Bibliography

Major publications by the team in recent years

• 1D. Bzdok, M. Eickenberg, O. Grisel, B. Thirion, G. Varoquaux.
  Semi-Supervised Factored Logistic Regression for High-Dimensional Neuroimaging Data, in: Neural Information Processing Systems, December 2015.
  https://hal.archives-ouvertes.fr/hal-01211248
• 2N. Chauffert, P. Ciuciu, J. Kahn, P. Weiss.
  Variable density sampling with continuous trajectories. Application to MRI, in: SIAM Journal of Imaging Sciences, 2014, vol. 7, n^o 4, pp. 1962–1992.
  https://hal.inria.fr/hal-00908486
• 3B. Da Mota, V. Fritsch, G. Varoquaux, T. Banaschewski, G. J. Barker, A. L. W. Bokde, U. Bromberg, P. J. Conrod, J. Gallinat, H. Garavan, J.-L. Martinot, F. Nees, T. Paus, Z. Pausova, M. Rietschel, M. N. Smolka, A. Ströhle, V. Frouin, J.-B. Poline, B. Thirion.
  Randomized parcellation based inference, in: NeuroImage, November 2013, pp. 203 - 215, Digitéo (HiDiNim project and ICoGeN project). [ DOI : 10.1016/j.neuroimage.2013.11.012 ]
  http://hal.inria.fr/hal-00915243
• 4M. Eickenberg, E. Dohmatob, B. Thirion, G. Varoquaux.
  Total Variation meets Sparsity: statistical learning with segmenting penalties, in: Medical Image Computing and Computer Aided Intervention (MICCAI), München, Germany, Proceedings of MICCAI 2015, October 2015.
  https://hal.inria.fr/hal-01170619
• 5B. Ng, G. Varoquaux, J.-B. Poline, M. D. Greicius, B. Thirion.
  Transport on Riemannian Manifold for Connectivity-based Brain Decoding, in: IEEE Transactions on Medical Imaging, 2015, vol. PP, n^o 99, 9 p. [ DOI : 10.1109/TMI.2015.2463723 ]
  https://hal.inria.fr/hal-01185200
• 6F. Pedregosa, M. Eickenberg, P. Ciuciu, B. Thirion, A. Gramfort.
  Data-driven HRF estimation for encoding and decoding models, in: NeuroImage, November 2014, pp. 209–220.
  https://hal.inria.fr/hal-00952554
• 7Y. Schwartz, B. Thirion, G. Varoquaux.
  Mapping cognitive ontologies to and from the brain, in: NIPS (Neural Information Processing Systems), United States, November 2013.
  http://hal.inria.fr/hal-00904763
• 8G. Varoquaux, A. Gramfort, F. Pedregosa, V. Michel, B. Thirion.
  Multi-subject dictionary learning to segment an atlas of brain spontaneous activity, in: Information Processing in Medical Imaging, Kaufbeuren, Germany, Lecture Notes in Computer Science, Springer, July 2011, vol. 6801, pp. 562-573. [ DOI : 10.1007/978-3-642-22092-0_46 ]
  http://hal.inria.fr/inria-00588898/en
• 9G. Varoquaux, A. Gramfort, B. Thirion.
  Small-sample brain mapping: sparse recovery on spatially correlated designs with randomization and clustering, in: International Conference on Machine Learning, Edimbourg, United Kingdom, L. John, P. Joelle (editors), Andrew McCallum, June 2012.
  http://hal.inria.fr/hal-00705192
• 10G. Varoquaux, Y. Schwartz, P. Pinel, B. Thirion.
  Cohort-level brain mapping: learning cognitive atoms to single out specialized regions, in: IPMI - Information Processing in Medical Imaging - 2013, Asilomar, United States, W. M. Wells, S. Joshi, K. M. Pohl (editors), Springer, July 2013, vol. 7917, pp. 438-449. [ DOI : 10.1007/978-3-642-38868-2_37 ]
  http://hal.inria.fr/hal-00841502

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 11N. Chauffert.
  Compressed sensing along physicaly plausible sampling trajectories, université paris XI, September 2015.
  https://tel.archives-ouvertes.fr/tel-01235202
• 12F. Pedregosa-Izquierdo.
  Feature extraction and supervised learning on fMRI: from practice to theory, Université Pierre et Marie Curie, February 2015.
  https://tel.archives-ouvertes.fr/tel-01100921
• 13Y. Schwartz.
  Large-scale functional MRI analysis to accumulate knowledge on brain functions, Université Paris Sud - Paris XI, April 2015.
  https://tel.archives-ouvertes.fr/tel-01160550

