A. Coulet

Pierre Monnin, Adrien Coulet. Étudier les mécanismes des effets indésirables des médicaments avec l'IA explicable : expériences avec la fouille de graphes de connaissances. Bulletin de l'Association Française pour l'Intelligence Artificielle, AFIA, 2022. ⟨hal-03669065⟩

Pierre Monnin, Adrien Coulet. Projet ANR (2016-2021) « PractiKPharma » : extraction, comparaison et découverte de connaissances en pharmacogénomique. 1024 : Bulletin de la Société Informatique de France, Société Informatique de France, 2022, pp.109 - 120. ⟨10.48556/sif.1024.19.109⟩. ⟨hal-03669026⟩

Emmanuel Bresso, Pierre Monnin, Cédric Bousquet, François-Elie Calvier, Ndeye-Coumba Ndiaye, et al.. Investigating ADR mechanisms with Explainable AI: a feasibility study with knowledge graph mining. BMC Medical Informatics and Decision Making, BioMed Central, 2021, 21 (1), pp.171. ⟨10.1186/s12911-021-01518-6⟩. ⟨hal-03240476⟩

Joël Legrand, Yannick Toussaint, Chedy Raïssi, Adrien Coulet. Syntax-based transfer learning for the task of biomedical relation extraction. Journal of Biomedical Semantics, BioMed Central, 2021, 12 (1), ⟨10.1186/s13326-021-00248-y⟩. ⟨hal-03330823⟩

Pierre Monnin, Chedy Raïssi, Amedeo Napoli, Adrien Coulet. Discovering alignment relations with Graph Convolutional Networks: A biomedical case study. Semantic Web – Interoperability, Usability, Applicability, IOS Press, 2021, pp.1-20. ⟨10.3233/SW-210452⟩. ⟨hal-03452182⟩

Adrien Coulet, Stéphanie Allassonniere, François Angoulvant, Anita Burgun, Xiaoyi Chen, et al.. L'équipe-projet HeKA. Bulletin de l'Association Française pour l'Intelligence Artificielle, AFIA, 2021, pp.29-32. ⟨hal-03485904⟩

Joël Legrand, Romain Gogdemir, Cedric Bousquet, Kevin Dalleau, Marie-Dominique Devignes, et al.. PGxCorpus, a manually annotated corpus for pharmacogenomics. Scientific Data , Nature Publishing Group, 2020, 7, pp.3. ⟨10.1038/s41597-019-0342-9⟩. ⟨hal-02547607⟩

Fatima Rodriguez, Sukyung Chung, Manuel Blum, Adrien Coulet, Sanjay Basu, et al.. Atherosclerotic Cardiovascular Disease Risk Prediction in Disaggregated Asian and Hispanic Subgroups Using Electronic Health Records. Journal of the American Heart Association, Wiley-Blackwell, 2019, 8 (14), ⟨10.1161/JAHA.118.011874⟩. ⟨hal-02196129⟩

Pierre Monnin, Joël Legrand, Graziella Husson, Patrice Ringot, Andon Tchechmedjiev, et al.. PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. BMC Bioinformatics, BioMed Central, 2019, 20 (S4), ⟨10.1186/s12859-019-2693-9⟩. ⟨hal-02103899⟩

Adrien Coulet, Nigam Shah, Maxime Wack, Mohammad Chawki, Nicolas Jay, et al.. Predicting the need for a reduced drug dose, at first prescription. Scientific Reports, Nature Publishing Group, 2018, 8 (1), ⟨10.1038/s41598-018-33980-0⟩. ⟨hal-01901566⟩

Kevin Dalleau, Yassine Marzougui, Sébastien da Silva, Patrice Ringot, Ndeye Ndiaye, et al.. Learning from biomedical linked data to suggest valid pharmacogenes. Journal of Biomedical Semantics, BioMed Central, 2017, 8 (1), pp.16. ⟨10.1186/s13326-017-0125-1⟩. ⟨hal-01511773⟩

Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, et al.. Discovering associations between adverse drug events using pattern structures and ontologies. Journal of Biomedical Semantics, BioMed Central, 2017, 93, pp.539 - 546. ⟨10.1186/s13326-017-0137-x⟩. ⟨hal-01576341⟩

Adrien Coulet, Malika Smaïl-Tabbone. Mining Electronic Health Records to Validate Knowledge in Pharmacogenomics. ERCIM News, ERCIM, 2016, ERCIM News 104, Special theme: Tackling Big Data in the Life Sciences, pp.56. ⟨hal-01369501⟩

Matthias Samwald, Adrien Coulet, Iker Huerga, Robert L Powers, Joanne S Luciano, et al.. Semantically enabling pharmacogenomic data for the realization of personalized medicine.. Pharmacogenomics, Future Medicine, 2012, 13 (2), pp.201-12. ⟨10.2217/pgs.11.179⟩. ⟨hal-00752095⟩

Yi Liu, Adrien Coulet, Paea Lependu, Nigam H Shah. Using ontology-based annotation to profile disease research. Journal of the American Medical Informatics Association, BMJ Publishing Group, 2012, 19 (e1), pp.e177-e186. ⟨10.1136/amiajnl-2011-000631⟩. ⟨hal-00752101⟩

Adrien Coulet, Kevin Bretonnel Cohen, Russ Altman. Guest Editorial: The state of the art in text mining and natural language processing for pharmacogenomics. Journal of Biomedical Informatics, Elsevier, 2012, 45 (5), pp.825-826. ⟨hal-00752106⟩

Adrien Coulet, Yael Garten, Michel Dumontier, Russ B Altman, Mark Musen, et al.. Integration and publication of heterogeneous text-mined relationships on the Semantic Web. Journal of Biomedical Semantics, BioMed Central, 2011, 2 (S2), pp.S10. ⟨hal-00585215⟩

Clement Jonquet, Paea Lependu, Sean Falconer, Adrien Coulet, Natalya F. Noy, et al.. NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. Journal of Web Semantics, Elsevier, 2011, 9 (3), pp.316-324. ⟨10.1016/j.websem.2011.06.005⟩. ⟨lirmm-00622155v2⟩

Adrien Coulet, Nigam Shah, Lawrence Hunter, Chitta Barral, Russ B Altman. Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application.. Pacific Symposium on Biocomputing, World Scientific, 2010, pp.485-7. ⟨inria-00549705⟩

Yael Garten, Adrien Coulet, Russ B Altman. Recent progress in automatically extracting information from the pharmacogenomic literature.. Pharmacogenomics / Personalized Medicine, 2010, 11 (10), pp.1467-89. ⟨10.2217/pgs.10.136⟩. ⟨inria-00549699⟩

Adrien Coulet, Nigam H Shah, Yael Garten, Mark Musen, Russ B Altman. Using text to build semantic networks for pharmacogenomics. Journal of Biomedical Informatics, Elsevier, 2010, 43 (6), pp.1009-19. ⟨10.1016/j.jbi.2010.08.005⟩. ⟨inria-00549695⟩

Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes. Ontology-guided data preparation for discovering genotype-phenotype relationships. BMC Bioinformatics, BioMed Central, 2008, 9 (Suppl 4), pp.S3. ⟨inria-00338669⟩

Walid Hafiane, Joël Legrand, Yannick Toussaint, Adrien Coulet. Expérimentations autour des architectures d'apprentissage par transfert pour l'extraction de relations biomédicales. EGC 2021 - 21ème édition de la conférence "Extraction et Gestion des Connaissances", Jan 2021, Montpellier / Virtuel, France. ⟨hal-03073601⟩

Alice Rogier, Adrien Coulet, Bastien Rance. Using an ontological representation of chemotherapy toxicities for guiding information extraction and integration from EHRs. Medinfo 2021 - 18th World Congress on Medical and Health Informatics, Oct 2021, Virtual conference, Australia. ⟨hal-03364585⟩

