Gaël Varoquaux

212

Documents

Researcher identifiers

gael-varoquaux
0000-0003-1076-5122
IdRef : 126239894

Presentation

Publications

	Causal inference methods for combining randomized trials and observational studies: a review Bénédicte Colnet , Imke Mayer , Guanhua Chen , Awa Dieng , Ruohong Li Statistical Science, In press Journal articles hal-03008276v2
	Individual Brain Charting dataset extension, third release for movie watching and retinotopy data Ana Luísa Pinho , Hugo Richard , Ana Fernanda Ponce , Michael Eickenberg , Alexis Amadon Scientific Data , 2024, 11 (590) Journal articles hal-04272993v2
	Understanding metric-related pitfalls in image analysis validation Annika Reinke , Minu D. Tizabi , Michael Baumgartner , Matthias Eisenmann , Doreen Heckmann-Nötzel Nature Methods, 2024, 21, pp.182-194. ⟨10.1038/s41592-023-02150-0⟩ Journal articles hal-04480158v1
	Metrics reloaded: recommendations for image analysis validation Lena Maier-Hein , Annika Reinke , Patrick Godau , Minu Tizabi , Florian Buettner Nature Methods, 2024, 21 (2), pp.195-212. ⟨10.1038/s41592-023-02151-z⟩ Journal articles hal-04477840v1
	The Past, Present, and Future of the Brain Imaging Data Structure (BIDS) Russell Poldrack , Christopher Markiewicz , Stefan Appelhoff , Yoni Ashar , Tibor Auer Imaging Neuroscience, 2024, 2, pp.1-19. ⟨10.1162/imag_a_00103⟩ Journal articles hal-04346097v1
	Relational Data Embeddings for Feature Enrichment with Background Information Alexis Cvetkov-Iliev , Alexandre Allauzen , Gaël Varoquaux Machine Learning, 2023, 112 (2), pp.687-720. ⟨10.1007/s10994-022-06277-7⟩ Journal articles hal-03848124v1
	How to remove or control confounds in predictive models, with applications to brain biomarkers Darya Chyzhyk , Gaël Varoquaux , Michael Milham , Bertrand Thirion GigaScience, 2022, 11, ⟨10.1093/gigascience/giac014⟩ Journal articles hal-03607651v1
	Analytics on Non-Normalized Data Sources: more Learning, rather than more Cleaning Alexis Cvetkov-Iliev , Alexandre Allauzen , Gaël Varoquaux IEEE Access, inPress, 10, pp.42420-42431. ⟨10.1109/ACCESS.2022.3168013⟩ Journal articles hal-03647434v2
	Understanding Brain Network Dynamics in Autism Begs for Generalization Yong Liu , Gaël Varoquaux Biological Psychiatry, 2022, 91 (11), pp.916-917. ⟨10.1016/j.biopsych.2022.03.007⟩ Journal articles hal-03818457v1
	Advancing brain network models to reconcile functional neuroimaging and clinical research Xenia Kobeleva , Gaël Varoquaux , Alain Dagher , Mohit Adhikari , Christian Grefkes Neuroimage-Clinical, 2022, 36, pp.103262. ⟨10.1016/j.nicl.2022.103262⟩ Journal articles hal-04100892v1
	Comprehensive decoding mental processes from Web repositories of functional brain images Romuald Menuet , Raphael Meudec , Jérôme Dockès , Gaël Varoquaux , Bertrand Thirion Scientific Reports, 2022, 12 (7050), ⟨10.1038/s41598-022-10710-1⟩ Journal articles hal-03666470v1
	Predicting future cognitive decline from non-brain and multimodal brain imaging data in healthy and pathological aging Bruno Hebling Vieira , Franziskus Liem , Kamalaker Dadi , Denis Engemann , Alexandre Gramfort Neurobiology of Aging, 2022, 118, pp.55-65. ⟨10.1016/j.neurobiolaging.2022.06.008⟩ Journal articles hal-03808175v1
	Benchmarking missing-values approaches for predictive models on health databases Alexandre Perez-Lebel , Gaël Varoquaux , Marine Le Morvan , Julie Josse , Jean-Baptiste Poline GigaScience, inPress, ⟨10.1093/gigascience/giac013⟩ Journal articles hal-03526292v2
	Machine learning for medical imaging: methodological failures and recommendations for the future Gaël Varoquaux , Veronika Cheplygina npj Digital Medicine, 2022, 5 (1), pp.48. ⟨10.1038/s41746-022-00592-y⟩ Journal articles hal-03818456v1
	Causal effect on a target population: a sensitivity analysis to handle missing covariates Bénédicte Colnet , Julie Josse , Gaël Varoquaux , Erwan Scornet Journal of Causal Inference, 2022, 10 (1), pp.372-414. ⟨10.1515/jci-2021-0059⟩ Journal articles hal-03473691v3
	424-P: Body-Weight Variability and Risk of Cardiovascular Outcomes in Type 1 Diabetes: Results from the DCCT/EDIC Studies Iulia Petria , Samuel Albuquerque , Gaël Varoquaux , Jill-Jênn Vie , Gilberto Velho Diabetes, 2022, 71 (Supplement_1), ⟨10.2337/db22-424-P⟩ Journal articles hal-03818459v1
	Insights from an autism imaging biomarker challenge: promises and threats to biomarker discovery Nicolas Traut , Katja Heuer , Guillaume Lemaître , Anita Beggiato , David Germanaud NeuroImage, 2022, 255, pp.119171. ⟨10.1016/j.neuroimage.2022.119171⟩ Journal articles hal-03637273v2
	Body-weight variability and risk of cardiovascular outcomes in patients with type 1 diabetes: a retrospective observational analysis of data from the DCCT/EDIC population. Iulia Petria , Samuel Albuquerque , Gaël Varoquaux , Jill-Jênn Vie , Nicolas Venteclef Cardiovascular Diabetology, 2022, 21 (1), pp.247. ⟨10.1186/s12933-022-01689-0⟩ Journal articles hal-04021480v1
	Extracting representations of cognition across neuroimaging studies improves brain decoding Arthur Mensch , Julien Mairal , Bertrand Thirion , Gaël Varoquaux PLoS Computational Biology, 2021, 17 (5), pp.e1008795:1-20. ⟨10.1371/journal.pcbi.1008795⟩ Journal articles hal-01874713v3
	Decoding with Confidence: Statistical Control on Decoder Maps Jérôme-Alexis Chevalier , Tuan-Binh Nguyen , Joseph Salmon , Gaël Varoquaux , Bertrand Thirion NeuroImage, 2021, pp.117921. ⟨10.1016/j.neuroimage.2021.117921⟩ Journal articles hal-03179728v1
	Preventing dataset shift from breaking machine-learning biomarkers Jérôme Dockès , Gaël Varoquaux , Jean-Baptiste Poline GigaScience, inPress, ⟨10.1093/gigascience/giab055⟩ Journal articles hal-03293375v1
	Numerical uncertainty in analytical pipelines lead to impactful variability in brain networks Gregory Kiar , Yohan Chatelain , Pablo de Oliveira Castro , Eric Petit , Ariel Rokem PLoS ONE, 2021, 16 (11), pp.e0250755. ⟨10.1371/journal.pone.0250755⟩ Journal articles hal-03651395v1
	Population modeling with machine learning can enhance measures of mental health Kamalaker Dadi , Gaël Varoquaux , Josselin Houenou , Danilo Bzdok , Bertrand Thirion GigaScience, 2021, ⟨10.1101/2020.08.25.266536⟩ Journal articles hal-03470466v1
	International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium Gabriel A. Brat , Griffin M. Weber , Nils Gehlenborg , Paul Avillach , Nathan P. Palmer npj Digital Medicine, 2020, 3 (1), pp.#109. ⟨10.1038/s41746-020-00308-0⟩ Journal articles hal-02918344v1
	Individual Brain Charting dataset extension, second release of high-resolution fMRI data for cognitive mapping Ana Luísa Pinho , Alexis Amadon , Baptiste Gauthier , Nicolas Clairis , André Knops Scientific Data , 2020, ⟨10.1038/s41597-020-00670-4⟩ Journal articles hal-02973046v1
	Fine-grain atlases of functional modes for fMRI analysis Kamalaker Dadi , Gaël Varoquaux , Antonia Machlouzarides-Shalit , Krzysztof J. Gorgolewski , Demian Wassermann NeuroImage, 2020, 221, pp.117126 Journal articles hal-02904869v1
	Subject‐specific segregation of functional territories based on deep phenotyping Ana Luísa Pinho , Alexis Amadon , Murielle Fabre , Elvis Dohmatob , Isabelle Denghien Human Brain Mapping, 2020, ⟨10.1002/hbm.25189⟩ Journal articles hal-03088606v1
	Combining magnetoencephalography with magnetic resonance imaging enhances learning of surrogate-biomarkers Denis Engemann , Oleh Kozynets , David Sabbagh , Guillaume Lemaître , Gaël Varoquaux eLife, 2020, ⟨10.7554/eLife.54055⟩ Journal articles hal-02395406v1
	Predictive regression modeling with MEG/EEG: from source power to signals and cognitive states David Sabbagh , Pierre Ablin , Gaël Varoquaux , Alexandre Gramfort , Denis Engemann NeuroImage, 2020, ⟨10.1016/j.neuroimage.2020.116893⟩ Journal articles hal-02367411v1
	NeuroQuery, comprehensive meta-analysis of human brain mapping Jérôme Dockès , Russell Poldrack , Romain Primet , Hande Gözükan , Tal Yarkoni eLife, 2020 Journal articles hal-02485642v2
	Encoding high-cardinality string categorical variables Patricio Cerda , Gaël Varoquaux IEEE Transactions on Knowledge and Data Engineering, In press, ⟨10.1109/TKDE.2020.2992529⟩ Journal articles hal-02171256v5
