2,718 research outputs found
A supervised clustering approach for fMRI-based inference of brain states
We propose a method that combines signals from many brain regions observed in
functional Magnetic Resonance Imaging (fMRI) to predict the subject's behavior
during a scanning session. Such predictions suffer from the huge number of
brain regions sampled on the voxel grid of standard fMRI data sets: the curse
of dimensionality. Dimensionality reduction is thus needed, but it is often
performed using a univariate feature selection procedure, that handles neither
the spatial structure of the images, nor the multivariate nature of the signal.
By introducing a hierarchical clustering of the brain volume that incorporates
connectivity constraints, we reduce the span of the possible spatial
configurations to a single tree of nested regions tailored to the signal. We
then prune the tree in a supervised setting, hence the name supervised
clustering, in order to extract a parcellation (division of the volume) such
that parcel-based signal averages best predict the target information.
Dimensionality reduction is thus achieved by feature agglomeration, and the
constructed features now provide a multi-scale representation of the signal.
Comparisons with reference methods on both simulated and real data show that
our approach yields higher prediction accuracy than standard voxel-based
approaches. Moreover, the method infers an explicit weighting of the regions
involved in the regression or classification task
Machine Learning for Neuroimaging with Scikit-Learn
Statistical machine learning methods are increasingly used for neuroimaging
data analysis. Their main virtue is their ability to model high-dimensional
datasets, e.g. multivariate analysis of activation images or resting-state time
series. Supervised learning is typically used in decoding or encoding settings
to relate brain images to behavioral or clinical observations, while
unsupervised learning can uncover hidden structures in sets of images (e.g.
resting state functional MRI) or find sub-populations in large cohorts. By
considering different functional neuroimaging applications, we illustrate how
scikit-learn, a Python machine learning library, can be used to perform some
key analysis steps. Scikit-learn contains a very large set of statistical
learning algorithms, both supervised and unsupervised, and its application to
neuroimaging data provides a versatile tool to study the brain.Comment: Frontiers in neuroscience, Frontiers Research Foundation, 2013, pp.1
Mapping cognitive ontologies to and from the brain
Imaging neuroscience links brain activation maps to behavior and cognition
via correlational studies. Due to the nature of the individual experiments,
based on eliciting neural response from a small number of stimuli, this link is
incomplete, and unidirectional from the causal point of view. To come to
conclusions on the function implied by the activation of brain regions, it is
necessary to combine a wide exploration of the various brain functions and some
inversion of the statistical inference. Here we introduce a methodology for
accumulating knowledge towards a bidirectional link between observed brain
activity and the corresponding function. We rely on a large corpus of imaging
studies and a predictive engine. Technically, the challenges are to find
commonality between the studies without denaturing the richness of the corpus.
The key elements that we contribute are labeling the tasks performed with a
cognitive ontology, and modeling the long tail of rare paradigms in the corpus.
To our knowledge, our approach is the first demonstration of predicting the
cognitive content of completely new brain images. To that end, we propose a
method that predicts the experimental paradigms across different studies.Comment: NIPS (Neural Information Processing Systems), United States (2013
Improving accuracy and power with transfer learning using a meta-analytic database
Typical cohorts in brain imaging studies are not large enough for systematic
testing of all the information contained in the images. To build testable
working hypotheses, investigators thus rely on analysis of previous work,
sometimes formalized in a so-called meta-analysis. In brain imaging, this
approach underlies the specification of regions of interest (ROIs) that are
usually selected on the basis of the coordinates of previously detected
effects. In this paper, we propose to use a database of images, rather than
coordinates, and frame the problem as transfer learning: learning a
discriminant model on a reference task to apply it to a different but related
new task. To facilitate statistical analysis of small cohorts, we use a sparse
discriminant model that selects predictive voxels on the reference task and
thus provides a principled procedure to define ROIs. The benefits of our
approach are twofold. First it uses the reference database for prediction, i.e.
to provide potential biomarkers in a clinical setting. Second it increases
statistical power on the new task. We demonstrate on a set of 18 pairs of
functional MRI experimental conditions that our approach gives good prediction.
In addition, on a specific transfer situation involving different scanners at
different locations, we show that voxel selection based on transfer learning
leads to higher detection power on small cohorts.Comment: MICCAI, Nice : France (2012
A supervised clustering approach for extracting predictive information from brain activation images
International audienceIt is a standard approach to consider that images encode some information such as face expression or biomarkers in medical images; decoding this information is particularly challenging in the case of medical imaging, because the whole image domain has to be considered a priori to avoid biasing image-based prediction and image interpretation. Feature selection is thus needed, but is often performed using mass-univariate procedures, that handle neither the spatial structure of the images, nor the multivariate nature of the signal. Here we propose a solution that computes a reduced set of high-level features which compress the image information while retaining its informative parts: first, we introduce a hierarchical clustering of the research domain that incorporates spatial connectivity constraints and reduces the complexity of the possible spatial configurations to a single tree of nested regions. Then we prune the tree in order to produce a parcellation (division of the image domain) such that parcel-based signal averages optimally predict the target information. We show the power of this approach with respect to reference techniques on simulated data and apply it to enhance the prediction of the subject's behaviour during functional Magnetic Resonance Imaging (fMRI) scanning sessions. Besides its superior performance, the method provides an interpretable weighting of the regions involved in the regression or classification task
Formal Models of the Network Co-occurrence Underlying Mental Operations
International audienceSystems neuroscience has identified a set of canonical large-scale networks in humans. These have predominantly been characterized by resting-state analyses of the task-uncon-strained, mind-wandering brain. Their explicit relationship to defined task performance is largely unknown and remains challenging. The present work contributes a multivariate statistical learning approach that can extract the major brain networks and quantify their configuration during various psychological tasks. The method is validated in two extensive datasets (n = 500 and n = 81) by model-based generation of synthetic activity maps from recombination of shared network topographies. To study a use case, we formally revisited the poorly understood difference between neural activity underlying idling versus goal-directed behavior. We demonstrate that task-specific neural activity patterns can be explained by plausible combinations of resting-state networks. The possibility of decomposing a mental task into the relative contributions of major brain networks, the "network co-occurrence architecture" of a given task, opens an alternative access to the neural substrates of human cognition
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