Pierre Monnin, Miguel Couceiro, Amedeo Napoli, Adrien Coulet. Knowledge-Based Matching of $n$-ary Tuples. ICCS 2020 - 25th International Conference on Conceptual Structures, Sep 2020, Bolzano / Virtual, Italy. pp.48-56, ⟨10.1007/978-3-030-57855-8_4⟩. ⟨hal-02493067⟩

Pierre Monnin, Emmanuel Bresso, Miguel Couceiro, Malika Smaïl-Tabbone, Amedeo Napoli, et al.. Tackling scalability issues in mining path patterns from knowledge graphs: a preliminary study. ALGOS 2020 - 1st International Conference on Algebras, Graphs and Ordered Sets, Aug 2020, Nancy, France. ⟨hal-02913224⟩

Pierre Monnin, Chedy Raïssi, Amedeo Napoli, Adrien Coulet. Knowledge Reconciliation with Graph Convolutional Networks: Preliminary Results. DL4KG2019 - Workshop on Deep Learning for Knowledge Graphs, Jun 2019, Portoroz, Slovenia. ⟨hal-02155546⟩

Stephen Pfohl, Ben Marafino, Adrien Coulet, Fatima Rodriguez, Latha Palaniappan, et al.. Creating Fair Models of Atherosclerotic Cardiovascular Disease Risk. AIES '19 - Proceedings of the 2019 AAAI/ACM Conference on AI, Ethics, and Society, Jan 2019, Honolulu, United States. pp.271-278, ⟨10.1145/3306618.3314278⟩. ⟨hal-02388730⟩

Pierre Monnin, Amedeo Napoli, Adrien Coulet. Combining Concept Annotation and Pattern Structures for Guiding Ontology Mapping. FCA4AI@IJCAI2018 - 6th International Workshop "What can FCA do for Artificial Intelligence?", Jul 2018, Stockholm, Sweden. ⟨hal-01858391⟩

Joël Legrand, Yannick Toussaint, Chedy Raïssi, Adrien Coulet. Syntax-based Transfer Learning for the Task of Biomedical Relation Extraction. LOUHI 2018 - The Ninth International Workshop on Health Text Mining and Information Analysis, Oct 2018, Brussels, Belgium. ⟨hal-01869071⟩

Gabin Personeni, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Philippe Jonveaux, Céline Bonnet, et al.. Cooperation of bio-ontologies for the classification of genetic intellectual disabilities : a diseasome approach. Proceedings of the 11th International Conference on Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4HCLS 2018), Dec 2018, Antwerp, Belgium. ⟨hal-01925471⟩

Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, et al.. Découverte d'associations entre Evénements Indésirables Médicamenteux par les structures de patrons et les ontologies. Journée I.A. et Santé, Jul 2018, Nancy, France. ⟨hal-01872312⟩

Joël Legrand, Yannick Toussaint, Chedy Raïssi, Adrien Coulet. Tree-LSTM and Cross-Corpus Training for Extracting Biomedical Relationships from Text. DLPM2017 Workshop - 2nd International Workshop on Deep Learning for Precision Medicine, Sep 2017, Skopje, Macedonia. ⟨hal-01592802⟩

Pierre Monnin, Clement Jonquet, Joël Legrand, Amedeo Napoli, Adrien Coulet. PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units. Methods, tools & platforms for Personalized Medicine in the Big Data Era, Oct 2017, Palermo, Italy. ⟨10.7287/peerj.preprints.3140v1⟩. ⟨hal-01593184v2⟩

Pierre Monnin, Mario Lezoche, Amedeo Napoli, Adrien Coulet. Using formal concept analysis for checking the structure of an ontology in LOD: the example of DBpedia. 23rd International Symposium on Methodologies for Intelligent Systems, ISMIS 2017, Warsaw university of technology, Jun 2017, Warsaw, Poland. pp.674-683, ⟨10.1007/978-3-319-60438-1_66⟩. ⟨hal-01511909⟩

