques recently considered by the researchers and summarizes the works done based on these techniques. In Sect. 5.9, we present the experimental results of the most significant methods on high-dimensional data. Finally, Sect. 5.10 summarizes this chapter.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
C.E. Crangle, R. Wang, M. Perreau-Guimaraes, M.U. Nguyen, D.T. Nguyen, P. Suppes, Machine learning for the recognition of emotion in the speech of couples in psychotherapy using the Stanford Suppes Brain Lab Psychotherapy Dataset. arXiv preprint arXiv:1901.04110 (2019)
A. Rouhi, M. Spitale, F. Catania, G. Cosentino, M. Gelsomini, F. Garzotto, Emotify: emotional game for children with autism spectrum disorder based-on machine learning, in Proceedings of the 24th International Conference on Intelligent User Interfaces: Companion (ACM, New York, 2019), pp. 31–32
U. Shruthi, V. Nagaveni, B. Raghavendra, A review on machine learning classification techniques for plant disease detection, in 2019 5th International Conference on Advanced Computing & Communication Systems (ICACCS), (IEEE, Piscataway, 2019), pp. 281–284
R.O. Duda, P.E. Hart, D.G. Stork, Pattern Classification (Wiley, Hoboken, 2012)
M. Fernandes, A. Canito, V. Bolón-Canedo, L. Conceição, I. Praça, G. Marreiros, Data analysis and feature selection for predictive maintenance: A case-study in the metallurgic industry. Int. J. Inf. Manag. 46, 252–262 (2019)
H. Liu, H. Motoda, Feature Selection for Knowledge Discovery and Data Mining (Springer, Berlin, 2012)
H. Handels, T. Roß, J. Kreusch, H.H. Wolff, S.J. Poeppl, Feature selection for optimized skin tumor recognition using genetic algorithms. Artif. Intell. Med. 16(3), 283–297 (1999)
B. Nikpour, H. Nezamabadi-pour, HTSS: a hyper-heuristic training set selection method for imbalanced data sets. Iran J. Comput. Sci. 1(2), 109–128 (2018)
K. Borowska, J. Stepaniuk, A rough–granular approach to the imbalanced data classification problem. Appl. Soft Comput. 83, 105607 (2019)
A. Reyes-Nava, H. Cruz-Reyes, R. Alejo, E. Rendón-Lara, A. Flores-Fuentes, and E. Granda-Gutiérrez, Using deep learning to classify class imbalanced gene-expression microarrays datasets, in Iberoamerican Congress on Pattern Recognition (Springer, Berlin, 2018), pp. 46–54
P.B. andLuis Torgo, R. Ribeiro, A survey of predictive modeling under imbalanced distributions. ACM Comput. Surv. 49(2), 1–31 (2016)
H. He, E.A. Garcia, Learning from imbalanced data. IEEE Trans. Knowl. Data Eng. 9, 1263–1284 (2008)
J. Błaszczyński, J. Stefanowski, Improving bagging ensembles for class imbalanced data by active learning, in Advances in Feature Selection for Data and Pattern Recognition, (Springer, Berlin, 2018), pp. 25–52
R.J. Hickey, Noise modelling and evaluating learning from examples. Artif. Intell. 82(1–2), 157–179 (1996)
Z. Sun, Q. Song, X. Zhu, H. Sun, B. Xu, Y. Zhou, A novel ensemble method for classifying imbalanced data. Pattern Recogn. 48(5), 1623–1637 (2015)
C.E. Brodley, M.A. Friedl, Identifying mislabeled training data. J. Artif. Intell. Res. 11, 131–167 (1999)
B. Frénay, A. Kabán, A comprehensive introduction to label noise, in ESANN (2014)
F. Barani, M. Mirhosseini, H. Nezamabadi-Pour, Application of binary quantum-inspired gravitational search algorithm in feature subset selection. Appl. Intell. 47(2), 304–318 (2017)
A.P. Dawid, A.M. Skene, Maximum likelihood estimation of observer error-rates using the EM algorithm. J. R. Stat. Soc. Ser. C Appl. Stat. 28(1), 20–28 (1979)
T.R. Golub et al., Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439), 531–537 (1999)