	Benchmarking functional connectome-based predictive models for resting-state fMRI Kamalaker Dadi , Mehdi Rahim , Alexandre Abraham , Darya Chyzhyk , Michael Milham NeuroImage, 2019, 192, pp.115-134. ⟨10.1016/j.neuroimage.2019.02.062⟩ Journal articles hal-01824205v3
	Predictive models avoid excessive reductionism in cognitive neuroimaging Gaël Varoquaux , Russell Poldrack Current Opinion in Neurobiology, inPress, 55, ⟨10.1016/j.conb.2018.11.002⟩ Journal articles hal-01856412v4
	Population shrinkage of covariance (PoSCE) for better individual brain functional-connectivity estimation Mehdi Rahim , Bertrand Thirion , Gaël Varoquaux Medical Image Analysis, 2019, ⟨10.1016/j.media.2019.03.001⟩ Journal articles hal-02068389v1
	Brain-based ranking of cognitive domains to predict schizophrenia Teresa M Karrer , Danielle S. Bassett , Birgit Derntl , Oliver Gruber , Andre Aleman Human Brain Mapping, 2019, 40, pp.4487-4507. ⟨10.1002/hbm.24716⟩ Journal articles hal-02180311v1
	Different shades of default mode disturbance in schizophrenia: Subnodal covariance estimation in structure and function Jeremy Lefort-Besnard , Danielle S Bassett , Jonathan Smallwood , Daniel S. Margulies , Birgit Derntl Human Brain Mapping, 2018, pp.1-52 Journal articles hal-01620441v1
	Patterns of Schizophrenia Symptoms: Hidden Structure in the PANSS Questionnaire Jeremy Lefort-Besnard , Gaël Varoquaux , Birgit Derntl , Oliver Gruber , Andre Aleman Translational Psychiatry, inPress, ⟨10.1038/s41398-018-0294-4⟩ Journal articles hal-01888918v1
	Similarity encoding for learning with dirty categorical variables Patricio Cerda , Gaël Varoquaux , Balázs Kégl Machine Learning, 2018, ⟨10.1007/s10994-018-5724-2⟩ Journal articles hal-01806175v1
	Inter-subject registration of functional images: do we need anatomical images ? Elvis Dohmatob , Gaël Varoquaux , Bertrand Thirion Frontiers in Neuroscience, inPress Journal articles hal-01701619v1
	Subspecialization within default mode nodes characterized in 10,000 UK Biobank participants Julius M Kernbach , B T Thomas Yeo , Jonathan Smallwood , Daniel Margulies , Michel Thiebaut de Schotten Proceedings of the National Academy of Sciences of the United States of America, 2018, ⟨10.1073/pnas.1804876115⟩ Journal articles hal-01926796v1
	Stochastic Subsampling for Factorizing Huge Matrices Arthur Mensch , Julien Mairal , Bertrand Thirion , Gaël Varoquaux IEEE Transactions on Signal Processing, 2018, 66 (1), pp.113-128. ⟨10.1109/TSP.2017.2752697⟩ Journal articles hal-01431618v3
	Shared Endo-phenotypes of Default Mode Dysfunction in Attention Deficit/Hyperactivity Disorder and Autism Spectrum Disorder Julius M Kernbach , Theodore D Satterthwaite , Danielle S. Bassett , Jonathan Smallwood , Daniel Margulies Translational Psychiatry, 2018, 8 (1), pp.133. ⟨10.1038/s41398-018-0179-6⟩ Journal articles hal-01790245v1
	Atlases of cognition with large-scale human brain mapping Gaël Varoquaux , Yannick Schwartz , Russell A Poldrack , Baptiste Gauthier , Danilo Bzdok PLoS Computational Biology, 2018, 14 (11), pp.e1006565. ⟨10.1371/journal.pcbi.1006565⟩ Journal articles inserm-02146700v1
	Atlases of cognition with large-scale brain mapping Gaël Varoquaux , Yannick Schwartz , Russell Poldrack , Baptiste Gauthier , Danilo Bzdok PLoS Computational Biology, inPress Journal articles hal-01908189v1
	Decoding fMRI activity in the time domain improves classification performance João Loula , Gaël Varoquaux , Bertrand Thirion NeuroImage, 2017, ⟨10.1016/j.neuroimage.2017.08.018⟩ Journal articles hal-01576641v1
	FReM – scalable and stable decoding with fast regularized ensemble of models Andrés A Hoyos-Idrobo , Gaël Varoquaux , Yannick Schwartz , Bertrand Thirion NeuroImage, 2017, pp.1-16. ⟨10.1016/j.neuroimage.2017.10.005⟩ Journal articles hal-01615015v1
	Distinct alterations in Parkinson's Medication-state and Disease-state Connectivity Running Title: PD altered connectivity Bernard Ng , Gaël Varoquaux , Jean Baptiste Poline , Bertrand Thirion , Michael D. Greicius Neuroimage-Clinical, 2017 Journal articles hal-01614971v1
	Joint prediction of multiple scores captures better individual traits from brain images Mehdi Rahim , Bertrand Thirion , Danilo Bzdok , Irène Buvat , Gaël Varoquaux NeuroImage, 2017, ⟨10.1016/j.neuroimage.2017.06.072⟩ Journal articles hal-01547524v1
	Cross-validation failure: small sample sizes lead to large error bars Gaël Varoquaux NeuroImage, 2017, ⟨10.1016/j.neuroimage.2017.06.061⟩ Journal articles hal-01545002v1
	Predicting brain-age from multimodal imaging data captures cognitive impairment Franziskus Liem , Gaël Varoquaux , Jana Kynast , Frauke Beyer , Shahrzad Kharabian Masouleh NeuroImage, 2016, ⟨10.1016/j.neuroimage.2016.11.005⟩ Journal articles hal-01403005v1
	Formal Models of the Network Co-occurrence Underlying Mental Operations Danilo Bzdok , Gaël Varoquaux , Olivier Grisel , Michael Eickenberg , Cyril Poupon PLoS Computational Biology, 2016, ⟨10.1371/journal.pcbi.1004994⟩ Journal articles hal-01338307v1
	Exploring the anatomical encoding of voice with a mathematical model of the vocal system. M Florencia Assaneo , Jacobo Sitt , Gaël Varoquaux , Mariano Sigman , Laurent Cohen NeuroImage, 2016, 141, pp.31-9. ⟨10.1016/j.neuroimage.2016.07.033⟩ Journal articles hal-01498364v1
	Assessing and tuning brain decoders: cross-validation, caveats, and guidelines Gaël Varoquaux , Pradeep A Reddy Raamana , Denis A Engemann , Andrés A Hoyos-Idrobo , Yannick A Schwartz NeuroImage, 2016, ⟨10.1016/j.neuroimage.2016.10.038⟩ Journal articles hal-01332785v2
	Neuroimaging Research: From Null-Hypothesis Falsification to Out-of-sample Generalization Danilo Bzdok , Gaël Varoquaux , Bertrand Thirion Educational and Psychological Measurement, 2016 Journal articles hal-01338313v1
	Seeing it all: Convolutional network layers map the function of the human visual system Michael Eickenberg , Alexandre Gramfort , Gaël Varoquaux , Bertrand Thirion NeuroImage, 2016, ⟨10.1016/j.neuroimage.2016.10.001⟩ Journal articles hal-01389809v1
	The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments Krzysztof J. Gorgolewski , Tibor Auer , Vince D. Calhoun , Cameron R. Craddock , Samir Das Scientific Data , 2016, 3, pp.160044. ⟨10.1038/sdata.2016.44⟩ Journal articles inserm-01345616v1
	Recursive nearest agglomeration (ReNA): fast clustering for approximation of structured signals Andrés Hoyos-Idrobo , Gaël Varoquaux , Jonas Kahn , Bertrand Thirion IEEE Transactions on Pattern Analysis and Machine Intelligence, In press, XX, ⟨10.1109/TPAMI.2018.2815524⟩ Journal articles hal-01366651v2
	Connectivity-Based Parcellation: Critique and Implications Simon B. Eickhoff , Bertrand Thirion , Gaël Varoquaux , Danilo Bzdok Human Brain Mapping, 2016, pp.22. ⟨10.1002/hbm.22933⟩ Journal articles hal-01184563v1
	Beyond computational reproducibility, let us aim for reusability Gaël Varoquaux IEEE CIS Newsletter on Cognitive and Developmental Systems, 2016, What is Computational Reproducibility?, 13 (2) Journal articles hal-01592368v1
	Deriving reproducible biomarkers from multi-site resting-state data: An Autism-based example Alexandre Abraham , Michael Milham , Adriana Di Martino , R. Cameron Craddock , Dimitris Samaras NeuroImage, 2016, ⟨10.1016/j.neuroimage.2016.10.045⟩ Journal articles hal-01398867v1
	Transmodal Learning of Functional Networks for Alzheimer's Disease Prediction Mehdi Rahim , Bertrand Thirion , Claude Comtat , Gaël Varoquaux IEEE Journal of Selected Topics in Signal Processing, 2016, 10 (7), pp.1204 - 1213. ⟨10.1109/JSTSP.2016.2600400⟩ Journal articles hal-01353728v1
	Convex relaxations of penalties for sparse correlated variables with bounded total variation Eugene Belilovsky , Andreas Argyriou , Gaël Varoquaux , Matthew B. Blaschko Machine Learning, 2015, pp.1-21. ⟨10.1007/s10994-015-5511-2⟩ Journal articles hal-01167861v1
	NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain Krzysztof J. Gorgolewski , Gael Varoquaux , Gabriel Rivera , Yannick Schwartz , Vanessa V. Sochat NeuroImage, 2015, 124 (Pt B), pp.1242-1244. ⟨10.1016/j.neuroimage.2015.04.016⟩ Journal articles inserm-01148969v1
	Transport on Riemannian Manifold for Connectivity-based Brain Decoding Bernard Ng , Gaël Varoquaux , Jean-Baptiste Poline , Michael D Greicius , Bertrand Thirion IEEE Transactions on Medical Imaging, 2015, PP (99), pp.9. ⟨10.1109/TMI.2015.2463723⟩ Journal articles hal-01185200v1
	NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain Krzysztof J. Gorgolewski , Gael Varoquaux , Gabriel Rivera , Yannick Schwarz , Satrajit S. Ghosh Frontiers in Neuroinformatics, 2015, 9 (8), ⟨10.3389/fninf.2015.00008⟩ Journal articles inserm-01134573v2
	Identification of Mood-Relevant Brain Connections Using a Continuous, Subject-Driven Rumination Paradigm. Anna-Clare Milazzo , Bernard Ng , Heidi Jiang , William Shirer , Gael Varoquaux Cerebral Cortex, 2014, pp.12 Journal articles hal-01094759v1
	Which fMRI clustering gives good brain parcellations? Bertrand Thirion , Gaël Varoquaux , Elvis Dohmatob , Jean-Baptiste Poline Frontiers in Neuroscience, 2014, 8 (167), pp.13. ⟨10.3389/fnins.2014.00167⟩ Journal articles hal-01015172v1
	Machine Learning Patterns for Neuroimaging-Genetic Studies in the Cloud Benoit da Mota , Radu Tudoran , Alexandru Costan , Gaël Varoquaux , Goetz Brasche Frontiers in Neuroinformatics, 2014, Recent advances and the future generation of neuroinformatics infrastructure, 8, ⟨10.3389/fninf.2014.00031⟩ Journal articles hal-01057325v1
	How machine learning is shaping cognitive neuroimaging Gaël Varoquaux , Bertrand Thirion GigaScience, 2014, 3, pp.28. ⟨10.1186/2047-217X-3-28⟩ Journal articles hal-01094737v1
	Learning and comparing functional connectomes across subjects Gaël Varoquaux , R. Cameron Craddock NeuroImage, 2013, 80, pp.405-415. ⟨10.1016/j.neuroimage.2013.04.007⟩ Journal articles hal-00812911v1
	Machine Learning for Neuroimaging with Scikit-Learn Alexandre Abraham , Fabian Pedregosa , Michael Eickenberg , Philippe Gervais , Andreas Muller Frontiers in Neuroscience, 2013, pp.15. ⟨10.3389/fninf.2014.00014⟩ Journal articles hal-01093971v1
	Spatial vs. Temporal Features in ICA of Resting-State fMRI - A Quantitative and Qualitative Investigation in the Context of Response Inhibition Lixia Tian , Yazhuo Kong , Juejing Ren , Gaël Varoquaux , Yufeng Zang PLoS ONE, 2013, ⟨10.1371/journal.pone.0066572⟩ Journal articles hal-00856513v1
	A framework for inter-subject prediction of functional connectivity from structural networks Fani Deligianni , Gaël Varoquaux , Bertrand Thirion , David J. Sharp , Christian Ledig IEEE Transactions on Medical Imaging, 2013, epub ahead of print, ⟨10.1109/TMI.2013.2276916⟩ Journal articles hal-00852072v1
	Publishing scientific software matters Christophe Pradal , Gaël Varoquaux , Hans Peter Langtangen Journal of computational science, 2013, 4 (5), pp.311 - 312. ⟨10.1016/j.jocs.2013.08.001⟩ Journal articles hal-00858663v1
	Randomized parcellation based inference. Benoit da Mota , Virgile Fritsch , Gaël Varoquaux , Tobias Banaschewski , Gareth J. Barker NeuroImage, 2013, epub ahead of print. ⟨10.1016/j.neuroimage.2013.11.012⟩ Journal articles hal-00915243v1
	In Situ Synchrotron Microtomography Reveals Multiple Reaction Pathways During Soda-Lime Glass Synthesis Emmanuelle Gouillart , Michael-J. Toplis , Julien Grynberg , Marie-Hélène Chopinet , Elin Sondergard Journal of the American Ceramic Society, 2012, 95 (5), pp.1504-1507. ⟨10.1111/j.1551-2916.2012.05151.x⟩ Journal articles hal-00705955v1
	Hyperfrontality and hypoconnectivity during refreshing in schizophrenia. Marie-Laure Grillon , Catherine Oppenheim , Gaël Varoquaux , Frédérique Charbonneau , Anne-Dominique Devauchelle Psychiatry Research: Neuroimaging, 2012, 211 (3), pp.226-233. ⟨10.1016/j.pscychresns.2012.09.001⟩ Journal articles hal-00753225v1
	Markov models for fMRI correlation structure: is brain functional connectivity small world, or decomposable into networks? Gaël Varoquaux , Alexandre Gramfort , Jean Baptiste Poline , Bertrand Thirion Journal of Physiology - Paris, 2012, 106, pp.212-221. ⟨10.1016/j.jphysparis.2012.01.001⟩ Journal articles hal-00665340v2
	Changing computational research. The challenges ahead. Cameron Neylon , Jan Aerts , C Titus Brown , Simon J Coles , Les Hatton Source Code for Biology and Medicine, 2012, 7 (2), pp.2. ⟨10.1186/1751-0473-7-2⟩ Journal articles hal-00856484v1
	PyXNAT: XNAT in Python Yannick Schwartz , Alexis Barbot , Benjamin Thyreau , Vincent Frouin , Gaël Varoquaux Frontiers in Neuroinformatics, 2012, 6 (12), pp.1-14. ⟨10.3389/fninf.2012.00012⟩ Journal articles hal-00782339v1
	Detecting Outliers in High-Dimensional Neuroimaging Datasets with Robust Covariance Estimators Virgile Fritsch , Gaël Varoquaux , Benjamin Thyreau , Jean-Baptiste Poline , Bertrand Thirion Medical Image Analysis, 2012, 16, pp.1359-1370. ⟨10.1016/j.media.2012.05.002⟩ Journal articles hal-00701225v1
	Scale-Free and Multifractal Time Dynamics of fMRI Signals during Rest and Task. Philippe Ciuciu , G. Varoquaux , Patrice Abry , S. Sadaghiani , A. Kleinschmidt Frontiers in Physiology, 2012, 3 (1), pp.186. ⟨10.3389/fphys.2012.00186⟩ Journal articles hal-00852175v1
	Total variation regularization for fMRI-based prediction of behaviour. Vincent Michel , Alexandre Gramfort , Gaël Varoquaux , Evelyn Eger , Bertrand Thirion IEEE Transactions on Medical Imaging, 2011, 30 (7), pp.1328 - 1340. ⟨10.1109/TMI.2011.2113378⟩ Journal articles inria-00563468v1
	Scikit-learn: Machine Learning in Python Fabian Pedregosa , Gaël Varoquaux , Alexandre Gramfort , Vincent Michel , Bertrand Thirion Journal of Machine Learning Research, 2011 Journal articles hal-00650905v2
	A supervised clustering approach for fMRI-based inference of brain states Vincent Michel , Alexandre Gramfort , Gaël Varoquaux , Evelyn Eger , Christine Keribin Pattern Recognition, 2011, epub ahead of print. ⟨10.1016/j.patcog.2011.04.006⟩ Journal articles inria-00589201v1
	The NumPy array: a structure for efficient numerical computation Stefan van Der Walt , S. Chris Colbert , Gaël Varoquaux Computing in Science and Engineering, 2011, 13 (2), pp.22-30. ⟨10.1109/MCSE.2011.37⟩ Journal articles inria-00564007v1
	Mayavi: 3D visualization of scientific data Prabhu Ramachandran , Gaël Varoquaux Computing in Science and Engineering, 2011, 13 (2), pp.40-51. ⟨10.1109/MCSE.2011.35⟩ Journal articles inria-00528985v1
	A group model for stable multi-subject ICA on fMRI datasets. Gaël Varoquaux , Sepideh Sadaghiani , Philippe Pinel , Andreas Kleinschmidt , Jean-Baptiste Poline NeuroImage, 2010, 51 (1), pp.288-99. ⟨10.1016/j.neuroimage.2010.02.010⟩ Journal articles hal-00489507v1
	Python comme langage scientifique Gaël Varoquaux Linux Magazine France, 2009, Explorer les richesses du langage Python, 40 Journal articles hal-00776672v1
	How to estimate the differential acceleration in a two-species atom interferometer to test the equivalence principle Gaël Varoquaux , Robert Nyman , Rémi Geiger , Patrick Cheinet , Arnaud Landragin New Journal of Physics, 2009, 11, pp.113010. ⟨10.1088/1367-2630/11/11/113010⟩ Journal articles hal-00423845v1
	Light-pulse atom interferometry in microgravity Guillaume Stern , Baptiste Battelier , Rémi Geiger , Gaël Varoquaux , André Villing The European Physical Journal D : Atomic, molecular, optical and plasma physics, 2009, 53 (3), pp.353. ⟨10.1140/epjd/e2009-00150-5⟩ Journal articles hal-00369287v1
	Sagnac effect in superfluid liquids Eric Varoquaux , Gaël Varoquaux Uspekhi Fizicheskikh Nauk, 2008, 51 (2), pp.205-208. ⟨10.1070/PU2008v051n02ABEH006425⟩ Journal articles hal-00502604v1
	Agile Computer Control of a Complex Experiment Gaël Varoquaux Computing in Science and Engineering, 2008, 10 (2), pp.55-59. ⟨10.1109/MCSE.2008.47⟩ Journal articles hal-00502504v1
	Light-shift tomography in an optical-dipole trap for neutral atoms Jean-Philippe Brantut , Jean-François Clément , Martin Robert-De-Saint-Vincent , Gaël Varoquaux , Robert Nyman Physical Review A : Atomic, molecular, and optical physics [1990-2015], 2008, 78, pp.031401 (R). ⟨10.1103/PhysRevA.78.031401⟩ Journal articles hal-00303321v1
	I.C.E.: a Transportable Atomic Inertial Sensor for Test in Microgravity Robert Nyman , Gaël Varoquaux , Fabien Lienhart , Damien Chambon , Salah Boussen Applied Physics B - Laser and Optics, 2006, 84, pp.673-681. ⟨10.1007/s00340-006-2395-7⟩ Journal articles hal-00023609v1
	Tapered-amplified AR-coated laser diodes for Potassium and Rubidium atomic-physics experiments Robert Nyman , Gaël Varoquaux , Brice Villier , Delphine Sacchet , Frédéric Moron Review of Scientific Instruments, 2006, 77, pp.033105. ⟨10.1063/1.2186809⟩ Journal articles hal-00014931v1

