Rethinking NLP for Chemistry: A Critical Look at the USPTO Benchmark.

Benoit Da Mota Derin Ozer Nicolas Gutowski Benoit Da Mota Thomas Cauchy Sylvain Lamprier Rethinking NLP for Chemistry: A Critical Look at the USPTO Benchmark. EMNLP (Findings) 2025 22813-22825 conf/emnlp/2025f https://aclanthology.org/2025.findings-emnlp.1242/ db/conf/emnlp/emnlp2025f.html#OzerGMCL25 streams/conf/emnlp Derin Ozer Sylvain Lamprier Nicolas Gutowski Benoit Da Mota Thomas Cauchy A Transformer Model for Predicting Chemical Products from Generic SMARTS Templates with Data Augmentation. 630-636 2025 ICTAI https://doi.org/10.1109/ICTAI66417.2025.00091 conf/ictai/2025 db/conf/ictai/ictai2025.html#OzerLGMC25 streams/conf/ictai Gaëlle Milon-Harnois Chaïmaâ Touhami Nicolas Gutowski Benoit Da Mota Thomas Cauchy Guiding Evolutionary Molecular Design: Adding Reinforcement Learning for Mutation Selection. 1132-1139 2025 ICTAI https://doi.org/10.1109/ICTAI66417.2025.00165 conf/ictai/2025 db/conf/ictai/ictai2025.html#MilonHarnoisTGMC25 streams/conf/ictai

Derin Ozer Sylvain Lamprier Thomas Cauchy Nicolas Gutowski Benoit Da Mota A Transformer Model for Predicting Chemical Reaction Products from Generic Templates. 2025 March abs/2503.05810 CoRR https://doi.org/10.48550/arXiv.2503.05810 db/journals/corr/corr2503.html#abs-2503-05810 streams/journals/corr

Gaëlle Milon-Harnois Chaïmaâ Touhami Nicolas Gutowski Benoit Da Mota Thomas Cauchy Guiding Evolutionary Molecular Design: Adding Reinforcement Learning for Mutation Selection. 2025 October abs/2510.00802 CoRR https://doi.org/10.48550/arXiv.2510.00802 db/journals/corr/corr2510.html#abs-2510-00802 streams/journals/corr

Jules Leguy Marta Glavatskikh Thomas Cauchy Benoit Da Mota Scalable estimator of the diversity for de novo molecular generation resulting in a more robust QM dataset (OD9) and a more efficient molecular optimization. 76 2021 13 J. Cheminformatics 1 https://doi.org/10.1186/s13321-021-00554-8 db/journals/jcheminf/jcheminf13.html#LeguyGCM21

Jules Leguy Béatrice Duval Benoit Da Mota Thomas Cauchy Surrogate-Based Black-Box Optimization Method for Costly Molecular Properties. 780-785 2021 ICTAI https://doi.org/10.1109/ICTAI52525.2021.00124 conf/ictai/2021 db/conf/ictai/ictai2021.html#LeguyDMC21

Jules Leguy Thomas Cauchy Béatrice Duval Benoit Da Mota Surrogate-Based Black-Box Optimization Method for Costly Molecular Properties. 2021 abs/2110.03522 CoRR https://arxiv.org/abs/2110.03522 db/journals/corr/corr2110.html#abs-2110-03522

Jules Leguy Thomas Cauchy Marta Glavatskikh Béatrice Duval Benoit Da Mota EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation. 55 2020 12 J. Cheminformatics 1 https://doi.org/10.1186/s13321-020-00458-z db/journals/jcheminf/jcheminf12.html#LeguyCGDM20

Marta Glavatskikh Jules Leguy Gilles Hunault Thomas Cauchy Benoit Da Mota Dataset's chemical diversity limits the generalizability of machine learning predictions. 69:1-69:15 2019 11 J. Cheminformatics 1 https://doi.org/10.1186/s13321-019-0391-2 https://www.wikidata.org/entity/Q94193269 db/journals/jcheminf/jcheminf11.html#GlavatskikhLHCM19

Jules Leguy Thomas Cauchy Béatrice Duval Benoit Da Mota Des réseaux de neurones pour prédire des distances interatomiques extraites d'une base de données ouverte de calculs en chimie quantique. 9-20 2019 EGC https://editions-rnti.fr/?inprocid=1002464 conf/f-egc/2019 db/conf/f-egc/egc2019.html#LeguyCDM19 Jules Leguy Thomas Cauchy Béatrice Duval Benoit Da Mota Predicting Interatomic Distances of Molecular Quantum Chemistry Calculations. 159-174 2019 EGC (best of volume) https://doi.org/10.1007/978-3-030-90287-2_8 conf/f-egc/2019sci db/conf/f-egc/sci2019.html#LeguyCDM19a

Virgile Fritsch Benoit Da Mota Eva Loth Gaël Varoquaux Tobias Banaschewski Gareth J. Barker Arun L. W. Bokde Rüdiger Brühl Brigitte Butzek Patricia J. Conrod Herta Flor Hugh Garavan Hervé Lemaître Karl Mann Frauke Nees Tomás Paus Daniel J. Schad Gunter Schümann Vincent Frouin Jean-Baptiste Poline Bertrand Thirion Robust regression for large-scale neuroimaging studies. 431-441 2015 111 NeuroImage https://doi.org/10.1016/j.neuroimage.2015.02.048 https://www.wikidata.org/entity/Q41321338 db/journals/neuroimage/neuroimage111.html#FritschMLVBBBBB15

