Overview of the 2005 cross-language image retrieval track (ImageCLEF)

The purpose of this paper is to outline efforts from the 2005 CLEF crosslanguage image retrieval campaign (ImageCLEF). The aim of this CLEF track is to explore the use of both text and content-based retrieval methods for cross-language image retrieval. Four tasks were offered in the ImageCLEF track: a ad-hoc retrieval from an historic photographic collection, ad-hoc retrieval from a medical collection, an automatic image annotation task, and a user-centered (interactive) evaluation task that is explained in the iCLEF summary. 24 research groups from a variety of backgrounds and nationalities (14 countries) participated in ImageCLEF. In this paper we describe the ImageCLEF tasks, submissions from participating groups and summarise the main fndings

DCU@TRECMed 2012: Using ad-hoc baselines for domain-specific retrieval

This paper describes the first participation of DCU in the TREC Medical Records Track (TRECMed). We performed some initial experiments on the 2011 TRECMed data based on the BM25 retrieval model. Surprisingly, we found that the standard BM25 model with default parameters, performs comparable to the best automatic runs submitted to TRECMed 2011 and would have resulted in rank four out of 29 participating groups. We expected that some form of domain adaptation would increase performance. However, results on the 2011 data proved otherwise: concept-based query expansion decreased performance, and filtering and reranking by term proximity also decreased performance slightly. We submitted four runs based on the BM25 retrieval model to TRECMed 2012 using standard BM25, standard query expansion, result filtering, and concept-based query expansion. Official results for 2012 confirm that domain-specific knowledge does not increase performance compared to the BM25 baseline as applied by us

Overview of the ImageCLEFphoto 2008 photographic retrieval task

ImageCLEFphoto 2008 is an ad-hoc photo retrieval task and part of the ImageCLEF evaluation campaign. This task provides both the resources and the framework necessary to perform comparative laboratory-style evaluation of visual information retrieval systems. In 2008, the evaluation task concentrated on promoting diversity within the top 20 results from a multilingual image collection. This new challenge attracted a record number of submissions: a total of 24 participating groups submitting 1,042 system runs. Some of the findings include that the choice of annotation language is almost negligible and the best runs are by combining concept and content-based retrieval methods

Automatic annotation of X-ray images: a study on attribute selection

Advances in the medical imaging technology has lead to an exponential growth in the number of digital images that need to be acquired, analyzed, classified, stored and retrieved in medical centers. As a result, medical image classification and retrieval has recently gained high interest in the scientific community. Despite several attempts, the proposed solutions are still far from being sufficiently accurate for real-life implementations. In a previous work, performance of different feature types were investigated in a SVM-based learning framework for classification. of X-Ray images into classes corresponding to body parts and local binary patterns were observed to outperform others. In this paper, we extend that work by exploring the effect of attribute selection on the classification performance. Our experiments show that principal component analysis based attribute selection manifests prediction values that are comparable to the baseline (all-features case) with considerably smaller subsets of original features, inducing lower processing times and reduced storage space

Mining clinical relationships from patient narratives

Background The Clinical E-Science Framework (CLEF) project has built a system to extract clinically significant information from the textual component of medical records in order to support clinical research, evidence-based healthcare and genotype-meets-phenotype informatics. One part of this system is the identification of relationships between clinically important entities in the text. Typical approaches to relationship extraction in this domain have used full parses, domain-specific grammars, and large knowledge bases encoding domain knowledge. In other areas of biomedical NLP, statistical machine learning (ML) approaches are now routinely applied to relationship extraction. We report on the novel application of these statistical techniques to the extraction of clinical relationships. Results We have designed and implemented an ML-based system for relation extraction, using support vector machines, and trained and tested it on a corpus of oncology narratives hand-annotated with clinically important relationships. Over a class of seven relation types, the system achieves an average F1 score of 72%, only slightly behind an indicative measure of human inter annotator agreement on the same task. We investigate the effectiveness of different features for this task, how extraction performance varies between inter- and intra-sentential relationships, and examine the amount of training data needed to learn various relationships. Conclusion We have shown that it is possible to extract important clinical relationships from text, using supervised statistical ML techniques, at levels of accuracy approaching those of human annotators. Given the importance of relation extraction as an enabling technology for text mining and given also the ready adaptability of systems based on our supervised learning approach to other clinical relationship extraction tasks, this result has significance for clinical text mining more generally, though further work to confirm our encouraging results should be carried out on a larger sample of narratives and relationship types

ImageCLEF 2014: Overview and analysis of the results

This paper presents an overview of the ImageCLEF 2014 evaluation lab. Since its first edition in 2003, ImageCLEF has become one of the key initiatives promoting the benchmark evaluation of algorithms for the annotation and retrieval of images in various domains, such as public and personal images, to data acquired by mobile robot platforms and medical archives. Over the years, by providing new data collections and challenging tasks to the community of interest, the ImageCLEF lab has achieved an unique position in the image annotation and retrieval research landscape. The 2014 edition consists of four tasks: domain adaptation, scalable concept image annotation, liver CT image annotation and robot vision. This paper describes the tasks and the 2014 competition, giving a unifying perspective of the present activities of the lab while discussing future challenges and opportunities.This work has been partially supported by the tranScriptorium FP7 project under grant #600707 (M. V., R. 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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

Improving patient record search: A meta-data based approach

The International Classification of Diseases (ICD) is a type of meta-data found in many Electronic Patient Records. Research to explore the utility of these codes in medical Information Retrieval (IR) applications is new, and many areas of investigation remain, including the question of how reliable the assignment of the codes has been. This paper proposes two uses of the ICD codes in two different contexts of search: Pseudo-Relevance Judgments (PRJ) and Pseudo-Relevance Feedback (PRF). We find that our approach to evaluate the TREC challenge runs using simulated relevance judgments has a positive correlation with the TREC official results, and our proposed technique for performing PRF based on the ICD codes significantly outperforms a traditional PRF approach. The results are found to be consistent over the two years of queries from the TREC medical test collection

Test collections for medical information retrieval evaluation

The web has rapidly become one of the main resources for medical information for many people: patients, clinicians, medical doctors, etc. Measuring the effectiveness with which information can be retrieved from web resources for these users is crucial: it brings better information to professionals for better diagnosis, treatment, patient care; and helps patients and relatives get informed on their condition. Several existing information retrieval (IR) evaluation campaigns have been developed to assess and improve medical IR methods, for example the TREC Medical Record Track [11] and TREC Genomics Track [10]. These campaigns only target certain type of users, mainly clinicians and some medical professionals: queries are mainly centered on cohorts of records describing a specific patient cases or on biomedical reports. Evaluating search effectiveness over the many heterogeneous online medical information sources now available, which are increasingly used by a diverse range of medical professionals and, very importantly, the general public, is vital to the understanding and development of medical IR. We describe the development of two benchmarks for medical IR evaluation from the Khresmoi project. The first of these has been developed using existing medical query logs for internal research within the Khresmoi project and targets both medical professionals and general public; the second has been created in the framework of a new CLEFeHealth evaluation campaign and is designed to evaluate patient search in context