A Survey on Deep Learning for Neuroimaging-based Brain Disorder Analysis

Deep learning has been recently used for the analysis of neuroimages, such as structural magnetic resonance imaging (MRI), functional MRI, and positron emission tomography (PET), and has achieved significant performance improvements over traditional machine learning in computer-aided diagnosis of brain disorders. This paper reviews the applications of deep learning methods for neuroimaging-based brain disorder analysis. We first provide a comprehensive overview of deep learning techniques and popular network architectures, by introducing various types of deep neural networks and recent developments. We then review deep learning methods for computer-aided analysis of four typical brain disorders, including Alzheimer's disease, Parkinson's disease, Autism spectrum disorder, and Schizophrenia, where the first two diseases are neurodegenerative disorders and the last two are neurodevelopmental and psychiatric disorders, respectively. More importantly, we discuss the limitations of existing studies and present possible future directions.Comment: 30 pages, 7 figure

Learning Neural Markers of Schizophrenia Disorder Using Recurrent Neural Networks

Smart systems that can accurately diagnose patients with mental disorders and identify effective treatments based on brain functional imaging data are of great applicability and are gaining much attention. Most previous machine learning studies use hand-designed features, such as functional connectivity, which does not maintain the potential useful information in the spatial relationship between brain regions and the temporal profile of the signal in each region. Here we propose a new method based on recurrent-convolutional neural networks to automatically learn useful representations from segments of 4-D fMRI recordings. Our goal is to exploit both spatial and temporal information in the functional MRI movie (at the whole-brain voxel level) for identifying patients with schizophrenia.Comment: To be published as a workshop paper at NIPS 2017 Machine Learning for Health (ML4H

Using Human Brain Activity to Guide Machine Learning

Machine learning is a field of computer science that builds algorithms that learn. In many cases, machine learning algorithms are used to recreate a human ability like adding a caption to a photo, driving a car, or playing a game. While the human brain has long served as a source of inspiration for machine learning, little effort has been made to directly use data collected from working brains as a guide for machine learning algorithms. Here we demonstrate a new paradigm of "neurally-weighted" machine learning, which takes fMRI measurements of human brain activity from subjects viewing images, and infuses these data into the training process of an object recognition learning algorithm to make it more consistent with the human brain. After training, these neurally-weighted classifiers are able to classify images without requiring any additional neural data. We show that our neural-weighting approach can lead to large performance gains when used with traditional machine vision features, as well as to significant improvements with already high-performing convolutional neural network features. The effectiveness of this approach points to a path forward for a new class of hybrid machine learning algorithms which take both inspiration and direct constraints from neuronal data.Comment: Supplemental material can be downloaded here: http://www.wjscheirer.com/misc/activity_weights/fong-et-al-supplementary.pd

Ensemble learning with 3D convolutional neural networks for connectome-based prediction

The specificty and sensitivity of resting state functional MRI (rs-fMRI) measurements depend on pre-processing choices, such as the parcellation scheme used to define regions of interest (ROIs). In this study, we critically evaluate the effect of brain parcellations on machine learning models applied to rs-fMRI data. Our experiments reveal a remarkable trend: On average, models with stochastic parcellations consistently perform as well as models with widely used atlases at the same spatial scale. We thus propose an ensemble learning strategy to combine the predictions from models trained on connectivity data extracted using different (e.g., stochastic) parcellations. We further present an implementation of our ensemble learning strategy with a novel 3D Convolutional Neural Network (CNN) approach. The proposed CNN approach takes advantage of the full-resolution 3D spatial structure of rs-fMRI data and fits non-linear predictive models. Our ensemble CNN framework overcomes the limitations of traditional machine learning models for connectomes that often rely on region-based summary statistics and/or linear models. We showcase our approach on a classification (autism patients versus healthy controls) and a regression problem (prediction of subject's age), and report promising results.Comment: 45 pages, 9 figures, 4 supplementary figures (To appear in Neuroimage

