Query expansion using medical information extraction for improving information retrieval in French medical domain

Many users’ queries contain references to named entities, and this is particularly true in the medical field. Doctors express their information needs using medical entities as they are elements rich with information that helps to better target the relevant documents. At the same time, many resources have been recognized as a large container of medical entities and relationships between them such as clinical reports; which are medical texts written by doctors. In this paper, we present a query expansion method that uses medical entities and their semantic relations in the query context based on an external resource in OWL. The goal of this method is to evaluate the effectiveness of an information retrieval system to support doctors in accessing easily relevant information. Experiments on a collection of real clinical reports show that our approach reveals interesting improvements in precision, recall and MAP in medical information retrieval

Natural language processing

Beginning with the basic issues of NLP, this chapter aims to chart the major research activities in this area since the last ARIST Chapter in 1996 (Haas, 1996), including: (i) natural language text processing systems - text summarization, information extraction, information retrieval, etc., including domain-specific applications; (ii) natural language interfaces; (iii) NLP in the context of www and digital libraries ; and (iv) evaluation of NLP systems

Adaptation of machine translation for multilingual information retrieval in the medical domain

Objective. We investigate machine translation (MT) of user search queries in the context of cross-lingual information retrieval (IR) in the medical domain. The main focus is on techniques to adapt MT to increase translation quality; however, we also explore MT adaptation to improve eectiveness of cross-lingual IR. Methods and Data. Our MT system is Moses, a state-of-the-art phrase-based statistical machine translation system. The IR system is based on the BM25 retrieval model implemented in the Lucene search engine. The MT techniques employed in this work include in-domain training and tuning, intelligent training data selection, optimization of phrase table configuration, compound splitting, and exploiting synonyms as translation variants. The IR methods include morphological normalization and using multiple translation variants for query expansion. The experiments are performed and thoroughly evaluated on three language pairs: Czech–English, German–English, and French–English. MT quality is evaluated on data sets created within the Khresmoi project and IR eectiveness is tested on the CLEF eHealth 2013 data sets. Results. The search query translation results achieved in our experiments are outstanding – our systems outperform not only our strong baselines, but also Google Translate and Microsoft Bing Translator in direct comparison carried out on all the language pairs. The baseline BLEU scores increased from 26.59 to 41.45 for Czech–English, from 23.03 to 40.82 for German–English, and from 32.67 to 40.82 for French–English. This is a 55% improvement on average. In terms of the IR performance on this particular test collection, a significant improvement over the baseline is achieved only for French–English. For Czech–English and German–English, the increased MT quality does not lead to better IR results. Conclusions. Most of the MT techniques employed in our experiments improve MT of medical search queries. Especially the intelligent training data selection proves to be very successful for domain adaptation of MT. Certain improvements are also obtained from German compound splitting on the source language side. Translation quality, however, does not appear to correlate with the IR performance – better translation does not necessarily yield better retrieval. We discuss in detail the contribution of the individual techniques and state-of-the-art features and provide future research directions

Multiple Retrieval Models and Regression Models for Prior Art Search

This paper presents the system called PATATRAS (PATent and Article Tracking, Retrieval and AnalysiS) realized for the IP track of CLEF 2009. Our approach presents three main characteristics: 1. The usage of multiple retrieval models (KL, Okapi) and term index definitions (lemma, phrase, concept) for the three languages considered in the present track (English, French, German) producing ten different sets of ranked results. 2. The merging of the different results based on multiple regression models using an additional validation set created from the patent collection. 3. The exploitation of patent metadata and of the citation structures for creating restricted initial working sets of patents and for producing a final re-ranking regression model. As we exploit specific metadata of the patent documents and the citation relations only at the creation of initial working sets and during the final post ranking step, our architecture remains generic and easy to extend

Bridging the Semantic Gap in Multimedia Information Retrieval: Top-down and Bottom-up approaches

Semantic representation of multimedia information is vital for enabling the kind of multimedia search capabilities that professional searchers require. Manual annotation is often not possible because of the shear scale of the multimedia information that needs indexing. This paper explores the ways in which we are using both top-down, ontologically driven approaches and bottom-up, automatic-annotation approaches to provide retrieval facilities to users. We also discuss many of the current techniques that we are investigating to combine these top-down and bottom-up approaches

Factors affecting the effectiveness of biomedical document indexing and retrieval based on terminologies

International audienceThe aim of this work is to evaluate a set of indexing and retrieval strategies based on the integration of several biomedical terminologies on the available TREC Genomics collections for an ad hoc information retrieval (IR) task.Materials and methodsWe propose a multi-terminology based concept extraction approach to selecting best concepts from free text by means of voting techniques. We instantiate this general approach on four terminologies (MeSH, SNOMED, ICD-10 and GO). We particularly focus on the effect of integrating terminologies into a biomedical IR process, and the utility of using voting techniques for combining the extracted concepts from each document in order to provide a list of unique concepts.ResultsExperimental studies conducted on the TREC Genomics collections show that our multi-terminology IR approach based on voting techniques are statistically significant compared to the baseline. For example, tested on the 2005 TREC Genomics collection, our multi-terminology based IR approach provides an improvement rate of +6.98% in terms of MAP (mean average precision) (p < 0.05) compared to the baseline. In addition, our experimental results show that document expansion using preferred terms in combination with query expansion using terms from top ranked expanded documents improve the biomedical IR effectiveness.ConclusionWe have evaluated several voting models for combining concepts issued from multiple terminologies. Through this study, we presented many factors affecting the effectiveness of biomedical IR system including term weighting, query expansion, and document expansion models. The appropriate combination of those factors could be useful to improve the IR performance

ShARe/CLEF eHealth evaluation lab 2014, task 3: user-centred health information retrieval

This paper presents the results of task 3 of the ShARe/CLEF eHealth Evaluation Lab 2014. This evaluation lab focuses on improving access to medical information on the web. The task objective was to investigate the effect of using additional information such as a related discharge summary and external resources such as medical ontologies on the IR effectiveness, in a monolingual and in a multilingual context. The participants were allowed to submit up to seven runs for each language, one mandatory run using no additional information or external resources, and three each using or not using discharge summaries

Use Case Oriented Medical Visual Information Retrieval & System Evaluation

Large amounts of medical visual data are produced daily in hospitals, while new imaging techniques continue to emerge. In addition, many images are made available continuously via publications in the scientific literature and can also be valuable for clinical routine, research and education. Information retrieval systems are useful tools to provide access to the biomedical literature and fulfil the information needs of medical professionals. The tools developed in this thesis can potentially help clinicians make decisions about difficult diagnoses via a case-based retrieval system based on a use case associated with a specific evaluation task. This system retrieves articles from the biomedical literature when querying with a case description and attached images. This thesis proposes a multimodal approach for medical case-based retrieval with focus on the integration of visual information connected to text. Furthermore, the ImageCLEFmed evaluation campaign was organised during this thesis promoting medical retrieval system evaluation