I. Kamkar, S.K. Gupta, D. Phung, S. Venkatesh, Stable feature selection for clinical prediction: exploiting ICD tree structure using tree-lasso. J. Biomed. Inform. 53, 277–290 (2015)
A. Rouhi and H. Nezamabadi-Pour, A hybrid feature selection approach based on ensemble method for high-dimensional data, in 2017 2nd Conference on Swarm Intelligence and Evolutionary Computation (CSIEC) (IEEE, Piscataway, 2017), pp. 16–20
S. Tabakhi, A. Najafi, R. Ranjbar, P. Moradi, Gene selection for microarray data classification using a novel ant colony optimization. Neurocomputing 168, 1024–1036 (2015)
M.K. Ebrahimpour, H. Nezamabadi-Pour, M. Eftekhari, CCFS: a cooperating coevolution technique for large scale feature selection on microarray datasets. Comput. Biol. Chem. 73, 171–178 (2018)
A. Rouhi and H. Nezamabadi-Pour, Filter-based feature selection for microarray data using improved binary gravitational search algorithm, in 2018 3rd Conference on Swarm Intelligence and Evolutionary Computation (CSIEC) (IEEE, Piscataway, 2018), pp. 1–6
J.R. Quinlan, Induction of decision trees. Mach. Learn. 1(1), 81–106 (1986)
Y.-W. Chen, C.-J. Lin, Combining SVMs with various feature selection strategies, in Feature Extraction, (Springer, Berlin, 2006), pp. 315–324
Q. Gu, Z. Li, J. Han, Generalized fisher score for feature selection. arXiv preprint arXiv:1202.3725, 2012
I. Kononenko, Estimating attributes: analysis and extensions of RELIEF, in European Conference on Machine Learning (Springer, Berlin, 1994), pp. 171–182
L. Yu, H. Liu, Feature selection for high-dimensional data: a fast correlation-based filter solution, in Proceedings of the 20th International Conference on Machine Learning (ICML-03) (2003), pp. 856–863
H. Peng, F. Long, C. Ding, Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans. Pattern Anal. Mach. Intell. 8, 1226–1238 (2005)
M. A. Hall, Correlation-based feature selection for machine learning (1999)
J. Li et al., Feature selection: a data perspective. ACM Comput. Sur. (CSUR) 50(6), 94 (2018)
A. Rouhi and H. Nezamabadi-Pour, A hybrid method for dimensionality reduction in microarray data based on advanced binary ant colony algorithm, in 2016 1st Conference on Swarm Intelligence and Evolutionary Computation (CSIEC) (IEEE, Piscataway, 2016), pp. 70–75
N. Taheri, H. Nezamabadi-Pour, A hybrid feature selection method for high-dimensional data, in 2014 4th International Conference on Computer and Knowledge Engineering (ICCKE) (IEEE, Piscataway, 2014), pp. 141–145
X. He, D. Cai, P. Niyogi, Laplacian score for feature selection, in Advances in Neural Information Processing Systems, (ACM, New York, 2006), pp. 507–514
M.A. Hall, L.A. Smith, Feature selection for machine learning: comparing a correlation-based filter approach to the wrapper, in FLAIRS Conference, vol. 1999 (1999), pp. 235–239
W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Numerical recipes in C++. Art Sci. Comput. 2, 1002 (1992)
J.C. Davis, R.J. Sampson, Statistics and Data Analysis in Geology (Wiley, New York, 1986)
H. Lee et al., Feature selection practice for unsupervised learning of credit card fraud detection. J. Theor. Appl. Inf. Technol. 96(2), 408–417 (2018)
Y. Saeys, I. Inza, P. Larrañaga, A review of feature selection techniques in bioinformatics. Bioinformatics 23(19), 2507–2517 (2007)
A. Rouhi, H. Nezamabadi-pour, A hybrid-ensemble based framework for microarray data gene selection. Int. J. Data Min. Bioinform. 19(3), 221–242 (2017)
S. Kashef, H. Nezamabadi-pour, B. Nikpour, Multilabel feature selection: a comprehensive review and guiding experiments. Wiley Interdiscip. Rev. Data Min. Knowl. Disc. 8(2), e1240 (2018)
