A semi-automatic semantic method for mapping SNOMED CT concepts to VCM Icons

VCM (Visualization of Concept in Medicine) is an iconic language for representing key medical concepts by icons. However, the use of this language with reference terminologies, such as SNOMED CT, will require the mapping of its icons to the terms of these terminologies. Here, we present and evaluate a semi-automatic semantic method for the mapping of SNOMED CT concepts to VCM icons. Both SNOMED CT and VCM are compositional in nature; SNOMED CT is expressed in description logic and VCM semantics are formalized in an OWL ontology. The proposed method involves the manual mapping of a limited number of underlying concepts from the VCM ontology, followed by automatic generation of the rest of the mapping. We applied this method to the clinical findings of the SNOMED CT CORE subset, and 100 randomly-selected mappings were evaluated by three experts. The results obtained were promising, with 82 of the SNOMED CT concepts correctly linked to VCM icons according to the experts. Most of the errors were easy to fix

Ontopy : programmation orientée ontologie en Python

Ontopy a par la suite été renommé Owlready ; le contenu du module reste identique.International audienceLes ontologies et les modèles objets partagent un vocabulaire commun mais diffèrent dans leurs utilisations : l'ontologie permet d'effectuer des inférences et les modèles objets sont utilisés pour la programmation. Il est souvent nécessaire d'interfacer ontologie et programme objet. Plusieurs approches ont été proposées, de OWL API à la programmation orientée ontologie. Dans cet article, nous présentons Ontopy, un module de programmation orientée ontologie dynamique en Python, et nous prendrons pour exemple la comparaison des contre-indications des médicaments

Rainbow boxes: a technique for visualizing overlapping sets and an application to the comparison of drugs properties

International audienceOverlapping set visualization is a well-known problem in information visualization. This problem considers elements and sets containing all or part of the elements, a given element possibly belonging to more than one set. A typical example is the properties of the 20 amino-acids. A more complex application is the visual comparison of the contraindications or the adverse effects of several similar drugs. The knowledge involved is voluminous, each drug has many contraindications and adverse effects, some of them are shared with other drugs.In this paper, we present rainbow boxes, a novel technique for visualizing overlapping sets, and its application to the properties of amino-acids and to the comparison of drug properties. We also describe a user study comparing rainbow boxes to tables and showing that the former allowed physicians to find information significantly faster. We finally discuss the limits and the perspectives of rainbow boxes

Use of the C4.5 machine learning algorithm to test a clinical guideline-based decision support system.

International audienceWell-designed medical decision support system (DSS) have been shown to improve health care quality. However, before they can be used in real clinical situations, these systems must be extensively tested, to ensure that they conform to the clinical guidelines (CG) on which they are based. Existing methods cannot be used for the systematic testing of all possible test cases. We describe here a new exhaustive dynamic verification method. In this method, the DSS is considered to be a black box, and the Quinlan C4.5 algorithm is used to build a decision tree from an exhaustive set of DSS input vectors and outputs. This method was successfully used for the testing of a medical DSS relating to chronic diseases: the ASTI critiquing module for type 2 diabetes

Explainable artificial intelligence for breast cancer: A visual case-based reasoning approach

International audienceCase-Based Reasoning (CBR) is a form of analogical reasoning in which the solution for a (new) query case is determined using a database of previous known cases with their solutions. Cases similar to the query are retrieved from the database, and then their solutions are adapted to the query. In medicine, a case usually corresponds to a patient and the problem consists of classifying the patient in a class of diagnostic or therapy. Compared to "black box" algorithms such as deep learning, the responses of CBR systems can be justified easily using the similar cases as examples. However, this possibility is often under-exploited and the explanations provided by most CBR systems are limited to the display of the similar cases. In this paper, we propose a CBR method that can be both executed automatically as an algorithm and presented visually in a user interface for providing visual explanations or for visual reasoning. After retrieving similar cases, a visual interface displays quantitative and qualitative similarities between the query and the similar cases, so as one can easily classify the query through visual reasoning, in a fully explainable manner. It combines a quantitative approach (visualized by a scatter plot based on Multidimensional Scaling in polar coordinates , preserving distances involving the query) and a qualitative approach (set visualization using rainbow boxes). We applied this method to breast cancer management. We showed on three public datasets that our qualitative method has a classification accuracy comparable to k-Nearest Neighbors algorithms, but is better explainable. We also tested the proposed interface during a small user study. Finally, we apply the proposed approach to a real dataset in breast cancer. Medical experts found the visual approach interesting as it explains why cases are similar through the visualization of shared patient characteristics

Implementing Guideline-based, Experience-based, and Case-based approaches to enrich decision support for the management of breast cancer patients in the DESIREE project

DESIREE is a European-funded project to improve the management of primary breast cancer. We have developed three decision support systems (DSSs), a guideline-based, an experience-based, and a case-based DSSs, resp. GL-DSS, EXP-DSS, and CB-DSS, that operate simultaneously to offer an enriched multi-modal decision support to clinicians. A breast cancer knowledge model has been built to describe within a common ontology the data model and the termino-ontological knowledge used for representing breast cancer patient cases. It allows for rule-based and subsumption-based reasoning in the GL-DSS to provide best patient-centered reconciled care plans. It also allows for using semantic similarity in the retrieval algorithm implemented in the CB-DSS. Rainbow boxes are used to display patient cases similar to a given query patient. This innovative visualization technique translates the question of deciding the most appropriate treatment into a question of deciding the colour dominance among boxes

Reconciliation of Multiple Guidelines for Decision Support: A case study on the multidisciplinary management of breast cancer within the DESIREE project

Breast cancer is the most common cancer among women. DESIREE is a European project which aims at developing web-based services for the management of primary breast cancer by multidisciplinary breast units (BUs). We describe the guideline-based decision support system (GL-DSS) of the project. Various breast cancer clinical practice guidelines (CPGs) have been selected to be concurrently applied to provide state-of-the-art patient-specific recommendations. The aim is to reconcile CPG recommendations with the objective of complementarity to enlarge the number of clinical situations covered by the GL-DSS. Input and output data exchange with the GL-DSS is performed using FHIR. We used a knowledge model of the domain as an ontology on which relies the reasoning process performed by rules that encode the selected CPGs. Semantic web tools were used, notably the Euler/EYE inference engine, to implement the GL-DSS. "Rainbow boxes" are a synthetic tabular display used to visualize the inferred recommendations