ASD-DiagNet: A hybrid learning approach for detection of Autism Spectrum Disorder using fMRI data

Mental disorders such as Autism Spectrum Disorders (ASD) are heterogeneous disorders that are notoriously difficult to diagnose, especially in children. The current psychiatric diagnostic process is based purely on the behavioural observation of symptomology (DSM-5/ICD-10) and may be prone to over-prescribing of drugs due to misdiagnosis. In order to move the field towards more quantitative fashion, we need advanced and scalable machine learning infrastructure that will allow us to identify reliable biomarkers of mental health disorders. In this paper, we propose a framework called ASD-DiagNet for classifying subjects with ASD from healthy subjects by using only fMRI data. We designed and implemented a joint learning procedure using an autoencoder and a single layer perceptron which results in improved quality of extracted features and optimized parameters for the model. Further, we designed and implemented a data augmentation strategy, based on linear interpolation on available feature vectors, that allows us to produce synthetic datasets needed for training of machine learning models. The proposed approach is evaluated on a public dataset provided by Autism Brain Imaging Data Exchange including 1035 subjects coming from 17 different brain imaging centers. Our machine learning model outperforms other state of the art methods from 13 imaging centers with increase in classification accuracy up to 20% with maximum accuracy of 80%. The machine learning technique presented in this paper, in addition to yielding better quality, gives enormous advantages in terms of execution time (40 minutes vs. 6 hours on other methods). The implemented code is available as GPL license on GitHub portal of our lab (https://github.com/pcdslab/ASD-DiagNet)

Classification of EEG-Based Brain Connectivity Networks in Schizophrenia Using a Multi-Domain Connectome Convolutional Neural Network

We exploit altered patterns in brain functional connectivity as features for automatic discriminative analysis of neuropsychiatric patients. Deep learning methods have been introduced to functional network classification only very recently for fMRI, and the proposed architectures essentially focused on a single type of connectivity measure. We propose a deep convolutional neural network (CNN) framework for classification of electroencephalogram (EEG)-derived brain connectome in schizophrenia (SZ). To capture complementary aspects of disrupted connectivity in SZ, we explore combination of various connectivity features consisting of time and frequency-domain metrics of effective connectivity based on vector autoregressive model and partial directed coherence, and complex network measures of network topology. We design a novel multi-domain connectome CNN (MDC-CNN) based on a parallel ensemble of 1D and 2D CNNs to integrate the features from various domains and dimensions using different fusion strategies. Hierarchical latent representations learned by the multiple convolutional layers from EEG connectivity reveal apparent group differences between SZ and healthy controls (HC). Results on a large resting-state EEG dataset show that the proposed CNNs significantly outperform traditional support vector machine classifiers. The MDC-CNN with combined connectivity features further improves performance over single-domain CNNs using individual features, achieving remarkable accuracy of $93.06\%$ with a decision-level fusion. The proposed MDC-CNN by integrating information from diverse brain connectivity descriptors is able to accurately discriminate SZ from HC. The new framework is potentially useful for developing diagnostic tools for SZ and other disorders.Comment: 15 pages, 9 figure

Classification of Alzheimer's Disease using fMRI Data and Deep Learning Convolutional Neural Networks

Over the past decade, machine learning techniques especially predictive modeling and pattern recognition in biomedical sciences from drug delivery system to medical imaging has become one of the important methods which are assisting researchers to have deeper understanding of entire issue and to solve complex medical problems. Deep learning is power learning machine learning algorithm in classification while extracting high-level features. In this paper, we used convolutional neural network to classify Alzheimer's brain from normal healthy brain. The importance of classifying this kind of medical data is to potentially develop a predict model or system in order to recognize the type disease from normal subjects or to estimate the stage of the disease. Classification of clinical data such as Alzheimer's disease has been always challenging and most problematic part has been always selecting the most discriminative features. Using Convolutional Neural Network (CNN) and the famous architecture LeNet-5, we successfully classified functional MRI data of Alzheimer's subjects from normal controls where the accuracy of test data on trained data reached 96.85%. This experiment suggests us the shift and scale invariant features extracted by CNN followed by deep learning classification is most powerful method to distinguish clinical data from healthy data in fMRI. This approach also enables us to expand our methodology to predict more complicated systems