	CARTE: Pretraining and Transfer for Tabular Learning Myung Jun Kim , Léo Grinsztajn , Gaël Varoquaux Forty-first International Conference on Machine Learning, ICML 2024, Jul 2024, Vienna, Austria Conference papers hal-04596816v2
	Confidence intervals uncovered: Are we ready for real-world medical imaging AI? Evangelia Christodoulou , Annika Reinke , Rola Houhou , Piotr Kalinowski , Selen Erkan MICCAI 2024 - Medical Image Computing and Computer-Assisted Intervention, Oct 2024, Marrakech, Morocco Conference papers hal-04715638v1
	Learning High-Quality and General-Purpose Phrase Representations Lihu Chen , Gaël Varoquaux , Fabian M. Suchanek EACL 2024 - The 18th Conference of the European Chapter of the Association for Computational Linguistics, Mar 2024, La Valette, Malta Conference papers hal-04465022v1
	Beyond calibration: estimating the grouping loss of modern neural networks Alexandre Perez-Lebel , Marine Le Morvan , Gaël Varoquaux ICLR 2023 – The Eleventh International Conference on Learning Representations, May 2023, Kigali, Rwanda Conference papers hal-03829870v4
	The Locality and Symmetry of Positional Encodings Lihu Chen , Gaël Varoquaux , Fabian M. Suchanek EMNLP 2023 - Conference on Empirical Methods in Natural Language Processing, Dec 2023, Singapore, Singapore Conference papers hal-04330367v1
	GLADIS: A General and Large Acronym Disambiguation Benchmark Lihu Chen , Gaël Varoquaux , Fabian M. Suchanek EACL 2023 - The 17th Conference of the European Chapter of the Association for Computational Linguistics, May 2023, Dubrovnik, Croatia Conference papers hal-04039173v1
	Why do tree-based models still outperform deep learning on typical tabular data? Léo Grinsztajn , Edouard Oyallon , Gaël Varoquaux 36th Conference on Neural Information Processing Systems (NeurIPS 2022) Track on Datasets and Benchmarks, Nov 2022, New Orleans, United States Conference papers hal-03723551v3
	Imputing out-of-vocabulary embeddings with LOVE makes language models robust with little cost Lihu Chen , Gaël Varoquaux , Fabian Suchanek ACL 2022 - 60th Annual Meeting of the Association for Computational Linguistics, May 2022, Dublin, Ireland Conference papers hal-03613101v2
	What's a good imputation to predict with missing values? Marine Le Morvan , Julie Josse , Erwan Scornet , Gaël Varoquaux NeurIPS 2021 - 35th Conference on Neural Information Processing Systems, Dec 2021, Virtual, France. ⟨10.48550/arXiv.2106.00311⟩ Conference papers hal-03243931v2
	Accounting for variance in machine learning benchmarks Xavier Bouthillier , Pierre Delaunay , Mirko Bronzi , Assya Trofimov , Brennan Nichyporuk MLsys 2021 - 4th Conference on Machine Learning and Systems, Apr 2021, San Francisco (virtual), United States Conference papers hal-03177159v1
	AI as statistical methods for imperfect theories Gaël Varoquaux NeurIPS 2021 - 35th Conference on Neural Information Processing Systems. Workshop: AI for Science, Dec 2021, Virtual, France Conference papers hal-03474791v2
	A lightweight neural model for biomedical entity linking Lihu Chen , Gaël Varoquaux , Fabian Suchanek AAAI 2021 - The Thirty-Fifth Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, Feb 2021, Palo Alto (virtual), United States. pp.12657-12665 Conference papers hal-03086044v2
	NeuMiss networks: differentiable programming for supervised learning with missing values Marine Le Morvan , Julie Josse , Thomas Moreau , Erwan Scornet , Gaël Varoquaux NeurIPS 2020 - 34th Conference on Neural Information Processing Systems, Dec 2020, Vancouver / Virtual, Canada Conference papers hal-02888867v3
	Linear predictor on linearly-generated data with missing values: non consistency and solutions Marine Le Morvan , Nicolas Prost , Julie Josse , Erwan Scornet , Gaël Varoquaux AISTATS 2020 - International Conference on Artificial Intelligence and Statistics, Aug 2020, Online, France. pp.3165-3174 Conference papers hal-02464569v2
	Feature Grouping as a Stochastic Regularizer for High-Dimensional Structured Data Sergül Aydöre , Bertrand Thirion , Gaël Varoquaux NeurIPS 2019 - 33th Annual Conference on Neural Information Processing Systems, Dec 2019, Vancouver, Canada Conference papers hal-02318458v1
	Comparing distributions: $l1$ geometry improves kernel two-sample testing Meyer Scetbon , Gaël Varoquaux NeurIPS 2019 - 33th Conference on Neural Information Processing Systems, Dec 2019, Vancouver, Canada Conference papers hal-02292545v2
	Manifold-regression to predict from MEG/EEG brain signals without source modeling David Sabbagh , Pierre Ablin , Gaël Varoquaux , Alexandre Gramfort , Denis Engemann NeurIPS 2019 - 33th Annual Conference on Neural Information Processing Systems, Dec 2019, Vancouver, Canada Conference papers hal-02147708v2
	Controlling a confound in predictive models with a test set minimizing its effect Darya Chyzhyk , Gaël Varoquaux , Bertrand Thirion , Michael Milham PRNI 2018 - 8th International Workshop on Pattern Recognition in Neuroimaging, Jun 2018, Singapore, Singapore. pp.1-4 Conference papers hal-01831701v1
	Text to brain: predicting the spatial distribution of neuroimaging observations from text reports Jérôme Dockès , Demian Wassermann , Russell Poldrack , Fabian M. Suchanek , Bertrand Thirion MICCAI 2018 - 21st International Conference on Medical Image Computing and Computer Assisted Intervention, Sep 2018, Granada, Spain. pp.1-18 Conference papers hal-01807295v3
	Hierarchical Region-Network Sparsity for High-Dimensional Inference in Brain Imaging Danilo Bzdok , Michael Eickenberg , Gaël Varoquaux , Bertrand Thirion International conference on Information Processing in Medical Imaging (IPMI) 2017, Jun 2017, Boone, North Carolina, United States Conference papers hal-01480885v1
	Learning Neural Representations of Human Cognition across Many fMRI Studies Arthur Mensch , Julien Mairal , Danilo Bzdok , Bertrand Thirion , Gaël Varoquaux Neural Information Processing Systems, Dec 2017, Long Beach, United States Conference papers hal-01626823v3
	Population-shrinkage of covariance to estimate better brain functional connectivity Mehdi Rahim , Bertrand Thirion , Gaël Varoquaux Medical Image Computing and Computer Assisted Interventions, Sep 2017, Quebec city, Canada Conference papers hal-01547612v1
	Multi-output predictions from neuroimaging: assessing reduced-rank linear models Mehdi Rahim , Bertrand Thirion , Gaël Varoquaux PRNI 2017 - The 7th International Workshop on Pattern Recognition in Neuroimaging, Jun 2017, Toronto, Canada. pp.1 - 4, ⟨10.1109/PRNI.2017.7981504⟩ Conference papers hal-01547572v2
	Learning to Discover Sparse Graphical Models Eugene B Belilovsky , Kyle Kastner , Gaël Varoquaux , Matthew B Blaschko International Conference on Machine Learning , Aug 2017, Sydney, Australia Conference papers hal-01306491v4
	Label scarcity in biomedicine: Data-rich latent factor discovery enhances phenotype prediction Marc-Andre Schulz , Gaël Varoquaux , Alexandre Gramfort , Bertrand Thirion , Danilo Bzdok Neural Information Processing Systems, Machine Learning in Health Workshop, Dec 2017, Long Beach, United States Conference papers hal-01633096v1
	Towards a Faster Randomized Parcellation Based Inference Andrés Hoyos-Idrobo , Gaël Varoquaux , Bertrand Thirion PRNI 2017 - 7th International Workshop on Pattern Recognition in NeuroImaging, Jun 2017, Toronto, Canada Conference papers hal-01552237v1
	Fast brain decoding with random sampling and random projections Andrés Hoyos-Idrobo , Gaël Varoquaux , Bertrand Thirion PRNI 2016: the 6th International Workshop on Pattern Recognition in Neuroimaging, Jun 2016, Trento, Italy Conference papers hal-01313814v1
	Subsampled online matrix factorization with convergence guarantees Arthur Mensch , Julien Mairal , Gaël Varoquaux , Bertrand Thirion NIPS Workshop on Optimization for Machine Learning, Dec 2016, Barcelone, Spain Conference papers hal-01405058v1
	Dictionary Learning for Massive Matrix Factorization Arthur Mensch , Julien Mairal , Bertrand Thirion , Gaël Varoquaux International Conference on Machine Learning, Jun 2016, New York, United States. pp.1737-1746 Conference papers hal-01308934v2
	The Brain Imaging Data Structure: a format for organizing and describing neuroimaging data Krzysztof Gorgolewski , Tibor Auer , Vince D Calhoun , Cameron Craddock , Samir Das 22nd Annual Meeting of the Organization for Human Brain Mapping (OHBM 2016), Jun 2016, Geneva, Switzerland Conference papers inserm-01570685v1
	Learning brain regions via large-scale online structured sparse dictionary-learning Elvis Dohmatob , Arthur Mensch , Gaël Varoquaux , Bertrand Thirion Neural Information Processing Systems (NIPS), Dec 2016, Barcelona, Spain Conference papers hal-01369134v3
