Performance evaluation of unified medical language system®'s synonyms expansion to query PubMed

<p>Abstract</p> <p>Background</p> <p>PubMed is the main access to medical literature on the Internet. In order to enhance the performance of its information retrieval tools, primarily non-indexed citations, the authors propose a method: expanding users' queries using Unified Medical Language System' (UMLS) synonyms i.e. all the terms gathered under one unique Concept Unique Identifier.</p> <p>Methods</p> <p>This method was evaluated using queries constructed to emphasize the differences between this new method and the current PubMed automatic term mapping. Four experts assessed citation relevance.</p> <p>Results</p> <p>Using UMLS, we were able to retrieve new citations in 45.5% of queries, which implies a small increase in recall. The new strategy led to a heterogeneous 23.7% mean increase in non-indexed citation retrieved. Of these, 82% have been published less than 4 months earlier. The overall mean precision was 48.4% but differed according to the evaluators, ranging from 36.7% to 88.1% (Inter rater agreement was poor: kappa = 0.34).</p> <p>Conclusions</p> <p>This study highlights the need for specific search tools for each type of user and use-cases. The proposed strategy may be useful to retrieve recent scientific advancement.</p

Improving semantic information retrieval by combining possibilistic networks, vector space model and pseudo-relevance feedback

International audienceTo improve the performance of information retrieval systems (IRSs), we propose in this article a novel approach that enriches the user’s queries with new concepts. Indeed, query expansion is one of the best methods that plays an important role in improving searches for a better semantic information retrieval. The proposed approach in this study combines possibilistic networks (PNs), the vector space model (VSM) and pseudo-relevance feedback (PRF) to evaluate and add relevant concepts to the initial index of the user’s query. First, query expansion is performed using PN, VSM and domain knowledge. PRF is then exploited to enrich, in a second round, the user’s query by applying the same approach used in the first expansion step. To evaluate the performance of the developed system, denoted conceptual information retrieval model (CIRM), several experiments of query expansion are performed. The experiments carried out on the OHSUMED and Clinical Trials corpora showed that using the two measures of possibility and necessity combined the cosinus similarity and PRF improves the query expansion process. Indeed, the improvement rate of our approach compared with the baseline is +28, 49% in terms of P@5

Indexing biomedical documents with Bayesian networks and terminologies

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Indexing biomedical documents with a possibilistic network

International audienceIn this article, we propose a new approach for indexing biomedical documents based on a possibilistic network that carries out partial matching between documents and biomedical vocabulary. The main contribution of our approach is to deal with the imprecision and uncertainty of the indexing task using possibility theory. We enhance estimation of the similarity between a document and a given concept using the two measures of possibility and necessity. Possibility estimates the extent to which a document is not similar to the concept. The second measure can provide confirmation that the document is similar to the concept. Our contribution also reduces the limitation of partial matching. Although the latter allows extracting from the document other variants of terms than those in dictionaries, it also generates irrelevant information. Our objective is to filter the index using the knowledge provided by the Unified Medical Language System®. Experiments were carried out on different corpora, showing encouraging results (the improvement rate is +26.37% in terms of main average precision when compared with the baseline)

Biomedical Concepts Extraction Based on Possibilistic Network and Vector Space Model

International audienceThis paper proposes a new approach for indexing biomedical documents based on the combination of a Possibilistic Network and a Vector Space Model. This later carries out partial matching between documents and biomedical vocabularies. The main contribution of the proposed approach is to combine the cosine similarity and the two measures of possibility and necessity to enhance the estimation of the similarity between a document and a given concept. The possibility estimates the extent to which a document is not similar to the concept. The necessity allows the confirmation that the document is similar to the concept. Experiments were carried out on the OSHUMED corpora and showed encouraging results