Articles in International Peer-Reviewed Journals

• 14E. Belilovsky, A. Argyriou, G. Varoquaux, M. B. Blaschko.
  Convex relaxations of penalties for sparse correlated variables with bounded total variation, in: Machine Learning, June 2015, pp. 1-21. [ DOI : 10.1007/s10994-015-5511-2 ]
  https://hal.inria.fr/hal-01167861
• 15S. Bludau, D. Bzdok, O. Gruber, N. Kohn, V. Riedl, C. Sorg, N. Palomero-Gallagher, M. Veronika, F. Hoffstaedter, K. Amunts, B. Simon.
  Medial Prefrontal Aberrations in Major Depressive Disorder Revealed by Cytoarchitectonically Informed Voxel-Based Morphometry, in: American journal of psychiatry, December 2015. [ DOI : 10.1176/appi.ajp.2015.15030349 ]
  https://hal.archives-ouvertes.fr/hal-01236100
• 16S. Eickhoff, B. Thirion, G. Varoquaux, D. Bzdok.
  Connectivity-Based Parcellation: Critique and Implications, in: Human Brain Mapping, January 2016, 22 p. [ DOI : 10.1002/hbm.22933 ]
  https://hal.archives-ouvertes.fr/hal-01184563
• 17K. J. Gorgolewski, G. Varoquaux, G. Rivera, Y. Schwartz, V. V. Sochat, S. S. Ghosh, C. Maumet, T. E. Nichols, J.-B. Poline, T. Yarkoni, D. S. Margulies, R. A. Poldrack.
  NeuroVault.org: A repository for sharing unthresholded statistical maps, parcellations, and atlases of the human brain, in: NeuroImage, April 2015, 3 p, [Epub ahead of print]. [ DOI : 10.1016/j.neuroimage.2015.04.016 ]
  http://www.hal.inserm.fr/inserm-01148969
• 18K. J. Gorgolewski, G. Varoquaux, G. Rivera, Y. Schwarz, S. S. Ghosh, C. Maumet, V. V. Sochat, T. E. Nichols, R. A. Poldrack, J.-B. Poline, T. Yarkoni, D. S. Margulies.
  NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain, in: Frontiers in Neuroinformatics, April 2015, vol. 9, n^o 8. [ DOI : 10.3389/fninf.2015.00008 ]
  http://www.hal.inserm.fr/inserm-01134573
• 19B. Ng, G. Varoquaux, J.-B. Poline, M. D. Greicius, B. Thirion.
  Transport on Riemannian Manifold for Connectivity-based Brain Decoding, in: IEEE Transactions on Medical Imaging, 2015, vol. PP, n^o 99, 9 p. [ DOI : 10.1109/TMI.2015.2463723 ]
  https://hal.inria.fr/hal-01185200
• 20D. Papadopoulos Orfanos, V. Michel, Y. Schwartz, P. Pinel, A. Moreno, D. Le Bihan, V. Frouin.
  The Brainomics/Localizer database, in: NeuroImage, October 2015. [ DOI : 10.1016/j.neuroimage.2015.09.052 ]
  https://hal-cea.archives-ouvertes.fr/cea-01213448
• 21F. Pedregosa, M. Eickenberg, P. Ciuciu, B. Thirion, A. Gramfort.
  Data-driven HRF estimation for encoding and decoding models, in: NeuroImage, January 2015, pp. 209–220.
  https://hal.inria.fr/hal-00952554

Invited Conferences

• 22C. Févotte, M. Kowalski.
  Hybrid sparse and low-rank time-frequency signal decomposition, in: Eusipco 2015, Nice, France, August 2015.
  https://hal.archives-ouvertes.fr/hal-01199622

