arXiv subjects

Bertrand Thirion

Publications and source records attributed to Bertrand Thirion.

At least 55 records · Page 3Linked to original sources

arXiv2021

Functional Magnetic Resonance Imaging data augmentation through conditional ICA

Advances in computational cognitive neuroimaging research are related to the availability of large amounts of labeled brain imaging data, but such data are scarce and expensive to generate. While powerful data generation mechanisms, such as Generative Adversarial Networks (GANs), have been designed in the last decade for computer vision, such improvements have not yet carried over to brain imaging. A likely reason is that GANs training is ill-suited to the noisy, high-dimensional and small-sample data available in functional neuroimaging. In this paper, we introduce Conditional Independent Components Analysis (Conditional ICA): a fast functional Magnetic Resonance Imaging (fMRI) data augmentation technique, that leverages abundant resting-state data to create images by sampling from an ICA decomposition. We then propose a mechanism to condition the generator on classes observed with few samples. We first show that the generative mechanism is successful at synthesizing data indistinguishable from observations, and that it yields gains in classification accuracy in brain decoding problems. In particular it outperforms GANs while being much easier to optimize and interpret. Lastly, Conditional ICA enhances classification accuracy in eight datasets without further parameters tuning.

eess.IV↗

arXiv2021

Spatially relaxed inference on high-dimensional linear models

We consider the inference problem for high-dimensional linear models, when covariates have an underlying spatial organization reflected in their correlation. A typical example of such a setting is high-resolution imaging, in which neighboring pixels are usually very similar. Accurate point and confidence intervals estimation is not possible in this context with many more covariates than samples, furthermore with high correlation between covariates. This calls for a reformulation of the statistical inference problem, that takes into account the underlying spatial structure: if covariates are locally correlated, it is acceptable to detect them up to a given spatial uncertainty. We thus propose to rely on the $δ$-FWER, that is the probability of making a false discovery at a distance greater than $δ$ from any true positive. With this target measure in mind, we study the properties of ensembled clustered inference algorithms which combine three techniques: spatially constrained clustering, statistical inference, and ensembling to aggregate several clustered inference solutions. We show that ensembled clustered inference algorithms control the $δ$-FWER under standard assumptions for $δ$ equal to the largest cluster diameter. We complement the theoretical analysis with empirical results, demonstrating accurate $δ$-FWER control and decent power achieved by such inference algorithms.

stat.ME↗

arXiv2021

Extracting representations of cognition across neuroimaging studies improves brain decoding

Cognitive brain imaging is accumulating datasets about the neural substrate of many different mental processes. Yet, most studies are based on few subjects and have low statistical power. Analyzing data across studies could bring more statistical power; yet the current brain-imaging analytic framework cannot be used at scale as it requires casting all cognitive tasks in a unified theoretical framework. We introduce a new methodology to analyze brain responses across tasks without a joint model of the psychological processes. The method boosts statistical power in small studies with specific cognitive focus by analyzing them jointly with large studies that probe less focal mental processes. Our approach improves decoding performance for 80% of 35 widely-different functional-imaging studies. It finds commonalities across tasks in a data-driven way, via common brain representations that predict mental processes. These are brain networks tuned to psychological manipulations. They outline interpretable and plausible brain structures. The extracted networks have been made available; they can be readily reused in new neuro-imaging studies. We provide a multi-study decoding tool to adapt to new data.

stat.ML↗

arXiv2021

Adaptive Multi-View ICA: Estimation of noise levels for optimal inference

We consider a multi-view learning problem known as group independent component analysis (group ICA), where the goal is to recover shared independent sources from many views. The statistical modeling of this problem requires to take noise into account. When the model includes additive noise on the observations, the likelihood is intractable. By contrast, we propose Adaptive multiView ICA (AVICA), a noisy ICA model where each view is a linear mixture of shared independent sources with additive noise on the sources. In this setting, the likelihood has a tractable expression, which enables either direct optimization of the log-likelihood using a quasi-Newton method, or generalized EM. Importantly, we consider that the noise levels are also parameters that are learned from the data. This enables sources estimation with a closed-form Minimum Mean Squared Error (MMSE) estimator which weights each view according to its relative noise level. On synthetic data, AVICA yields better sources estimates than other group ICA methods thanks to its explicit MMSE estimator. On real magnetoencephalograpy (MEG) data, we provide evidence that the decomposition is less sensitive to sampling noise and that the noise variance estimates are biologically plausible. Lastly, on functional magnetic resonance imaging (fMRI) data, AVICA exhibits best performance in transferring information across views.

