Classification of Schizophrenia Based on Individual Hierarchical Brain Networks Constructed From Structural MRI Images

An ensemble approach using multidimensional convolutional neural networks in wavelet domain for schizophrenia classification from sMRI data

Schizophrenia is a complicated mental condition marked by disruptions in thought processes, perceptions, and emotional responses, which can cause severe impairment in everyday functioning. sMRI is a non-invasive neuroimaging technology that visualizes the brain's structure while providing precise information on its anatomy and potential problems. This paper investigates the role of multidimensional Convolutional Neural Network (CNN) architectures: 1D-CNN, 2D-CNN and 3D-CNN, using the DWT subbands of sMRI data. 1D-CNN involves energy features extracted from the CD subband of sMRI data. The sum of gradient magnitudes of CD subband, known as energy feature, highlights diagonal high frequency elements associated with schizophrenia. 2D-CNN uses the CH subband decomposed by DWT that enables feature extraction from horizontal high frequency coefficients of sMRI data. In the case of 3D-CNNs, the CV subband is used which leads to volumetric feature extraction from vertical high frequency coefficients. Feature extraction in DWT domain explores textural changes, edges, coarse and fine details present in sMRI data from which the multidimensional feature extraction is carried out for classification.Through maximum voting technique, the proposed model optimizes schizophrenia classification from the multidimensional CNN models. The generalization of the proposed model for the two datasets proves convincing in improving the classification accuracy. The multidimensional CNN architectures achieve an average accuracy of 93.2%, 95.8%, and 98.0%, respectively, while the proposed model achieves an average accuracy of 98.9%.

Magnetic resonance imaging-based machine learning classification of schizophrenia spectrum disorders: a meta-analysis

BACKGROUND

Recent advances in multivariate pattern recognition have fostered the search for reliable neuroimaging-based biomarkers in psychiatric conditions, including schizophrenia. These approaches consider the complex pattern of alterations in brain function and structure, overcoming the limitations of traditional univariate methods. To assess the reliability of neuroimaging-based biomarkers and the contribution of study characteristics in distinguishing individuals with schizophrenia spectrum disorder (SSD) from healthy controls (HCs), we conducted a systematic review of the studies that used multivariate pattern recognition for this objective.

METHODS

We systematically searched PubMed, Scopus, and Web of Science for studies on SSD classification using multivariate pattern analysis on magnetic resonance imaging data. We employed a bivariate random-effects meta-analytic model to explore the classification of sensitivity (SE) and specificity (SP) across studies while also evaluating the moderator effects of clinical and non-clinical variables.

RESULTS

A total of 119 studies (with 12,723 patients with SSD and 13,196 HCs) were identified. The meta-analysis estimated a SE of 79.1% (95% confidence interval [CI], 77.1%-81.0%) and a SP of 80.0% (95% CI, 77.8%-82.0%). In particular, the Positive and Negative Syndrome Scale and the Global Assessment of Functioning scores, age, age of onset, duration of untreated psychosis, deep learning, algorithm type, features selection, and validation methods had significant effects on classification performance.

CONCLUSIONS

Multivariate pattern analysis reliably identifies neuroimaging-based biomarkers of SSD, achieving ∼80% SE and SP. Despite clinical heterogeneity, discernible brain modifications effectively differentiate SSD from HCs. Classification performance depends on patient-related and methodological factors crucial for the development, validation, and application of prospective models in clinical settings.

Classification of Schizophrenia using Intrinsic Connectivity Networks and Incremental Boosting Convolution Neural Networks

One of the key challenges in the use of resting brain functional magnetic resonance imaging (fMRI) network analysis for predicting mental illnesses such as schizophrenia (SZ) is the high noise levels variability among individuals including age, sex, and different protocols used in labs. To deal with these challenging problems, we designed a recognition method for using brain functional networks to classify SZs and healthy controls (HCs). Our method includes two stages of training. In the first stage, we use a deep convolutional neural network (DCNN) to extract valuable deep features from functional network connectivity (FNC) images. In the next stage, these deep features are used as inputs to a gradient-boosting trees classifier. After the training process, the boosting trees classifier gains a remarkable performance compared to the DCNN classifier. We evaluate this approach using a large dataset of schizophrenia and healthy controls divided into separate validation and training sets. Experimental results showed that the recognition accuracy is over 98 %, compared to a support vector machine baseline of 77% demonstrating the ability of our system to distinguish differences between the two groups. We also estimate heatmaps for each FNC image, representing a 2D FNC matrix indicated which pairs of networks are most predictive of SZ. Our method thus provides both high accuracy, and provides insights into the relevant brain regions for SZ.