International Conferences with Proceedings

• 23M. Albughdadi, L. Chaari, F. Forbes, J.-Y. Tourneret, P. Ciuciu.
  Multi-subject joint parcellation detection estimation in functional MRI, in: 13th IEEE International Symposium on Biomedical Imaging, Prague, Czech Republic, April 2016.
  https://hal.inria.fr/hal-01261982
• 24N. Chauffert, P. Ciuciu, J. Kahn, P. Weiss.
  Comment représenter une image avec un spaghetti ?, in: GRETSI, Lyon, France, 25 ème actes du colloque GRETSI, September 2015.
  https://hal.inria.fr/hal-01255315
• 25F. Feng, M. Kowalski.
  An Unified Approach for Blind Source Separation Using Sparsity and Decorrelation, in: Eusipco 2015, Nice, France, August 2015.
  https://hal.archives-ouvertes.fr/hal-01199620
• 26F. Forbes, A. Frau-Pascual, P. Ciuciu.
  Méthode d'approximation variationnelle pour l'analyse de données d'IRM fonctionnelle acquise par Arterial Spin Labelling, in: GRETSI, Lyon, France, September 2015.
  https://hal.archives-ouvertes.fr/hal-01254176
• 27A. Frau-Pascual, F. Forbes, P. Ciuciu.
  Comparison of Stochastic and Variational Solutions to ASL fMRI Data Analysis, in: 18th International Conference on Medical Image Computing and Computer-Assisted Intervention - MICCAI 2015, Munich, Germany, N. Navab, J. Hornegger, W. M. Wells III, A. F. Frangi (editors), Springer, October 2015, vol. 9349, pp. 85-92, ISBN 978-3-319-24552-2. [ DOI : 10.1007/978-3-319-24553-9_11 ]
  https://hal.archives-ouvertes.fr/hal-01249018
• 28A. Frau-Pascual, F. Forbes, P. Ciuciu.
  Physiological models comparison for the analysis of ASL FMRI data, in: 12th IEEE International Symposium on Biomedical Imaging, ISBI 2015, New York, United States, IEEE, April 2015, pp. 1348-1351. [ DOI : 10.1109/ISBI.2015.7164125 ]
  https://hal.archives-ouvertes.fr/hal-01249014
• 29A. Frau-Pascual, F. Forbes, P. Ciuciu.
  Variational Physiologically Informed Solution to Hemodynamic and Perfusion Response Estimation from ASL fMRI Data, in: 2015 International Workshop on Pattern Recognition in NeuroImaging, Stanford, CA, United States, IEEE, June 2015, pp. 57-60. [ DOI : 10.1109/PRNI.2015.12 ]
  https://hal.archives-ouvertes.fr/hal-01249015
• 30M. Kowalski, A. Gramfort.
  Inverse Problems with Time-frequency Dictionaries and non-white Gaussian Noise, in: Eusipco 2015, Nice, France, August 2015.
  https://hal.archives-ouvertes.fr/hal-01199635
• 31C. Laroche, M. Kowalski, H. PAPADOPOULOS, G. Richard.
  A structured nonnegative matrix factorization for source separation, in: Eusipco 2015 - European Signal Processing Conference, Nice, France, August 2015.
  https://hal.archives-ouvertes.fr/hal-01199631
• 32C. Laroche, M. Kowalski, H. PAPADOPOULOS, G. Richard.
  Méthode Structurée de décomposition en matrices non- négatives appliquéè a la séparation de sources audio, in: Gretsi 2015, Lyon, France, September 2015.
  https://hal.archives-ouvertes.fr/hal-01199648
• 33H. Pellé, P. Ciuciu, M. Rahim, E. Dohmatob, P. Abry, V. Van Wassenhove.
  Multivariate Hurst Exponent Estimation in FMRI. Application to Brain Decoding of Perceptual Learning, in: 13th IEEE International Symposium on Biomedical Imaging, Prague, Czech Republic, April 2016.
  https://hal.inria.fr/hal-01261976
• 34P. Weiss, N. Chauffert, C. Boyer, J. Kahn, P. Ciuciu.
  Sur la génération de schémas d'échantillonnage compressé en IRM, in: GRETSI, Lyon, France, 25 ème actes du colloque GRETSI, Patrice Abry and Paulo Gonçalves, September 2015, 4 p.
  https://hal.inria.fr/hal-01255325