	Local Q-Linear Convergence and Finite-time Active Set Identification of ADMM on a Class of Penalized Regression Problems Elvis Dohmatob , Michael Eickenberg , Bertrand Thirion , Gaël Varoquaux ICASSP, International Conference on Acoustics, Speach, and Signal Processing, Mar 2016, http://icassp2016.org/default.asp, China Conference papers hal-01265372v1
	Comparing functional connectivity based predictive models across datasets Kamalaker Dadi , Alexandre Abraham , Mehdi Rahim , Bertrand Thirion , Gaël Varoquaux PRNI 2016: 6th International Workshop on Pattern Recognition in Neuroimaging, Jun 2016, Trento, Italy Conference papers hal-01319131v1
	Testing for Differences in Gaussian Graphical Models: Applications to Brain Connectivity Eugene Belilovsky , Gaël Varoquaux , Matthew B. Blaschko Neural Information Processing Systems (NIPS) 2016, Dec 2016, Barcelona, Spain Conference papers hal-01248844v4
	Compressed Online Dictionary Learning for Fast Resting-State fMRI Decomposition Arthur Mensch , Gaël Varoquaux , Bertrand Thirion International Symposium on Biomedical Imaging, IEEE, Apr 2016, Prague, Czech Republic. pp.1282-1285, ⟨10.1109/ISBI.2016.7493501⟩ Conference papers hal-01271033v2
	Social-sparsity brain decoders: faster spatial sparsity Gaël Varoquaux , Matthieu Kowalski , Bertrand Thirion Pattern Recognition in NeuroImaging, Jun 2016, Trento, Italy Conference papers hal-01334551v1
	FAASTA: A fast solver for total-variation regularization of ill-conditioned problems with application to brain imaging Gaël Varoquaux , Michael Eickenberg , Elvis Dohmatob , Bertand Thirion Colloque GRETSI, P. Gonçalves, P. Abry, Sep 2015, Lyon, France Conference papers hal-01247388v1
	Speeding-up model-selection in GraphNet via early-stopping and univariate feature-screening Elvis Dohmatob , Michael Eickenberg , Bertrand Thirion , Gaël Varoquaux PRNI, Jun 2015, Stanford, United States Conference papers hal-01147731v1
	NeuroVault.org: new features and a proof of concept analysis Krzysztof Gorgolewski , Gaël Varoquaux , Gabriel Rivera , Joseph Wexler , Yannick Schwartz 21st Annual Meeting of the Organization for Human Brain Mapping (OHBM 2015), Jun 2015, Honolulu, United States Conference papers inserm-01570688v1
	Improving sparse recovery on structured images with bagged clustering Andrés Hoyos-Idrobo , Yannick Schwartz , Gaël Varoquaux , Bertrand Thirion International Workshop On Pattern Recognition In Neuroimaging (PRNI), 2015, Jun 2015, Palo alto, United States Conference papers hal-01174335v1
	Total Variation meets Sparsity: statistical learning with segmenting penalties Michael Eickenberg , Elvis Dohmatob , Bertrand Thirion , Gaël Varoquaux Medical Image Computing and Computer Aided Intervention (MICCAI), Oct 2015, München, Germany Conference papers hal-01170619v1
	Fast clustering for scalable statistical analysis on structured images Bertrand Thirion , Andrés Hoyos-Idrobo , Jonas Kahn , Gaël Varoquaux ICML Workshop on Statistics, Machine Learning and Neuroscience (Stamlins 2015), Bertrand Thirion, Lars Kai Hansen, Sanmi Koyejo, Jul 2015, Lille, France Conference papers hal-01229023v2
	Integrating Multimodal Priors in Predictive Models for the Functional Characterization of Alzheimer's Disease Mehdi Rahim , Bertrand Thirion , Alexandre Abraham , Michael Eickenberg , Elvis Dohmatob Medical Image Computing and Computer Assisted Intervention, Oct 2015, Munich, Germany. ⟨10.1007/978-3-319-24553-9_26⟩ Conference papers hal-01174636v1
	Semi-Supervised Factored Logistic Regression for High-Dimensional Neuroimaging Data Danilo Bzdok , Michael Eickenberg , Olivier Grisel , Bertrand Thirion , Gaël Varoquaux NIPS'15: 28th International Conference on Neural Information Processing Systems, Dec 2015, Montreal, Canada Conference papers hal-01211248v1
	Correlations of correlations are not reliable statistics: implications for multivariate pattern analysis. Bertrand Thirion , Fabian Pedregosa , Michael Eickenberg , Gaël Varoquaux ICML Workshop on Statistics, Machine Learning and Neuroscience (Stamlins 2015), Bertrand Thirion, Lars Kai Hansen, Sanmi Koyejo, Jul 2015, Lille, France Conference papers hal-01187297v1
	Principal Component Regression predicts functional responses across individuals Bertrand Thirion , Gaël Varoquaux , Olivier Grisel , Cyril Poupon , Philippe Pinel MICCAI, Sep 2014, Boston, United States Conference papers hal-01015173v1
	Transport on Riemannian Manifold for Functional Connectivity-based Classification Bernard Ng , Martin Dressler , Gaël Varoquaux , Jean-Baptiste Poline , Michael D. Greicius MICCAI - 17th International Conference on Medical Image Computing and Computer Assisted Intervention, Polina Golland, Sep 2014, Boston, United States Conference papers hal-01058521v1
	Benchmarking solvers for TV-l1 least-squares and logistic regression in brain imaging Elvis Dohmatob , Alexandre Gramfort , Bertrand Thirion , Gaël Varoquaux PRNI 2014 - 4th International Workshop on Pattern Recognition in NeuroImaging, Jun 2014, Tübingen, Germany Conference papers hal-00991743v1
	Deriving a multi-subject functional-connectivity atlas to inform connectome estimation Ronald Phlypo , Bertrand Thirion , Gaël Varoquaux Medical Image Computing and Computer-Assisted Intervention, Sep 2014, Boston, United States. pp.185-192, ⟨10.1007/978-3-319-10443-0_24⟩ Conference papers hal-00991124v4
	A Comparison of Metrics and Algorithms for Fiber Clustering Viviana Siless , Sergio Medina , Gaël Varoquaux , Bertrand Thirion Pattern Recognition in NeuroImaging, Jun 2013, Philadelphia, United States Conference papers hal-00858115v1
	Extracting brain regions from rest fMRI with Total-Variation constrained dictionary learning Alexandre Abraham , Elvis Dohmatob , Bertrand Thirion , Dimitris Samaras , Gaël Varoquaux MICCAI - 16th International Conference on Medical Image Computing and Computer Assisted Intervention - 2013, Sep 2013, Nagoya, Japan Conference papers hal-00853242v1
	Implications of Inconsistencies between fMRI and dMRI on Multimodal Connectivity Estimation Bernard Ng , Gaël Varoquaux , Jean-Baptiste Poline , Bertrand Thirion MICCAI - 16th International Conference on Medical Image Computing and Computer Assisted Intervention - 2013, Kensaku Mori, Sep 2013, Nagoya, Japan Conference papers hal-00853108v1
	Hemodynamic estimation based on Consensus Clustering Solveig Badillo , Gaël Varoquaux , Philippe Ciuciu PRNI 2013 -- 3rd International Workshop on Pattern Recognition in NeuroImaging, Jun 2013, Philadelphia, United States Conference papers hal-00854621v1
	A Novel Sparse Group Gaussian Graphical Model for Functional Connectivity Estimation Bernard Ng , Gaël Varoquaux , Jean-Baptiste Poline , Bertrand Thirion Information Processing in Medical Imaging, Jun 2013, Asilomar, United States Conference papers hal-00842607v1
	Cohort-level brain mapping: learning cognitive atoms to single out specialized regions Gaël Varoquaux , Yannick Schwartz , Philippe Pinel , Bertrand Thirion IPMI - Information Processing in Medical Imaging - 2013, William M. Wells, Sarang Joshi, Kilian M. Pohl, Jun 2013, Asilomar, United States. pp.438-449, ⟨10.1007/978-3-642-38868-2_37⟩ Conference papers hal-00841502v1
	API design for machine learning software: experiences from the scikit-learn project Lars Buitinck , Gilles Louppe , Mathieu Blondel , Fabian Pedregosa , Andreas Mueller European Conference on Machine Learning and Principles and Practices of Knowledge Discovery in Databases, Sep 2013, Prague, Czech Republic Conference papers hal-00856511v1
	Enhancing the Reproducibility of Group Analysis with Randomized Brain Parcellations Benoit da Mota , Virgile Fritsch , Gaël Varoquaux , Vincent Frouin , Jean-Baptiste Poline MICCAI - 16th International Conference on Medical Image Computing and Computer Assisted Intervention - 2013, Sep 2013, Nagoya, Japan Conference papers hal-00832616v1
	Identifying predictive regions from fMRI with TV-L1 prior Alexandre Gramfort , Bertrand Thirion , Gaël Varoquaux Pattern Recognition in Neuroimaging (PRNI), Jun 2013, Philadelphia, United States Conference papers hal-00839984v1
	Robust Group-Level Inference in Neuroimaging Genetic Studies Virgile Fritsch , Benoit da Mota , Gaël Varoquaux , Vincent Frouin , Eva Loth Pattern Recognition in Neuroimaging, Jun 2013, Philadelphie, United States Conference papers hal-00833953v1
	Mapping cognitive ontologies to and from the brain Yannick Schwartz , Bertrand Thirion , Gaël Varoquaux NIPS (Neural Information Processing Systems), Dec 2013, United States Conference papers hal-00904763v2
	A Novel Sparse Graphical Approach for Multimodal Brain Connectivity Inference Bernard Ng , Gaël Varoquaux , Jean-Baptiste Poline , Bertrand Thirion Medical Image Computing and Computer Assisted Intervention, Oct 2012, Nice, France Conference papers hal-00741631v1
	A fast computational framework for genome-wide association studies with neuroimaging data Benoit da Mota , Vincent Frouin , Edouard Duchesnay , Soizic Laguitton , Gaël Varoquaux 20th International Conference on Computational Statistics (COMPSTAT 2012), Aug 2012, Limassol, Cyprus Conference papers hal-00720265v1
