Unsupervised and self-supervised deep learning approaches for biomedical text mining. Issue 2 (11th February 2021)

• Record Type: Journal Article
• Authors: Nadif, Mohamed; Role, François
• Is Part Of: Briefings in bioinformatics. Volume 22:Issue 2(2021)
• Page Start: 1592
• Page End: 1603
• Publication Date: 2021-02-11
• Subjects: unsupervised learning -- self-supervised learning -- deep learning -- text mining; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbab016
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Biomedical scientific literature is growing at a very rapid pace, which makes increasingly difficult for human experts to spot the most relevant results hidden in the papers. Automatized information extraction tools based on text mining techniques are therefore needed to assist them in this task. In the last few years, deep neural networks-based techniques have significantly contributed to advance the state-of-the-art in this research area. Although the contribution to this progress made by supervised methods is relatively well-known, this is less so for other kinds of learning, namely unsupervised and self-supervised learning. Unsupervised learning is a kind of learning that does not require the cost of creating labels, which is very useful in the exploratory stages of a biomedical study where agile techniques are needed to rapidly explore many paths. In particular, clustering techniques applied to biomedical text mining allow to gather large sets of documents into more manageable groups. Deep learning techniques have allowed to produce new clustering-friendly representations of the data. On the other hand, self-supervised learning is a kind of supervised learning where the labels do not have to be manually created by humans, but are automatically derived from relations found in the input texts. In combination with innovative network architectures (e.g. transformer-based architectures), self-supervised techniques have allowed to design increasingly effective vector-based word representations (word embeddings). We show in this survey how word representations obtained in this way have proven to successfully interact with common supervised modules (e.g. classification networks) to whose performance they greatly contribute.