Combining entity co-occurrence with specialized word embeddings to measure entity relation in Alzheimer’s disease

BACKGROUND: Extracting useful information from biomedical literature plays an important role in the development of modern medicine. In natural language processing, there have been rigorous attempts to find meaningful relationships between entities automatically by co-occurrence-based methods. It has been increasingly important to understand whether relationships exist, and if so how strong, between any two entities extracted from a large number of texts. One of the defining methods is to measure semantic similarity and relatedness between two entities. METHODS: We propose a hybrid ranking method that combines a co-occurrence approach considering both direct and indirect entity pair relationship with specialized word embeddings for measuring the relatedness of two entities. RESULTS: We evaluate the proposed ranking method comparatively with other well-known methods such as co-occurrence, Word2Vec, COALS (Correlated Occurrence Analog to Lexical Semantics), and random indexing by calculating top-ranked entities related to Alzheimer’s disease. In addition, we analyze gene, pathway, and gene–phenotype relationships. Overall, the proposed method tends to find more hidden relationships than the other methods. CONCLUSION: Our proposed method is able to select more useful related entities that not only highly co-occur but also have more indirect relations for the target entity. In pathway analysis, our proposed method shows superior performance at identifying (functional) cross clustering and higher-level pathways. Our proposed method, resulting from phenotype analysis, has an advantage in identifying the common genotype relating to phenotypes from biological literature.