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

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

The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LITS) organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2016 and International Conference On Medical Image Computing Computer Assisted Intervention (MICCAI) 2017. Twenty four valid state-of-the-art liver and liver tumor segmentation algorithms were applied to a set of 131 computed tomography (CT) volumes with different types of tumor contrast levels (hyper-/hypo-intense), abnormalities in tissues (metastasectomie) size and varying amount of lesions. The submitted algorithms have been tested on 70 undisclosed volumes. The dataset is created in collaboration with seven hospitals and research institutions and manually reviewed by independent three radiologists. We found that not a single algorithm performed best for liver and tumors. The best liver segmentation algorithm achieved a Dice score of 0.96(MICCAI) whereas for tumor segmentation the best algorithm evaluated at 0.67(ISBI) and 0.70(MICCAI). The LITS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource.Comment: conferenc

Data fusion by using machine learning and computational intelligence techniques for medical image analysis and classification

Data fusion is the process of integrating information from multiple sources to produce specific, comprehensive, unified data about an entity. Data fusion is categorized as low level, feature level and decision level. This research is focused on both investigating and developing feature- and decision-level data fusion for automated image analysis and classification. The common procedure for solving these problems can be described as: 1) process image for region of interest\u27 detection, 2) extract features from the region of interest and 3) create learning model based on the feature data. Image processing techniques were performed using edge detection, a histogram threshold and a color drop algorithm to determine the region of interest. The extracted features were low-level features, including textual, color and symmetrical features. For image analysis and classification, feature- and decision-level data fusion techniques are investigated for model learning using and integrating computational intelligence and machine learning techniques. These techniques include artificial neural networks, evolutionary algorithms, particle swarm optimization, decision tree, clustering algorithms, fuzzy logic inference, and voting algorithms. This work presents both the investigation and development of data fusion techniques for the application areas of dermoscopy skin lesion discrimination, content-based image retrieval, and graphic image type classification --Abstract, page v