Jean-Cédric Chappelier | EPFL Graph Search

Jean-Cédric Chappelier est ingénieur diplômé et docteur de l'Ecole Nationale Supérieure des Télécommunications de Paris. Il est actuellement collaborateur scientifique et chargé de cours à l'Ecole Polytechnique Fédérale de Lausanne où il participe à l'activité de recherche et enseigne, entre autres, dans le domaine du traitement automatique des langues.

Agile text mining with Sherlok

Jean-Cédric Chappelier, Sean Lewis Hill, Renaud Luc Richardet

The successful development of an intelligent text mining application requires the collaboration of two main stakeholders: subject matter experts and text miners. In this paper, we describe a new methodology, agile text mining to improve that collaboration. Agile text mining is characterized by short development cycles, frequent tasks redefinition and continuous performance monitoring through integration tests. We introduce Sherlok, a system supporting the development of agile text mining applications and present an application to extract mention of neurons from a very large corpus of scientific articles. The resulting code and models are publicly available.

IEEE2015

Automatic target validation based on neuroscientific literature mining for tractography

Jocelyne Bloch, Jean-Cédric Chappelier, Bogdan Draganski, Sean Lewis Hill, Renaud Luc Richardet, David Slater, Xavier Vasques

Target identification for tractography studies requires solid anatomical knowledge validated by an extensive literature review across species for each seed structure to be studied. Manual literature review to identify targets for a given seed region is tedious and potentially subjective. Therefore, complementary approaches would be useful. We propose to use text-mining models to automatically suggest potential targets from the neuroscientific literature, full-text articles and abstracts, so that they can be used for anatomical connection studies and more specifically for tractography. We applied text-mining models to three structures: two well-studied structures, since validated deep brain stimulation targets, the internal globus pallidus and the subthalamic nucleus and, the nucleus accumbens, an exploratory target for treating psychiatric disorders. We performed a systematic review of the literature to document the projections of the three selected structures and compared it with the targets proposed by text-mining models, both in rat and primate (including human). We ran probabilistic tractography on the nucleus accumbens and compared the output with the results of the text-mining models and literature review. Overall, text-mining the literature could find three times as many targets as two man-weeks of curation could. The overall efficiency of the text-mining against literature review in our study was 98% recall (at 36% precision), meaning that over all the targets for the three selected seeds, only one target has been missed by text-mining. We demonstrate that connectivity for a structure of interest can be extracted from a very large amount of publications and abstracts. We believe this tool will be useful in helping the neuroscience community to facilitate connectivity studies of particular brain regions. The text mining tools used for the study are part of the HBP Neuroinformatics Platform, publicly available at http://connectivity-brainer.rhcloud.com/.

Frontiers Research Foundation2015

Large-scale extraction of brain connectivity from the neuroscientific literature

Jean-Cédric Chappelier, Sean Lewis Hill, Renaud Luc Richardet, Martin Telefont

In neuroscience, as in many other scientific domains, the primary form of knowledge dissemination is through published articles. One challenge for modern neuroinformatics is finding methods to make the knowledge from the tremendous backlog of publications accessible for search, analysis and the integration of such data into computational models. A key example of this is metascale brain connectivity, where results are not reported in a normalized repository. Instead, these experimental results are published in natural language, scattered among individual scientific publications. This lack of normalization and centralization hinders the large-scale integration of brain connectivity results. In this article, we present text-mining models to extract and aggregate brain connectivity results from 13.2 million PubMed abstracts and 630 216 full-text publications related to neuroscience. The brain regions are identified with three different named entity recognizers (NERs) and then normalized against two atlases: the Allen Brain Atlas (ABA) and the atlas from the Brain Architecture Management System (BAMS). We then use three different extractors to assess inter-region connectivity.

Oxford Univ Press2015

Automatic target validation based on neuroscientific literature mining for tractography

Jocelyne Bloch, Jean-Cédric Chappelier, Bogdan Draganski, Sean Lewis Hill, Renaud Luc Richardet, David Slater, Xavier Vasques

Frontiers Research Foundation2015