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Representation learning applications in biological sequence analysis.

ABSTRACT: Although remarkable advances have been reported in high-throughput sequencing, the ability to aptly analyze a substantial amount of rapidly generated biological (DNA/RNA/protein) sequencing data remains a critical hurdle. To tackle this issue, the application of natural language processing (NLP) to biological sequence analysis has received increased attention. In this method, biological sequences are regarded as sentences while the single nucleic acids/amino acids or k-mers in these sequences represent the words. Embedding is an essential step in NLP, which performs the conversion of these words into vectors. Specifically, representation learning is an approach used for this transformation process, which can be applied to biological sequences. Vectorized biological sequences can then be applied for function and structure estimation, or as input for other probabilistic models. Considering the importance and growing trend for the application of representation learning to biological research, in the present study, we have reviewed the existing knowledge in representation learning for biological sequence analysis.

SUBMITTER: Iuchi H

PROVIDER: S-EPMC8190442 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Proper expression of the genes plays a vital role in the function of an organism. Recent advancements in DNA microarray technology allow for monitoring the expression level of thousands of genes. One of the important tasks in this context is to understand the underlying mechanisms of gene regulation. Recently, researchers have focused on identifying local DNA elements, or motifs to infer the relation between the expression and the nucleotide sequence of the gene. This study proposes a novel data adaptive representation approach for supervised learning to predict the response associated with the biological sequences. Biological sequences such as DNA and protein are a class of categorical sequences. In machine learning, categorical sequences are generally mapped to a lower dimensional representation for learning tasks to avoid problems with high dimensionality. The proposed method, namely SW-RF (sliding window-random forest), is a feature-based approach requiring two main steps to learn a representation for categorical sequences. In the first step, each sequence is represented by overlapping subsequences of constant length. Then a tree-based learner on this representation is trained to obtain a bag-of-words like representation which is the frequency of subsequences on the terminal nodes of the tree for each sequence. After representation learning, any classifier can be trained on the learned representation. A lasso logistic regression is trained on the learned representation to facilitate the identification of important patterns for the classification task. Our experiments show that proposed approach provides significantly better results in terms of accuracy on both synthetic data and DNA promoter sequence data. Moreover, a common problem for microarray datasets, namely missing values, is handled efficiently by the tree learners in SW-RF. Although the focus of this paper is on biological sequences, SW-RF is flexible in handling any categorical sequence data from different applications.

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Representation learning applications in biological sequence analysis.

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