The Role of Document Structure and Citation Analysis in Literature Information Retrieval

Literature Information Retrieval (IR) is the task of searching relevant publications given a particular information need expressed as a set of queries. With the staggering growth of scientific literature, it is critical to design effective retrieval solutions to facilitate efficient access to them. We hypothesize that particular genre specific characteristics of scientific literature such as metadata and citations are potentially helpful for enhancing scientific literature search. We conducted systematic and extensive IR experiments on open information retrieval test collections to investigate their roles in enhancing literature information retrieval effectiveness. This thesis consists of three major parts of studies. First, we examined the role of document structure in literature search through comprehensive studies on the retrieval effectiveness of a set of structure-aware retrieval models on ad hoc scientific literature search tasks. Second, under the language modeling retrieval framework, we studied exploiting citation and co-citation analysis results as sources of evidence for enhancing literature search. Specifically, we examined relevant document distribution patterns over partitioned clusters of document citation and co-citation graphs; we examined seven ways of modeling document prior probabilities of being relevant based on document citation and co-citation analysis; we studied the effectiveness of boosting retrieved documents with scores of their neighborhood documents in terms co-citation counts, co-citation similarities and Howard White's pennant scores. Third, we combined both structured retrieval features and citation related features in developing machine learned retrieval models for literatures search and assessed the effectiveness of learning to rank algorithms and various literature-specific features. Our major findings are as follows. State-of-the-art structure-ware retrieval models though reportedly perform well in known item finding tasks do not significantly outperform non-fielded baseline retrieval models in ad hoc literature information retrieval. Though relevant document distributions over citation and co-citation network graph partitions reveal favorable pattern, citation and co-citation analysis results on the current iSearch test collection only modestly improve retrieval effectiveness. However, priors derived from co-citation analysis outperform that derived from citation analysis, and pennant score for document expansion outperforms raw co-citation count or cosine similarity of co-citation counts. Our learning to rank experiments show that in a heterogeneous collection setting, citation related features can significantly outperform baselines.Ph.D., Information Studies -- Drexel University, 201

Topic Signature Language Models for Ad Hoc Retrieval

Semantic smoothing, which incorporates synonym and sense information into the language models, is effective and potentially significant to improve retrieval performance. Previously implemented semantic smoothing models such as the translation model have shown good experimental results. However, these models are unable to incorporate contextual information. To overcome this limitation, we propose a novel context-sensitive semantic smoothing method that decomposes a document into a set of weighted context-sensitive topic signatures and then maps those topic signatures into query terms. The language model with such a contextsensitive semantic smoothing is referred to as the topic signature language model. In detail, we implement two types of topic signatures, depending on whether ontology exists in the application domain. One is the ontology-based concept and the other is the multiword phrase. The mapping probabilities from each topic signature to individual terms are estimated through the EM algorithm. Document models based on topic signature mapping are then derived. The new smoothing method is evaluated on the TREC 2004/ 2005 Genomics Track with ontology-based concepts, as well as the TREC Ad Hoc Track (Disks 1, 2, and 3) with multiword phrases. Both experiments show significant improvements over the two-stage language model, as well as the language model with contextinsensitive semantic smoothing

Accès à l'information biomédicale : vers une approche d'indexation et de recherche d'information conceptuelle basée sur la fusion de ressources termino-ontologiques

La recherche d'information (RI) est une discipline scientifique qui a pour objectif de produire des solutions permettant de sélectionner à partir de corpus d'information celle qui sont dites pertinentes pour un utilisateur ayant exprimé une requête. Dans le contexte applicatif de la RI biomédicale, les corpus concernent différentes sources d'information du domaine : dossiers médicaux de patients, guides de bonnes pratiques médicales, littérature scientifique du domaine médical etc. Les besoins en information peuvent concerner divers profils : des experts médicaux, des patients et leurs familles, des utilisateurs néophytes etc. Plusieurs défis sont liés spécifiquement à la RI biomédicale : la représentation "spécialisée" des documents, basés sur l'usage des ressources terminologiques du domaine, le traitement des synonymes, des acronymes et des abréviations largement pratiquée dans le domaine, l'accès à l'information guidé par le contexte du besoin et des profils des utilisateurs. Nos travaux de thèse s'inscrivent dans le domaine général de la RI biomédicale et traitent des défis de représentation de l'information biomédicale et de son accès. Sur le volet de la représentation de l'information, nous proposons des techniques d'indexation de documents basées sur : 1) la reconnaissance de concepts termino-ontologiques : cette reconnaissance s'apparente à une recherche approximative de concepts pertinents associés à un contenu, vu comme un sac de mots. La technique associée exploite à la fois la similitude structurelle des contenus informationnels des concepts vis-à-vis des documents mais également la similitude du sujet porté par le document et le concept, 2) la désambiguïsation des entrées de concepts reconnus en exploitant la branche liée au sous-domaine principal de la ressource termino-ontologique, 3) l'exploitation de différentes ressources termino-ontologiques dans le but de couvrir au mieux la sémantique du contenu documentaire. Sur le volet de l'accès à l'information, nous proposons des techniques d'appariement basées sur l'expansion combinée de requêtes et des documents guidées par le contexte du besoin en information d'une part et des contenus documentaires d'autre part. Notre analyse porte essentiellement sur l'étude de l'impact des différents paramètres d'expansion sur l'efficacité de la recherche : distribution des concepts dans les ressources ontologiques, modèle de fusion des concepts, modèle de pondération des concepts, etc. L'ensemble de nos contributions, en termes de techniques d'indexation et d'accès à l'information ont fait l'objet d'évaluation expérimentale sur des collections de test dédiées à la recherche d'information médicale, soit du point de vue de la tâche telles que TREC Medical track, CLEF Image, Medical case ou des collections de test telles que TREC Genomics.Information Retrieval (IR) is a scientific field aiming at providing solutions to select relevant information from a corpus of documents in order to answer the user information need. In the context of biomedical IR, there are different sources of information: patient records, guidelines, scientific literature, etc. In addition, the information needs may concern different profiles : medical experts, patients and their families, and other users ... Many challenges are specifically related to the biomedical IR : the document representation, the usage of terminologies with synonyms, acronyms, abbreviations as well as the access to the information guided by the context of information need and the user profiles. Our work is most related to the biomedical IR and deals with the challenges of the representation of biomedical information and the access to this rich source of information in the biomedical domain.Concerning the representation of biomedical information, we propose techniques and approaches to indexing documents based on: 1) recognizing and extracting concepts from terminologies : the method of concept extraction is basically based on an approximate lookup of candidate concepts that could be useful to index the document. This technique expoits two sources of evidence : (a) the content-based similarity between concepts and documents and (b) the semantic similarity between them. 2) disambiguating entry terms denoting concepts by exploiting the polyhierarchical structure of a medical thesaurus (MeSH - Medical Subject Headings). More specifically, the domains of each concept are exploited to compute the semantic similarity between ambiguous terms in documents. The most appropriate domain is detected and associated to each term denoting a particular concept. 3) exploiting different termino-ontological resources in an attempt to better cover the semantics of document contents. Concerning the information access, we propose a document-query matching method based on the combination of document and query expansion techniques. Such a combination is guided by the context of information need on one hand and the semantic context in the document on the other hand. Our analysis is essentially based on the study of factors related to document and query expansion that could have an impact on the IR performance: distribution of concepts in termino-ontological resources, fusion techniques for concept extraction issued from multiple terminologies, concept weighting models, etc