stat.ML↗

arXiv2020

Modeling Shared Responses in Neuroimaging Studies through MultiView ICA

Group studies involving large cohorts of subjects are important to draw general conclusions about brain functional organization. However, the aggregation of data coming from multiple subjects is challenging, since it requires accounting for large variability in anatomy, functional topography and stimulus response across individuals. Data modeling is especially hard for ecologically relevant conditions such as movie watching, where the experimental setup does not imply well-defined cognitive operations. We propose a novel MultiView Independent Component Analysis (ICA) model for group studies, where data from each subject are modeled as a linear combination of shared independent sources plus noise. Contrary to most group-ICA procedures, the likelihood of the model is available in closed form. We develop an alternate quasi-Newton method for maximizing the likelihood, which is robust and converges quickly. We demonstrate the usefulness of our approach first on fMRI data, where our model demonstrates improved sensitivity in identifying common sources among subjects. Moreover, the sources recovered by our model exhibit lower between-session variability than other methods.On magnetoencephalography (MEG) data, our method yields more accurate source localization on phantom data. Applied on 200 subjects from the Cam-CAN dataset it reveals a clear sequence of evoked activity in sensor and source space. The code is freely available at https://github.com/hugorichard/multiviewica.

stat.ML↗

arXiv2020

Statistical control for spatio-temporal MEG/EEG source imaging with desparsified multi-task Lasso

Detecting where and when brain regions activate in a cognitive task or in a given clinical condition is the promise of non-invasive techniques like magnetoencephalography (MEG) or electroencephalography (EEG). This problem, referred to as source localization, or source imaging, poses however a high-dimensional statistical inference challenge. While sparsity promoting regularizations have been proposed to address the regression problem, it remains unclear how to ensure statistical control of false detections. Moreover, M/EEG source imaging requires to work with spatio-temporal data and autocorrelated noise. To deal with this, we adapt the desparsified Lasso estimator -- an estimator tailored for high dimensional linear model that asymptotically follows a Gaussian distribution under sparsity and moderate feature correlation assumptions -- to temporal data corrupted with autocorrelated noise. We call it the desparsified multi-task Lasso (d-MTLasso). We combine d-MTLasso with spatially constrained clustering to reduce data dimension and with ensembling to mitigate the arbitrary choice of clustering; the resulting estimator is called ensemble of clustered desparsified multi-task Lasso (ecd-MTLasso). With respect to the current procedures, the two advantages of ecd-MTLasso are that i)it offers statistical guarantees and ii)it allows to trade spatial specificity for sensitivity, leading to a powerful adaptive method. Extensive simulations on realistic head geometries, as well as empirical results on various MEG datasets, demonstrate the high recovery performance of ecd-MTLasso and its primary practical benefit: offer a statistically principled way to threshold MEG/EEG source maps.

stat.ML↗

arXiv2020

Aggregation of Multiple Knockoffs

We develop an extension of the Knockoff Inference procedure, introduced by Barber and Candes (2015). This new method, called Aggregation of Multiple Knockoffs (AKO), addresses the instability inherent to the random nature of Knockoff-based inference. Specifically, AKO improves both the stability and power compared with the original Knockoff algorithm while still maintaining guarantees for False Discovery Rate control. We provide a new inference procedure, prove its core properties, and demonstrate its benefits in a set of experiments on synthetic and real datasets.

math.ST↗

arXiv2020

Fine-grain atlases of functional modes for fMRI analysis

Population imaging markedly increased the size of functional-imaging datasets, shedding new light on the neural basis of inter-individual differences. Analyzing these large data entails new scalability challenges, computational and statistical. For this reason, brain images are typically summarized in a few signals, for instance reducing voxel-level measures with brain atlases or functional modes. A good choice of the corresponding brain networks is important, as most data analyses start from these reduced signals. We contribute finely-resolved atlases of functional modes, comprising from 64 to 1024 networks. These dictionaries of functional modes (DiFuMo) are trained on millions of fMRI functional brain volumes of total size 2.4TB, spanned over 27 studies and many research groups. We demonstrate the benefits of extracting reduced signals on our fine-grain atlases for many classic functional data analysis pipelines: stimuli decoding from 12,334 brain responses, standard GLM analysis of fMRI across sessions and individuals, extraction of resting-state functional-connectomes biomarkers for 2,500 individuals, data compression and meta-analysis over more than 15,000 statistical maps. In each of these analysis scenarii, we compare the performance of our functional atlases with that of other popular references, and to a simple voxel-level analysis. Results highlight the importance of using high-dimensional "soft" functional atlases, to represent and analyse brain activity while capturing its functional gradients. Analyses on high-dimensional modes achieve similar statistical performance as at the voxel level, but with much reduced computational cost and higher interpretability. In addition to making them available, we provide meaningful names for these modes, based on their anatomical location. It will facilitate reporting of results.

q-bio.NC↗

arXiv2020

NeuroQuery: comprehensive meta-analysis of human brain mapping

Reaching a global view of brain organization requires assembling evidence on widely different mental processes and mechanisms. The variety of human neuroscience concepts and terminology poses a fundamental challenge to relating brain imaging results across the scientific literature. Existing meta-analysis methods perform statistical tests on sets of publications associated with a particular concept. Thus, large-scale meta-analyses only tackle single terms that occur frequently. We propose a new paradigm, focusing on prediction rather than inference. Our multivariate model predicts the spatial distribution of neurological observations, given text describing an experiment, cognitive process, or disease. This approach handles text of arbitrary length and terms that are too rare for standard meta-analysis. We capture the relationships and neural correlates of 7 547 neuroscience terms across 13 459 neuroimaging publications. The resulting meta-analytic tool, neuroquery.org, can ground hypothesis generation and data-analysis priors on a comprehensive view of published findings on the brain.

q-bio.QM↗

arXiv2019

Fast shared response model for fMRI data

The shared response model provides a simple but effective framework to analyse fMRI data of subjects exposed to naturalistic stimuli. However when the number of subjects or runs is large, fitting the model requires a large amount of memory and computational power, which limits its use in practice. In this work, we introduce the FastSRM algorithm that relies on an intermediate atlas-based representation. It provides considerable speed-up in time and memory usage, hence it allows easy and fast large-scale analysis of naturalistic-stimulus fMRI data. Using four different datasets, we show that our method matches the performance of the original SRM algorithm while being about 5x faster and 20x to 40x more memory efficient. Based on this contribution, we use FastSRM to predict age from movie watching data on the CamCAN sample. Besides delivering accurate predictions (mean absolute error of 7.5 years), FastSRM extracts topographic patterns that are predictive of age, demonstrating that brain activity during free perception reflects age.

cs.CV↗

arXiv2019

Multi-subject MEG/EEG source imaging with sparse multi-task regression

Magnetoencephalography and electroencephalography (M/EEG) are non-invasive modalities that measure the weak electromagnetic fields generated by neural activity. Estimating the location and magnitude of the current sources that generated these electromagnetic fields is a challenging ill-posed regression problem known as \emph{source imaging}. When considering a group study, a common approach consists in carrying out the regression tasks independently for each subject. An alternative is to jointly localize sources for all subjects taken together, while enforcing some similarity between them. By pooling all measurements in a single multi-task regression, one makes the problem better posed, offering the ability to identify more sources and with greater precision. The Minimum Wasserstein Estimates (MWE) promotes focal activations that do not perfectly overlap for all subjects, thanks to a regularizer based on Optimal Transport (OT) metrics. MWE promotes spatial proximity on the cortical mantel while coping with the varying noise levels across subjects. On realistic simulations, MWE decreases the localization error by up to 4 mm per source compared to individual solutions. Experiments on the Cam-CAN dataset show a considerable improvement in spatial specificity in population imaging. Our analysis of a multimodal dataset shows how multi-subject source localization closes the gap between MEG and fMRI for brain mapping.