Connectome-based schizophrenia prediction using structural connectivity - Deep Graph Neural Network(sc-DGNN)

BACKGROUND

Connectome is understanding the complex organization of the human brain's structural and functional connectivity is essential for gaining insights into cognitive processes and disorders.

OBJECTIVE

To improve the prediction accuracy of brain disorder issues, the current study investigates dysconnected subnetworks and graph structures associated with schizophrenia.

METHOD

By using the proposed structural connectivity-deep graph neural network (sc-DGNN) model and compared with machine learning (ML) and deep learning (DL) models.This work attempts to focus on eighty-eight subjects of diffusion magnetic resonance imaging (dMRI), three classical ML, and five DL models.

RESULT

The structural connectivity-deep graph neural network (sc-DGNN) model is proposed to effectively predict dysconnectedness associated with schizophrenia and exhibits superior performance compared to traditional ML and DL (GNNs) methods in terms of accuracy, sensitivity, specificity, precision, F1-score, and Area under receiver operating characteristic (AUC).

CONCLUSION

The classification task on schizophrenia using structural connectivity matrices and experimental results showed that linear discriminant analysis (LDA) performed 72% accuracy rate in ML models and sc-DGNN performed at a 93% accuracy rate in DL models to distinguish between schizophrenia and healthy patients.

Constructing the Schizophrenia Recognition Method Employing GLCM Features from Multiple Brain Regions and Machine Learning Techniques

Accurately diagnosing schizophrenia, a complex psychiatric disorder, is crucial for effectively managing the treatment process and methods. Various types of magnetic resonance (MR) images have the potential to serve as biomarkers for schizophrenia. The aim of this study is to numerically analyze differences in the textural characteristics that may occur in the bilateral amygdala, caudate, pallidum, putamen, and thalamus regions of the brain between individuals with schizophrenia and healthy controls via structural MR images. Towards this aim, Gray Level Co-occurence Matrix (GLCM) features obtained from five regions of the right, left, and bilateral brain were classified using machine learning methods. In addition, it was analyzed in which hemisphere these features were more distinctive and which method among Adaboost, Gradient Boost, eXtreme Gradient Boosting, Random Forest, k-Nearest Neighbors, Linear Discriminant Analysis (LDA), and Naive Bayes had higher classification success. When the results were examined, it was demonstrated that the GLCM features of these five regions in the left hemisphere could be classified as having higher performance in schizophrenia compared to healthy individuals. Using the LDA algorithm, classification success was achieved with a 100% AUC, 94.4% accuracy, 92.31% sensitivity, 100% specificity, and an F1 score of 91.9% in healthy and schizophrenic individuals. Thus, it has been revealed that the textural characteristics of the five predetermined regions, instead of the whole brain, are an important indicator in identifying schizophrenia.

Estimating uncertainty in read-out patterns: Application to controls-based denoising and voxel-based morphometry patterns in neurodegenerative and neuropsychiatric diseases

Quantifying pathology-related patterns in patient data with pattern expression score (PES) is a standard approach in medical image analysis. In order to estimate the PES error, we here propose to express the uncertainty contained in read-out patterns in terms of the expected squared Euclidean distance between the read-out pattern and the unknown "true" pattern (squared standard error of the read-out pattern, SE2 ). Using SE2 , we predicted and optimized the net benefit (NBe) of the recently suggested method controls-based denoising (CODE) by weighting patterns of nonpathological variance (NPV). Multi-center MRI (1192 patients with various neurodegenerative and neuropsychiatric diseases, 1832 healthy controls) were analysed with voxel-based morphometry. For each pathology, accounting for SE2 , NBe correctly predicted classification improvement and allowed to optimize NPV pattern weights. Using these weights, CODE improved classification performances in all but one analyses, for example, for prediction of conversion to Alzheimer's disease (AUC 0.81 vs. 0.75, p = .01), diagnosis of autism (AUC 0.66 vs. 0.60, p < .001), and of major depressive disorder (AUC 0.62 vs. 0.50, p = .03). We conclude that the degree of uncertainty in a read-out pattern should generally be reported in PES-based analyses and suggest using weighted CODE as a complement to PES-based analyses.

