Event-Based Information Extraction for the Biomedical Domain: the Caderige Project. - Érick Alphonse; Sophie Aubin; Philippe Bessières; Gilles Bisson; Thierry Hamon; Sandrine Lagarrigue; Adeline Nazarenko; Alain-Pierre Manine; Claire Nédellec; Mohamed Ould Abdel Vetah; Thierry Poibeau; Davy Weissenbacher (NLPBA/BioNLP, 2004)

La relation de synonymie en génomique. - Davy Weissenbacher (RECITAL, 2004)

Une infrastructure pour l'annotation linguistique de documents issus du web : le projet ALVIS. - Sophie Aubin; Julien Derivière; Thierry Hamon; Adeline Nazarenko; Thierry Poibeau; Davy Weissenbacher (AAFD, 2006)

Bayesian Network, a Model for NLP? - Davy Weissenbacher (EACL, 2006)

The ALVIS Format for Linguistically Annotated Documents. - Adeline Nazarenko; Érick Alphonse; Julien Derivière; Thierry Hamon; Guillaume Vauvert; Davy Weissenbacher (LREC, 2006)

Identifier les pronoms anaphoriques et trouver leurs antécédents : l'intérêt de la classification bayésienne. - Davy Weissenbacher; Adeline Nazarenko (TALN (Articles longs), 2007)

Les réseaux bayésiens : un formalisme adapté au traitement automatique des langues ? - Davy Weissenbacher (Rev. d'Intelligence Artif., 2007)

Influence des annotations imparfaites sur les systèmes de Traitement Automatique des Langues, un cadre applicatif: la résolution de l'anaphore pronominale. (Effects of imperfect annotations on Natural Language Processing systems, an applicative case study: the pronominal anaphora resolution). - Davy Weissenbacher (2008)

ASSIST : un moteur de recherche spécialisé pour l'analyse des cadres d'expériences. - Davy Weissenbacher; Elisa Pieri; Sophia Ananiadou; Brian Rea; Farida Vis; Yuwei Lin; Rob Procter; Peter Halfpenny (TALN (Demonstrations), 2009)

Understand the effects of erroneous annotations produced by NLP pipelines, a case study on the pronominal anaphora resolution. - Davy Weissenbacher; Adeline Nazarenko (Trait. Autom. des Langues, 2011)

Which Factors Contribute to Resolving Coreference Chains with Bayesian Networks?. - Davy Weissenbacher; Yutaka Sasaki (Int. J. Comput. Linguistics Appl., 2013)

Natural Language Processing Methods for Enhancing Geographic Metadata for Phylogeography of Zoonotic Viruses. - Tasnia Tahsin; Robert Rivera; Rachel Beard; Rob Lauder; Davy Weissenbacher; Matthew Scotch; Garrick L. Wallstrom; Graciela Gonzalez 001 (BioNLP@ACL, 2014)

Tree-Structured Named Entities Extraction from Competing Speech Transcriptions. - Davy Weissenbacher; Christian Raymond (NLDB, 2015)

DIEGOLab: An Approach for Message-level Sentiment Classification in Twitter. - Abeed Sarker; Azadeh Nikfarjam; Davy Weissenbacher; Graciela Gonzalez-Hernandez (SemEval@NAACL-HLT, 2015)

Knowledge-driven geospatial location resolution for phylogeographic models of virus migration. - Davy Weissenbacher; Tasnia Tahsin; Rachel Beard; Mari Figaro; Robert Rivera; Matthew Scotch; Graciela Gonzalez 001 (Bioinform., 2015)

Automatic Prediction of Linguistic Decline in Writings of Subjects with Degenerative Dementia. - Davy Weissenbacher; Travis A. Johnson; Laura Wojtulewicz; Amylou Dueck; Dona Locke; Richard J. Caselli; Graciela Gonzalez 001 (HLT-NAACL, 2016)

