Decoding the Encoding of Functional Brain Networks: an fMRI Classification Comparison of Non-negative Matrix Factorization (NMF), Independent Component Analysis (ICA), and Sparse Coding Algorithms

Brain networks in fMRI are typically identified using spatial independent component analysis (ICA), yet mathematical constraints such as sparse coding and positivity both provide alternate biologically-plausible frameworks for generating brain networks. Non-negative Matrix Factorization (NMF) would suppress negative BOLD signal by enforcing positivity. Spatial sparse coding algorithms ($L1$ Regularized Learning and K-SVD) would impose local specialization and a discouragement of multitasking, where the total observed activity in a single voxel originates from a restricted number of possible brain networks. The assumptions of independence, positivity, and sparsity to encode task-related brain networks are compared; the resulting brain networks for different constraints are used as basis functions to encode the observed functional activity at a given time point. These encodings are decoded using machine learning to compare both the algorithms and their assumptions, using the time series weights to predict whether a subject is viewing a video, listening to an audio cue, or at rest, in 304 fMRI scans from 51 subjects. For classifying cognitive activity, the sparse coding algorithm of $L1$ Regularized Learning consistently outperformed 4 variations of ICA across different numbers of networks and noise levels (p$<$0.001). The NMF algorithms, which suppressed negative BOLD signal, had the poorest accuracy. Within each algorithm, encodings using sparser spatial networks (containing more zero-valued voxels) had higher classification accuracy (p$<$0.001). The success of sparse coding algorithms may suggest that algorithms which enforce sparse coding, discourage multitasking, and promote local specialization may capture better the underlying source processes than those which allow inexhaustible local processes such as ICA

Graph- and finite element-based total variation models for the inverse problem in diffuse optical tomography

Total variation (TV) is a powerful regularization method that has been widely applied in different imaging applications, but is difficult to apply to diffuse optical tomography (DOT) image reconstruction (inverse problem) due to complex and unstructured geometries, non-linearity of the data fitting and regularization terms, and non-differentiability of the regularization term. We develop several approaches to overcome these difficulties by: i) defining discrete differential operators for unstructured geometries using both finite element and graph representations; ii) developing an optimization algorithm based on the alternating direction method of multipliers (ADMM) for the non-differentiable and non-linear minimization problem; iii) investigating isotropic and anisotropic variants of TV regularization, and comparing their finite element- and graph-based implementations. These approaches are evaluated on experiments on simulated data and real data acquired from a tissue phantom. Our results show that both FEM and graph-based TV regularization is able to accurately reconstruct both sparse and non-sparse distributions without the over-smoothing effect of Tikhonov regularization and the over-sparsifying effect of L$_1$ regularization. The graph representation was found to out-perform the FEM method for low-resolution meshes, and the FEM method was found to be more accurate for high-resolution meshes.Comment: 24 pages, 11 figures. Reviced version includes revised figures and improved clarit

Data-Driven Time-Frequency Analysis

In this paper, we introduce a new adaptive data analysis method to study trend and instantaneous frequency of nonlinear and non-stationary data. This method is inspired by the Empirical Mode Decomposition method (EMD) and the recently developed compressed (compressive) sensing theory. The main idea is to look for the sparsest representation of multiscale data within the largest possible dictionary consisting of intrinsic mode functions of the form $\{a(t) \cos(\theta(t))\}$, where $a \in V(\theta)$, $V(\theta)$ consists of the functions smoother than $\cos(\theta(t))$ and $\theta'\ge 0$. This problem can be formulated as a nonlinear $L^0$ optimization problem. In order to solve this optimization problem, we propose a nonlinear matching pursuit method by generalizing the classical matching pursuit for the $L^0$ optimization problem. One important advantage of this nonlinear matching pursuit method is it can be implemented very efficiently and is very stable to noise. Further, we provide a convergence analysis of our nonlinear matching pursuit method under certain scale separation assumptions. Extensive numerical examples will be given to demonstrate the robustness of our method and comparison will be made with the EMD/EEMD method. We also apply our method to study data without scale separation, data with intra-wave frequency modulation, and data with incomplete or under-sampled data

Simultaneous Codeword Optimization (SimCO) for Dictionary Update and Learning

We consider the data-driven dictionary learning problem. The goal is to seek an over-complete dictionary from which every training signal can be best approximated by a linear combination of only a few codewords. This task is often achieved by iteratively executing two operations: sparse coding and dictionary update. In the literature, there are two benchmark mechanisms to update a dictionary. The first approach, such as the MOD algorithm, is characterized by searching for the optimal codewords while fixing the sparse coefficients. In the second approach, represented by the K-SVD method, one codeword and the related sparse coefficients are simultaneously updated while all other codewords and coefficients remain unchanged. We propose a novel framework that generalizes the aforementioned two methods. The unique feature of our approach is that one can update an arbitrary set of codewords and the corresponding sparse coefficients simultaneously: when sparse coefficients are fixed, the underlying optimization problem is similar to that in the MOD algorithm; when only one codeword is selected for update, it can be proved that the proposed algorithm is equivalent to the K-SVD method; and more importantly, our method allows us to update all codewords and all sparse coefficients simultaneously, hence the term simultaneous codeword optimization (SimCO). Under the proposed framework, we design two algorithms, namely, primitive and regularized SimCO. We implement these two algorithms based on a simple gradient descent mechanism. Simulations are provided to demonstrate the performance of the proposed algorithms, as compared with two baseline algorithms MOD and K-SVD. Results show that regularized SimCO is particularly appealing in terms of both learning performance and running speed.Comment: 13 page