Unsupervised learning and mapping of active brain functional MRI signals based on hidden semi-Markov event sequence models

Predicting change: Approximate inference under explicit representation of temporal structure in changing environments

In our daily lives timing of our actions plays an essential role when we navigate the complex everyday environment. It is an open question though how the representations of the temporal structure of the world influence our behavior. Here we propose a probabilistic model with an explicit representation of state durations which may provide novel insights in how the brain predicts upcoming changes. We illustrate several properties of the behavioral model using a standard reversal learning design and compare its task performance to standard reinforcement learning models. Furthermore, using experimental data, we demonstrate how the model can be applied to identify participants' beliefs about the latent temporal task structure. We found that roughly one quarter of participants seem to have learned the latent temporal structure and used it to anticipate changes, whereas the remaining participants' behavior did not show signs of anticipatory responses, suggesting a lack of precise temporal expectations. We expect that the introduced behavioral model will allow, in future studies, for a systematic investigation of how participants learn the underlying temporal structure of task environments and how these representations shape behavior.

A decomposition model and voxel selection framework for fMRI analysis to predict neural response of visual stimuli

This paper presents an fMRI signal analysis methodology using geometric mean curve decomposition (GMCD) and mutual information-based voxel selection framework. Previously, the fMRI signal analysis has been conducted using empirical mean curve decomposition (EMCD) model and voxel selection on raw fMRI signal. The erstwhile methodology loses frequency component, while the latter methodology suffers from signal redundancy. Both challenges are addressed by our methodology in which the frequency component is considered by decomposing the raw fMRI signal using geometric mean rather than arithmetic mean and the voxels are selected from EMCD signal using GMCD components, rather than raw fMRI signal. The proposed methodologies are adopted for predicting the neural response. Experimentations are conducted in the openly available fMRI data of six subjects, and comparisons are made with existing decomposition models and voxel selection frameworks. Subsequently, the effect of degree of selected voxels and the selection constraints are analyzed. The comparative results and the analysis demonstrate the superiority and the reliability of the proposed methodology.

Robust activation detection methods for real-time and offline fMRI analysis

We propose two contributions with novel approaches to fMRI activation analysis. The first is to apply confidence intervals to locate activations in real-time, and second is a new metric based on robust regression of fMRI signals. These contributions are implemented in our four proposed methods; Instantaneous Activation Method (IAM), Instantaneous Activation Method with Past Blocks (IAMP) for real-time analysis, Task Robust Regression Distance Method (TRRD) for the new metric with robust regression and Instantaneous Robust Regression Distance Method (IRRD) for both contributions. For comparison, a statistical offline method called Task Activation Method (TAM) and a correlation analysis method are also implemented. The methods are initially evaluated with synthetic data generated using two different approaches; first using varying hemodynamic response function signals to simulate a wide range of stimuli responses, along with a Gaussian white noise, and second using no activity state data of a real fMRI experiment, which removes the need to generate noise. The methods are also tested with real fMRI experiments and compared with the results obtained by the widely used SPM tool. The results show that instantaneous methods reveal activations that are lost statistically in an offline analysis. They also reveal further improvements by robust fitting application, which minimizes the outlier effect. TRRD has an area under the ROC curve of 0,7127 for very noisy synthetic images, is reaching up to 0,9608 as the noise decreases, while the instantaneous score is in the range of 0,6124 to 0,8019 in the same noise levels.

Asynchronous brain computer interface using hidden semi-Markov models

Ideal Brain Computer Interfaces need to perform asynchronously and at real time. We propose Hidden Semi-Markov Models (HSMM) to better segment and classify EEG data. The proposed HSMM method was tested against a simple windowed method on standard datasets. We found that our HSMM outperformed the simple windowed method. Furthermore, due to the computational demands of the algorithm, we adapted the HSMM algorithm to an online setting and demonstrate that this faster version of the algorithm can run in real time.

