Automated Classification of Resting-State fMRI ICA Components Using a Deep Siamese Network

Manual classification of functional resting state networks (RSNs) derived from Independent Component Analysis (ICA) decomposition can be labor intensive and requires expertise, particularly in large multi-subject analyses. Hence, a fully automatic algorithm that can reliably classify these RSNs is desirable. In this paper, we present a deep learning approach based on a Siamese Network to learn a discriminative feature representation for single-subject ICA component classification. Advantages of this supervised framework are that it requires relatively few training data examples and it does not require the number of ICA components to be specified. In addition, our approach permits one-shot learning, which allows generalization to new classes not seen in the training set with only one example of each new class. The proposed method is shown to out-perform traditional convolutional neural network (CNN) and template matching methods in identifying eleven subject-specific RSNs, achieving 100% accuracy on a holdout data set and over 99% accuracy on an outside data set. We also demonstrate that the method is robust to scan-rescan variation. Finally, we show that the functional connectivity of default mode and salience networks identified by the proposed technique is altered in a group analysis of mild traumatic brain injury (TBI), severe TBI, and healthy subjects.

Aberrant Resting-State Functional Connectivity of the Dorsal Attention Network in Tinnitus

Previous functional magnetic resonance imaging (fMRI) analyses have shown that the dorsal attention network (DAN) is involved in the pathophysiological changes of tinnitus, but few relevant studies have been conducted, and the conclusions to date are not uniform. The purpose of this research was to test whether there is a change in intrinsic functional connectivity (FC) patterns between the DAN and other brain regions in tinnitus patients. Thirty-one patients with persistent tinnitus and thirty-three healthy controls were enrolled in this study. A group independent component analysis (ICA), degree centrality (DC) analysis, and seed-based FC analysis were conducted. In the group ICA, the tinnitus patients showed increased connectivity in the left superior parietal gyrus in the DAN compared to the healthy controls. Compared with the healthy controls, the tinnitus patients showed increased DC in the left inferior parietal gyrus and decreased DC in the left precuneus within the DAN. The clusters within the DAN with significant differences in the ICA or DC analysis between the tinnitus patients and the healthy controls were selected as regions of interest (ROIs) for seeds. The tinnitus patients exhibited significantly increased FC from the left superior parietal gyrus to several brain regions, including the left inferior parietal gyrus, the left superior marginal gyrus, and the right superior frontal gyrus, and decreased FC to the right anterior cingulate cortex. The tinnitus patients exhibited decreased FC from the left precuneus to the left inferior occipital gyrus, left calcarine cortex, and left superior frontal gyrus compared with the healthy controls. The findings of this study show that compared with healthy controls, tinnitus patients have altered functional connections not only within the DAN but also between the DAN and other brain regions. These results suggest that it may be possible to improve the disturbance and influence of tinnitus by regulating the DAN.

A method to compare the discriminatory power of data-driven methods: Application to ICA and IVA

BACKGROUND

The widespread application of data-driven factorization-based methods, such as independent component analysis (ICA), to functional magnetic resonance imaging data facilitates the study of neural function and how it is disrupted by psychiatric disorders such as schizophrenia. While the increasing number of these methods motivates a comparison of their relative performance, such a comparison is difficult to perform on real fMRI data, since the ground truth is, relatively, unknown and the alignment of factors across different methods is impractical and imprecise.

NEW METHOD

We present a novel method, global difference maps (GDMs), to compare the results of different fMRI analysis techniques on real fMRI data, quantify their relative performances, and highlight the differences between the decompositions visually.

COMPARISON WITH EXISTING METHODS

We apply this method to compare the performances of two different factorization-based methods, ICA and its multiset extension independent vector analysis (IVA), for the analysis of fMRI data from 109 patients with schizophrenia and 138 healthy controls during the performance of three tasks.

RESULTS

Through this application of GDMs, we find that IVA can determine regions that are more discriminatory between patients and controls than ICA, though IVA is less effective at emphasizing regions found in only a subset of the tasks.

CONCLUSIONS

These results demonstrate that GDMs are an effective way to compare the performances of different factorization-based methods as well as regression-based analyses.