stat.ML↗

arXiv2019

Feature Grouping as a Stochastic Regularizer for High-Dimensional Structured Data

In many applications where collecting data is expensive, for example neuroscience or medical imaging, the sample size is typically small compared to the feature dimension. It is challenging in this setting to train expressive, non-linear models without overfitting. These datasets call for intelligent regularization that exploits known structure, such as correlations between the features arising from the measurement device. However, existing structured regularizers need specially crafted solvers, which are difficult to apply to complex models. We propose a new regularizer specifically designed to leverage structure in the data in a way that can be applied efficiently to complex models. Our approach relies on feature grouping, using a fast clustering algorithm inside a stochastic gradient descent loop: given a family of feature groupings that capture feature covariations, we randomly select these groups at each iteration. We show that this approach amounts to enforcing a denoising regularizer on the solution. The method is easy to implement in many model architectures, such as fully connected neural networks, and has a linear computational cost. We apply this regularizer to a real-world fMRI dataset and the Olivetti Faces datasets. Experiments on both datasets demonstrate that the proposed approach produces models that generalize better than those trained with conventional regularizers, and also improves convergence speed.

cs.LG↗

arXiv2019

ECKO: Ensemble of Clustered Knockoffs for multivariate inference on fMRI data

Continuous improvement in medical imaging techniques allows the acquisition of higher-resolution images. When these are used in a predictive setting, a greater number of explanatory variables are potentially related to the dependent variable (the response). Meanwhile, the number of acquisitions per experiment remains limited. In such high dimension/small sample size setting, it is desirable to find the explanatory variables that are truly related to the response while controlling the rate of false discoveries. To achieve this goal, novel multivariate inference procedures, such as knockoff inference, have been proposed recently. However, they require the feature covariance to be well-defined, which is impossible in high-dimensional settings. In this paper, we propose a new algorithm, called Ensemble of Clustered Knockoffs, that allows to select explanatory variables while controlling the false discovery rate (FDR), up to a prescribed spatial tolerance. The core idea is that knockoff-based inference can be applied on groups (clusters) of voxels, which drastically reduces the problem's dimension; an ensembling step then removes the dependence on a fixed clustering and stabilizes the results. We benchmark this algorithm and other FDR-controlling methods on brain imaging datasets and observe empirical gains in sensitivity, while the false discovery rate is controlled at the nominal level.

math.ST↗

arXiv2019

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.

stat.ML↗

arXiv2018

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.

stat.ML↗

arXiv2018

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.

cs.NE↗

arXiv2018

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.

stat.ME↗

arXiv2018

Statistical Inference with Ensemble of Clustered Desparsified Lasso

Medical imaging involves high-dimensional data, yet their acquisition is obtained for limited samples. Multivariate predictive models have become popular in the last decades to fit some external variables from imaging data, and standard algorithms yield point estimates of the model parameters. It is however challenging to attribute confidence to these parameter estimates, which makes solutions hardly trustworthy. In this paper we present a new algorithm that assesses parameters statistical significance and that can scale even when the number of predictors p $\ge$ 10^5 is much higher than the number of samples n $\le$ 10^3 , by lever-aging structure among features. Our algorithm combines three main ingredients: a powerful inference procedure for linear models --the so-called Desparsified Lasso-- feature clustering and an ensembling step. We first establish that Desparsified Lasso alone cannot handle n p regimes; then we demonstrate that the combination of clustering and ensembling provides an accurate solution, whose specificity is controlled. We also demonstrate stability improvements on two neuroimaging datasets.

stat.AP↗