	Improving accuracy and power with transfer learning using a meta-analytic database Yannick Schwartz , Gaël Varoquaux , Christophe Pallier , Philippe Pinel , Jean-Baptiste Poline MICCAI, Oct 2012, Nice, France. pp.1-8 Conference papers hal-00734911v2
	Improved brain pattern recovery through ranking approaches Fabian Pedregosa , Elodie Cauvet , Gaël Varoquaux , Christophe Pallier , Bertrand Thirion PRNI 2012 : 2nd International Workshop on Pattern Recognition in NeuroImaging, Jul 2012, London, United Kingdom Conference papers hal-00717954v1
	Decoding Visual Percepts Induced by Word Reading with fMRI Alexandre Gramfort , Christophe Pallier , Gaël Varoquaux , Bertrand Thirion Pattern Recognition in NeuroImaging (PRNI), 2012 International Workshop on, Jul 2012, Londres, United Kingdom. pp.13-16, ⟨10.1109/PRNI.2012.20⟩ Conference papers hal-00730768v1
	A MapReduce Approach for Ridge Regression in Neuroimaging-Genetic Studies Benoit da Mota , Michael Eickenberg , Soizic Laguitton , Vincent Frouin , Gaël Varoquaux DCICTIA-MICCAI - Data- and Compute-Intensive Clinical and Translational Imaging Applications in conjonction with the 15th International Conference on Medical Image Computing and Computer Assisted Intervention - 2012, Oct 2012, Nice, France Conference papers hal-00730385v1
	Connectivity-informed Sparse Classifiers for fMRI Brain Decoding Bernard Ng , Viviana Siless , Gaël Varoquaux , Jean-Baptiste Poline , Bertrand Thirion Pattern Recognition in Neuroimaging, Christos Davatzikos, Moritz Grosse-Wentrup, Janaina Mourao-Miranda, Dimitri Van De Ville, Jul 2012, London, United Kingdom Conference papers hal-00726656v1
	Non-parametric Density Modeling and Outlier Detection in Medical Imaging Datasets Virgile Fritsch , Gaël Varoquaux , Jean-Baptiste Poline , Bertrand Thirion Machine Learning in Medical Imaging - Miccai 2012 workshop, Oct 2012, Nice, France. pp.207-214 Conference papers hal-00738438v1
	On spatial selectivity and prediction across conditions with fMRI Yannick Schwartz , Gaël Varoquaux , Bertrand Thirion PRNI 2012 : 2nd International Workshop on Pattern Recognition in NeuroImaging, Jul 2012, London, United Kingdom. pp.53-56 Conference papers hal-00728765v1
	Learning to rank from medical imaging data Fabian Pedregosa , Elodie Cauvet , Gaël Varoquaux , Christophe Pallier , Bertrand Thirion Third International Workshop on Machine Learning in Medical Imaging - MLMI 2012, INRIA, Oct 2012, Nice, France Conference papers hal-00717990v2
	Small-sample brain mapping: sparse recovery on spatially correlated designs with randomization and clustering Gaël Varoquaux , Alexandre Gramfort , Bertrand Thirion International Conference on Machine Learning, Andrew McCallum, Jun 2012, Edimbourg, United Kingdom Conference papers hal-00705192v1
	A probabilistic framework to infer brain functional connectivity from anatomical connections Fani Deligianni , Gaël Varoquaux , Bertrand Thirion , Emma Robinson , David J. Sharp Information Processing in Medical Imaging, Gábor Székely, Horst Hahn, Jul 2011, Kaufbeuren, Germany. pp.296-307, ⟨10.1007/978-3-642-22092-0_25⟩ Conference papers inria-00627914v1
	Detecting Outlying Subjects in High-Dimensional Neuroimaging Datasets with Regularized Minimum Covariance Determinant Virgile Fritsch , Gaël Varoquaux , Thyreau Benjamin , Jean-Baptiste Poline , Bertrand Thirion Medical Image Computing and Computer Assisted Intervention, Sep 2011, Toronto, Canada. pp. 264-271, ⟨10.1007/978-3-642-23626-6_33⟩ Conference papers inria-00626857v1
	MULTIFRACTAL ANALYSIS OF RESTING STATE NETWORKS IN FUNCTIONAL MRI Philippe Ciuciu , Gaël Varoquaux , Patrice Abry , Moty Almog IEEE International Symposium on Biomedical Imaging, Mar 2011, Chicago, United States. paper ID 1544 Conference papers cea-00558870v1
	Statistical Learning for Resting-State fMRI: Successes and Challenges Gaël Varoquaux , Bertrand Thirion Machine Learning and Interpretation in Neuroimaging, NIPS workshop, Dec 2011, Sierra Nevada, Spain. pp.172-177, ⟨10.1007/978-3-642-34713-9_22⟩ Conference papers hal-00753132v1
	Connectivity-informed fMRI Activation Detection Bernard Ng , Abugharbieh Rafeef , Gaël Varoquaux , Jean Baptiste Poline , Bertrand Thirion Medical Image Computing and Computed Aided Intervention, Sep 2011, Toronto, Canada. pp.285-292, ⟨10.1007/978-3-642-23629-7_35⟩ Conference papers inria-00627523v1
	Multi-subject dictionary learning to segment an atlas of brain spontaneous activity Gaël Varoquaux , Alexandre Gramfort , Fabian Pedregosa , Vincent Michel , Bertrand Thirion Information Processing in Medical Imaging, Gábor Székely, Horst Hahn, Jul 2011, Kaufbeuren, Germany. pp.562-573, ⟨10.1007/978-3-642-22092-0_46⟩ Conference papers inria-00588898v2
	A Comparative Study of Algorithms for Intra- and Inter-subjects fMRI Decoding Vincent Michel , Alexandre Gramfort , Evelyn Eger , Gaël Varoquaux , Bertrand Thirion MLINI - Machine Learning and Interpretation in Neuroimaging - 2011, Dec 2011, Sierra Nevada, Spain. pp.1-8, ⟨10.1007/978-3-642-34713-9_1⟩ Conference papers hal-00753142v1
	Beyond brain reading: randomized sparsity and clustering to simultaneously predict and identify Alexandre Gramfort , Gaël Varoquaux , Bertrand Thirion NIPS 2011 MLINI Workshop, Dec 2011, Granada, Spain. pp.9-16, ⟨10.1007/978-3-642-34713-9_2⟩ Conference papers hal-00704875v1
	Detection of brain functional-connectivity difference in post-stroke patients using group-level covariance modeling Gaël Varoquaux , Flore Baronnet , Andreas Kleinschmidt , Pierre Fillard , Bertrand Thirion Medical Image Computing and Computer Added Intervention, Tianzi Jiang, Sep 2010, Beijing, China. ⟨10.1007/978-3-642-15705-9_25⟩ Conference papers inria-00512417v1
	ICA-based sparse feature recovery from fMRI datasets Gaël Varoquaux , Merlin Keller , Jean Baptiste Poline , Philippe Ciuciu , Bertrand Thirion Biomedical Imaging, IEEE International Symposium on, Apr 2010, Rotterdam, Netherlands. pp.1177 Conference papers hal-00489506v1
	Total Variation regularization enhances regression-based brain activity prediction Vincent Michel , Alexandre Gramfort , Gaël Varoquaux , Bertrand Thirion 1st ICPR Workshop on Brain Decoding - Pattern recognition challenges in neuroimaging - 20th International Conference on Pattern Recognition, Aug 2010, Istanbul, Turkey. pp.9-12, ⟨10.1109/WBD.2010.13⟩ Conference papers hal-00504095v1
	Accurate Definition of Brain Regions Position Through the Functional Landmark Approach Bertrand Thirion , Gaël Varoquaux , Jean-Baptiste Poline 13th International Conference on Medical Image Computing and Computer Assisted Intervention, Sep 2010, Beijing, China Conference papers inria-00521909v1
	Brain covariance selection: better individual functional connectivity models using population prior Gaël Varoquaux , Alexandre Gramfort , Jean Baptiste Poline , Bertrand Thirion Advances in Neural Information Processing Systems, John Lafferty, Dec 2010, Vancouver, Canada Conference papers inria-00512451v4
	Proceedings of the 8th Python in Science conference Gaël Varoquaux , Stefan van Der Walt , Jarrod Millman SciPy 2009: 8th Python in Science Conference, Aug 2009, Pasadena, United States. pp.1-78 Conference papers hal-00502607v1
	CanICA: Model-based extraction of reproducible group-level ICA patterns from fMRI time series Gaël Varoquaux , Sepideh Sadaghiani , Jean Baptiste Poline , Bertrand Thirion Medical Image Computing and Computer Aided Intervention, Sep 2009, London, United Kingdom. pp.1 Conference papers hal-00435262v1
	Mayavi: Making 3D Data Visualization Reusable Gaël Varoquaux , Prabhu Ramachandran SciPy 2008: 7th Python in Science Conference, Aug 2008, Pasadena, United States. pp.51 Conference papers hal-00502548v1
	Effects of disorder in 2D Jean-Philippe Brantut , Gaël Varoquaux , Robert A. Nyman , Jean-François Clément , Martin Robert-De-Saint-Vincent Latsis, Jan 2008, Lausanne, Switzerland Conference papers hal-00637732v1
	All-optical evaporative cooling in a versatile optical-dipole trap at telecom wavelength Martin Robert-De-Saint-Vincent , Alain Aspect , Thomas Bourdel , Philippe Bouyer , Gaël Varoquaux YAO, 2008, Florence, Italy Conference papers hal-00637735v1
	Proceedings of the 7th Python in Science conference Gaël Varoquaux , Travis Vaught , Jarrod Millman SciPy 2008: 7th Python in Science Conference, Aug 2008, Pasadena, United States. pp.1-78 Conference papers hal-00502586v1
	I.C.E.: An Ultra-Cold Atom Source for Long-Baseline Interferometric Inertial Sensors in Reduced Gravity Gaël Varoquaux , Nassim Zahzam , Walid Chaibi , Jean-François Clément , Olivier Carraz Rencontres de Moriond Gravitational Waves and Experimental Gravity, Mar 2007, La Thuile, Val d'Aosta, Italy Conference papers hal-00147641v3

