The MeSH-gram Neural Network Model: Extending Word Embedding Vectors with MeSH Concepts for UMLS Semantic Similarity and Relatedness in the Biomedical Domain

Eliciting semantic similarity between concepts in the biomedical domain remains a challenging task. Recent approaches founded on embedding vectors have gained in popularity as they risen to efficiently capture semantic relationships The underlying idea is that two words that have close meaning gather similar contexts. In this study, we propose a new neural network model named MeSH-gram which relies on a straighforward approach that extends the skip-gram neural network model by considering MeSH (Medical Subject Headings) descriptors instead words. Trained on publicly available corpus PubMed MEDLINE, MeSH-gram is evaluated on reference standards manually annotated for semantic similarity. MeSH-gram is first compared to skip-gram with vectors of size 300 and at several windows contexts. A deeper comparison is performed with tewenty existing models. All the obtained results of Spearman's rank correlations between human scores and computed similarities show that MeSH-gram outperforms the skip-gram model, and is comparable to the best methods but that need more computation and external resources.Comment: 6 pages, 2 table

Comparative Analysis of Word Embeddings for Capturing Word Similarities

Distributed language representation has become the most widely used technique for language representation in various natural language processing tasks. Most of the natural language processing models that are based on deep learning techniques use already pre-trained distributed word representations, commonly called word embeddings. Determining the most qualitative word embeddings is of crucial importance for such models. However, selecting the appropriate word embeddings is a perplexing task since the projected embedding space is not intuitive to humans. In this paper, we explore different approaches for creating distributed word representations. We perform an intrinsic evaluation of several state-of-the-art word embedding methods. Their performance on capturing word similarities is analysed with existing benchmark datasets for word pairs similarities. The research in this paper conducts a correlation analysis between ground truth word similarities and similarities obtained by different word embedding methods.Comment: Part of the 6th International Conference on Natural Language Processing (NATP 2020

Insights into Analogy Completion from the Biomedical Domain

Analogy completion has been a popular task in recent years for evaluating the semantic properties of word embeddings, but the standard methodology makes a number of assumptions about analogies that do not always hold, either in recent benchmark datasets or when expanding into other domains. Through an analysis of analogies in the biomedical domain, we identify three assumptions: that of a Single Answer for any given analogy, that the pairs involved describe the Same Relationship, and that each pair is Informative with respect to the other. We propose modifying the standard methodology to relax these assumptions by allowing for multiple correct answers, reporting MAP and MRR in addition to accuracy, and using multiple example pairs. We further present BMASS, a novel dataset for evaluating linguistic regularities in biomedical embeddings, and demonstrate that the relationships described in the dataset pose significant semantic challenges to current word embedding methods.Comment: Accepted to BioNLP 2017. (10 pages