PMCVec: Distributed phrase representation for biomedical text processing

Distributed semantic representation of biomedical text can be beneficial for text classification, named entity recognition, query expansion, human comprehension, and information retrieval. Despite the success of high-quality vector space models such as Word2Vec and GloVe, they only provide unigram word representations and the semantics for multi-word phrases can only be approximated by composition. This is problematic in biomedical text processing where technical phrases for diseases, symptoms, and drugs should be represented as single entities to capture the correct meaning. In this paper, we introduce PMCVec, an unsupervised technique that generates important phrases from PubMed abstracts and learns embeddings for single words and multi-word phrases simultaneously. Evaluations performed on benchmark datasets produce significant performance gains both qualitatively and quantitatively.