M. Dowlatshahi, V. Derhami, H. Nezamabadi-Pour, Ensemble of filter-based rankers to guide an epsilon-greedy swarm optimizer for high-dimensional feature subset selection. Information 8(4), 152 (2017)
M. Dorigo, G. di Caro, Ant colony optimization: a new meta-heuristic, in Proceedings of the 1999 Congress on Evolutionary Computation-CEC99 (Cat. No. 99TH8406), vol. 2 (IEEE, Piscataway, 1999), pp. 1470–1477
S. Kashef, H. Nezamabadi-pour, An advanced ACO algorithm for feature subset selection. Neurocomputing 147, 271–279 (2015)
J. Kennedy, Particle swarm optimization. Enc. Mach. Learn., 760–766 (2010)
E. Rashedi, H. Nezamabadi-Pour, S. Saryazdi, GSA: a gravitational search algorithm. Inf. Sci. 179(13), 2232–2248 (2009)
A. Mahanipour, H. Nezamabadi-Pour, A multiple feature construction method based on gravitational search algorithm. Expert Syst. Appl. 127, 199–209 (2019)
E. Rashedi, H. Nezamabadi-Pour, S. Saryazdi, BGSA: binary gravitational search algorithm. Nat. Comput. 9(3), 727–745 (2010)
E. Rashedi, H. Nezamabadi-pour, Feature subset selection using improved binary gravitational search algorithm. J. Intell. Fuzzy Syst. 26(3), 1211–1221 (2014)
A. Rouhi, P.H. Nezamabadi, A Hybrid-Based Feature Selection Method for High-Dimensional Data Using Ensemble Methods (2018)
V. Bolón-Canedo, N. Sánchez-Marono, A. Alonso-Betanzos, J.M. BenÃtez, F. Herrera, A review of microarray datasets and applied feature selection methods. Inf. Sci. 282, 111–135 (2014)
P.A. Mundra, J.C. Rajapakse, SVM-RFE with MRMR filter for gene selection. IEEE Trans. Nanobioscience 9(1), 31–37 (2009)
H. Uğuz, A two-stage feature selection method for text categorization by using information gain, principal component analysis and genetic algorithm. Knowl.-Based Syst. 24(7), 1024–1032 (2011)
L.-Y. Chuang, C.-H. Yang, K.-C. Wu, C.-H. Yang, A hybrid feature selection method for DNA microarray data. Comput. Biol. Med. 41(4), 228–237 (2011)
C.-P. Lee, Y. Leu, A novel hybrid feature selection method for microarray data analysis. Appl. Soft Comput. 11(1), 208–213 (2011)
S.S. Shreem, S. Abdullah, M.Z.A. Nazri, M. Alzaqebah, Hybridizing ReliefF, MRMR filters and GA wrapper approaches for gene selection. J. Theor. Appl. Inf. Technol. 46(2), 1034–1039 (2012)
J. Apolloni, G. Leguizamón, E. Alba, Two hybrid wrapper-filter feature selection algorithms applied to high-dimensional microarray experiments. Appl. Soft Comput. 38, 922–932 (2016)
B. Venkatesh, J. Anuradha, A hybrid feature selection approach for handling a high-dimensional data, in Innovations in Computer Science and Engineering, (Springer, Berlin, 2019), pp. 365–373
Z. Manbari, F. AkhlaghianTab, C. Salavati, Hybrid fast unsupervised feature selection for high-dimensional data. Expert Syst. Appl. 124, 97–118 (2019)
C. Yan, J. Liang, M. Zhao, X. Zhang, T. Zhang, H. Li, A novel hybrid feature selection strategy in quantitative analysis of laser-induced breakdown spectroscopy. Anal. Chim. Acta 1080, 35–42 (2019)
T. Gangavarapu, N. Patil, A novel filter-wrapper hybrid greedy ensemble approach optimized using the genetic algorithm to reduce the dimensionality of high-dimensional biomedical datasets. Appl. Soft Comput. 81, 105538 (2019)
L. Sun, X. Kong, J. Xu, R. Zhai, S. Zhang, A hybrid gene selection method based on ReliefF and ant colony optimization algorithm for tumor classification. Sci. Rep. 9(1), 8978 (2019)
W. You, Z. Yang, G. Ji, PLS-based recursive feature elimination for high-dimensional small sample. Knowl.-Based Syst. 55, 15–28 (2014)
