Computational and structural biotechnology journal
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Comput Struct Biotechnol J · Jan 2021
ReviewThe language of proteins: NLP, machine learning & protein sequences.
Natural language processing (NLP) is a field of computer science concerned with automated text and language analysis. In recent years, following a series of breakthroughs in deep and machine learning, NLP methods have shown overwhelming progress. Here, we review the success, promise and pitfalls of applying NLP algorithms to the study of proteins. ⋯ We present methods for encoding the information of proteins as text and analyzing it with NLP methods, reviewing classic concepts such as bag-of-words, k-mers/n-grams and text search, as well as modern techniques such as word embedding, contextualized embedding, deep learning and neural language models. In particular, we focus on recent innovations such as masked language modeling, self-supervised learning and attention-based models. Finally, we discuss trends and challenges in the intersection of NLP and protein research.