A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records. - Tasnia Tahsin; Davy Weissenbacher; Robert Rivera; Rachel Beard; Mari Firago; Garrick L. Wallstrom; Matthew Scotch; Graciela Gonzalez 001 (J. Am. Medical Informatics Assoc., 2016)

Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research. - Tasnia Tahsin; Davy Weissenbacher; Demetrius Jones-Shargani; Daniel Magee; Matteo Vaiente; Graciela Gonzalez 001; Matthew Scotch (Database J. Biol. Databases Curation, 2017)

Dealing with Medication Non-Adherence Expressions in Twitter. - Takeshi Onishi; Davy Weissenbacher; Ari Z. Klein; Karen O'Connor; Graciela Gonzalez-Hernandez (SMM4H@EMNLP, 2018)

Overview of the Third Social Media Mining for Health (SMM4H) Shared Tasks at EMNLP 2018. - Davy Weissenbacher; Abeed Sarker; Michael J. Paul; Graciela Gonzalez-Hernandez (SMM4H@EMNLP, 2018)

Deep neural networks and distant supervision for geographic location mention extraction. - Arjun Magge; Davy Weissenbacher; Abeed Sarker; Matthew Scotch; Graciela Gonzalez-Hernandez (Bioinform., 2018)

GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records. - Tasnia Tahsin; Davy Weissenbacher; Karen O'Connor; Arjun Magge; Matthew Scotch; Graciela Gonzalez-Hernandez (Bioinform., 2018)

Automatically Detecting Self-Reported Birth Defect Outcomes on Twitter for Large-scale Epidemiological Research. - Ari Z. Klein; Abeed Sarker; Davy Weissenbacher; Graciela Gonzalez-Hernandez (CoRR, 2018)

Social media mining for birth defects research: A rule-based, bootstrapping approach to collecting data for rare health-related events on Twitter. - Ari Z. Klein; Abeed Sarker; Haitao Cai; Davy Weissenbacher; Graciela Gonzalez-Hernandez (J. Biomed. Informatics, 2018)

Text Mining and Machine Learning for Precision Medicine. - Graciela Gonzalez 001; Zhiyong Lu; Robert Leaman; Davy Weissenbacher; Mary Regina Boland; Yong Chen 016; Jingcheng Du; Juliane Fluck; Casey S. Greene; John H. Holmes; Aditya Kashyap; Rikke Linnemann Nielsen; et al. (PSB, 2019)

Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature. - Arjun Magge; Davy Weissenbacher; Abeed Sarker; Matthew Scotch; Graciela Gonzalez-Hernandez (PSB, 2019)

SemEval-2019 Task 12: Toponym Resolution in Scientific Papers. - Davy Weissenbacher; Arjun Magge; Karen O'Connor; Matthew Scotch; Graciela Gonzalez-Hernandez (SemEval@NAACL-HLT, 2019)

Overview of the Fourth Social Media Mining for Health (SMM4H) Shared Tasks at ACL 2019. - Davy Weissenbacher; Abeed Sarker; Arjun Magge; Ashlynn R. Daughton; Karen O'Connor; Michael J. Paul; Graciela Gonzalez-Hernandez (SMM4H@ACL, 2019)

Deep neural networks ensemble for detecting medication mentions in tweets. - Davy Weissenbacher; Abeed Sarker; Ari Z. Klein; Karen O'Connor; Arjun Magge; Graciela Gonzalez-Hernandez (J. Am. Medical Informatics Assoc., 2019)

Towards scaling Twitter for digital epidemiology of birth defects. - Ari Z. Klein; Abeed Sarker; Davy Weissenbacher; Graciela Gonzalez-Hernandez (npj Digit. Medicine, 2019)

