Section: Partnerships and Cooperations

Regional Initiatives

CoSmic project

Participants : Philippe Ciuciu [Correspondant] , Carole Lazarus, Loubna El Gueddari.

This is a collaborative project with Jean-Luc Stark, (CEA) funded by the CEA program drf-impulsion.

Compressed Sensing is a recent theory in maths that allows the perfect recovery of signals or images from compressive acquisition scenarios. This approach has been popularized in MRI over the last decade as well as in astrophysics (noticeably in radio-astronomy). So far, both of these fields have developed skills in CS separately. The aim of the COSMIC project is to foster collaborations between CEA experts in MRI (Inria-CEA Parietal team within NeuroSpin) and in astrophysics (CosmoStat lab within the Astrophysics Department). These interactions will allow us to share different expertise in order to improve image quality, either in MRI or in radio-astronomy (thanks to the interferometry principle). In this field, given the data delivered by radio-telescopet he goal will consist of extracting high temporal resolution information in order to study fast transient events.

BrainAMP project

Participants : Bertrand Thirion [Correspondant] , Gaël Varoquaux, Andre Monteiro Manoel.

This is a collaborative project with Lenka Zdeborová, Theoretical Physics Institute (CEA) funded by the CEA program drf-impulsion.

In many scientific fields, the data acquisition devices have benefited of hardware improvement to increase the resolution of the observed phenomena, leading to ever larger datasets. While the dimensionality has increased, the number of samples available is often limited, due to physical or financial limits. This is a problem when these data are processed with estimators that have a large sample complexity, such as multivariate statistical models. In that case it is very useful to rely on structured priors, so that the results reflect the state of knowledge on the phenomena of interest. The study of the human brain activity through high-field MRI belongs among these problems, with up to 106 features, yet a set of observations limited by cost and participant comfort.

We are missing fast estimators for multivariate models with structured priors, that furthermore provide statistical control on the solution. Approximate message passing methods are designed to work optimally with low-sample-complexity, they accommodate rather generic class of priors and come with an estimation of statistical significance. They are therefore well suited for our purposes.

We want to join forces to design a new generation of inverse problem solvers that can take into account the complex structure of brain images and provide guarantees in the low-sample-complexity regime. To this end, we will first adapt AMP to the brain mapping setting, using first standard sparsity priors (e.g. Gauss-Bernoulli) on the model. We will then consider more complex structured priors that control the variation of the learned image patterns in space. Crucial gains are expected from the use of the EM algorithm for parameter setting, that comes naturally with AMP. We will also examine the estimators provided by AMP for statistical significance. BrainAMP will design a reference inference toolbox released as a generic open source library. We expect a 3- to 10-fold improvement in CPU time, that will benefit to large-scale brain mapping investigations.

iConnectom project

Participants : Bertrand Thirion [Correspondant] , Gaël Varoquaux, Elvis Dohmatob.

This is a Digiteo project (2014-2017).

Mapping brain functional connectivity from functional Magnetic Resonance Imaging (MRI) data has become a very active field of research. However, analysis tools are limited and many important tasks, such as the empirical definition of brain networks, remain difficult due to the lack of a good framework for the statistical modeling of these networks. We propose to develop population models of anatomical and functional connectivity data to improve the alignment of subjects brain structures of interest while inferring an average template of these structures. Based on this essential contribution, we will design new statistical inference procedures to compare the functional connections between conditions or populations and improve the sensitivity of connectivity analysis performed on noisy data. Finally, we will test and validate the methods on multiple datasets and distribute them to the brain imaging community.

MetaCog project

Participants : Bertrand Thirion [Correspondant] , Gaël Varoquaux, Jérome Dockès.

This is a Digicosme project (2016-2019) and a collaboration with Fabian Suchanek (Telecom Paritech).

Understanding how cognition emerges from the billions of neurons that constitute the human brain is a major open problem in science that could bridge natural science –biology– to humanities –psychology. Psychology studies performed on humans with functional Magnetic Resonance Imaging (fMRI) can be used to probe the full repertoire of high-level cognitive functions. While analyzing the resulting image data for a given experiment is a relatively well-mastered process, the challenges in comparing data across multiple datasets poses serious limitation to the field. Indeed, such comparisons require to pool together brain images acquired under different settings and assess the effect of different experimental conditions that correspond to psychological effects studied by neuroscientists.

Such meta-analyses are now becoming possible thanks to the development of public data resources –OpenfMRI http://openfmri.org and NeuroVault http://neurovault.org. As many others, researchers of the Parietal team understand these data sources well and contribute to them. However, in such open-ended context, the description of experiments in terms of cognitive concepts is very difficult: there is no universal definition of cognitive terms that could be employed consistently by neuroscientists. Hence meta-analytic studies loose power and specificity. On the other hand, http://brainspell.org provide a set of curated annotation, albeit on much less data, that can serve as a seed or a ground truth to define a consensual ontology of cognitive concepts. Relating these terms to brain activity poses another challenge, of statistical nature, as brain patterns form high-dimensional data in perspective with the scarcity and the noise of the data.

The purpose of this project is to learn a semantic structure in cognitive terms from their occurrence in brain activations. This structure will simplify massive multi-label statistical-learning problems that arise in brain mapping by providing compact representations of cognitive concepts while capturing the imprecision on the definition these concepts.


Participants : Bertrand Thirion [Correspondant] , Gaël Varoquaux, Guillaume Lemaitre.

CDS2 is an "Strategic research initiatice” of the Paris Saclay University Idex http://datascience-paris-saclay.fr. Although it groups together many partners of the Paris Saclay ecosystem, Parietal has been deeply involved in the project. It currently funds a post-doc for Guillume Lemaitre.