National Conferences with Proceedings

• 35P. Ciuciu, N. Zilber, P. Abry, V. Van Wassenhove.
  La convergence de l'activité neurale vers des attracteurs multifractals localisés prédit la capacité d'apprentissage, in: GRETSI, Lyon, France, 25 ème actes du colloque GRETSI, September 2015.
  https://hal.inria.fr/hal-01255289
• 36F. Feng, M. Kowalski.
  Vers une approche unifiée pour la séparation aveugle de sources en sur et sous-déterminé, basée sur la parcimonie et la décorrélation, in: Gretsi 2015, Lyon, France, September 2015.
  https://hal.archives-ouvertes.fr/hal-01199645
• 37M. Kowalski, A. Gramfort.
  Problèmes inverses avec dictionnaires temps-fréquences en présence de bruit Gaussien non blanc, in: Gretsi 2015, Lyon, France, September 2015.
  https://hal.archives-ouvertes.fr/hal-01199641

Conferences without Proceedings

• 38N. Chauffert, P. Weiss, M. Boucher, S. Mériaux, P. Ciuciu.
  Variable density sampling based on physically plausible gradient waveform. Application to 3D MRI angiography, in: IEEE International Symposium on Biomedical Imaging (ISBI), New-York, United States, April 2015.
  https://hal.inria.fr/hal-01119578
• 39E. Dohmatob, M. Eickenberg, B. Thirion, G. Varoquaux.
  Speeding-up model-selection in GraphNet via early-stopping and univariate feature-screening, in: PRNI, Stanford, United States, June 2015.
  https://hal.inria.fr/hal-01147731
• 40M. Eickenberg, E. Dohmatob, B. Thirion, G. Varoquaux.
  Total Variation meets Sparsity: statistical learning with segmenting penalties, in: Medical Image Computing and Computer Aided Intervention (MICCAI), München, Germany, October 2015.
  https://hal.inria.fr/hal-01170619
• 41L. Estève.
  Big data in practice: the example of nilearn for mining brain imaging data, in: Scipy 2015, Austin, Texas, United States, July 2015.
  https://hal.archives-ouvertes.fr/hal-01207106
• 42A. Hoyos-Idrobo, Y. Schwartz, G. Varoquaux, B. Thirion.
  Improving sparse recovery on structured images with bagged clustering, in: International Workshop On Pattern Recognition In Neuroimaging (PRNI), 2015, Palo alto, United States, June 2015.
  https://hal.archives-ouvertes.fr/hal-01174335
• 43B. Ng, J. Baptiste Poline, B. Thirion, M. Greicius.
  Bootstrapped Permutation Test for Multiresponse Inference on Brain Behavior Associations, in: Information Processing in Medical Imaging 2015, Sabhal Mor Ostaig, Isle of Skye, United Kingdom, S. Ourselin, D. C. Alexander, C.-F. Westin, M. J. Cardoso (editors), Lecture Notes in Computer Science, Springer, June 2015, vol. 9123, 12 p.
  https://hal.inria.fr/hal-01185206
• 44M. Rahim, B. Thirion, A. Abraham, M. Eickenberg, E. Dohmatob, C. Comtat, G. Varoquaux.
  Integrating Multimodal Priors in Predictive Models for the Functional Characterization of Alzheimer's Disease, in: Medical Image Computing and Computer Assisted Intervention, Munich, Germany, October 2015.
  https://hal.archives-ouvertes.fr/hal-01174636
• 45B. Thirion, A. Hoyos-Idrobo, J. Kahn, G. Varoquaux.
  Fast clustering for scalable statistical analysis on structured images, in: ICML Workshop on Statistics, Machine Learning and Neuroscience (Stamlins 2015), Lille, France, Bertrand Thirion, Lars Kai Hansen, Sanmi Koyejo, July 2015.
  https://hal.inria.fr/hal-01229023
• 46B. Thirion, F. Pedregosa, M. Eickenberg, G. Varoquaux.
  Correlations of correlations are not reliable statistics: implications for multivariate pattern analysis, in: ICML Workshop on Statistics, Machine Learning and Neuroscience (Stamlins 2015), Lille, France, Bertrand Thirion, Lars Kai Hansen, Sanmi Koyejo, July 2015.
  https://hal.inria.fr/hal-01187297
• 47G. Varoquaux, M. Eickenberg, E. Dohmatob, B. Thirion.
  FAASTA: A fast solver for total-variation regularization of ill-conditioned problems with application to brain imaging, in: Colloque GRETSI, Lyon, France, P. Gonçalves, P. Abry, September 2015.
  https://hal.inria.fr/hal-01247388

Scientific Books (or Scientific Book chapters)