3D Inception-based CNN with sMRI and MD-DTI data fusion for Alzheimer's Disease diagnostics

In the last decade, computer-aided early diagnostics of Alzheimer's Disease (AD) and its prodromal form, Mild Cognitive Impairment (MCI), has been the subject of extensive research. Some recent studies have shown promising results in the AD and MCI determination using structural and functional Magnetic Resonance Imaging (sMRI, fMRI), Positron Emission Tomography (PET) and Diffusion Tensor Imaging (DTI) modalities. Furthermore, fusion of imaging modalities in a supervised machine learning framework has shown promising direction of research. In this paper we first review major trends in automatic classification methods such as feature extraction based methods as well as deep learning approaches in medical image analysis applied to the field of Alzheimer's Disease diagnostics. Then we propose our own design of a 3D Inception-based Convolutional Neural Network (CNN) for Alzheimer's Disease diagnostics. The network is designed with an emphasis on the interior resource utilization and uses sMRI and DTI modalities fusion on hippocampal ROI. The comparison with the conventional AlexNet-based network using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset (http://adni.loni.usc.edu) demonstrates significantly better performance of the proposed 3D Inception-based CNN.Comment: arXiv admin note: substantial text overlap with arXiv:1801.0596

Robust Spatial Filtering with Graph Convolutional Neural Networks

Convolutional Neural Networks (CNNs) have recently led to incredible breakthroughs on a variety of pattern recognition problems. Banks of finite impulse response filters are learned on a hierarchy of layers, each contributing more abstract information than the previous layer. The simplicity and elegance of the convolutional filtering process makes them perfect for structured problems such as image, video, or voice, where vertices are homogeneous in the sense of number, location, and strength of neighbors. The vast majority of classification problems, for example in the pharmaceutical, homeland security, and financial domains are unstructured. As these problems are formulated into unstructured graphs, the heterogeneity of these problems, such as number of vertices, number of connections per vertex, and edge strength, cannot be tackled with standard convolutional techniques. We propose a novel neural learning framework that is capable of handling both homogeneous and heterogeneous data, while retaining the benefits of traditional CNN successes. Recently, researchers have proposed variations of CNNs that can handle graph data. In an effort to create learnable filter banks of graphs, these methods either induce constraints on the data or require preprocessing. As opposed to spectral methods, our framework, which we term Graph-CNNs, defines filters as polynomials of functions of the graph adjacency matrix. Graph-CNNs can handle both heterogeneous and homogeneous graph data, including graphs having entirely different vertex or edge sets. We perform experiments to validate the applicability of Graph-CNNs to a variety of structured and unstructured classification problems and demonstrate state-of-the-art results on document and molecule classification problems

Radiological images and machine learning: trends, perspectives, and prospects

The application of machine learning to radiological images is an increasingly active research area that is expected to grow in the next five to ten years. Recent advances in machine learning have the potential to recognize and classify complex patterns from different radiological imaging modalities such as x-rays, computed tomography, magnetic resonance imaging and positron emission tomography imaging. In many applications, machine learning based systems have shown comparable performance to human decision-making. The applications of machine learning are the key ingredients of future clinical decision making and monitoring systems. This review covers the fundamental concepts behind various machine learning techniques and their applications in several radiological imaging areas, such as medical image segmentation, brain function studies and neurological disease diagnosis, as well as computer-aided systems, image registration, and content-based image retrieval systems. Synchronistically, we will briefly discuss current challenges and future directions regarding the application of machine learning in radiological imaging. By giving insight on how take advantage of machine learning powered applications, we expect that clinicians can prevent and diagnose diseases more accurately and efficiently.Comment: 13 figure