Pascal Vaillant

Ludovic Brieulle, Chan Le Duc, Pascal Vaillant

We present in this paper a reformulation of the usual set-theoretical semantics of the description logic $\mathcal{ALC}$ with general TBoxes by using categorical language. In this setting, $\mathcal{ALC}$ concepts are represented as objects, concept subsumptions as arrows, and memberships as logical quantifiers over objects and arrows of categories. Such a category-based semantics provides a more modular representation of the semantics of $\mathcal{ALC}$. This feature allows us to define a sublogic of $\mathcal{ALC}$ by dropping the interaction between existential and universal restrictions, which would be responsible for an exponential complexity in space. Such a sublogic is undefinable in the usual set-theoretical semantics, We show that this sublogic is {\sc{PSPACE}} by proposing a deterministic algorithm for checking concept satisfiability which runs in polynomial space.

Pascal Vaillant

We propose an algorithm for approximative dictionary lookup, where altered strings are matched against reference forms. The algorithm makes use of a divergence function between strings -- broadly belonging to the family of edit distances; it finds dictionary entries whose distance to the search string is below a certain threshold. The divergence function is not the classical edit distance (DL distance); it is adaptable to a particular corpus, and is based on elementary alteration costs defined on character blocks, rather than on individual characters. Nous proposons un algorithme de recherche approximative de chaînes dans un dictionnaire à partir de formes altérées. Cet algorithme est fondé sur une fonction de divergence entre chaînes~ -- une sorte de distance d'édition: il recherche des entrées pour lesquelles la distance à la chaîne cherchée est inférieure à un certain seuil. La fonction utilisée n'est pas la distance d'édition classique (distance DL); elle est adaptée à un corpus, et se fonde sur la prise en compte de coûts d'altération élémentaires définis non pas sur des caractères, mais sur des sous-chaînes (des blocs de caractères).

Xavier Tannier, Nicolas Paris, Hugo Cisneros et al.

Objective: Natural language processing can help minimize human intervention in identifying patients meeting eligibility criteria for clinical trials, but there is still a long way to go to obtain a general and systematic approach that is useful for researchers. We describe two methods taking a step in this direction and present their results obtained during the n2c2 challenge on cohort selection for clinical trials. Materials and Methods: The first method is a weakly supervised method using an unlabeled corpus (MIMIC) to build a silver standard, by producing semi-automatically a small and very precise set of rules to detect some samples of positive and negative patients. This silver standard is then used to train a traditional supervised model. The second method is a terminology-based approach where a medical expert selects the appropriate concepts, and a procedure is defined to search the terms and check the structural or temporal constraints. Results: On the n2c2 dataset containing annotated data about 13 selection criteria on 288 patients, we obtained an overall F1-measure of 0.8969, which is the third best result out of 45 participant teams, with no statistically significant difference with the best-ranked team. Discussion: Both approaches obtained very encouraging results and apply to different types of criteria. The weakly supervised method requires explicit descriptions of positive and negative examples in some reports. The terminology-based method is very efficient when medical concepts carry most of the relevant information. Conclusion: It is unlikely that much more annotated data will be soon available for the task of identifying a wide range of patient phenotypes. One must focus on weakly or non-supervised learning methods using both structured and unstructured data and relying on a comprehensive representation of the patients.

Pascal Vaillant, Jean-Baptiste Lamy

A graphical language addresses the need to communicate medical information in a synthetic way. Medical concepts are expressed by icons conveying fast visual information about patients' current state or about the known effects of drugs. In order to increase the visual language's acceptance and usability, a natural language generation interface is currently developed. In this context, this paper describes the use of an informatics method ---graph transformation--- to prepare data consisting of concepts in an OWL-DL ontology for use in a natural language generation component. The OWL concept may be considered as a star-shaped graph with a central node. The method transforms it into a graph representing the deep semantic structure of a natural language phrase. This work may be of future use in other contexts where ontology concepts have to be mapped to half-formalized natural language expressions.