Graph-Regularized Manifold-Aware Conditional Wasserstein GAN for Brain Functional Connectivity Generation

Common measures of brain functional connectivity (FC) including covariance and correlation matrices are semi-positive definite (SPD) matrices residing on a cone-shape Riemannian manifold. Despite its remarkable success for Euclidean-valued data generation, use of standard generative adversarial networks (GANs) to generate manifold-valued FC data neglects its inherent SPD structure and hence the inter-relatedness of edges in real FC. We propose a novel graph-regularized manifold-aware conditional Wasserstein GAN (GR-SPD-GAN) for FC data generation on the SPD manifold that can preserve the global FC structure. Specifically, we optimize a generalized Wasserstein distance between the real and generated SPD data under an adversarial training, conditioned on the class labels. The resulting generator can synthesize new SPD-valued FC matrices associated with different classes of brain networks, e.g., brain disorder or healthy control. Furthermore, we introduce additional population graph-based regularization terms on both the SPD manifold and its tangent space to encourage the generator to respect the inter-subject similarity of FC patterns in the real data. This also helps in avoiding mode collapse and produces more stable GAN training. Evaluated on resting-state functional magnetic resonance imaging (fMRI) data of major depressive disorder (MDD), qualitative and quantitative results show that the proposed GR-SPD-GAN clearly outperforms several state-of-the-art GANs in generating more realistic fMRI-based FC samples. When applied to FC data augmentation for MDD identification, classification models trained on augmented data generated by our approach achieved the largest margin of improvement in classification accuracy among the competing GANs over baselines without data augmentation.Comment: 10 pages, 4 figure

Towards AI-Assisted Disease Diagnosis: Learning Deep Feature Representations for Medical Image Analysis

Artificial Intelligence (AI) has impacted our lives in many meaningful ways. For our research, we focus on improving disease diagnosis systems by analyzing medical images using AI, specifically deep learning technologies. The recent advances in deep learning technologies are leading to enhanced performance for medical image analysis and computer-aided disease diagnosis. In this dissertation, we explore a major research area in medical image analysis - Image classification. Image classification is the process to assign an image a label from a fixed set of categories. For our research, we focus on the problem of Alzheimer\u27s Disease (AD) diagnosis from 3D structural Magnetic Resonance Imaging (sMRI) and Positron Emission Tomography (PET) brain scans. Alzheimer\u27s Disease is a severe neurological disorder. In this dissertation, we address challenges related to Alzheimer\u27s Disease diagnosis and propose several models for improved diagnosis. We focus on analyzing the 3D Structural MRI (sMRI) and Positron Emission Tomography (PET) brain scans to identify the current stage of Alzheimer\u27s Disease: Normal Controls (CN), Mild Cognitive Impairment (MCI), and Alzheimer\u27s Disease (AD). This dissertation demonstrates ways to improve the performance of a Convolutional Neural Network (CNN) for Alzheimer\u27s Disease diagnosis. Besides, we present approaches to solve the class-imbalance problem and improving classification performance with limited training data for medical image analysis. To understand the decision of the CNN, we present methods to visualize the behavior of a CNN model for disease diagnosis. As a case study, we analyzed brain PET scans of AD and CN patients to see how CNN discriminates among data samples of different classes. Additionally, this dissertation proposes a novel approach to generate synthetic medical images using Generative Adversarial Networks (GANs). Working with the limited dataset and small amount of annotated samples makes it difficult to develop a robust automated disease diagnosis model. Our proposed model can solve such issue and generate brain MRI and PET images for three different stages of Alzheimer\u27s Disease - Normal Control (CN), Mild Cognitive Impairment (MCI), and Alzheimer\u27s Disease (AD). Our proposed approach can be generalized to create synthetic data for other medical image analysis problems and help to develop better disease diagnosis model

Assessing the Potential of Data Augmentation in EEG Functional Connectivity for Early Detection of Alzheimer’s Disease

Electroencephalographic (EEG) signals are acquired non-invasively from electrodes placed on the scalp. Experts in the field can use EEG signals to distinguish between patients with Alzheimer’s disease (AD) and normal control (NC) subjects using classification models. However, the training of deep learning or machine learning models requires a large number of trials. Datasets related to Alzheimer’s disease are typically small in size due to the lack of AD patient samples. The lack of data samples required for the training process limits the use of deep learning techniques for further development in clinical settings. We propose to increase the number of trials in the training set by means of a decomposition–recombination system consisting of three steps. Firstly, the original signals from the training set are decomposed into multiple intrinsic mode functions via multivariate empirical mode decomposition. Next, these intrinsic mode functions are randomly recombined across trials. Finally, the recombined intrinsic mode functions are added together as artificial trials, which are used for training the models. We evaluated the decomposition–recombination system on a small dataset using each subject’s functional connectivity matrices as inputs. Three different neural networks, including ResNet, BrainNet CNN, and EEGNet, were used. Overall, the system helped improve ResNet training in both the mild AD dataset, with an increase of 5.24%, and in the mild cognitive impairment dataset, with an increase of 4.50%. The evaluation of the proposed data augmentation system shows that the performance of neural networks can be improved by enhancing the training set with data augmentation. This work shows the need for data augmentation on the training of neural networks in the case of small-size AD datasets.Fil: Jia, Hao. Universitat de Vic; España. Nankai University; ChinaFil: Huang, Zihao. Nankai University; ChinaFil: Caiafa, César Federico. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Argentino de Radioastronomía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Argentino de Radioastronomía; ArgentinaFil: Duan, Feng. Nankai University; ChinaFil: Zhang, Yu. Lehigh University; Estados UnidosFil: Sun, Zhe. Juntendo University; ChinaFil: Solé Casals, Jordi. Universitat de Vic; Españ

