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Title (Primary) Information theory for biological sequence classification: A novel feature extraction technique based on Tsallis entropy
Author Bonidia, R.P.; Avila Santos, A.P.; Almeida, B.L.S.; Stadler, P.F.; Nunes da Rocha, U.; Sipoli Sanches, D.; de Carvalho, A.C.P.L.F.
Journal Entropy
Year 2022
Department UMB
Volume 24
Issue 10
Page From art. 1398
Language englisch
Topic T7 Bioeconomy
Data links https://github. com/Bonidia/TsallisEntropy—https://bonidia.github.io/MathFeature/entropy.html
Supplements https: //www.mdpi.com/article/10.3390/e24101398/s1
Keywords feature extraction; tsallis entropy; biological sequence; information theory
Abstract In recent years, there has been an exponential growth in sequencing projects due to accelerated technological advances, leading to a significant increase in the amount of data and resulting in new challenges for biological sequence analysis. Consequently, the use of techniques capable of analyzing large amounts of data has been explored, such as machine learning (ML) algorithms. ML algorithms are being used to analyze and classify biological sequences, despite the intrinsic difficulty in extracting and finding representative biological sequence methods suitable for them. Thereby, extracting numerical features to represent sequences makes it statistically feasible to use universal concepts from Information Theory, such as Tsallis and Shannon entropy. In this study, we propose a novel Tsallis entropy-based feature extractor to provide useful information to classify biological sequences. To assess its relevance, we prepared five case studies: (1) an analysis of the entropic index q; (2) performance testing of the best entropic indices on new datasets; (3) a comparison made with Shannon entropy and (4) generalized entropies; (5) an investigation of the Tsallis entropy in the context of dimensionality reduction. As a result, our proposal proved to be effective, being superior to Shannon entropy and robust in terms of generalization, and also potentially representative for collecting information in fewer dimensions compared with methods such as Singular Value Decomposition and Uniform Manifold Approximation and Projection.
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=26624
Bonidia, R.P., Avila Santos, A.P., Almeida, B.L.S., Stadler, P.F., Nunes da Rocha, U., Sipoli Sanches, D., de Carvalho, A.C.P.L.F. (2022):
Information theory for biological sequence classification: A novel feature extraction technique based on Tsallis entropy
Entropy 24 (10), art. 1398