Davy Weissenbacher

Also published as: D. Weissenbacher


2020

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Proceedings of the Fifth Social Media Mining for Health Applications Workshop & Shared Task
Graciela Gonzalez-Hernandez | Ari Z. Klein | Ivan Flores | Davy Weissenbacher | Arjun Magge | Karen O'Connor | Abeed Sarker | Anne-Lyse Minard | Elena Tutubalina | Zulfat Miftahutdinov | Ilseyar Alimova
Proceedings of the Fifth Social Media Mining for Health Applications Workshop & Shared Task

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Overview of the Fifth Social Media Mining for Health Applications (#SMM4H) Shared Tasks at COLING 2020
Ari Klein | Ilseyar Alimova | Ivan Flores | Arjun Magge | Zulfat Miftahutdinov | Anne-Lyse Minard | Karen O’Connor | Abeed Sarker | Elena Tutubalina | Davy Weissenbacher | Graciela Gonzalez-Hernandez
Proceedings of the Fifth Social Media Mining for Health Applications Workshop & Shared Task

The vast amount of data on social media presents significant opportunities and challenges for utilizing it as a resource for health informatics. The fifth iteration of the Social Media Mining for Health Applications (#SMM4H) shared tasks sought to advance the use of Twitter data (tweets) for pharmacovigilance, toxicovigilance, and epidemiology of birth defects. In addition to re-runs of three tasks, #SMM4H 2020 included new tasks for detecting adverse effects of medications in French and Russian tweets, characterizing chatter related to prescription medication abuse, and detecting self reports of birth defect pregnancy outcomes. The five tasks required methods for binary classification, multi-class classification, and named entity recognition (NER). With 29 teams and a total of 130 system submissions, participation in the #SMM4H shared tasks continues to grow.

2019

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Proceedings of the Fourth Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task
Davy Weissenbacher | Graciela Gonzalez-Hernandez
Proceedings of the Fourth Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task

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Overview of the Fourth Social Media Mining for Health (SMM4H) Shared Tasks at ACL 2019
Davy Weissenbacher | Abeed Sarker | Arjun Magge | Ashlynn Daughton | Karen O’Connor | Michael J. Paul | Graciela Gonzalez-Hernandez
Proceedings of the Fourth Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task

The number of users of social media continues to grow, with nearly half of adults worldwide and two-thirds of all American adults using social networking. Advances in automated data processing, machine learning and NLP present the possibility of utilizing this massive data source for biomedical and public health applications, if researchers address the methodological challenges unique to this media. We present the Social Media Mining for Health Shared Tasks collocated with the ACL at Florence in 2019, which address these challenges for health monitoring and surveillance, utilizing state of the art techniques for processing noisy, real-world, and substantially creative language expressions from social media users. For the fourth execution of this challenge, we proposed four different tasks. Task 1 asked participants to distinguish tweets reporting an adverse drug reaction (ADR) from those that do not. Task 2, a follow-up to Task 1, asked participants to identify the span of text in tweets reporting ADRs. Task 3 is an end-to-end task where the goal was to first detect tweets mentioning an ADR and then map the extracted colloquial mentions of ADRs in the tweets to their corresponding standard concept IDs in the MedDRA vocabulary. Finally, Task 4 asked participants to classify whether a tweet contains a personal mention of one’s health, a more general discussion of the health issue, or is an unrelated mention. A total of 34 teams from around the world registered and 19 teams from 12 countries submitted a system run. We summarize here the corpora for this challenge which are freely available at https://competitions.codalab.org/competitions/22521, and present an overview of the methods and the results of the competing systems.