T. Prasartvit, A. Banharnsakun, B. Kaewkamnerdpong, T. Achalakul, Reducing bioinformatics data dimension with ABC-kNN. Neurocomputing 116, 367–381 (2013)
I. Guyon, J. Weston, S. Barnhill, V. Vapnik, Gene selection for cancer classification using support vector machines. Mach. Learn. 46(1–3), 389–422 (2002)
S. Maldonado, R. Weber, J. Basak, Simultaneous feature selection and classification using kernel-penalized support vector machines. Inf. Sci. 181(1), 115–128 (2011)
J. Canul-Reich, L.O. Hall, D.B. Goldgof, J.N. Korecki, S. Eschrich, Iterative feature perturbation as a gene selector for microarray data. Int. J. Pattern Recognit. Artif. Intell. 26(05), 1260003 (2012)
S. Maldonado, J. López, Dealing with high-dimensional class-imbalanced datasets: embedded feature selection for SVM classification. Appl. Soft Comput. 67, 94–105 (2018)
H. Liu, M. Zhou, Q. Liu, An embedded feature selection method for imbalanced data classification. IEEE/CAA J. Autom. Sin. 6(3), 703–715 (2019)
C. Peng, X. Wu, W. Yuan, X. Zhang, Y. Li, MGRFE: multilayer recursive feature elimination based on an embedded genetic algorithm for cancer classification. IEEE/ACM Trans. Comput. Biol. Bioinform. (2019). https://doi.org/10.1109/TCBB.2019.2921961
A.B. Brahim, M. Limam, Robust ensemble feature selection for high dimensional data sets, in 2013 International Conference on High Performance Computing & Simulation (HPCS) (IEEE, Piscataway, 2013), pp. 151–157
V. Bolón-Canedo, N. Sánchez-Marono, A. Alonso-Betanzos, Data classification using an ensemble of filters. Neurocomputing 135, 13–20 (2014)
F. Yang, K. Mao, Robust feature selection for microarray data based on multicriterion fusion. IEEE/ACM Trans. Comput. Biol. Bioinform. 8(4), 1080–1092 (2010)
V. Bolón-Canedo, N. Sánchez-Maroño, A. Alonso-Betanzos, An ensemble of filters and classifiers for microarray data classification. Pattern Recogn. 45(1), 531–539 (2012)
S. Sayed, M. Nassef, A. Badr, I. Farag, A nested genetic algorithm for feature selection in high-dimensional cancer microarray datasets. Expert Syst. Appl. 121, 233–243 (2019)
B. Pes, Ensemble feature selection for high-dimensional data: a stability analysis across multiple domains. Neural Comput. Applic., 1–23 (2019)
B. Singh, K. Kumar, S. Mohan, R. Ahmad, Ensemble of clustering approaches for feature selection of high dimensional data. Available at SSRN 3349018 (2019)
J. Wang, J. Xu, C. Zhao, Y. Peng, H. Wang, An ensemble feature selection method for high-dimensional data based on sort aggregation. Syst. Sci. Control Eng. 7(2), 32–39 (2019)
X. Song, L.R. Waitman, Y. Hu, A.S. Yu, D. Robins, M. Liu, Robust clinical marker identification for diabetic kidney disease with ensemble feature selection. J. Am. Med. Inform. Assoc. 26(3), 242–253 (2019)
V.P. Singh, D.J. Kalita, S. Tripathi, Classifying gene expression data of cancer using multistage ensemble of neural networks. Available at SSRN 3349578 (2019)
Feature Selection at Arizona State University. http://featureselection.asu.edu/datasets.php
B. Institute. Cancer Program Data Sets. http://www.broadinstitute.org/cgi-bin/cancer/datasets.cgi
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Rouhi, A., Nezamabadi-Pour, H. (2020). Feature Selection in High-Dimensional Data. In: Amini, M. (eds) Optimization, Learning, and Control for Interdependent Complex Networks. Advances in Intelligent Systems and Computing, vol 1123. Springer, Cham. https://doi.org/10.1007/978-3-030-34094-0_5
Download citation
DOI: https://doi.org/10.1007/978-3-030-34094-0_5
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-34093-3
Online ISBN: 978-3-030-34094-0
eBook Packages: EngineeringEngineering (R0)