Evaluating Graph Signal Processing for Neuroimaging Through Classification and Dimensionality Reduction

Graph Signal Processing (GSP) is a promising framework to analyze multi-dimensional neuroimaging datasets, while taking into account both the spatial and functional dependencies between brain signals. In the present work, we apply dimensionality reduction techniques based on graph representations of the brain to decode brain activity from real and simulated fMRI datasets. We introduce seven graphs obtained from a) geometric structure and/or b) functional connectivity between brain areas at rest, and compare them when performing dimension reduction for classification. We show that mixed graphs using both a) and b) offer the best performance. We also show that graph sampling methods perform better than classical dimension reduction including Principal Component Analysis (PCA) and Independent Component Analysis (ICA).Comment: 5 pages, GlobalSIP 201

Sparse Predictive Structure of Deconvolved Functional Brain Networks

The functional and structural representation of the brain as a complex network is marked by the fact that the comparison of noisy and intrinsically correlated high-dimensional structures between experimental conditions or groups shuns typical mass univariate methods. Furthermore most network estimation methods cannot distinguish between real and spurious correlation arising from the convolution due to nodes' interaction, which thus introduces additional noise in the data. We propose a machine learning pipeline aimed at identifying multivariate differences between brain networks associated to different experimental conditions. The pipeline (1) leverages the deconvolved individual contribution of each edge and (2) maps the task into a sparse classification problem in order to construct the associated "sparse deconvolved predictive network", i.e., a graph with the same nodes of those compared but whose edge weights are defined by their relevance for out of sample predictions in classification. We present an application of the proposed method by decoding the covert attention direction (left or right) based on the single-trial functional connectivity matrix extracted from high-frequency magnetoencephalography (MEG) data. Our results demonstrate how network deconvolution matched with sparse classification methods outperforms typical approaches for MEG decoding

The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data.

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being 'good' or 'bad.' Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to 'bad' quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer's Disease Neuroimaging Initiative (ADNI). LONI-QC's functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community

Towards Deeper Understanding in Neuroimaging

Neuroimaging is a growing domain of research, with advances in machine learning having tremendous potential to expand understanding in neuroscience and improve public health. Deep neural networks have recently and rapidly achieved historic success in numerous domains, and as a consequence have completely redefined the landscape of automated learners, giving promise of significant advances in numerous domains of research. Despite recent advances and advantages over traditional machine learning methods, deep neural networks have yet to have permeated significantly into neuroscience studies, particularly as a tool for discovery. This dissertation presents well-established and novel tools for unsupervised learning which aid in feature discovery, with relevant applications to neuroimaging. Through our works within, this dissertation presents strong evidence that deep learning is a viable and important tool for neuroimaging studies

MVPAlab: A machine learning decoding toolbox for multidimensional electroencephalography data

This research was supported by the Spanish Ministry of Sci- ence and Innovation under the PID2019–111187GB-I00 grant, by the MCIN/AEI/10.13039/50110 0 011033/ and FEDER “Una manera de hacer Europa’’ under the RTI2018-098913-B100 project, by the Consejería de Economía, Innovación, Ciencia y Empleo (Junta de Andalucía) and FEDER under CV20-45250, A-TIC-080-UGR18, B- TIC-586-UGR20 and P20-00525 projects. The first author of this work is supported by a scholarship from the Spanish Ministry of Science and Innovation (BES-2017–079769). Funding for open ac- cess charge: Universidad de Granada / CBUA. The sample EEG dataset was extracted from an original experiment previously ap- proved by the Ethics Committee of the University of Granada.Background and Objective: The study of brain function has recently expanded from classical univariate to multivariate analyses. These multivariate, machine learning-based algorithms afford neuroscientists extracting more detailed and richer information from the data. However, the implementation of these procedures is usually challenging, especially for researchers with no coding experience. To address this problem, we have developed MVPAlab, a MATLAB-based, flexible decoding toolbox for multidimensional electroencephalography and magnetoencephalography data. Methods: The MVPAlab Toolbox implements several machine learning algorithms to compute multivariate pattern analyses, cross-classification, temporal generalization matrices and feature and frequency contri- bution analyses. It also provides access to an extensive set of preprocessing routines for, among others, data normalization, data smoothing, dimensionality reduction and supertrial generation. To draw statisti- cal inferences at the group level, MVPAlab includes a non-parametric cluster-based permutation approach. Results: A sample electroencephalography dataset was compiled to test all the MVPAlab main function- alities. Significant clusters (p < 0.01) were found for the proposed decoding analyses and different config- urations, proving the software capability for discriminating between different experimental conditions. Conclusions: This toolbox has been designed to include an easy-to-use and intuitive graphic user interface and data representation software, which makes MVPAlab a very convenient tool for users with few or no previous coding experience. In addition, MVPAlab is not for beginners only, as it implements several high and low-level routines allowing more experienced users to design their own projects in a highly flexible manner.Spanish Government PID2019-111187GB-I00 BES-2017-079769MCIN/AEIFEDER "Una manera de hacer Europa'' RTI2018-098913-B100Junta de AndalucíaEuropean Commission CV20-45250 A-TIC-080-UGR18 BTIC-586-UGR20 P20-00525Universidad de Granada/CBU