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SemEval-2019 Task 12: Toponym Resolution in Scientific Papers
Davy Weissenbacher | Arjun Magge | Karen O’Connor | Matthew Scotch | Graciela Gonzalez-Hernandez
Proceedings of the 13th International Workshop on Semantic Evaluation

We present the SemEval-2019 Task 12 which focuses on toponym resolution in scientific articles. Given an article from PubMed, the task consists of detecting mentions of names of places, or toponyms, and mapping the mentions to their corresponding entries in GeoNames.org, a database of geospatial locations. We proposed three subtasks. In Subtask 1, we asked participants to detect all toponyms in an article. In Subtask 2, given toponym mentions as input, we asked participants to disambiguate them by linking them to entries in GeoNames. In Subtask 3, we asked participants to perform both the detection and the disambiguation steps for all toponyms. A total of 29 teams registered, and 8 teams submitted a system run. We summarize the corpus and the tools created for the challenge. They are freely available at https://competitions.codalab.org/competitions/19948. We also analyze the methods, the results and the errors made by the competing systems with a focus on toponym disambiguation.

2018

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Proceedings of the 2018 EMNLP Workshop SMM4H: The 3rd Social Media Mining for Health Applications Workshop & Shared Task
Graciela Gonzalez-Hernandez | Davy Weissenbacher | Abeed Sarker | Michael Paul
Proceedings of the 2018 EMNLP Workshop SMM4H: The 3rd Social Media Mining for Health Applications Workshop & Shared Task

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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
Proceedings of the 2018 EMNLP Workshop SMM4H: The 3rd Social Media Mining for Health Applications Workshop & Shared Task

The goals of the SMM4H shared tasks are to release annotated social media based health related datasets to the research community, and to compare the performances of natural language processing and machine learning systems on tasks involving these datasets. The third execution of the SMM4H shared tasks, co-hosted with EMNLP-2018, comprised of four subtasks. These subtasks involve annotated user posts from Twitter (tweets) and focus on the (i) automatic classification of tweets mentioning a drug name, (ii) automatic classification of tweets containing reports of first-person medication intake, (iii) automatic classification of tweets presenting self-reports of adverse drug reaction (ADR) detection, and (iv) automatic classification of vaccine behavior mentions in tweets. A total of 14 teams participated and 78 system runs were submitted (23 for task 1, 20 for task 2, 18 for task 3, 17 for task 4).

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Dealing with Medication Non-Adherence Expressions in Twitter
Takeshi Onishi | Davy Weissenbacher | Ari Klein | Karen O’Connor | Graciela Gonzalez-Hernandez
Proceedings of the 2018 EMNLP Workshop SMM4H: The 3rd Social Media Mining for Health Applications Workshop & Shared Task

Through a semi-automatic analysis of tweets, we show that Twitter users not only express Medication Non-Adherence (MNA) in social media but also their reasons for not complying; further research is necessary to fully extract automatically and analyze this information, in order to facilitate the use of this data in epidemiological studies.

2016

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Automatic Prediction of Linguistic Decline in Writings of Subjects with Degenerative Dementia
Davy Weissenbacher | Travis A. Johnson | Laura Wojtulewicz | Amylou Dueck | Dona Locke | Richard Caselli | Graciela Gonzalez
Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

2015

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DIEGOLab: An Approach for Message-level Sentiment Classification in Twitter
Abeed Sarker | Azadeh Nikfarjam | Davy Weissenbacher | Graciela Gonzalez
Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015)

2014

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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 Wallstrom | Graciela Gonzalez
Proceedings of BioNLP 2014

2006

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The ALVIS Format for Linguistically Annotated Documents
A. Nazarenko | E. Alphonse | J. Derivière | T. Hamon | G. Vauvert | D. Weissenbacher
Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC’06)

The paper describes the ALVIS annotation format and discusses the problems that we encountered for the indexing of large collections of documents for topic specific search engines. This paper is exemplified on the biological domain and on MedLine abstracts, as developing a specialized search engine for biologist is one of the ALVIS case studies. The ALVIS principle for linguistic annotations is based on existing works and standard propositions. We made the choice of stand-off annotations rather than inserted mark-up, and annotations are encoded as XML elements which form the linguistic subsection of the document record.

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Bayesian Network, a Model for NLP?
Davy Weissenbacher
Demonstrations

2004

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Event-Based Information Extraction for the Biomedical Domain: the Caderige Project
Erick 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
Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP)