Machine learning patterns for neuroimaging-genetic studies in the cloud.
Brain imaging is a natural intermediate phenotype to understand the link between genetic information and behavior or brain pathologies risk factors. Massive efforts have been made in the last few years to acquire high-dimensional neuroimaging and genetic data on large cohorts of subjects. The statistical analysis of such data is carried out with increasingly sophisticated techniques and represents a great computational challenge. Fortunately, increasing computational power in distributed architectures can be harnessed, if new neuroinformatics infrastructures are designed and training to use these new tools is provided. Combining a MapReduce framework (TomusBLOB) with machine learning algorithms (Scikit-learn library), we design a scalable analysis tool that can deal with non-parametric statistics on high-dimensional data. End-users describe the statistical procedure to perform and can then test the model on their own computers before running the very same code in the cloud at a larger scale. We illustrate the potential of our approach on real data with an experiment showing how the functional signal in subcortical brain regions can be significantly fit with genome-wide genotypes. This experiment demonstrates the scalability and the reliability of our framework in the cloud with a 2 weeks deployment on hundreds of virtual machines.
Parietal Team, INRIA Saclay, Île-de-France Saclay, France ; CEA, DSV, I2BM, Neurospin Gif-sur-Yvette, France.
Benoit
B
Da Mota
KerData Team, INRIA Rennes - Bretagne Atlantique Rennes, France.
Radu
R
Tudoran
KerData Team, INRIA Rennes - Bretagne Atlantique Rennes, France.
Alexandru
A
Costan
Parietal Team, INRIA Saclay, Île-de-France Saclay, France ; CEA, DSV, I2BM, Neurospin Gif-sur-Yvette, France.
Gaël
G
Varoquaux
Microsoft, Advance Technology Lab Europe Munich, Germany.
Goetz
G
Brasche
Institute of Psychiatry, King's College London London, UK ; Department of Psychiatry, Universite de Montreal, CHU Ste Justine Hospital Montreal, QC, Canada.
Patricia
P
Conrod
Institut National de la Santé et de la Recherche Médicale, INSERM CEA Unit 1000 "Imaging & Psychiatry," University Paris Sud, Orsay, and AP-HP Department of Adolescent Psychopathology and Medicine, Maison de Solenn, University Paris Descartes Paris, France.
Herve
H
Lemaitre
Rotman Research Institute, University of Toronto Toronto, ON, Canada ; School of Psychology, University of Nottingham Nottingham, UK ; Montreal Neurological Institute, McGill University Montréal, QC, Canada.
Tomas
T
Paus
Central Institute of Mental Health Mannheim, Germany ; Medical Faculty Mannheim, University of Heidelberg Heidelberg, Germany.
Marcella
M
Rietschel
CEA, DSV, I2BM, Neurospin Gif-sur-Yvette, France.
Vincent
V
Frouin
CEA, DSV, I2BM, Neurospin Gif-sur-Yvette, France ; Henry H. Wheeler Jr. Brain Imaging Center, University of California at Berkeley Berkeley, CA, USA.
Jean-Baptiste
JB
Poline
KerData Team, INRIA Rennes - Bretagne Atlantique Rennes, France.
Gabriel
G
Antoniu
Parietal Team, INRIA Saclay, Île-de-France Saclay, France ; CEA, DSV, I2BM, Neurospin Gif-sur-Yvette, France.
Bertrand
B
Thirion
cloud computing; fMRI; heritability; machine learning; neuroimaging-genetic