Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches

DOI10.1016/J.INS.2022.06.005MaRDI QIDQ6195191zbMATH OpenOpenAlexFDO

Authors

Publication date 13 March 2024

Published in Information Sciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2202.13884

zbMATH Keywords

biological sequence embeddingLyndon factorizationmachine learningread representation

Mathematics Subject Classification ID

Learning and adaptive systems in artificial intelligence (68T05) Protein sequences, DNA sequences (92D20)

Abstract: Feature embedding methods have been proposed in literature to represent sequences as numeric vectors to be used in some bioinformatics investigations, such as family classification and protein structure prediction. Recent theoretical results showed that the well-known Lyndon factorization preserves common factors in overlapping strings. Surprisingly, the fingerprint of a sequencing read, which is the sequence of lengths of consecutive factors in variants of the Lyndon factorization of the read, is effective in preserving sequence similarities, suggesting it as basis for the definition of novels representations of sequencing reads. We propose a novel feature embedding method for Next-Generation Sequencing (NGS) data using the notion of fingerprint. We provide a theoretical and experimental framework to estimate the behaviour of fingerprints and of the $k$-mers extracted from it, called $k$-fingers, as possible feature embeddings for sequencing reads. As a case study to assess the effectiveness of such embeddings, we use fingerprints to represent RNA-Seq reads and to assign them to the most likely gene from which they were originated as fragments of transcripts of the gene. We provide an implementation of the proposed method in the tool lyn2vec, which produces Lyndon-based feature embeddings of sequencing reads.

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Cited in

(1)

• Unveiling the connection between the Lyndon factorization and the canonical inverse Lyndon factorization via a border property

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