• 48P. Ciuciu, F. Forbes, T. Vincent, L. Chaari.
  Joint Detection-Estimation in Functional MRI, in: Regularization and Bayesian Methods for Inverse Problems in Signal and Image Processing, J.-F. Giovannelli, J. Idier (editors), John Wiley and Sons, 2015, pp. 169-200.
  https://hal.archives-ouvertes.fr/hal-01254177
• 49X. Pennec, P. Fillard.
  Statistical Computing on Non-Linear Spaces for Computational Anatomy, in: Handbook of Biomedical Imaging: Methodologies and Clinical Research, N. Paragios, J. Duncan, N. Ayache (editors), Springer, 2015, pp. 147-168. [ DOI : 10.1007/978-0-387-09749-7_8 ]
  https://hal.inria.fr/inria-00616201

Scientific Popularization

• 50D. Bzdok, M. Eickenberg, O. Grisel, B. Thirion, G. Varoquaux.
  Semi-Supervised Factored Logistic Regression for High-Dimensional Neuroimaging Data, in: Neural Information Processing Systems, December 2015.
  https://hal.archives-ouvertes.fr/hal-01211248
• 51G. Varoquaux, E. Gouillart, O. Vahtras, V. Haenel, N. P. Rougier, R. Gommers, F. Pedregosa, Z. Jędrzejewski-Szmek, P. Virtanen, C. Combelles, D. Pinte, R. Cimrman, A. Espaze, A. Chauve, C. Burns.
  Scipy Lecture Notes, Zenodo, 2015. [ DOI : 10.5281/zenodo.31736 ]
  https://hal.inria.fr/hal-01206546

Other Publications

• 52E. Belilovsky, G. Varoquaux, M. B. Blaschko.
  Hypothesis Testing for Differences in Gaussian Graphical Models: Applications to Brain Connectivity, December 2015, working paper or preprint.
  https://hal.inria.fr/hal-01248844
• 53L. Chaari, S. Badillo, T. Vincent, G. Dehaene-Lambertz, F. Forbes, P. Ciuciu.
  Hemodynamic-Informed Parcellation of fMRI Data in a Joint Detection Estimation Framework, November 2015, Submitted to IEEE Transactions on Medical Imaging. [ DOI : 10.1007/978-3-642-33454-2_23 ]
  https://hal.archives-ouvertes.fr/hal-01228007
• 54L. Chaari, S. Badillo, T. Vincent, G. Dehaene-Lambertz, F. Forbes, P. Ciuciu.
  Subject-level Joint Parcellation-Detection-Estimation in fMRI, January 2016, working paper or preprint.
  https://hal.inria.fr/hal-01255465
• 55N. Chauffert, P. Ciuciu, J. Kahn, P. Weiss.
  A projection algorithm on measures sets, March 2015, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01188069
• 56N. Chauffert, P. Ciuciu, J. Kahn, P. Weiss.
  A projection method on measures sets, March 2015, working paper or preprint.
  https://hal.inria.fr/hal-01133398
• 57N. Chauffert, P. Weiss, J. Kahn, P. Ciuciu.
  A projection algorithm for gradient waveforms design in Magnetic Resonance Imaging, December 2015, In revision to IEEE Transaction on Medical Imaging.
  https://hal.inria.fr/hal-01255336
• 58E. Dohmatob.
  In theory, You crack under pressure!, July 2015, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01179903
• 59E. Dohmatob, M. Eickenberg, B. Thirion, G. Varoquaux.
  SpaceNet: Multivariate brain decoding and segmentation, June 2015, OHBM, Poster.
  https://hal.inria.fr/hal-01187230
• 60M. Kowalski, A. Meynard, H.-t. Wu.
  Convex Optimization approach to signals with fast varying instantaneous frequency, September 2015, working paper or preprint.
  https://hal.archives-ouvertes.fr/hal-01199615
• 61F. Pedregosa, F. Bach, A. Gramfort.
  On the Consistency of Ordinal Regression Methods, September 2015, working paper or preprint.
  https://hal.inria.fr/hal-01054942

References in notes

• 62S. Moeller, E. Yacoub, C. A. Olman, E. Auerbach, J. Strupp, N. Harel, K. Uğurbil.
  Multiband multislice GE-EPI at 7 tesla, with 16-fold acceleration using partial parallel imaging with application to high spatial and temporal whole-brain fMRI, in: Magn Reson Med, May 2010, vol. 63, n^o 5, pp. 1144–1153.
  http://dx.doi.org/10.1002/mrm.22361