Fast shared response model for fMRI data

The shared response model provides a simple but effective framework toanalyse fMRI data of subjects exposed to naturalistic stimuli. However whenthe number of subjects or runs is large, fitting the model requires a large amountof memory and computational power, which limits its use in practice. In thiswork, we introduce the FastSRM algorithm that relies on an intermediate atlas-based representation. It provides considerable speed-up in time and memoryusage, hence it allows easy and fast large-scale analysis of naturalistic-stimulusfMRI data. Using four different datasets, we show that our method outperformsthe original SRM algorithm while being about 5x faster and 20x to 40x morememory efficient. Based on this contribution, we use FastSRM to predict agefrom movie watching data on the CamCAN sample. Besides delivering accuratepredictions (mean absolute error of 7.5 years), FastSRM extracts topographicpatterns that are predictive of age, demonstrating that brain activity duringfree perception reflects age.

Group level MEG/EEG source imaging via optimal transport: minimum Wasserstein estimates

Magnetoencephalography (MEG) and electroencephalogra-phy (EEG) are non-invasive modalities that measure the weak electromagnetic fields generated by neural activity. Inferring the location of the current sources that generated these magnetic fields is an ill-posed inverse problem known as source imaging. When considering a group study, a baseline approach consists in carrying out the estimation of these sources independently for each subject. The ill-posedness of each problem is typically addressed using sparsity promoting regularizations. A straightforward way to define a common pattern for these sources is then to average them. A more advanced alternative relies on a joint localization of sources for all subjects taken together, by enforcing some similarity across all estimated sources. An important advantage of this approach is that it consists in a single estimation in which all measurements are pooled together, making the inverse problem better posed. Such a joint estimation poses however a few challenges, notably the selection of a valid regularizer that can quantify such spatial similarities. We propose in this work a new procedure that can do so while taking into account the geometrical structure of the cortex. We call this procedure Minimum Wasserstein Estimates (MWE). The benefits of this model are twofold. First, joint inference allows to pool together the data of different brain geometries, accumulating more spatial information. Second, MWE are defined through Optimal Transport (OT) metrics which provide a tool to model spatial proximity between cortical sources of different subjects, hence not enforcing identical source location in the group. These benefits allow MWE to be more accurate than standard MEG source localization techniques. To support these claims, we perform source localization on realistic MEG simulations based on forward operators derived from MRI scans. On a visual task dataset, we demonstrate how MWE infer neural patterns similar to functional Magnetic Resonance Imaging (fMRI) maps.

Extracting Universal Representations of Cognition across Brain-Imaging Studies

We show in this paper how to extract shared brain representations that predict mental processes across many cognitive neuroimaging studies. Focused cognitive-neuroimaging experiments study precise mental processes with carefully-designed cognitive paradigms; however the cost of imaging limits their statistical power. On the other hand, large-scale databasing efforts increase considerably the sample sizes, but cannot ask precise cognitive questions. To address this tension, we develop new methods that turn the heterogeneous cognitive information held in different task-fMRI studies into common-universal-cognitive models. Our approach does not assume any prior knowledge of the commonalities shared by the studies in the corpus; those are inferred during model training. The method uses deep-learning techniques to extract representations - task-optimized networks - that form a set of basis cognitive dimensions relevant to the psychological manipulations. In this sense, it forms a novel kind of functional atlas, optimized to capture mental state across many functional-imaging experiments. As it bridges information on the neural support of mental processes, this representation improves decoding performance for 80% of the 35 widely-different functional imaging studies that we consider. Our approach opens new ways of extracting information from brain maps, increasing statistical power even for focused cognitive neuroimaging studies, in particular for those with few subjects.

Approximate message-passing for convex optimization with non-separable penalties

We introduce an iterative optimization scheme for convex objectives consisting of a linear loss and a non-separable penalty, based on the expectation-consistent approximation and the vector approximate message-passing (VAMP) algorithm. Specifically, the penalties we approach are convex on a linear transformation of the variable to be determined, a notable example being total variation (TV). We describe the connection between message-passing algorithms -- typically used for approximate inference -- and proximal methods for optimization, and show that our scheme is, as VAMP, similar in nature to the Peaceman-Rachford splitting, with the important difference that stepsizes are set adaptively. Finally, we benchmark the performance of our VAMP-like iteration in problems where TV penalties are useful, namely classification in task fMRI and reconstruction in tomography, and show faster convergence than that of state-of-the-art approaches such as FISTA and ADMM in most settings.