	Relating Brain Structures To Open-Ended Descriptions Of Cognition Jérôme Dockès , Olivier Grisel , Joan Massich , Fabian Suchanek , Bertrand Thirion CCN 2017 - Conference on Cognitive Computational Neuroscience, Sep 2017, New York, United States. , 10 (2), pp.59 - 63, 2017, ⟨10.1016/j.tics.2005.12.004⟩ Conference poster hal-01699045v1
	SpaceNet: Multivariate brain decoding and segmentation Elvis Dohmatob , Michael Eickenberg , Bertrand Thirion , Gaël Varoquaux OHBM, Jun 2015, Honolulu, Hawaii, United States Conference poster hal-01187230v1

	Region segmentation for sparse decompositions: better brain parcellations from rest fMRI Alexandre Abraham , Elvis Dohmatob , Bertrand Thirion , Dimitris Samaras , Gael Varoquaux Sparsity Techniques in Medical Imaging, Sep 2014, Boston, United States. pp.8 Documents associated with scientific events hal-01093944v1

	Scipy Lecture Notes Gaël Varoquaux , Emmanuelle Gouillart , Olav Vahtras , Valentin Haenel , Nicolas P. Rougier Zenodo, 2015, ⟨10.5281/zenodo.31736⟩ Books hal-01206546v1

