Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics. - Antoine Neuraz; Laurent Chouchana; Georgia Malamut; Christine Le Beller; Denis Roche; Philippe Beaune; Patrice Degoulet; Anita Burgun; Marie-Anne Loriot; Paul Avillach (PLoS Comput. Biol., 2013)

Improving a full-text search engine: the importance of negation detection and family history context to identify cases in a biomedical data warehouse. - Nicolas Garcelon; Antoine Neuraz; Vincent Benoit; Rémi Salomon; Anita Burgun (J. Am. Medical Informatics Assoc., 2017)

Finding patients using similarity measures in a rare diseases-oriented clinical data warehouse: Dr. Warehouse and the needle in the needle stack. - Nicolas Garcelon; Antoine Neuraz; Vincent Benoit; Rémi Salomon; Sven Kracker; Felipe Suarez; Nadia Bahi-Buisson; Smail Hadj-Rabia; Alain Fischer; Arnold Munnich; Anita Burgun (J. Biomed. Informatics, 2017)

Natural language understanding for task oriented dialog in the biomedical domain in a low resources context. - Antoine Neuraz; Leonardo Campillos-Llanos; Anita Burgun; Sophie Rosset (CoRR, 2018)

A Model-Based Reinforcement Learning Approach for a Rare Disease Diagnostic Task. - Rémi Besson; Erwan Le Pennec; Stéphanie Allassonnière; Julien Stirnemann; Emmanuel Spaggiari; Antoine Neuraz (CoRR, 2018)

A clinician friendly data warehouse oriented toward narrative reports: Dr. Warehouse. - Nicolas Garcelon; Antoine Neuraz; Rémi Salomon; Hassan Faour; Vincent Benoit; Arthur Delapalme; Arnold Munnich; Anita Burgun; Bastien Rance (J. Biomed. Informatics, 2018)

Evaluating the Impact of Text Duplications on a Corpus of More than 600, 000 Clinical Narratives in a French Hospital. - William Digan; Maxime Wack; Vincent Looten; Antoine Neuraz; Anita Burgun; Bastien Rance (MedInfo, 2019)

Do You Need Embeddings Trained on a Massive Specialized Corpus for Your Clinical Natural Language Processing Task? - Antoine Neuraz; Vincent Looten; Bastien Rance; Nicolas Daniel; Nicolas Garcelon; Leonardo Campillos-Llanos; Anita Burgun; Sophie Rosset (MedInfo, 2019)

What can millions of laboratory test results tell us about the temporal aspect of data quality? Study of data spanning 17 years in a clinical data warehouse. - Vincent Looten; Liliane Kong Win Chang; Antoine Neuraz; Marie-Anne Landau-Loriot; Benoit Vedie; Jean-Louis Paul; Laëtitia Mauge; Nadia Rivet; Angela Bonifati; Gilles Chatellier; Anita Burgun; Bastien Rance (Comput. Methods Programs Biomed., 2019)

Phenotypic similarity for rare disease: Ciliopathy diagnoses and subtyping. - Xiaoyi Chen; Nicolas Garcelon; Antoine Neuraz; Katy Billot; Marc Lelarge; Thomas Bonald; Hugo Garcia; Yoann Martin; Vincent Benoit; Marc Vincent; Hassan Faour; Maxime Douillet; et al. (J. Biomed. Informatics, 2019)

Optimization of a Sequential Decision Making Problem for a Rare Disease Diagnostic Application. - Rémi Besson; Erwan Le Pennec; Emmanuel Spaggiari; Antoine Neuraz; Julien Stirnemann; Stéphanie Allassonnière (ICAART (2), 2020)

What is best for spoken language understanding: small but task-dependant embeddings or huge but out-of-domain embeddings? - Sahar Ghannay; Antoine Neuraz; Sophie Rosset (ICASSP, 2020)

The Impact of Specialized Corpora for Word Embeddings in Natural Langage Understanding. - Antoine Neuraz; Bastien Rance; Nicolas Garcelon; Leonardo Campillos-Llanos; Anita Burgun; Sophie Rosset (MIE, 2020)

Learning the grammar of prescription: recurrent neural network grammars for medication information extraction in clinical texts. - Ivan Lerner; Jordan Jouffroy; Anita Burgun; Antoine Neuraz (CoRR, 2020)

Compréhension du langage naturel pour le dossier patient informatisé : accès à l'information et extraction d'information. (Natural language understanding for the electronic health records : access to information and information extraction). - Antoine Neuraz (2020)

Using Deep Learning to Improve Phenotyping from Clinical Reports. - Marc Vincent; Maxime Douillet; Ivan Lerner; Antoine Neuraz; Anita Burgun; Nicolas Garcelon (MedInfo, 2021)

Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites. - William Digan; Aurélie Névéol; Antoine Neuraz; Maxime Wack; David Baudoin; Anita Burgun; Bastien Rance (J. Am. Medical Informatics Assoc., 2021)

Lessons Learned from the Usability Evaluation of a Simulated Patient Dialogue System. - Leonardo Campillos-Llanos; Catherine Thomas; Éric Bilinski; Antoine Neuraz; Sophie Rosset; Pierre Zweigenbaum (J. Medical Syst., 2021)

Determining the Set of Items to Include in Breast Operative Reports, Using Clustering Algorithms on Retrospective Data Extracted from Clinical DataWarehouse. - Adrien Boukobza; Maxime Wack; Antoine Neuraz; Daniela Geromin; Cécile Badoual; Anne-Sophie Bats; Anita Burgun; Meriem Koual; Rosy Tsopra (ICIMTH, 2022)

Learning structures of the French clinical language: development and validation of word embedding models using 21 million clinical reports from electronic health records. - Basile Dura; Charline Jean; Xavier Tannier; Alice Calliger; Romain Bey; Antoine Neuraz; Rémi Flicoteaux (CoRR, 2022)

SurvMaximin: Robust federated approach to transporting survival risk prediction models. - Xuan Wang; Harrison G. Zhang; Xin Xiong; Chuan Hong; Griffin M. Weber; Gabriel A. Brat; Clara-Lea Bonzel; Yuan Luo 001; Rui Duan 004; Nathan P. Palmer; Meghan R. Hutch; Alba Gutiérrez-Sacristán; et al. (J. Biomed. Informatics, 2022)

International electronic health record-derived post-acute sequelae profiles of COVID-19 patients. - Harrison G. Zhang; Arianna Dagliati; Zahra Shakeri Hossein Abad; Xin Xiong; Clara-Lea Bonzel; Zongqi Xia; Bryce W. Q. Tan; Paul Avillach; Gabriel A. Brat; Chuan Hong; Michele Morris; Shyam Visweswaran; et al. (npj Digit. Medicine, 2022)

TAXN: Translate Align Extract Normalize, a Multilingual Extraction Tool for Clinical Texts. - Antoine Neuraz; Ivan Lerner; Olivier Birot; Camila Arias; Larry Han; Clara-Lea Bonzel; Tianxi Cai; Kim Tâm Huynh; Adrien Coulet (MedInfo, 2023)

The Smart Data Extractor, a Clinician Friendly Solution to Accelerate and Improve the Data Collection During Clinical Trials. - Sophie Quennelle; Maxime Douillet; Lisa Friedlander; Olivia Boyer; Antoine Neuraz; Anita Burgun; Nicolas Garcelon (MIE, 2023)

Extracting Diagnosis Pathways from Electronic Health Records Using Deep Reinforcement Learning. - Lillian Muyama; Antoine Neuraz; Adrien Coulet (CoRR, 2023)

Comparing NER Approaches on French Clinical Text, with Easy-to-Reuse Pipelines. - Thibault Hubert; Ghislain Vaillant; Olivier Birot; Camila Arias; Antoine Neuraz; Adrien Coulet (MIE, 2024)

Deep Reinforcement Learning for personalized diagnostic decision pathways using Electronic Health Records: A comparative study on anemia and Systemic Lupus Erythematosus. - Lillian Muyama; Antoine Neuraz; Adrien Coulet (Artif. Intell. Medicine, 2024)

Facilitating phenotyping from clinical texts: the medkit library. - Antoine Neuraz; Ghislain Vaillant; Camila Arias; Olivier Birot; Kim Tâm Huynh; Thibaut Fabacher; Alice Rogier; Nicolas Garcelon; Ivan Lerner; Bastien Rance; Adrien Coulet (CoRR, 2024)

Step-by-Step Guidance to Differential Anemia Diagnosis with Real-World Data and Deep Reinforcement Learning. - Lillian Muyama; Estelle Lu; Geoffrey Cheminet; Jacques Pouchot; Bastien Rance; Anne-Isabelle Tropeano; Antoine Neuraz; Adrien Coulet (CoRR, 2024)

Machine learning approaches for the discovery of clinical pathways from patient data: A systematic review. - Lillian Muyama; Antoine Neuraz; Adrien Coulet (J. Biomed. Informatics, 2024)

Active learning for extracting rare adverse events from electronic health records: A study in pediatric cardiology. - Sophie Quennelle; Sophie Malekzadeh-Milani; Nicolas Garcelon; Hassan Faour; Anita Burgun; Carole Faviez; Rosy Tsopra; Damien Bonnet; Antoine Neuraz (Int. J. Medical Informatics, 2025)