AI-based dimensional neuroimaging system for characterizing heterogeneity in brain structure and function in major depressive disorder:COORDINATE-MDD consortium design and rationale

BACKGROUND: Efforts to develop neuroimaging-based biomarkers in major depressive disorder (MDD), at the individual level, have been limited to date. As diagnostic criteria are currently symptom-based, MDD is conceptualized as a disorder rather than a disease with a known etiology; further, neural measures are often confounded by medication status and heterogeneous symptom states. METHODS: We describe a consortium to quantify neuroanatomical and neurofunctional heterogeneity via the dimensions of novel multivariate coordinate system (COORDINATE-MDD). Utilizing imaging harmonization and machine learning methods in a large cohort of medication-free, deeply phenotyped MDD participants, patterns of brain alteration are defined in replicable and neurobiologically-based dimensions and offer the potential to predict treatment response at the individual level. International datasets are being shared from multi-ethnic community populations, first episode and recurrent MDD, which are medication-free, in a current depressive episode with prospective longitudinal treatment outcomes and in remission. Neuroimaging data consist of de-identified, individual, structural MRI and resting-state functional MRI with additional positron emission tomography (PET) data at specific sites. State-of-the-art analytic methods include automated image processing for extraction of anatomical and functional imaging variables, statistical harmonization of imaging variables to account for site and scanner variations, and semi-supervised machine learning methods that identify dominant patterns associated with MDD from neural structure and function in healthy participants. RESULTS: We are applying an iterative process by defining the neural dimensions that characterise deeply phenotyped samples and then testing the dimensions in novel samples to assess specificity and reliability. Crucially, we aim to use machine learning methods to identify novel predictors of treatment response based on prospective longitudinal treatment outcome data, and we can externally validate the dimensions in fully independent sites. CONCLUSION: We describe the consortium, imaging protocols and analytics using preliminary results. Our findings thus far demonstrate how datasets across many sites can be harmonized and constructively pooled to enable execution of this large-scale project

EEG-based Brain-Computer Interfaces (BCIs): A Survey of Recent Studies on Signal Sensing Technologies and Computational Intelligence Approaches and Their Applications.

Brain-Computer interfaces (BCIs) enhance the capability of human brain activities to interact with the environment. Recent advancements in technology and machine learning algorithms have increased interest in electroencephalographic (EEG)-based BCI applications. EEG-based intelligent BCI systems can facilitate continuous monitoring of fluctuations in human cognitive states under monotonous tasks, which is both beneficial for people in need of healthcare support and general researchers in different domain areas. In this review, we survey the recent literature on EEG signal sensing technologies and computational intelligence approaches in BCI applications, compensating for the gaps in the systematic summary of the past five years. Specifically, we first review the current status of BCI and signal sensing technologies for collecting reliable EEG signals. Then, we demonstrate state-of-the-art computational intelligence techniques, including fuzzy models and transfer learning in machine learning and deep learning algorithms, to detect, monitor, and maintain human cognitive states and task performance in prevalent applications. Finally, we present a couple of innovative BCI-inspired healthcare applications and discuss future research directions in EEG-based BCI research

Assessing atypical brain functional connectivity development : an approach based on generative adversarial networks

Generative Adversarial Networks (GANs) are promising analytical tools in machine learning applications. Characterizing atypical neurodevelopmental processes might be useful in establishing diagnostic and prognostic biomarkers of psychiatric disorders. In this article, we investigate the potential of GANs models combined with functional connectivity (FC) measures to build a predictive neurotypicality score 3-years after scanning. We used a ROI-to-ROI analysis of resting-state functional magnetic resonance imaging (fMRI) data from a community-based cohort of children and adolescents (377 neurotypical and 126 atypical participants). Models were trained on data from neurotypical participants, capturing their sample variability of FC. The discriminator subnetwork of each GAN model discriminated between the learned neurotypical functional connectivity pattern and atypical or unrelated patterns. Discriminator models were combined in ensembles, improving discrimination performance. Explanations for the model’s predictions are provided using the LIME (Local Interpretable Model-Agnostic) algorithm and local hubs are identified in light of these explanations. Our findings suggest this approach is a promising strategy to build potential biomarkers based on functional connectivity

An Explainable Deep Learning-Based Method For Schizophrenia Diagnosis Using Generative Data-Augmentation

In this study, we leverage a deep learning-based method for the automatic diagnosis of schizophrenia using EEG brain recordings. This approach utilizes generative data augmentation, a powerful technique that enhances the accuracy of the diagnosis. To enable the utilization of time-frequency features, spectrograms were extracted from the raw signals. After exploring several neural network architectural setups, a proper convolutional neural network (CNN) was used for the initial diagnosis. Subsequently, using Wasserstein GAN with Gradient Penalty (WGAN-GP) and Variational Autoencoder (VAE), two different synthetic datasets were generated in order to augment the initial dataset and address the over-fitting issue. The augmented dataset using VAE achieved a 3.0\% improvement in accuracy reaching up to 99.0\% and yielded a lower loss value as well as a faster convergence. Finally, we addressed the lack of trust in black-box models using the Local Interpretable Model-agnostic Explanations (LIME) algorithm to determine the most important superpixels (frequencies) in the diagnosis process