Full lists of publication

Year of Publication
Variomes: a high recall search engine to support the curation of genomic variants 2021
Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora 2021
CINECA synthetic cohort Europe CH SIB [CC-BY-NC- SA] 2021
Analyzing the information content of text-based files in supplementary materials of biomedical literature 2021
Contextualized French Language Models for Biomedical Named Entity Recognition 2020
UPCLASS: a deep learning-based classifier for UniProtKB entry publications 2020
Named entity recognition in chemical patents using ensemble of contextual language models 2020
An extended overview of the CLEF 2020 ChEMU Lab : information extraction of chemical reactions from patents 2020
BiTeM at WNUT 2020 Shared Task-1: Named Entity Recognition over Wet Lab Protocols using an Ensemble of Contextual Language Models 2020
Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology. 2020
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. 2020
SIB text mining at TREC precision medicine 2020 2020
A Baseline Approach for Early Detection of Signs of Anorexia and Self-harm in Reddit Posts 2019
A Data-Driven Approach for Measuring the Severity of the Signs of Depression using Reddit Posts 2019
Designing retrieval models to contrast precision-driven ad hoc search vs. recall-driven treatment extraction in Precision Medicine. 2019
Assistance à la curation de publications scientifiques par des méthodes de triage et d’annotation automatiques 2019
Customizing a Variant Annotation-Support Tool: an Inquiry into Probability Ranking Principles for TREC Precision Medicine 2018
ORBDA: An openEHR benchmark dataset for performance assessment of electronic health record servers 2018
Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt 2018
Triage by ranking to support the curation of protein interactions 2017
Development and Evaluation of a Case-Based Retrieval Service. 2017
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. 2016
BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction 2016
Le plaisir de tout conserver sans modération : une question de taille ? 2016
Deep Question Answering for protein annotation. 2015
Instance-Based Learning for Tweet Monitoring and Categorization 2015
Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. 2014
Instance-based Learning for Tweet Categorization in {CLEF} RepLab 2014 2014
Electronic processing of informed consents in a global pharmaceutical company environment. 2014
Development and tuning of an original search engine for patent libraries in medicinal chemistry. 2014
Practical implementation of a bridge between legacy EHR system and a clinical research environment. 2014
Overview of the gene ontology task at BioCreative IV. 2014
Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. 2013
Managing biomedical knowledge: computer-assisted knowledge acquisition and authoring in highly specialized domains 2013
Assisted Knowledge Discovery for the Maintenance of Clinical Guidelines 2013
Utilization of ontology look-up services in information retrieval for biomedical literature. 2013
Application of text-mining for updating protein post-translational modification annotation in UniProtKB. 2013
Use of controlled vocabularies to improve biomedical information retrieval tasks. 2013
Electronic processing of informed consents in a global pharmaceutical company environment. 2013
Using a Question-Answering Approach In Machine Reading Task Of Biomedical Texts About The Alzheimer Disease 2013
The COMBREX project: design, methodology, and initial results. 2013
Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database 2012
A medical informatics perspective on decision support systems. Findings from the yearbook 2012 section on decision support 2012
Building a transnational biosurveillance network using semantic web technologies: requirements, design, and preliminary evaluation 2012
Building a transnational biosurveillance network using semantic web technologies: requirements, design, and preliminary evaluation 2012
Pathogens and Gene Product Normalization in the Biomedical Literature 2012
An advanced search engine for patent analytics in medicinal chemistry. 2012
Assister la création de guides de bonnes pratiques par des techniques de recherche d’information 2012
Development of a text search engine for medicinal chemistry patents 2012
Selection of relevant articles for curation for the Comparative Toxicogenomic Database 2012
A user-friendly tool for medical-related patent retrieval. 2012
System zur Unterstützung der Kuration der Toxikogenomik in der medizinischen Literatur 2012
Classification and prioritization of biomedical literature for the comparative toxicogenomics database. 2012
The gene normalization task in BioCreative III 2011
A cross-site antimicrobial resistance surveillance system using semantic web technologies 2011
A medical informatics perspective on health informatics 3.0. Findings from the yearbook 2011 section on health informatics 3.0 2011
BiTeM group report for TREC Medical Records Track 2011 2011
Interoperability driven integration of biomedical data sources 2011
Exchanging biomedical information at large scale using the Semantic Web 2011
Using multimodal mining to drive clinical guidelines development. 2011
Improving the transparency of health information found on the internet through the honcode: a comparative study. 2011