Benoit Da Mota Radu Tudoran Alexandru Costan Gaël Varoquaux Goetz Brasche Patricia J. Conrod Hervé Lemaître Tomás Paus Marcella Rietschel Vincent Frouin Jean-Baptiste Poline Gabriel Antoniu Bertrand Thirion Generic Machine Learning Pattern for Neuroimaging-Genetic Studies in the Cloud. 2014 8 Frontiers Neuroinformatics https://doi.org/10.3389/fninf.2014.00031 https://www.wikidata.org/entity/Q35159992 db/journals/fini/fini8.html#MotaTCVBCLPRFPAT14 31

Benoit Da Mota Virgile Fritsch Gaël Varoquaux Tobias Banaschewski Gareth J. Barker Arun L. W. Bokde Uli Bromberg Patricia J. Conrod Jürgen Gallinat Hugh Garavan Jean-Luc Martinot Frauke Nees Tomás Paus Zdenka Pausova Marcella Rietschel Michael N. Smolka Andreas Ströhle Vincent Frouin Jean-Baptiste Poline Bertrand Thirion Randomized parcellation based inference. 203-215 2014 89 NeuroImage https://doi.org/10.1016/j.neuroimage.2013.11.012 https://www.wikidata.org/entity/Q46346887 db/journals/neuroimage/neuroimage89.html#MotaFVBBBBCGGMNPPRSSFPT14

Benoit Da Mota Virgile Fritsch Gaël Varoquaux Vincent Frouin Jean-Baptiste Poline Bertrand Thirion Enhancing the Reproducibility of Group Analysis with Randomized Brain Parcellations. 591-598 2013 MICCAI (2) https://doi.org/10.1007/978-3-642-40763-5_73 https://www.wikidata.org/entity/Q57317216 conf/miccai/2013-2 db/conf/miccai/miccai2013-2.html#MotaFVFPT13 Virgile Fritsch Benoit Da Mota Gaël Varoquaux Vincent Frouin Eva Loth Jean-Baptiste Poline Bertrand Thirion Robust Group-Level Inference in Neuroimaging Genetic Studies. 21-24 2013 PRNI https://doi.org/10.1109/PRNI.2013.15 https://www.wikidata.org/entity/Q57317226 conf/prni/2013 db/conf/prni/prni2013.html#FritschMVFLPT13

Gabriel Antoniu Alexandru Costan Benoit Da Mota Bertrand Thirion Radu Tudoran A-Brain: Using the Cloud to Understand the Impact of Genetic Variability on the Brain. 2012 2012 ERCIM News 89 http://ercim-news.ercim.eu/en89/special/a-brain-using-the-cloud-to-understand-the-impact-of-genetic-variability-on-the-brain db/journals/ercim/ercim2012.html#AntoniuCMTT12

Benoit Da Mota Équivalences et forme prénexe pour les formules booléennes quantifiées. 717-742 2011 25 Rev. d'Intelligence Artif. 6 https://doi.org/10.3166/ria.25.717-742 db/journals/ria/ria25.html#Mota11

Benoit Da Mota Formules booléennes quantifiées : transformations formelles et calculs parallèles. (Quantified boolean formulae : formal processings and parallel computations). 2010 University of Angers, France https://tel.archives-ouvertes.fr/tel-00578083 Benoit Da Mota Pascal Nicolas Igor Stéphan A new parallel architecture for QBF tools. 324-330 2010 HPCS https://doi.org/10.1109/HPCS.2010.5547114 conf/ieeehpcs/2010 db/conf/ieeehpcs/ieeehpcs2010.html#MotaNS10

Igor Stéphan Benoit Da Mota Pascal Nicolas From (Quantified) Boolean Formulae to Answer Set Programming. 565-590 2009 19 J. Log. Comput. 4 https://doi.org/10.1093/logcom/exn041 db/journals/logcom/logcom19.html#StephanMN09

Igor Stéphan Benoit Da Mota A Unified Framework for Certificate and Compilation for QBF. 210-223 2009 ICLA https://doi.org/10.1007/978-3-540-92701-3_15 conf/icla/2009 db/conf/icla/icla2009.html#StephanM09 Gabriel Antoniu Tobias Banaschewski Gareth J. Barker Arun L. W. Bokde Goetz Brasche Uli Bromberg Rüdiger Brühl Brigitte Butzek Thomas Cauchy Patricia J. Conrod Alexandru Costan Béatrice Duval Herta Flor Virgile Fritsch Vincent Frouin Jürgen Gallinat Hugh Garavan Marta Glavatskikh Nicolas Gutowski Gilles Hunault Sylvain Lamprier Jules Leguy Hervé Lemaître Eva Loth Karl Mann Jean-Luc Martinot Gaëlle Milon-Harnois Frauke Nees Pascal Nicolas Derin Ozer Tomás Paus Zdenka Pausova Jean-Baptiste Poline Marcella Rietschel Daniel J. Schad Gunter Schümann Michael N. Smolka Igor Stéphan Andreas Ströhle Bertrand Thirion Chaïmaâ Touhami Radu Tudoran Gaël Varoquaux