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Batet M.,Rovira i Virgili University | Harispe S.,2search Center | Ranwez S.,2search Center | Sanchez D.,Rovira i Virgili University | Ranwez V.,Montpellier SupAgro
Information Sciences | Year: 2014

Semantic similarity has become, in recent years, the backbone of numerous knowledge-based applications dealing with textual data. From the different methods and paradigms proposed to assess semantic similarity, ontology-based measures and, more specifically, those based on quantifying the Information Content (IC) of concepts are the most widespread solutions due to their high accuracy. However, these measures were designed to exploit a single ontology. They thus cannot be leveraged in many contexts in which multiple knowledge bases are considered. In this paper, we propose a new approach to achieve accurate IC-based similarity assessments for concept pairs spread throughout several ontologies. Based on Information Theory, our method defines a strategy to accurately measure the degree of commonality between concepts belonging to different ontologies - this is the cornerstone for estimating their semantic similarity. Our approach therefore enables classic IC-based measures to be directly applied in a multiple ontology setting. An empirical evaluation, based on well-established benchmarks and ontologies related to the biomedical domain, illustrates the accuracy of our approach, and demonstrates that similarity estimations provided by our approach are significantly more correlated with human ratings of similarity than those obtained via related works. © 2014 Elsevier Inc. All rights reserved.

Harispe S.,2search Center | Sanchez D.,Rovira i Virgili University | Ranwez S.,2search Center | Janaqi S.,2search Center | Montmain J.,2search Center
Journal of Biomedical Informatics | Year: 2014

Ontologies are widely adopted in the biomedical domain to characterize various resources (e.g. diseases, drugs, scientific publications) with non-ambiguous meanings. By exploiting the structured knowledge that ontologies provide, a plethora of ad hoc and domain-specific semantic similarity measures have been defined over the last years. Nevertheless, some critical questions remain: which measure should be defined/chosen for a concrete application? Are some of the, a priori different, measures indeed equivalent? In order to bring some light to these questions, we perform an in-depth analysis of existing ontology-based measures to identify the core elements of semantic similarity assessment. As a result, this paper presents a unifying framework that aims to improve the understanding of semantic measures, to highlight their equivalences and to propose bridges between their theoretical bases. By demonstrating that groups of measures are just particular instantiations of parameterized functions, we unify a large number of state-of-the-art semantic similarity measures through common expressions. The application of the proposed framework and its practical usefulness is underlined by an empirical analysis of hundreds of semantic measures in a biomedical context. © 2013 Elsevier Inc.

Ranwez S.,2search Center | Ranwez V.,Montpellier University | Sy M.-F.,2search Center | Montmain J.,2search Center | Crampes M.,2search Center
CEUR Workshop Proceedings | Year: 2010

Because of the increasing number of electronic data, designing efficient tools to retrieve and exploit documents is a major challenge. Current search engines suffer from two main drawbacks: there is limited interaction with the list of retrieved documents and no explanation for their adequacy to the query. Users may thus be confused by the selection and have no idea how to adapt their query so that the results match their expectations. This paper describes a request method and an environment based on aggregating models to assess the relevance of documents annotated by concepts of ontology. The selection of documents is then displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive exploration of data corpus.

Janaqi S.,2search Center | Harispe S.,2search Center | Ranwez S.,2search Center | Montmain J.,2search Center
Communications in Computer and Information Science | Year: 2014

Knowledge-based semantic measures are cornerstone to exploit ontologies not only for exact inferences or retrieval processes, but also for data analyses and inexact searches. Abstract theoretical frameworks have recently been proposed in order to study the large diversity of measures available; they demonstrate that groups of measures are particular instantiations of general parameterized functions. In this paper, we study how such frameworks can be used to support the selection/design of measures. Based on (i) a theoretical framework unifying the measures, (ii) a software solution implementing this framework and (iii) a domain-specific benchmark, we define a semi-supervised learning technique to distinguish best measures for a concrete application. Next, considering uncertainty in both experts' judgments and measures' selection process, we extend this proposal for robust selection of semantic measures that best resists to these uncertainties. We illustrate our approach through a real use case in the biomedical domain. © Springer International Publishing Switzerland 2014.

Harispe S.,2search Center | Ranwez S.,2search Center | Janaqi S.,2search Center | Montmain J.,2search Center
Bioinformatics | Year: 2014

The semantic measures library and toolkit are robust open-source and easy to use software solutions dedicated to semantic measures. They can be used for large-scale computations and analyses of semantic similarities between terms/concepts defined in terminologies and ontologies. The comparison of entities (e.g. genes) annotated by concepts is also supported. A large collection of measures is available. Not limited to a specific application context, the library and the toolkit can be used with various controlled vocabularies and ontology specifications (e.g. Open Biomedical Ontology, Resource Description Framework). The project targets both designers and practitioners of semantic measures providing a JAVA library, as well as a command-line tool that can be used on personal computers or computer clusters. © 2013 The Author 2013. Published by Oxford University Press. All rights reserved.

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