Optimizing deep video representation to match brain activity

The comparison of observed brain activity with the statistics generated by artificial intelligence systems is useful to probe brain functional organization under ecological conditions. Here we study fMRI activity in ten subjects watching color natural movies and compute deep representations of these movies with an architecture that relies on optical flow and image content. The association of activity in visual areas with the different layers of the deep architecture displays complexity-related contrasts across visual areas and reveals a striking foveal/peripheral dichotomy.

Using Feature Grouping as a Stochastic Regularizer for High-Dimensional Noisy Data

The use of complex models --with many parameters-- is challenging with high-dimensional small-sample problems: indeed, they face rapid overfitting. Such situations are common when data collection is expensive, as in neuroscience, biology, or geology. Dedicated regularization can be crafted to tame overfit, typically via structured penalties. But rich penalties require mathematical expertise and entail large computational costs. Stochastic regularizers such as dropout are easier to implement: they prevent overfitting by random perturbations. Used inside a stochastic optimizer, they come with little additional cost. We propose a structured stochastic regularization that relies on feature grouping. Using a fast clustering algorithm, we define a family of groups of features that capture feature covariations. We then randomly select these groups inside a stochastic gradient descent loop. This procedure acts as a structured regularizer for high-dimensional correlated data without additional computational cost and it has a denoising effect. We demonstrate the performance of our approach for logistic regression both on a sample-limited face image dataset with varying additive noise and on a typical high-dimensional learning problem, brain image classification.

Text to brain: predicting the spatial distribution of neuroimaging observations from text reports

Despite the digital nature of magnetic resonance imaging, the resulting observations are most frequently reported and stored in text documents. There is a trove of information untapped in medical health records, case reports, and medical publications. In this paper, we propose to mine brain medical publications to learn the spatial distribution associated with anatomical terms. The problem is formulated in terms of minimization of a risk on distributions which leads to a least-deviation cost function. An efficient algorithm in the dual then learns the mapping from documents to brain structures. Empirical results using coordinates extracted from the brain-imaging literature show that i) models must adapt to semantic variation in the terms used to describe a given anatomical structure, ii) voxel-wise parameterization leads to higher likelihood of locations reported in unseen documents, iii) least-deviation cost outperforms least-square. As a proof of concept for our method, we use our model of spatial distributions to predict the distribution of specific neurological conditions from text-only reports.

Scikit-learn: Machine Learning in Python

Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.org.

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

In this work, we revisit fast dimension reduction approaches, as with random projections and random sampling. Our goal is to summarize the data to decrease computational costs and memory footprint of subsequent analysis. Such dimension reduction can be very efficient when the signals of interest have a strong structure, such as with images. We focus on this setting and investigate feature clustering schemes for data reductions that capture this structure. An impediment to fast dimension reduction is that good clustering comes with large algorithmic costs. We address it by contributing a linear-time agglomerative clustering scheme, Recursive Nearest Agglomeration (ReNA). Unlike existing fast agglomerative schemes, it avoids the creation of giant clusters. We empirically validate that it approximates the data as well as traditional variance-minimizing clustering schemes that have a quadratic complexity. In addition, we analyze signal approximation with feature clustering and show that it can remove noise, improving subsequent analysis steps. As a consequence, data reduction by clustering features with ReNA yields very fast and accurate models, enabling to process large datasets on budget. Our theoretical analysis is backed by extensive experiments on publicly-available data that illustrate the computation efficiency and the denoising properties of the resulting dimension reduction scheme.

Learning Neural Representations of Human Cognition across Many fMRI Studies

Cognitive neuroscience is enjoying rapid increase in extensive public brain-imaging datasets. It opens the door to large-scale statistical models. Finding a unified perspective for all available data calls for scalable and automated solutions to an old challenge: how to aggregate heterogeneous information on brain function into a universal cognitive system that relates mental operations/cognitive processes/psychological tasks to brain networks? We cast this challenge in a machine-learning approach to predict conditions from statistical brain maps across different studies. For this, we leverage multi-task learning and multi-scale dimension reduction to learn low-dimensional representations of brain images that carry cognitive information and can be robustly associated with psychological stimuli. Our multi-dataset classification model achieves the best prediction performance on several large reference datasets, compared to models without cognitive-aware low-dimension representations, it brings a substantial performance boost to the analysis of small datasets, and can be introspected to identify universal template cognitive concepts.