Learning a functional grammar of protein domains using natural language word embedding techniques
In this paper, using word2vec, a widely-used natural language processing method, we demonstrate that proteins domains may have a learnable implicit semantic "meaning" in the context of their functional contributions to multi-domain proteins in which they are found. Word2vec is a group of models which can be used to produce semantically meaningful embeddings of words or tokens in a fixed-dimension vector space. In this work, we treat multi-domain proteins as "sentences" where domain identifiers are tokens which may be considered as "words". Using all InterPro  pfam domain assignments we observe that the embedding could be used to suggest putative GO assignments for Pfam  Domains of Unknown Function. This article is protected by copyright. All rights reserved.
Issue number 4