Diagnosis of Schizophrenia Based on Deep Learning Using fMRI

Schizophrenia is a brain disease that frequently occurs in young people. Early diagnosis and treatment can reduce family burdens and reduce social costs. There is no objective evaluation index for schizophrenia. In order to improve the classification effect of traditional classification methods on magnetic resonance data, a method of classification of functional magnetic resonance imaging data is proposed in conjunction with the convolutional neural network algorithm. We take functional magnetic resonance imaging (fMRI) data for schizophrenia as an example, to extract effective time series from preprocessed fMRI data, and perform correlation analysis on regions of interest, using transfer learning and VGG16 net, and the functional connection between schizophrenia and healthy controls is classified. Experimental results show that the classification accuracy of fMRI based on VGG16 is up to 84.3%. On the one hand, it can improve the early diagnosis of schizophrenia, and on the other hand, it can solve the classification problem of small samples and high-dimensional data and effectively improve the generalization ability of deep learning models.

Multi-modal neuroimaging feature fusion via 3D Convolutional Neural Network architecture for schizophrenia diagnosis

Early and precise diagnosis of schizophrenia disorder (SZ) has an essential role in the quality of a patient’s life and future treatments. Structural and functional neuroimaging provides robust biomarkers for understanding the anatomical and functional changes associated with SZ. Each of the neuroimaging techniques shows only a different perspective on the functional or structural of the brain, while multi-modal fusion can reveal latent connections in the brain. In this paper, we propose an approach for the fusion of structural and functional brain data with a deep learning-based model to take advantage of data fusion and increase the accuracy of schizophrenia disorder diagnosis. The proposed method consists of an architecture of 3D convolutional neural networks (CNNs) that applied to magnetic resonance imaging (MRI), functional magnetic resonance imaging (fMRI), and diffusion tensor imaging (DTI) extracted features. We use 3D MRI patches, fMRI spatial independent component analysis (ICA) map, and DTI fractional anisotropy (FA) as model inputs. Our method is validated on the COBRE dataset, and an average accuracy of 99.35% is obtained. The proposed method demonstrates promising classification performance and can be applied to real data.

Two-Dimensional Stockwell Transform and Deep Convolutional Neural Network for Multi-Class Diagnosis of Pathological Brain

Since the brain lesion detection and classification is a vital diagnosis task, in this paper, the problem of brain magnetic resonance imaging (MRI) classification is investigated. Recent advantages in machine learning and deep learning allows the researchers to develop the robust computer-aided diagnosis (CAD) tools for classification of brain lesions. Feature extraction is an essential step in any machine learning scheme. Time-frequency analysis methods provide localized information that makes them more attractive for image classification applications. Owing to the advantages of two-dimensional discrete orthonormal Stockwell transform (2D DOST), we propose to use it to extract the efficient features from brain MRIs and obtain the feature matrix. Since there are some irrelevant features, two-directional two-dimensional principal component analysis ((2D)₂PCA) is used to reduce the dimension of the feature matrix. Finally, convolution neural networks (CNNs) are designed and trained for MRI classification. Simulation results indicate that the proposed CAD tool outperforms the recently introduced ones and can efficiently diagnose the MRI scans.

Identification of early mild cognitive impairment using multi-modal data and graph convolutional networks

BACKGROUND

The identification of early mild cognitive impairment (EMCI), which is an early stage of Alzheimer's disease (AD) and is associated with brain structural and functional changes, is still a challenging task. Recent studies show great promises for improving the performance of EMCI identification by combining multiple structural and functional features, such as grey matter volume and shortest path length. However, extracting which features and how to combine multiple features to improve the performance of EMCI identification have always been a challenging problem. To address this problem, in this study we propose a new EMCI identification framework using multi-modal data and graph convolutional networks (GCNs). Firstly, we extract grey matter volume and shortest path length of each brain region based on automated anatomical labeling (AAL) atlas as feature representation from T1w MRI and rs-fMRI data of each subject, respectively. Then, in order to obtain features that are more helpful in identifying EMCI, a common multi-task feature selection method is applied. Afterwards, we construct a non-fully labelled subject graph using imaging and non-imaging phenotypic measures of each subject. Finally, a GCN model is adopted to perform the EMCI identification task.