	Evaluating machine learning models and their diagnostic value Gaël Varoquaux , Olivier Colliot Olivier Colliot. Machine Learning for Brain Disorders, Springer, 2023 Book sections hal-03682454v5

	What is the Role of Small Models in the LLM Era: A Survey Lihu Chen , Gaël Varoquaux 2024 Preprints, Working Papers, ... hal-04712720v1
	Teaching Models To Survive: Proper Scoring Rule and Stochastic Optimization with Competing Risks Julie Alberge , Vincent Maladière , Olivier Grisel , Judith Abécassis , Gaël Varoquaux 2024 Preprints, Working Papers, ... hal-04617672v2
	Imputation for prediction: beware of diminishing returns Marine Le Morvan , Gaël Varoquaux 2024 Preprints, Working Papers, ... hal-04662937v1
	On the consistency of supervised learning with missing values Julie Josse , Jacob M. Chen , Nicolas Prost , Erwan Scornet , Gaël Varoquaux 2024 Preprints, Working Papers, ... hal-02024202v6
	Risk ratio, odds ratio, risk difference... Which causal measure is easier to generalize? Bénédicte Colnet , Julie Josse , Gaël Varoquaux , Erwan Scornet 2024 Preprints, Working Papers, ... hal-04369607v1
	Retrieve, Merge, Predict: Augmenting Tables with Data Lakes (Experiment, Analysis & Benchmark Paper) Riccardo Cappuzzo , Gaël Varoquaux , Aimee Coelho , Paolo Papotti 2024 Preprints, Working Papers, ... hal-04509600v1
	Causal thinking for decision making on Electronic Health Records: why and how Matthieu Doutreligne , Tristan Struja , Judith Abecassis , Claire Morgand , Leo Anthony Celi 2023 Preprints, Working Papers, ... hal-04174834v2
	Vectorizing string entries for data processing on tables: when are larger language models better? Léo Grinsztajn , Myung Jun Kim , Edouard Oyallon , Gaël Varoquaux 2023 Preprints, Working Papers, ... hal-04345931v1
	Confidence intervals for performance estimates in 3D medical image segmentation Rosana El Jurdi , Gaël Varoquaux , Olivier Colliot 2023 Preprints, Working Papers, ... hal-04166803v1
	Understanding metric-related pitfalls in image analysis validation Annika Reinke , Minu D. Tizabi , Michael Baumgartner , Matthias Eisenmann , Doreen Heckmann-Nötzel 2023 Preprints, Working Papers, ... hal-04345927v1
	How to select predictive models for decision making or causal inference? Matthieu Doutreligne , Gaël Varoquaux 2023 Preprints, Working Papers, ... hal-03946902v4
	Reweighting the RCT for generalization: finite sample error and variable selection Bénédicte Colnet , Julie Josse , Gaël Varoquaux , Erwan Scornet 2022 Preprints, Working Papers, ... hal-03822662v2
	Beyond brain age: Empirically-derived proxy measures of mental health Kamalaker Dadi , Gael Varoquaux , Josselin Houenou , Danilo Bzdok , Bertrand Thirion 2020 Preprints, Working Papers, ... hal-02929857v1
	Fine-grain atlases of functional modes for fMRI analysis Kamalaker Dadi , Gaël Varoquaux , Antonia Machlouzarides-Shalit , Krzysztof Jacek Gorgolewski , Demian Wassermann 2020 Preprints, Working Papers, ... hal-02496156v1
	Hydroxychloroquine with or without azithromycin and in-hospital mortality or discharge in patients hospitalized for COVID-19 infection: a cohort study of 4,642 in-patients in France Emilie Sbidian , Julie Josse , Guillaume Lemaître , Imke Mayer , Melodie Bernaux 2020 Preprints, Working Papers, ... hal-02995319v1
	Prediction and inference diverge in biomedicine: Simulations and real-world data Danilo Bzdok , Denis Engemann , Olivier Grisel , Gaël Varoquaux , Bertrand Thirion 2018 Preprints, Working Papers, ... hal-01848319v1
	Approximate message-passing for convex optimization with non-separable penalties Andre Manoel , Florent Krzakala , Bertrand Thirion , Gaël Varoquaux , Lenka Zdeborová 2018 Preprints, Working Papers, ... cea-01932983v1

	Lessons from shortcomings in machine learning for medical imaging Gaël Varoquaux , Veronika Cheplygina OECD. 2023 Reports hal-04342020v1
	Survey of machine-learning experimental methods at NeurIPS2019 and ICLR2020 Xavier Bouthillier , Gaël Varoquaux [Research Report] Inria Saclay Ile de France. 2020 Reports hal-02447823v1

	Atomic sources for long-time-of-flight interferometric inertial sensors Gaël Varoquaux Atomic Physics [physics.atom-ph]. Université Paris Sud - Paris XI; Institut d'Optique, 2008. English. ⟨NNT : ⟩ Theses tel-00265714v3

Gaël Varoquaux

Presentation

Publications

Causal inference methods for combining randomized trials and observational studies: a review

Individual Brain Charting dataset extension, third release for movie watching and retinotopy data

Understanding metric-related pitfalls in image analysis validation

Metrics reloaded: recommendations for image analysis validation

The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

Relational Data Embeddings for Feature Enrichment with Background Information

How to remove or control confounds in predictive models, with applications to brain biomarkers

Analytics on Non-Normalized Data Sources: more Learning, rather than more Cleaning

Understanding Brain Network Dynamics in Autism Begs for Generalization

Advancing brain network models to reconcile functional neuroimaging and clinical research

Comprehensive decoding mental processes from Web repositories of functional brain images

Predicting future cognitive decline from non-brain and multimodal brain imaging data in healthy and pathological aging

Benchmarking missing-values approaches for predictive models on health databases

Machine learning for medical imaging: methodological failures and recommendations for the future

Causal effect on a target population: a sensitivity analysis to handle missing covariates

424-P: Body-Weight Variability and Risk of Cardiovascular Outcomes in Type 1 Diabetes: Results from the DCCT/EDIC Studies

Insights from an autism imaging biomarker challenge: promises and threats to biomarker discovery

Body-weight variability and risk of cardiovascular outcomes in patients with type 1 diabetes: a retrospective observational analysis of data from the DCCT/EDIC population.

Extracting representations of cognition across neuroimaging studies improves brain decoding

Decoding with Confidence: Statistical Control on Decoder Maps

Preventing dataset shift from breaking machine-learning biomarkers

Numerical uncertainty in analytical pipelines lead to impactful variability in brain networks

Population modeling with machine learning can enhance measures of mental health

International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium

Individual Brain Charting dataset extension, second release of high-resolution fMRI data for cognitive mapping

Fine-grain atlases of functional modes for fMRI analysis

Subject‐specific segregation of functional territories based on deep phenotyping

Combining magnetoencephalography with magnetic resonance imaging enhances learning of surrogate-biomarkers

Predictive regression modeling with MEG/EEG: from source power to signals and cognitive states

NeuroQuery, comprehensive meta-analysis of human brain mapping

Encoding high-cardinality string categorical variables

Benchmarking functional connectome-based predictive models for resting-state fMRI

Predictive models avoid excessive reductionism in cognitive neuroimaging

Population shrinkage of covariance (PoSCE) for better individual brain functional-connectivity estimation

Brain-based ranking of cognitive domains to predict schizophrenia

Different shades of default mode disturbance in schizophrenia: Subnodal covariance estimation in structure and function

Patterns of Schizophrenia Symptoms: Hidden Structure in the PANSS Questionnaire

Similarity encoding for learning with dirty categorical variables

Inter-subject registration of functional images: do we need anatomical images ?

Subspecialization within default mode nodes characterized in 10,000 UK Biobank participants

Stochastic Subsampling for Factorizing Huge Matrices

Shared Endo-phenotypes of Default Mode Dysfunction in Attention Deficit/Hyperactivity Disorder and Autism Spectrum Disorder

Atlases of cognition with large-scale human brain mapping

Atlases of cognition with large-scale brain mapping

Decoding fMRI activity in the time domain improves classification performance

FReM – scalable and stable decoding with fast regularized ensemble of models

Distinct alterations in Parkinson's Medication-state and Disease-state Connectivity Running Title: PD altered connectivity

Joint prediction of multiple scores captures better individual traits from brain images

Cross-validation failure: small sample sizes lead to large error bars

Predicting brain-age from multimodal imaging data captures cognitive impairment

Formal Models of the Network Co-occurrence Underlying Mental Operations

Exploring the anatomical encoding of voice with a mathematical model of the vocal system.

Assessing and tuning brain decoders: cross-validation, caveats, and guidelines

Neuroimaging Research: From Null-Hypothesis Falsification to Out-of-sample Generalization

Seeing it all: Convolutional network layers map the function of the human visual system

The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments

Recursive nearest agglomeration (ReNA): fast clustering for approximation of structured signals

Connectivity-Based Parcellation: Critique and Implications

Beyond computational reproducibility, let us aim for reusability

Deriving reproducible biomarkers from multi-site resting-state data: An Autism-based example

Transmodal Learning of Functional Networks for Alzheimer's Disease Prediction

Convex relaxations of penalties for sparse correlated variables with bounded total variation

NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain

Transport on Riemannian Manifold for Connectivity-based Brain Decoding

NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain

Identification of Mood-Relevant Brain Connections Using a Continuous, Subject-Driven Rumination Paradigm.

Which fMRI clustering gives good brain parcellations?

Machine Learning Patterns for Neuroimaging-Genetic Studies in the Cloud

How machine learning is shaping cognitive neuroimaging

Learning and comparing functional connectomes across subjects

Machine Learning for Neuroimaging with Scikit-Learn

Spatial vs. Temporal Features in ICA of Resting-State fMRI - A Quantitative and Qualitative Investigation in the Context of Response Inhibition

A framework for inter-subject prediction of functional connectivity from structural networks

Publishing scientific software matters

Randomized parcellation based inference.

In Situ Synchrotron Microtomography Reveals Multiple Reaction Pathways During Soda-Lime Glass Synthesis

Hyperfrontality and hypoconnectivity during refreshing in schizophrenia.