Improving Biomedical Document Retrieval by Mining Domain Knowledge

When research articles introduce new findings or concepts they typically relate them only to knowledge and domain concepts of immediate relevance. However, many domain concepts relevant for the article and its findings are omitted in the text. This may prevent us from retrieving articles of interest when executing a search query. Approaches such as probabilistic latent semantic indexing (PLSI) overcome this limitation by projecting terms in articles to a lower dimensional latent space and best possible matches in this space are identified. Nevertheless, this approach may not perform well enough if the number of explicit knowledge concepts in the articles is too small compared to the amount of knowledge in the domain. The objective of this paper is to address the problem by exploiting a domain knowledge layer: a rich network of associations among knowledge concepts in the domain of interest. We present a new document retrieval framework that i) extracts associations among knowledge concepts from many documents in the literature corpus; ii) and exploits them to improve the retrieval of relevant documents. We test our approach on the problem of retrieval of biomedical documents and show that it outperforms standard Lucene and BM25 information-retrieval methods