Ensemble learning with 3D convolutional neural networks for connectome-based prediction

arXiv.org Machine Learning

The specificty and sensitivity of resting state functional MRI (rs-fMRI) measurements depend on pre-processing choices, such as the parcellation scheme used to define regions of interest (ROIs). In this study, we critically evaluate the effect of brain parcellations on machine learning models applied to rs-fMRI data. Our experiments reveal a remarkable trend: On average, models with stochastic parcellations consistently perform as well as models with widely used atlases at the same spatial scale. We thus propose an ensemble learning strategy to combine the predictions from models trained on connectivity data extracted using different (e.g., stochastic) parcellations. We further present an implementation of our ensemble learning strategy with a novel 3D Convolutional Neural Network (CNN) approach. The proposed CNN approach takes advantage of the full-resolution 3D spatial structure of rs-fMRI data and fits non-linear predictive models. Our ensemble CNN framework overcomes the limitations of traditional machine learning models for connectomes that often rely on region-based summary statistics and/or linear models. We showcase our approach on a classification (autism patients versus healthy controls) and a regression problem (prediction of subject's age), and report promising results.


Connectivity-Driven Brain Parcellation via Consensus Clustering

arXiv.org Machine Learning

We present two related methods for deriving connectivity-based brain atlases from individual connectomes. The proposed methods exploit a previously proposed dense connectivity representation, termed continuous connectivity, by first performing graph-based hierarchical clustering of individual brains, and subsequently aggregating the individual parcellations into a consensus parcellation. The search for consensus minimizes the sum of cluster membership distances, effectively estimating a pseudo-Karcher mean of individual parcellations. We assess the quality of our parcellations using (1) Kullback-Liebler and Jensen-Shannon divergence with respect to the dense connectome representation, (2) inter-hemispheric symmetry, and (3) performance of the simplified connectome in a biological sex classification task. We find that the parcellation based-atlas computed using a greedy search at a hierarchical depth 3 outperforms all other parcellation-based atlases as well as the standard Dessikan-Killiany anatomical atlas in all three assessments.


Discriminative Network Models of Schizophrenia

Neural Information Processing Systems

Schizophrenia is a complex psychiatric disorder that has eluded a characterization in terms of local abnormalities of brain activity, and is hypothesized to affect the collective, ``emergent working of the brain. We propose a novel data-driven approach to capture emergent features using functional brain networks [Eguiluzet al] extracted from fMRI data, and demonstrate its advantage over traditional region-of-interest (ROI) and local, task-specific linear activation analyzes. Our results suggest that schizophrenia is indeed associated with disruption of global, emergent brain properties related to its functioning as a network, which cannot be explained by alteration of local activation patterns. Moreover, further exploitation of interactions by sparse Markov Random Field classifiers shows clear gain over linear methods, such as Gaussian Naive Bayes and SVM, allowing to reach 86% accuracy (over 50% baseline - random guess), which is quite remarkable given that it is based on a single fMRI experiment using a simple auditory task.


Machine learning in resting-state fMRI analysis

arXiv.org Machine Learning

Machine learning techniques have gained prominence for the analysis of resting-state functional Magnetic Resonance Imaging (rsfMRI) data. Here, we present an overview of various unsupervised and supervised machine learning applicationsto rsfMRI. We present a methodical taxonomy of machine learning methods in resting-state fMRI. We identify three major divisions of unsupervised learning methods with regard to their applications to rsfMRI, based on whether they discover principal modes of variation across space, time or population. Next, we survey the algorithms and rsfMRI feature representations that have driven the success of supervised subject-level predictions. Thegoal is to provide a high-level overview of the burgeoning field of rsfMRI from the perspective of machine learning applications. Keywords: Machine learning, resting-state, functional MRI, intrinsic networks, brain connectivity 1. Introduction Resting-state fMRI (rsfMRI) is a widely used neuroimaging tool that ...


Categories and Functional Units: An Infinite Hierarchical Model for Brain Activations

Neural Information Processing Systems

We present a model that describes the structure in the responses of different brain areas to a set of stimuli in terms of stimulus categories" (clusters of stimuli) and "functional units" (clusters of voxels). We assume that voxels within a unit respond similarly to all stimuli from the same category, and design a nonparametric hierarchical model to capture inter-subject variability among the units. The model explicitly captures the relationship between brain activations and fMRI time courses. A variational inference algorithm derived based on the model can learn categories, units, and a set of unit-category activation probabilities from data. When applied to data from an fMRI study of object recognition, the method finds meaningful and consistent clusterings of stimuli into categories and voxels into units."