17,225 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
A multimodal neuroimaging classifier for alcohol dependence
With progress in magnetic resonance imaging technology and a broader dissemination of state-of-the-art imaging facilities, the acquisition of multiple neuroimaging modalities is becoming increasingly feasible. One particular hope associated with multimodal neuroimaging is the development of reliable data-driven diagnostic classifiers for psychiatric disorders, yet previous studies have often failed to find a benefit of combining multiple modalities. As a psychiatric disorder with established neurobiological effects at several levels of description, alcohol dependence is particularly well-suited for multimodal classification. To this aim, we developed a multimodal classification scheme and applied it to a rich neuroimaging battery (structural, functional task-based and functional resting-state data) collected in a matched sample of alcohol-dependent patients (N = 119) and controls (N = 97). We found that our classification scheme yielded 79.3% diagnostic accuracy, which outperformed the strongest individual modality - grey-matter density - by 2.7%. We found that this moderate benefit of multimodal classification depended on a number of critical design choices: a procedure to select optimal modality-specific classifiers, a fine-grained ensemble prediction based on cross-modal weight matrices and continuous classifier decision values. We conclude that the combination of multiple neuroimaging modalities is able to moderately improve the accuracy of machine-learning-based diagnostic classification in alcohol dependence
A multimodal neuroimaging classifier for alcohol dependence
With progress in magnetic resonance imaging technology and a broader dissemination of state-of-the-art imaging facilities, the acquisition of multiple neuroimaging modalities is becoming increasingly feasible. One particular hope associated with multimodal neuroimaging is the development of reliable data-driven diagnostic classifiers for psychiatric disorders, yet previous studies have often failed to find a benefit of combining multiple modalities. As a psychiatric disorder with established neurobiological effects at several levels of description, alcohol dependence is particularly well-suited for multimodal classification. To this aim, we developed a multimodal classification scheme and applied it to a rich neuroimaging battery (structural, functional task-based and functional resting-state data) collected in a matched sample of alcohol-dependent patients (N = 119) and controls (N = 97). We found that our classification scheme yielded 79.3% diagnostic accuracy, which outperformed the strongest individual modality - grey-matter density - by 2.7%. We found that this moderate benefit of multimodal classification depended on a number of critical design choices: a procedure to select optimal modality-specific classifiers, a fine-grained ensemble prediction based on cross-modal weight matrices and continuous classifier decision values. We conclude that the combination of multiple neuroimaging modalities is able to moderately improve the accuracy of machine-learning-based diagnostic classification in alcohol dependence
A reversal coarse-grained analysis with application to an altered functional circuit in depression
Introduction:
When studying brain function using functional magnetic resonance imaging (fMRI) data containing tens of thousands of voxels, a coarse-grained approach – dividing the whole brain into regions of interest – is applied frequently to investigate the organization of the functional network on a relatively coarse scale. However, a coarse-grained scheme may average out the fine details over small spatial scales, thus rendering it difficult to identify the exact locations of functional abnormalities.
Methods:
A novel and general approach to reverse the coarse-grained approach by locating the exact sources of the functional abnormalities is proposed.
Results:
Thirty-nine patients with major depressive disorder (MDD) and 37 matched healthy controls are studied. A circuit comprising the left superior frontal gyrus (SFGdor), right insula (INS), and right putamen (PUT) exhibit the greatest changes between the patients with MDD and controls. A reversal coarse-grained analysis is applied to this circuit to determine the exact location of functional abnormalities.
Conclusions:
The voxel-wise time series extracted from the reversal coarse-grained analysis (source) had several advantages over the original coarse-grained approach: (1) presence of a larger and detectable amplitude of fluctuations, which indicates that neuronal activities in the source are more synchronized; (2) identification of more significant differences between patients and controls in terms of the functional connectivity associated with the sources; and (3) marked improvement in performing discrimination tasks. A software package for pattern classification between controls and patients is available in Supporting Information
Inter and intra-hemispheric structural imaging markers predict depression relapse after electroconvulsive therapy: a multisite study.
Relapse of depression following treatment is high. Biomarkers predictive of an individual's relapse risk could provide earlier opportunities for prevention. Since electroconvulsive therapy (ECT) elicits robust and rapidly acting antidepressant effects, but has a >50% relapse rate, ECT presents a valuable model for determining predictors of relapse-risk. Although previous studies have associated ECT-induced changes in brain morphometry with clinical response, longer-term outcomes have not been addressed. Using structural imaging data from 42 ECT-responsive patients obtained prior to and directly following an ECT treatment index series at two independent sites (UCLA: n = 17, age = 45.41±12.34 years; UNM: n = 25; age = 65.00±8.44), here we test relapse prediction within 6-months post-ECT. Random forests were used to predict subsequent relapse using singular and ratios of intra and inter-hemispheric structural imaging measures and clinical variables from pre-, post-, and pre-to-post ECT. Relapse risk was determined as a function of feature variation. Relapse was well-predicted both within site and when cohorts were pooled where top-performing models yielded balanced accuracies of 71-78%. Top predictors included cingulate isthmus asymmetry, pallidal asymmetry, the ratio of the paracentral to precentral cortical thickness and the ratio of lateral occipital to pericalcarine cortical thickness. Pooling cohorts and predicting relapse from post-treatment measures provided the best classification performances. However, classifiers trained on each age-disparate cohort were less informative for prediction in the held-out cohort. Post-treatment structural neuroimaging measures and the ratios of connected regions commonly implicated in depression pathophysiology are informative of relapse risk. Structural imaging measures may have utility for devising more personalized preventative medicine approaches
Regularized brain reading with shrinkage and smoothing
Functional neuroimaging measures how the brain responds to complex stimuli.
However, sample sizes are modest, noise is substantial, and stimuli are high
dimensional. Hence, direct estimates are inherently imprecise and call for
regularization. We compare a suite of approaches which regularize via
shrinkage: ridge regression, the elastic net (a generalization of ridge
regression and the lasso), and a hierarchical Bayesian model based on small
area estimation (SAE). We contrast regularization with spatial smoothing and
combinations of smoothing and shrinkage. All methods are tested on functional
magnetic resonance imaging (fMRI) data from multiple subjects participating in
two different experiments related to reading, for both predicting neural
response to stimuli and decoding stimuli from responses. Interestingly, when
the regularization parameters are chosen by cross-validation independently for
every voxel, low/high regularization is chosen in voxels where the
classification accuracy is high/low, indicating that the regularization
intensity is a good tool for identification of relevant voxels for the
cognitive task. Surprisingly, all the regularization methods work about equally
well, suggesting that beating basic smoothing and shrinkage will take not only
clever methods, but also careful modeling.Comment: Published at http://dx.doi.org/10.1214/15-AOAS837 in the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
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