Machine Learning Methods for Depression Detection Using SMRI and RS-FMRI Images

Major Depression Disorder (MDD) is a common disease throughout the world that negatively influences people’s lives. Early diagnosis of MDD is beneficial, so detecting practical biomarkers would aid clinicians in the diagnosis of MDD. Having an automated method to find biomarkers for MDD is helpful even though it is difficult. The main aim of this research is to generate a method for detecting discriminative features for MDD diagnosis based on Magnetic Resonance Imaging (MRI) data. In this research, representational similarity analysis provides a framework to compare distributed patterns and obtain the similarity/dissimilarity of brain regions. Regions are obtained by either data-driven or model-driven methods such as cubes and atlases respectively. For structural MRI (sMRI) similarity of voxels of spatial cubes (data-driven) are explored. For resting-state fMRI (rs-fMRI) images, the similarity of the time series of both cubes (data-driven) and atlases (model-driven) are examined. Moreover, the similarity method of the inverse of Minimum Covariant Determinant is applied that excludes outliers from patterns and finds conditionally independent regions given the rest of regions. Next, a statistical test that is robust to outliers, identifies discriminative similarity features between two groups of MDDs and controls. Therefore, the key contribution is the way to get discriminative features that include obtaining similarity of voxel’s cubes/time series using the inverse of robust covariance along with the statistical test. The experimental results show that obtaining these features along with the Bernoulli Naïve Bayes classifier achieves superior performance compared with other methods. The performance of our method is verified by applying it to three imbalanced datasets. Moreover, the similarity-based methods are compared with deep learning and regional-based approaches for detecting MDD using either sMRI or rs-fMRI. Given that depression is famous to be a connectivity disorder problem, investigating the similarity of the brain’s regions is valuable to understand the behavior of the brain. The combinations of structural and functional brain similarities are explored to investigate the brain’s structural and functional properties together. Moreover, the combination of data-driven (cube) and model-driven (atlas) similarities of rs-fMRI are looked over to evaluate how they affect the performance of the classifier. Besides, discriminative similarities are visualized for both sMRI and rs-fMRI. Also, to measure the informativeness of a cube, the relationship of atlas regions with overlapping cubes and vise versa (cubes with overlapping regions) are explored and visualized. Furthermore, the relationship between brain structure and function has been probed through common similarities between structural and resting-state functional networks

Spectral Graph Convolutions for Population-based Disease Prediction

Exploiting the wealth of imaging and non-imaging information for disease prediction tasks requires models capable of representing, at the same time, individual features as well as data associations between subjects from potentially large populations. Graphs provide a natural framework for such tasks, yet previous graph-based approaches focus on pairwise similarities without modelling the subjects' individual characteristics and features. On the other hand, relying solely on subject-specific imaging feature vectors fails to model the interaction and similarity between subjects, which can reduce performance. In this paper, we introduce the novel concept of Graph Convolutional Networks (GCN) for brain analysis in populations, combining imaging and non-imaging data. We represent populations as a sparse graph where its vertices are associated with image-based feature vectors and the edges encode phenotypic information. This structure was used to train a GCN model on partially labelled graphs, aiming to infer the classes of unlabelled nodes from the node features and pairwise associations between subjects. We demonstrate the potential of the method on the challenging ADNI and ABIDE databases, as a proof of concept of the benefit from integrating contextual information in classification tasks. This has a clear impact on the quality of the predictions, leading to 69.5% accuracy for ABIDE (outperforming the current state of the art of 66.8%) and 77% for ADNI for prediction of MCI conversion, significantly outperforming standard linear classifiers where only individual features are considered.Comment: International Conference on Medical Image Computing and Computer-Assisted Interventions (MICCAI) 201