Encoding Multi-Resolution Brain Networks Using Unsupervised Deep Learning

The main goal of this study is to extract a set of brain networks in multiple time-resolutions to analyze the connectivity patterns among the anatomic regions for a given cognitive task. We suggest a deep architecture which learns the natural groupings of the connectivity patterns of human brain in multiple time-resolutions. The suggested architecture is tested on task data set of Human Connectome Project (HCP) where we extract multi-resolution networks, each of which corresponds to a cognitive task. At the first level of this architecture, we decompose the fMRI signal into multiple sub-bands using wavelet decompositions. At the second level, for each sub-band, we estimate a brain network extracted from short time windows of the fMRI signal. At the third level, we feed the adjacency matrices of each mesh network at each time-resolution into an unsupervised deep learning algorithm, namely, a Stacked De- noising Auto-Encoder (SDAE). The outputs of the SDAE provide a compact connectivity representation for each time window at each sub-band of the fMRI signal. We concatenate the learned representations of all sub-bands at each window and cluster them by a hierarchical algorithm to find the natural groupings among the windows. We observe that each cluster represents a cognitive task with a performance of 93% Rand Index and 71% Adjusted Rand Index. We visualize the mean values and the precisions of the networks at each component of the cluster mixture. The mean brain networks at cluster centers show the variations among cognitive tasks and the precision of each cluster shows the within cluster variability of networks, across the subjects.Comment: 6 pages, 3 figures, submitted to The 17th annual IEEE International Conference on BioInformatics and BioEngineerin

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

Transfer learning of deep neural network representations for fMRI decoding

Background: Deep neural networks have revolutionised machine learning, with unparalleled performance in object classification. However, in brain imaging (e.g., fMRI), the direct application of Convolutional Neural Networks (CNN) to decoding subject states or perception from imaging data seems impractical given the scarcity of available data. New method: In this work we propose a robust method to transfer information from deep learning (DL) features to brain fMRI data with the goal of decoding. By adopting Reduced Rank Regression with Ridge Regularisation we establish a multivariate link between imaging data and the fully connected layer (fc7) of a CNN. We exploit the reconstructed fc7 features by performing an object image classification task on two datasets: one of the largest fMRI databases, taken from different scanners from more than two hundred subjects watching different movie clips, and another with fMRI data taken while watching static images. Results: The fc7 features could be significantly reconstructed from the imaging data, and led to significant decoding performance. Comparison with existing methods: The decoding based on reconstructed fc7 outperformed the decoding based on imaging data alone. Conclusion: In this work we show how to improve fMRI-based decoding benefiting from the mapping between functional data and CNN features. The potential advantage of the proposed method is twofold: the extraction of stimuli representations by means of an automatic procedure (unsupervised) and the embedding of high-dimensional neuroimaging data onto a space designed for visual object discrimination, leading to a more manageable space from dimensionality point of view