RESULTS

Our proposed EMCI identification method is evaluated on 210 subjects, including 105 subjects with EMCI and 105 normal controls (NCs), with both T1w MRI and rs-fMRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Experimental results show that our proposed framework achieves an accuracy of 84.1% and an area under the receiver operating characteristic (ROC) curve (AUC) of 0.856 for EMCI/NC classification. In addition, by comparison, the accuracy and AUC values of our proposed framework are better than those of some existing methods in EMCI identification.

CONCLUSION

Our proposed EMCI identification framework is effective and promising for automatic diagnosis of EMCI in clinical practice.

Towards a brain-based predictome of mental illness

Neuroimaging-based approaches have been extensively applied to study mental illness in recent years and have deepened our understanding of both cognitively healthy and disordered brain structure and function. Recent advancements in machine learning techniques have shown promising outcomes for individualized prediction and characterization of patients with psychiatric disorders. Studies have utilized features from a variety of neuroimaging modalities, including structural, functional, and diffusion magnetic resonance imaging data, as well as jointly estimated features from multiple modalities, to assess patients with heterogeneous mental disorders, such as schizophrenia and autism. We use the term "predictome" to describe the use of multivariate brain network features from one or more neuroimaging modalities to predict mental illness. In the predictome, multiple brain network-based features (either from the same modality or multiple modalities) are incorporated into a predictive model to jointly estimate features that are unique to a disorder and predict subjects accordingly. To date, more than 650 studies have been published on subject-level prediction focusing on psychiatric disorders. We have surveyed about 250 studies including schizophrenia, major depression, bipolar disorder, autism spectrum disorder, attention-deficit hyperactivity disorder, obsessive-compulsive disorder, social anxiety disorder, posttraumatic stress disorder, and substance dependence. In this review, we present a comprehensive review of recent neuroimaging-based predictomic approaches, current trends, and common shortcomings and share our vision for future directions.

AIMAFE: Autism spectrum disorder identification with multi-atlas deep feature representation and ensemble learning

BACKGROUND

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that could cause problems in social communications. Clinically, diagnosing ASD mainly relies on behavioral criteria while this approach is not objective enough and could cause delayed diagnosis. Since functional magnetic resonance imaging (fMRI) can measure brain activity, it provides data for the study of brain dysfunction disorders and has been widely used in ASD identification. However, satisfactory accuracy for ASD identification has not been achieved.

NEW METHOD

To improve the performance of ASD identification, we propose an ASD identification method based on multi-atlas deep feature representation and ensemble learning. We first calculate multiple functional connectivity based on different brain atlases from fMRI data of each subject. Then, to get the more discriminative features for ASD identification, we propose a multi-atlas deep feature representation method based on stacked denoising autoencoder (SDA). Finally, we propose multilayer perceptron (MLP) and an ensemble learning method to perform the final ASD identification task.

RESULTS

Our proposed method is evaluated on 949 subjects (including 419 ASDs and 530 typical control (TCs)) from the Autism Brain Imaging Data Exchange (ABIDE) and achieves accuracy of 74.52% (sensitivity of 80.69%, specificity of 66.71%, AUC of 0.8026) for ASD identification.

COMPARISON WITH EXISTING METHODS

Compared with some previously published methods, our proposed method obtains the better performance for ASD identification.

CONCLUSION

The results suggest that our proposed method is efficient to improve the performance of ASD identification, and is promising for ASD clinical diagnosis.

Stratifying patients using fast multiple kernel learning framework: case studies of Alzheimer's disease and cancers

BACKGROUND

Predictive patient stratification is greatly emerging, because it allows us to prospectively identify which patients will benefit from what interventions before their condition worsens. In the biomedical research, a number of stratification methods have been successfully applied and have assisted treatment process. Because of heterogeneity and complexity of medical data, it is very challenging to integrate them and make use of them in practical clinic. There are two major challenges of data integration. Firstly, since the biomedical data has a high number of dimensions, combining multiple data leads to the hard problem of vast dimensional space handling. The computation is enormously complex and time-consuming. Secondly, the disparity of different data types causes another critical problem in machine learning for biomedical data. It has a great need to develop an efficient machine learning framework to handle the challenges.