Overview of the Fifth Social Media Mining for Health Applications (#SMM4H) Shared Tasks at COLING 2020. - Ari Z. Klein; Ilseyar Alimova; Ivan Flores; Arjun Magge; Zulfat Miftahutdinov; Anne-Lyse Minard; Karen O'Connor; Abeed Sarker; Elena Tutubalina; Davy Weissenbacher; Graciela Gonzalez-Hernandez (SMM4H@COLING, 2020)

GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography. - Arjun Magge; Davy Weissenbacher; Karen O'Connor; Tasnia Tahsin; Graciela Gonzalez-Hernandez; Matthew Scotch (Bioinform., 2020)

Addressing Extreme Imbalance for Detecting Medications Mentioned in Twitter User Timelines. - Davy Weissenbacher; Siddharth Rawal; Arjun Magge; Graciela Gonzalez-Hernandez (AIME, 2021)

Overview of the Sixth Social Media Mining for Health Applications (#SMM4H) Shared Tasks at NAACL 2021. - Arjun Magge; Ari Z. Klein; Antonio Miranda-Escalada; Mohammed Ali Al-Garadi; Ilseyar Alimova; Zulfat Miftahutdinov; Eulàlia Farré; Salvador Lima-López; Ivan Flores; Karen O'Connor; Davy Weissenbacher; Elena Tutubalina; et al. (SMM4H@NAACL-HLT, 2021)

DeepADEMiner: a deep learning pharmacovigilance pipeline for extraction and normalization of adverse drug event mentions on Twitter. - Arjun Magge; Elena Tutubalina; Zulfat Miftahutdinov; Ilseyar Alimova; Anne Dirkson; Suzan Verberne; Davy Weissenbacher; Graciela Gonzalez-Hernandez (J. Am. Medical Informatics Assoc., 2021)

Active neural networks to detect mentions of changes to medication treatment in social media. - Davy Weissenbacher; Suyu Ge; Ari Z. Klein; Karen O'Connor; Robert Gross; Sean Hennessy; Graciela Gonzalez-Hernandez (J. Am. Medical Informatics Assoc., 2021)

Overview of the Seventh Social Media Mining for Health Applications (#SMM4H) Shared Tasks at COLING 2022. - Davy Weissenbacher; Juan M. Banda; Vera Davydova; Darryl Estrada-Zavala; Luis Gascó Sánchez; Yao Ge 003; Yuting Guo; Ari Z. Klein; Martin Krallinger; Mathias Leddin; Arjun Magge; Raul Rodriguez-Esteban; et al. (SMM4H@COLING, 2022)

Automatic Extraction of Medication Mentions from Tweets - Overview of the BioCreative VII Shared Task 3 Competition. - Davy Weissenbacher; Karen O'Connor; Siddharth Rawal; Yu Zhang 202; Richard Tzong-Han Tsai; Timothy Miller 002; Dongfang Xu; Carol Anderson; Bo Liu; Qing Han; Jinfeng Zhang; Igor Kulev; et al. (Database J. Biol. Databases Curation, 2023)

Automatic sentence segmentation of clinical record narratives in real-world data. - Dongfang Xu; Davy Weissenbacher; Karen O'Connor; Siddharth Rawal; Graciela Gonzalez-Hernandez (EMNLP, 2024)

Detecting goals of care conversations in clinical notes with active learning. - Davy Weissenbacher; Katherine R. Courtright; Siddharth Rawal; Andrew Crane-Droesch; Karen O'Connor; Nicholas Kuhl; Corinne Merlino; Anessa Foxwell; Lindsay Haines; Joseph C. Puhl; Graciela Gonzalez-Hernandez (J. Biomed. Informatics, 2024)

Probing Large Language Model Hidden States for Adverse Drug Reaction Knowledge. - Jacob S. Berkowitz; Davy Weissenbacher; Apoorva Srinivasan; Nadine A. Friedrich; Jose Miguel Acitores Cortina; Sophia Kivelson; Graciela Gonzalez-Hernandez; Nicholas P. Tatonetti (AIME (1), 2025)