Robert Bossy


2023

pdf bib
Exploitation de plongements de graphes pour l’extraction de relations biomédicales
Anfu Tang | Robert Bossy | Louise Deléger | Claire Nédellec | Pierre Zweigenbaum
Actes de CORIA-TALN 2023. Actes de la 30e Conférence sur le Traitement Automatique des Langues Naturelles (TALN), volume 1 : travaux de recherche originaux -- articles longs

L’intégration de connaissances externes dans les modèles neuronaux est très étudiée pour améliorer les performances des modèles de langue pré-entraînés, notamment en domaine biomédical. Dans cet article, nous explorons la contribution de plongements de bases de connaissances à une tâche d’extraction de relations. Pour deux mentions d’entités candidates dans un texte, nous faisons l’hypothèse que la connaissance de relations entre elles, issue d’une base de connaissances (BC) externe, aide à prédire l’existence d’une relation dans le texte, y compris lorsque les relations de BC sont différentes de celles du texte. Notre approche consiste à calculer des plongements du graphe de BC et à estimer la possibilité pour chaque paire d’entité du texte qu’elle soit reliée par une relation de BC. Les expériences menées sur trois tâches d’extraction de relations en domaine biomédical montrent que notre méthode surpasse le modèle PubMedBERT de base et donne des performances comparables aux méthodes de l’état de l’art.

2020

pdf bib
Handling Entity Normalization with no Annotated Corpus: Weakly Supervised Methods Based on Distributional Representation and Ontological Information
Arnaud Ferré | Robert Bossy | Mouhamadou Ba | Louise Deléger | Thomas Lavergne | Pierre Zweigenbaum | Claire Nédellec
Proceedings of the Twelfth Language Resources and Evaluation Conference

Entity normalization (or entity linking) is an important subtask of information extraction that links entity mentions in text to categories or concepts in a reference vocabulary. Machine learning based normalization methods have good adaptability as long as they have enough training data per reference with a sufficient quality. Distributional representations are commonly used because of their capacity to handle different expressions with similar meanings. However, in specific technical and scientific domains, the small amount of training data and the relatively small size of specialized corpora remain major challenges. Recently, the machine learning-based CONTES method has addressed these challenges for reference vocabularies that are ontologies, as is often the case in life sciences and biomedical domains. And yet, its performance is dependent on manually annotated corpus. Furthermore, like other machine learning based methods, parametrization remains tricky. We propose a new approach to address the scarcity of training data that extends the CONTES method by corpus selection, pre-processing and weak supervision strategies, which can yield high-performance results without any manually annotated examples. We also study which hyperparameters are most influential, with sometimes different patterns compared to previous work. The results show that our approach significantly improves accuracy and outperforms previous state-of-the-art algorithms.

2019

pdf bib
Bacteria Biotope at BioNLP Open Shared Tasks 2019
Robert Bossy | Louise Deléger | Estelle Chaix | Mouhamadou Ba | Claire Nédellec
Proceedings of the 5th Workshop on BioNLP Open Shared Tasks

This paper presents the fourth edition of the Bacteria Biotope task at BioNLP Open Shared Tasks 2019. The task focuses on the extraction of the locations and phenotypes of microorganisms from PubMed abstracts and full-text excerpts, and the characterization of these entities with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on biodiversity for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, and the challenge organization. We also provide an analysis of the results obtained by participants, and inspect the evolution of the results since the last edition in 2016.

2016

pdf bib
Proceedings of the 4th BioNLP Shared Task Workshop
Claire Nėdellec | Robert Bossy | Jin-Dong Kim
Proceedings of the 4th BioNLP Shared Task Workshop

pdf bib
Overview of the Regulatory Network of Plant Seed Development (SeeDev) Task at the BioNLP Shared Task 2016.
Estelle Chaix | Bertrand Dubreucq | Abdelhak Fatihi | Dialekti Valsamou | Robert Bossy | Mouhamadou Ba | Louise Deléger | Pierre Zweigenbaum | Philippe Bessières | Loic Lepiniec | Claire Nédellec
Proceedings of the 4th BioNLP Shared Task Workshop

pdf bib
Overview of the Bacteria Biotope Task at BioNLP Shared Task 2016
Louise Deléger | Robert Bossy | Estelle Chaix | Mouhamadou Ba | Arnaud Ferré | Philippe Bessières | Claire Nédellec
Proceedings of the 4th BioNLP Shared Task Workshop

2013

pdf bib
Proceedings of the BioNLP Shared Task 2013 Workshop
Claire Nédellec | Robert Bossy | Jin-Dong Kim | Jung-jae Kim | Tomoko Ohta | Sampo Pyysalo | Pierre Zweigenbaum
Proceedings of the BioNLP Shared Task 2013 Workshop

pdf bib
Overview of BioNLP Shared Task 2013
Claire Nédellec | Robert Bossy | Jin-Dong Kim | Jung-jae Kim | Tomoko Ohta | Sampo Pyysalo | Pierre Zweigenbaum
Proceedings of the BioNLP Shared Task 2013 Workshop

pdf bib
BioNLP Shared Task 2013 – An overview of the Genic Regulation Network Task
Robert Bossy | Philippe Bessières | Claire Nédellec
Proceedings of the BioNLP Shared Task 2013 Workshop

pdf bib
BioNLP shared Task 2013 – An Overview of the Bacteria Biotope Task
Robert Bossy | Wiktoria Golik | Zorana Ratkovic | Philippe Bessières | Claire Nédellec
Proceedings of the BioNLP Shared Task 2013 Workshop

2012

pdf bib
AlvisAE: a collaborative Web text annotation editor for knowledge acquisition
Frédéric Papazian | Robert Bossy | Claire Nédellec
Proceedings of the Sixth Linguistic Annotation Workshop

2011

pdf bib
Overview of BioNLP Shared Task 2011
Jin-Dong Kim | Sampo Pyysalo | Tomoko Ohta | Robert Bossy | Ngan Nguyen | Jun’ichi Tsujii
Proceedings of BioNLP Shared Task 2011 Workshop

pdf bib
BioNLP Shared Task 2011 - Bacteria Biotope
Robert Bossy | Julien Jourde | Philippe Bessières | Maarten van de Guchte | Claire Nédellec
Proceedings of BioNLP Shared Task 2011 Workshop

pdf bib
BioNLP Shared Task 2011 – Bacteria Gene Interactions and Renaming
Julien Jourde | Alain-Pierre Manine | Philippe Veber | Karën Fort | Robert Bossy | Erick Alphonse | Philippe Bessières
Proceedings of BioNLP Shared Task 2011 Workshop