Determining the optimal number of independent components for reproducible transcriptomic data analysis

BACKGROUND

Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the number of components (factors) to compute. The optimal choice of this parameter, related to determining the effective data dimension, remains an open question in the application of blind source separation techniques to transcriptomic data.

RESULTS

Here we address the question of optimizing the number of statistically independent components in the analysis of transcriptomic data for reproducibility of the components in multiple runs of ICA (within the same or within varying effective dimensions) and in multiple independent datasets. To this end, we introduce ranking of independent components based on their stability in multiple ICA computation runs and define a distinguished number of components (Most Stable Transcriptome Dimension, MSTD) corresponding to the point of the qualitative change of the stability profile. Based on a large body of data, we demonstrate that a sufficient number of dimensions is required for biological interpretability of the ICA decomposition and that the most stable components with ranks below MSTD have more chances to be reproduced in independent studies compared to the less stable ones. At the same time, we show that a transcriptomics dataset can be reduced to a relatively high number of dimensions without losing the interpretability of ICA, even though higher dimensions give rise to components driven by small gene sets.

CONCLUSIONS

We suggest a protocol of ICA application to transcriptomics data with a possibility of prioritizing components with respect to their reproducibility that strengthens the biological interpretation. Computing too few components (much less than MSTD) is not optimal for interpretability of the results. The components ranked within MSTD range have more chances to be reproduced in independent studies.

Quantifying the Interaction and Contribution of Multiple Datasets in Fusion: Application to the Detection of Schizophrenia

The extraction of information from multiple sets of data is a problem inherent to many disciplines. This is possible by either analyzing the data sets jointly as in data fusion or separately and then combining as in data integration. However, selecting the optimal method to combine and analyze multiset data is an ever-present challenge. The primary reason for this is the difficulty in determining the optimal contribution of each data set to an analysis as well as the amount of potentially exploitable complementary information among data sets. In this paper, we propose a novel classification rate-based technique to unambiguously quantify the contribution of each data set to a fusion result as well as facilitate direct comparisons of fusion methods on real data and apply a new method, independent vector analysis (IVA), to multiset fusion. This classification rate-based technique is used on functional magnetic resonance imaging data collected from 121 patients with schizophrenia and 150 healthy controls during the performance of three tasks. Through this application, we find that though optimal performance is achieved by exploiting all tasks, each task does not contribute equally to the result and this framework enables effective quantification of the value added by each task. Our results also demonstrate that data fusion methods are more powerful than data integration methods, with the former achieving a classification rate of 73.5 % and the latter achieving one of 70.9 %, a difference which we show is significant when all three tasks are analyzed together. Finally, we show that IVA, due to its flexibility, has equivalent or superior performance compared with the popular data fusion method, joint independent component analysis.

A Hitchhiker's Guide to Functional Magnetic Resonance Imaging

Functional Magnetic Resonance Imaging (fMRI) studies have become increasingly popular both with clinicians and researchers as they are capable of providing unique insights into brain functions. However, multiple technical considerations (ranging from specifics of paradigm design to imaging artifacts, complex protocol definition, and multitude of processing and methods of analysis, as well as intrinsic methodological limitations) must be considered and addressed in order to optimize fMRI analysis and to arrive at the most accurate and grounded interpretation of the data. In practice, the researcher/clinician must choose, from many available options, the most suitable software tool for each stage of the fMRI analysis pipeline. Herein we provide a straightforward guide designed to address, for each of the major stages, the techniques, and tools involved in the process. We have developed this guide both to help those new to the technique to overcome the most critical difficulties in its use, as well as to serve as a resource for the neuroimaging community.

Including signal intensity increases the performance of blind source separation on brain imaging data

When analyzing brain imaging data, blind source separation (BSS) techniques critically depend on the level of dimensional reduction. If the reduction level is too slight, the BSS model would be overfitted and become unavailable. Thus, the reduction level must be set relatively heavy. This approach risks discarding useful information and crucially limits the performance of BSS techniques. In this study, a new BSS method that can work well even at a slight reduction level is presented. We proposed the concept of "signal intensity" which measures the significance of the source. Only picking the sources with significant intensity, the new method can avoid the overfitted solutions which are nonexistent artifacts. This approach enables the reduction level to be set slight and retains more useful dimensions in the preliminary reduction. Comparisons between the new and conventional algorithms were performed on both simulated and real data.