Unsupervised spatiotemporal fMRI data analysis using support vector machines

In this work we present a new support vector machine (SVM)-based method for fMRI data analysis. SVM has been shown to be a powerful, efficient data-driven tool in pattern recognition, and has been applied to the supervised classification of brain cognitive states in fMRI experiments. We examine the unsupervised mapping of activated brain regions using SVM. Specifically, the mapping process is formulated as an outlier detection problem of one-class SVM (OCSVM) that provides initial mapping results. These results are further refined by applying prototype selection and SVM reclassification. Multiple spatial and temporal features are extracted and selected to facilitate SVM learning. The proposed method was compared with correlation analysis (CA), t-test (TT), and spatial independent component analysis (SICA) methods using synthetic and experimental data. Our results show that the proposed method can provide more accurate and robust activation mapping than CA, TT and SICA, and is computationally more efficient than SICA. Besides its applicability to typical fMRI experiments, the proposed method is also a powerful tool in fMRI studies where a reliable quantification of activated brain regions is required.

A hybrid approach for compressive neural activity detection with functional MR images

In this paper, we present a framework for neural activity detection using fMRI data, based on both statistical data analysis (data-driven) and graphical information modeling (model-based). The data-driven approaches do rough prediction when an extraordinary amount of neural activities arise. By proper exploration of spatial, temporal, inter-subject correlations, the model-based approaches can provide more insights to details, and physiological meaning from high data volume, low signal-to-noise ratio (SNR) fMRI measurements. Through temporal cluster analysis (TCA), matched filtering, linear predictive coding (LPC), and variational Bayesian Gaussian mixture modeling (VBGMM), the temporal fMRI signals are converted into event prototypes associated with three neural statuses: activation, deactivation, and normality. As a result, the high volume fMRI data generated from multiple subjects can be statistically modeled as coupled finite-state sequences. Based on the graphical-model representation, the neural activities captured through fMRI can be classified and detected at reduced computational cost. The whole framework consists of three components: 1) image enhancement, event prediction and capture; 2) event feature extraction and modeling; and 3) graphical model based Bayesian inference. The experiment results demonstrate the advantages of the proposed hybrid, compressive signal processing approach in terms of computational cost and robustness against inter-subject variability as well as various artifacts.

Hidden Markov multiple event sequence models: A paradigm for the spatio-temporal analysis of fMRI data

This paper presents a novel, completely unsupervised fMRI brain mapping method that addresses the three problems of hemodynamic response function (HRF) variability, hemodynamic event timing, and fMRI response non-linearity. Spatial and temporal information are directly taken into account into the core of the activation detection process. In practice, activation detection at voxel v is formulated in terms of temporal alignment between sequences of hemodynamic response onsets (HROs) detected in the fMRI signal at v and in the spatial neighborhood of v, and the input sequence of stimuli or stimulus onsets. Event-related and epoch paradigms are considered. The multiple event sequence alignment problem is solved within the probabilistic framework of hidden Markov multiple event sequence models (HMMESMs), a new class of hidden Markov models. Results obtained on real and synthetic data significantly outperform those obtained with the popular statistical parametric mapping (SPM2) method without requiring any prior definition of the expected activation patterns, the HMMESM mapping approach being completely unsupervised.

Contextual modeling of functional MR images with conditional random fields

This paper presents a conditional random field (CRF) approach to fuse contextual dependencies in functional magnetic resonance imaging (fMRI) data for the detection of brain activation. The interactions among both activation (activated/inactive) labels and observed data of brain voxels are unified in a probabilistic framework based on the CRF, where the interaction strength can be adaptively adjusted in terms of the data similarity of neighboring sites. Compared to earlier detection methods, including statistical parametric mapping and Markov random field, the proposed method avoids the suppression of high frequency information and relaxes the strong assumption of conditional independence of observed data. Experimental results show that the proposed approach effectively integrates contextual constraints within the detection process and robustly detects brain activities from fMRI data.