Gabin Personeni, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet. Discovering ADE associations from EHRs using pattern structures and ontologies. Phenotype Day, Bio-Ontologies SIG, ISMB, Jul 2016, Orlando, United States. ⟨hal-01369448⟩

Gabin Personeni, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet. Extraction d'association d'EIM à partir de dossiers patients : expérimentation avec les structures de patrons et les ontologies. Deuxième Atelier sur l'Intelligence Artificielle et la Santé, Jun 2016, Montpellier, France. ⟨hal-01391172⟩

Mohsen Hassan, Olfa Makkaoui, Adrien Coulet, Yannick Toussaint. Extracting Disease-Symptom Relationships by Learning Syntactic Patterns from Dependency Graphs. BioNLP 15, Association for Computational Linguistics, Jul 2015, Beijing, China. pp.184. ⟨hal-01184655⟩

Kevin Dalleau, Ndeye Coumba Ndiaye, Adrien Coulet. Suggesting valid pharmacogenes by mining linked data. Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2015, Dec 2015, Cambridge, United Kingdom. ⟨hal-01239568⟩

Mehwish Alam, Melisachew Wudage Chekol, Adrien Coulet, Amedeo Napoli, Malika Smaïl-Tabbone. Lattice Based Data Access (LBDA): An Approach for Organizing and Accessing Linked Open Data in Biology. DMoLD'13 - Data Mining on Linked Data Workshop (ECML/PKDD, 2013), Sep 2013, Prague, Czech Republic. ⟨hal-00903450⟩

Adrien Coulet, Florent Domenach, Mehdi Kaytoue, Amedeo Napoli. Using Pattern Structures for Analyzing Ontology-Based Annotations of Biomedical Data. International Conference on Formal Concept Analysis, May 2013, Dresden, Germany. ⟨hal-00880643⟩

Adrien Coulet, Florent Domenach, Mehdi Kaytoue, Amedeo Napoli. Using pattern structures for analyzing ontology-based annotations of biomedical data. Septièmes Journées d'Intelligence Artificielle Fondamentale, Jun 2013, Aix-en-Provence, France. pp.97--106. ⟨hal-00922392⟩

Mehwish Alam, Adrien Coulet, Amedeo Napoli, Malika Smaïl-Tabbone. Formal Concept Analysis Applied to Transcriptomic Data. What can FCA do for Artificial Intelligence (FCA4AI) (ECAI 2012), Aug 2012, Montpellier, France. ⟨hal-00760993⟩

Mehwish Alam, Adrien Coulet, Amedeo Napoli, Malika Smaïl-Tabbone. Formal Concept Analysis Applied to Transcriptomic Data. The Ninth International Conference on Concept Lattices and Their Applications - CLA 2012, Oct 2012, Fuengirola (Málaga), Spain. ⟨hal-00761003⟩

Clement Jonquet, Adrien Coulet, Nigam Shah, Mark Musen. Indexation et intégration de ressources textuelles à l'aide d'ontologies : application au domaine biomédical. 21èmes Journées Francophones d'Ingénierie des Connaissances, Jun 2010, Nimes, France. pp.271-282. ⟨hal-00488419⟩

Clement Jonquet, Paea Lependu, Sean M. Falconer, Adrien Coulet, Natalya F. Noy, et al.. NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. Semantic Web Challenge, 9th International Semantic Web Conference, ISWC'10, Nov 2010, Shangai, China. pp.8. ⟨hal-00557982⟩

Adrien Coulet, Malika Smail-Tabbone, Amedeo Napoli, Marie-Dominique Devignes. Ontology Refinement through Role Assertion Analysis: Example in Pharmacogenomics. 21st International Workshop on Description Logics - DL2008, May 2008, Dresden, Germany. ⟨inria-00338677⟩

Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes. Ontology-guided Data Preparation for Discovering Genotype-Phenotype Relationships. Network Tools and Applications in Biology: A Semantic Web for Bioinformatics - NETTAB 2007, Jun 2007, Pisa, Italy. ⟨inria-00186988⟩

Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes. Suggested Ontology for Pharmacogenomics (SO-Pharm): Modular Construction and Preliminary Testing. Proceedings of International Workshop on Knowledge Systems in Bioinformatics - KSinBIT'06, Oct 2006, Montpellier, France. ⟨inria-00089824⟩

Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes. SNP-Converter: an Ontology-Based solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies. 3rd International Workshop on Data Integration in the Life Sciences 2006 - DILS'06, Jul 2006, European Bioinformatics Institute (EBI), Hinxton/UK. ⟨inria-00080050⟩

Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes. Ontology-driven Data Integration for Pharmacogenomics: Application to Genome Variations. Journées Ouvertes : Biologie, Informatique et Mathématiques - JOBIM'06, Centre de Bioinformatique de Bordeaux (CBiB), Jul 2006, Bordeaux/France. ⟨inria-00080064⟩

Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes. SNP-Ontology for semantic integration of genomic variation data. 14th Annual International Conference on Intelligent Systems for Molecular Biology - ISMB'06, Aug 2006, Fortaleza/Brésil. ⟨inria-00067863v2⟩

Adrien Coulet, Marie-Dominique Devignes, Malika Smaïl-Tabbone. Extraction de données pharmacogénomiques à partir d'études cliniques : problématique. Deuxième atelier sur la "Fouille de données complexes dans un processus d'extraction des connaissances", Jan 2005, Paris/France. ⟨inria-00080156⟩

Pierre Monnin, Amedeo Napoli, Adrien Coulet. Discovering Subsumption Axioms with Concept Annotation. BDA 2017 - 33ème Conférence sur la Gestion de Données — Principes, Technologies et Applications, Nov 2017, Nancy, France. Gestion de Données — Principes, Technologies et Applications (BDA 2017). ⟨hal-01671454v2⟩

Gabin Personeni, Simon Daget, Céline Bonnet, Philippe Jonveaux, Marie-Dominique Devignes, et al.. Mining Linked Open Data: a Case Study with Genes Responsible for Intellectual Disability. ECCB'14 (European Conference on Computational Biology 2014), Sep 2014, Strasbourg, France. 2014. ⟨hal-01092800⟩

Patricia Whetzel, Nigam Shah, Natalya Noy, Clement Jonquet, Adrien Coulet, et al.. Ontology-based Web Services for Data Annotation and Integration. ISMB: Intelligent Systems for Molecular Biology, Jul 2010, Boston, United States. 18th International Conference on Intelligent Systems for Molecular Biology, 2010. ⟨lirmm-01605892⟩

Adrien Coulet, Malika Smaïl-Tabbone, Amedeo Napoli, Marie-Dominique Devignes. Ontology-based knowledge discovery in pharmacogenomics.. Hamid R. Arabnia and Quoc-Nam Tran. Software Tools and Algorithms for Biological Systems, 696, Springer, pp.357-66, 2011, Advances in Experimental Medicine and Biology, 978-1-4419-7046-6. ⟨10.1007/978-1-4419-7046-6_36⟩. ⟨inria-00585072⟩

Pierre Monnin, Amedeo Napoli, Adrien Coulet. Data-Interlinking: the Seed of Knowledge Reconciliation in Pharmacogenomics. 2018. ⟨hal-01955262⟩

Adrien Coulet. Construction et utilisation d'une base de connaissances pharmacogénomique pour l'intégration de données et la découverte de connaissances. Interface homme-machine [cs.HC]. Université Henri Poincaré - Nancy 1, 2008. Français. ⟨NNT : 2008NAN10047⟩. ⟨tel-01748450v2⟩

Adrien Coulet. Mises en correspondances de données, textes et connaissances pour la découverte de connaissances biomédicales. Base de données [cs.DB]. Université de Lorraine, 2019. ⟨tel-02429926v2⟩