Learning Deep Temporal Representations for Brain Decoding

Functional magnetic resonance imaging produces high dimensional data, with a less then ideal number of labelled samples for brain decoding tasks (predicting brain states). In this study, we propose a new deep temporal convolutional neural network architecture with spatial pooling for brain decoding which aims to reduce dimensionality of feature space along with improved classification performance. Temporal representations (filters) for each layer of the convolutional model are learned by leveraging unlabelled fMRI data in an unsupervised fashion with regularized autoencoders. Learned temporal representations in multiple levels capture the regularities in the temporal domain and are observed to be a rich bank of activation patterns which also exhibit similarities to the actual hemodynamic responses. Further, spatial pooling layers in the convolutional architecture reduce the dimensionality without losing excessive information. By employing the proposed temporal convolutional architecture with spatial pooling, raw input fMRI data is mapped to a non-linear, highly-expressive and low-dimensional feature space where the final classification is conducted. In addition, we propose a simple heuristic approach for hyper-parameter tuning when no validation data is available. Proposed method is tested on a ten class recognition memory experiment with nine subjects. The results support the efficiency and potential of the proposed model, compared to the baseline multi-voxel pattern analysis techniques.

Discriminative Functional Connectivity Measures for Brain Decoding

We propose a statistical learning model for classifying cognitive processes based on distributed patterns of neural activation in the brain, acquired via functional magnetic resonance imaging (fMRI). In the proposed learning method, local meshes are formed around each voxel. The distance between voxels in the mesh is determined by using a functional neighbourhood concept. In order to define the functional neighbourhood, the similarities between the time series recorded for voxels are measured and functional connectivity matrices are constructed. Then, the local mesh for each voxel is formed by including the functionally closest neighbouring voxels in the mesh. The relationship between the voxels within a mesh is estimated by using a linear regression model. These relationship vectors, called Functional Connectivity aware Local Relational Features (FC-LRF) are then used to train a statistical learning machine. The proposed method was tested on a recognition memory experiment, including data pertaining to encoding and retrieval of words belonging to ten different semantic categories. Two popular classifiers, namely k-nearest neighbour (k-nn) and Support Vector Machine (SVM), are trained in order to predict the semantic category of the item being retrieved, based on activation patterns during encoding. The classification performance of the Functional Mesh Learning model, which range in 62%-71% is superior to the classical multi-voxel pattern analysis (MVPA) methods, which range in 40%-48%, for ten semantic categories.

Mesh Learning for Classifying Cognitive Processes

A relatively recent advance in cognitive neuroscience has been multi-voxel pattern analysis (MVPA), which enables researchers to decode brain states and/or the type of information represented in the brain during a cognitive operation. MVPA methods utilize machine learning algorithms to distinguish among types of information or cognitive states represented in the brain, based on distributed patterns of neural activity. In the current investigation, we propose a new approach for representation of neural data for pattern analysis, namely a Mesh Learning Model. In this approach, at each time instant, a star mesh is formed around each voxel, such that the voxel corresponding to the center node is surrounded by its p-nearest neighbors. The arc weights of each mesh are estimated from the voxel intensity values by least squares method. The estimated arc weights of all the meshes, called Mesh Arc Descriptors (MADs), are then used to train a classifier, such as Neural Networks, k-Nearest Neighbor, Naive Bayes and Support Vector Machines. The proposed Mesh Model was tested on neuroimaging data acquired via functional magnetic resonance imaging (fMRI) during a recognition memory experiment using categorized word lists, employing a previously established experimental paradigm (Oztekin & Badre, 2011). Results suggest that the proposed Mesh Learning approach can provide an effective algorithm for pattern analysis of brain activity during cognitive processing.