User Centered and Ontology Based InformationRetrieval System for Life Sciences

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 talk 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.
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OBIRS-feedback, une méthode de reformulation utilisant une ontologie de domaine

National audienceLes performances d'un système de recherche d'information (SRI) peuvent être dégradées en termes de précision du fait de la difficulté pour des utilisateurs à formuler précisément leurs besoins en information. La reformulation ou l'expansion de requêtes constitue une des réponses à ce problème dans le cadre des SRI. Dans cet article, nous proposons une nouvelle méthode de reformulation de requêtes conceptuelles qui, à partir de documents jugés pertinents par l'utilisateur et d'une ontologie de domaine, cherche un ensemble de concepts maximisant les performances du SRI. Celles-ci sont évaluées, de manière originale, à l'aide d'indicateurs dont une formalisation est proposée. Cette méthode a été évaluée en utilisant notre moteur OBIRS, l'ontologie de domaine MeSH et la collection de tests MuCHMORE

USI: a fast and accurate approach for conceptual document annotation

International audienceBackground : Semantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a domain ontology. In order to keep such applications up-to-date, new entities need to be frequently annotated to enrich the corpus. However, this task is time-consuming and requires a high-level of expertise in both the domain and the related ontology. Different strategies have thus been proposed to ease this indexing process, each one taking advantage from the features of the document.Results : In this paper we present USI (User-oriented Semantic Indexer), a fast and intuitive method for indexing tasks. We introduce a solution to suggest a conceptual annotation for new entities based on related already indexed documents. Our results, compared to those obtained by previous authors using the MeSH thesaurus and a dataset of biomedical papers, show that the method surpasses text-specific methods in terms of both quality and speed. Evaluations are done via usual metrics and semantic similarity.Conclusions : By only relying on neighbor documents, the User-oriented Semantic Indexer does not need a representative learning set. Yet, it provides better results than the other approaches by giving a consistent annotation scored with a global criterion instead of one score per concept

How ontology based information retrieval systems may benefit from lexical text analysis

International audienceThe exponential growth of available electronic data is almost useless without efficient tools to retrieve the right information at the right time. It is now widely acknowledged that information retrieval systems need to take semantics into account to enhance the use of available information. However, there is still a gap between the amounts of relevant information that can be accessed through optimized IRSs on the one hand, and users' ability to grasp and process a handful of relevant data at once on the other. This chapter shows how conceptual and lexical approaches may be jointly used to enrich document description. After a survey on semantic based methodologies designed to efficiently retrieve and exploit information, hybrid approaches are discussed. The original approach presented here benefits from both lexical and ontological document description, and combines them in a software architecture dedicated to information retrieval and rendering in specific domains

OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics

<p>Abstract</p> <p>Background</p> <p>Molecular sequence data have become the standard in modern day phylogenetics. In particular, several long-standing questions of mammalian evolutionary history have been recently resolved thanks to the use of molecular characters. Yet, most studies have focused on only a handful of standard markers. The availability of an ever increasing number of whole genome sequences is a golden mine for modern systematics. Genomic data now provide the opportunity to select new markers that are potentially relevant for further resolving branches of the mammalian phylogenetic tree at various taxonomic levels.</p> <p>Description</p> <p>The EnsEMBL database was used to determine a set of orthologous genes from 12 available complete mammalian genomes. As targets for possible amplification and sequencing in additional taxa, more than 3,000 exons of length > 400 bp have been selected, among which 118, 368, 608, and 674 are respectively retrieved for 12, 11, 10, and 9 species. A bioinformatic pipeline has been developed to provide evolutionary descriptors for these candidate markers in order to assess their potential phylogenetic utility. The resulting OrthoMaM (Orthologous Mammalian Markers) database can be queried and alignments can be downloaded through a dedicated web interface <url>http://kimura.univ-montp2.fr/orthomam</url>.</p> <p>Conclusion</p> <p>The importance of marker choice in phylogenetic studies has long been stressed. Our database centered on complete genome information now makes possible to select promising markers to a given phylogenetic question or a systematic framework by querying a number of evolutionary descriptors. The usefulness of the database is illustrated with two biological examples. First, two potentially useful markers were identified for rodent systematics based on relevant evolutionary parameters and sequenced in additional species. Second, a complete, gapless 94 kb supermatrix of 118 orthologous exons was assembled for 12 mammals. Phylogenetic analyses using probabilistic methods unambiguously supported the new placental phylogeny by retrieving the monophyly of Glires, Euarchontoglires, Laurasiatheria, and Boreoeutheria. Muroid rodents thus do not represent a basal placental lineage as it was mistakenly reasserted in some recent phylogenomic analyses based on fewer taxa. We expect the OrthoMaM database to be useful for further resolving the phylogenetic tree of placental mammals and for better understanding the evolutionary dynamics of their genomes, i.e., the forces that shaped coding sequences in terms of selective constraints.</p

Motion2Language, unsupervised learning of synchronized semantic motion segmentation

In this paper, we investigate building a sequence to sequence architecture for motion to language translation and synchronization. The aim is to translate motion capture inputs into English natural-language descriptions, such that the descriptions are generated synchronously with the actions performed, enabling semantic segmentation as a byproduct, but without requiring synchronized training data. We propose a new recurrent formulation of local attention that is suited for synchronous/live text generation, as well as an improved motion encoder architecture better suited to smaller data and for synchronous generation. We evaluate both contributions in individual experiments, using the standard BLEU4 metric, as well as a simple semantic equivalence measure, on the KIT motion language dataset. In a follow-up experiment, we assess the quality of the synchronization of generated text in our proposed approaches through multiple evaluation metrics. We find that both contributions to the attention mechanism and the encoder architecture additively improve the quality of generated text (BLEU and semantic equivalence), but also of synchronization. Our code is available at https://github.com/rd20karim/M2T-Segmentation/tree/mainComment: Published at Neural Computing and Application