Enriching the trustworthiness of health-related web pages. 2011
KART, a knowledge authoring and refinement tool for clinical guidelines development 2011
The gene normalization task in BioCreative III. 2011
Pathogens and Genome Normalization for Literature-based Knowledge Discovery 2011
The CMS CERN Analysis Facility (CAF) 2010
Ensuring HL7-based information model requirements within an ontology framework. 2010
Automatic Prior Art Searching and Patent Encoding at CLEF-IP '10 2010
The DebugIT core ontology: semantic integration of antibiotics resistance patterns 2010
Simple Pre and Post Processing Strategies for Patent Searching in CLEF Intellectual Property Track 2009 2010
Automatic IPC encoding and novelty tracking for effective patent mining 2010
The Information Quality Triangle: a methodology to assess clinical information quality. 2010
BiTeM site report for TREC Chemistry 2010: Impact of Citations Feedback for Patent Prior Art Search and Chemical Compounds Expansion for Ad Hoc Retrieval 2010
Closing the loops in biomedical informatics from theory to daily practice. 2009
BIND: Biomedical Novelty Detection 2009
Question answering for biology and medicine 2009
Comparing a Rule Based vs. Statistical System for Automatic Categorization of MEDLINE Documents According to Biomedical Specialty. 2009
Automatic medical knowledge acquisition using question-answering. 2009
Biomedical data management: a proposal framework. 2009
Report on the trec 2009 experiments: Chemical ir track 2009
DebugIT: building a European distributed clinical data mining network to foster the fight against microbial diseases. 2009
QA-driven guidelines generation for bacteriotherapy. 2009
Introducing meta-services for biomedical information extraction. 2008
Supervised approach to recognize question type in a QA system for health. 2008
Overview of BioCreative II gene normalization. 2008
The CMS data transfer test environment in preparation for LHC data taking 2008
Mapping proteins to disease terminologies: from UniProt to MeSH. 2008
Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. 2008
The CMS data transfer test environment in preparation for LHC data taking 2008
Automatic medical encoding with SNOMED categories. 2008
From episodes of care to diagnosis codes: automatic text categorization for medico-economic encoding. 2008
Combination of heterogeneous criteria for the automatic detection of ethical principles on health web sites. 2007
Automatic Retrieval of Web Pages with Standards of Ethics and Trustworthiness Within a Medical Portal: What a Page Name Tells Us 2007
Analyzing web log files of the health on the net HONmedia search engine to define typical image search tasks for image retrieval evaluation. 2007
Health on the Net Foundation: assessing the quality of health web pages all over the world. 2007
Machine learning approach for automatic quality criteria detection of health web pages. 2007
A multi-sample automatic system for in situ electrochemical X-ray diffraction synchrotron measurements. 2007
WRAPIN: a tool for patient empowerment within EHR. 2007
Reconciliation of ontology and terminology to cope with linguistics. 2007
Using discourse analysis to improve text categorization in MEDLINE. 2007
Challenges and methodology for indexing the computerized patient record. 2007
Design of a decentralized reusable research database architecture to support data acquisition in large research projects. 2007
Using argumentation to extract key sentences from biomedical abstracts. 2007
Health search engine with e-document analysis for reliable search results. 2006
Advancing biomedical image retrieval: development and analysis of a test collection. 2006
Automatic assignment of biomedical categories: toward a generic approach. 2006
Methodology to ease the construction of a terminology of problems. 2006
Using argumentation to retrieve articles with similar citations: an inquiry into improving related articles search in the MEDLINE digital library. 2006
Recent advances in natural language processing for biomedical applications. 2006
Data-poor categorization and passage retrieval for gene ontology annotation in Swiss-Prot. 2005
UMLF: a unified medical lexicon for French. 2005
Extracting key sentences with latent argumentative structuring. 2005
A benchmark evaluation of the French MeSH indexers 2005
Coping with the variability of medical terms. 2004
Birefringence in nonlinear anisotropic dielectric media 2004
WRAPIN: new generation health search engine using UMLS knowledge sources for MeSH term extraction from health documentation. 2004
UMLF: a Unified Medical Lexicon for French. 2003
A frame-based representation of ICD-10. 2003
Towards a unified medical lexicon for French. 2003
Using lexical disambiguation and named-entity recognition to improve spelling correction in the electronic patient record. 2003
The future of natural language processing for biomedical applications. 2002
Automatic extraction of MeSH terms from Medline abstracts 2002
«Intonation du discours et synthèse de la parole: premiers résultats d'une approche par balises» 2001
La synthese de l’intonation a partir de structures syntaxiques riches 2001
FipsVox: a French TTS based on a syntactic parser 2001
Comparing corpora and lexical ambiguity 2000
Syntax-based speech recognition: how a syntactic parser can help a recognition system 1999