METHODS

In this paper, we propose a fast-multiple kernel learning framework, referred to as fMKL-DR, that optimise equations to calculate matrix chain multiplication and reduce dimensions in data space. We applied our framework to two case studies, Alzheimer's disease (AD) patient stratification and cancer patient stratification. We performed several comparative evaluations on various biomedical datasets.

RESULTS

In the case study of AD patients, we enhanced significantly the multiple-ROIs approach based on MRI image data. The method could successfully classify not only AD patients and non-AD patients but also different phases of AD patients with AUC close to 1. In the case study of cancer patients, the framework was applied to six types of cancers, i.e., glioblastoma multiforme cancer, ovarian cancer, lung cancer, breast cancer, kidney cancer, and liver cancer. We efficiently integrated gene expression, miRNA expression, and DNA methylation. The results showed that the classification model basing on integrated datasets was much more accurate than classification model basing on the single data type.

CONCLUSIONS

The results demonstrated that the fMKL-DR remarkably improves computational cost and accuracy for both AD patient and cancer patient stratification. We optimised the data integration, dimension reduction, and kernel fusion. Our framework has great potential for mining large-scale cohort data and aiding personalised prevention.

Brain MRI analysis using a deep learning based evolutionary approach

Convolutional neural network (CNN) models have recently demonstrated impressive performance in medical image analysis. However, there is no clear understanding of why they perform so well, or what they have learned. In this paper, a three-dimensional convolutional neural network (3D-CNN) is employed to classify brain MRI scans into two predefined groups. In addition, a genetic algorithm based brain masking (GABM) method is proposed as a visualization technique that provides new insights into the function of the 3D-CNN. The proposed GABM method consists of two main steps. In the first step, a set of brain MRI scans is used to train the 3D-CNN. In the second step, a genetic algorithm (GA) is applied to discover knowledgeable brain regions in the MRI scans. The knowledgeable regions are those areas of the brain which the 3D-CNN has mostly used to extract important and discriminative features from them. For applying GA on the brain MRI scans, a new chromosome encoding approach is proposed. The proposed framework has been evaluated using ADNI (including 140 subjects for Alzheimer's disease classification) and ABIDE (including 1000 subjects for Autism classification) brain MRI datasets. Experimental results show a 5-fold classification accuracy of 0.85 for the ADNI dataset and 0.70 for the ABIDE dataset. The proposed GABM method has extracted 6 to 65 knowledgeable brain regions in ADNI dataset (and 15 to 75 knowledgeable brain regions in ABIDE dataset). These regions are interpreted as the segments of the brain which are mostly used by the 3D-CNN to extract features for brain disease classification. Experimental results show that besides the model interpretability, the proposed GABM method has increased final performance of the classification model in some cases with respect to model parameters.

Schizophrenia Identification Using Multi-View Graph Measures of Functional Brain Networks

Schizophrenia (SZ) is a functional mental disorder that seriously affects the social life of patients. Therefore, accurate diagnosis of SZ has raised extensive attention of researchers. At present, study of brain network based on resting-state functional magnetic resonance imaging (rs-fMRI) has provided promising results for SZ identification by studying functional network alteration. However, previous studies based on brain network analysis are not very effective for SZ identification. Therefore, we propose an improved SZ identification method using multi-view graph measures of functional brain networks. Firstly, we construct an individual functional connectivity network based on Brainnetome atlas for each subject. Then, multi-view graph measures are calculated by the brain network analysis method as feature representations. Next, in order to consider the relationships between measures within the same brain region in feature selection, multi-view measures are grouped according to the corresponding regions and Sparse Group Lasso is applied to identify discriminative features based on this feature grouping structure. Finally, a support vector machine (SVM) classifier is employed to perform SZ identification task. To evaluate our proposed method, computational experiments are conducted on 145 subjects (71 schizophrenic patients and 74 healthy controls) using a leave-one-out cross-validation (LOOCV) scheme. The results show that our proposed method can obtain an accuracy of 93.10% for SZ identification. By comparison, our method is more effective for SZ identification than some existing methods.

Integrating machining learning and multimodal neuroimaging to detect schizophrenia at the level of the individual

Schizophrenia is a severe psychiatric disorder associated with both structural and functional brain abnormalities. In the past few years, there has been growing interest in the application of machine learning techniques to neuroimaging data for the diagnostic and prognostic assessment of this disorder. However, the vast majority of studies published so far have used either structural or functional neuroimaging data, without accounting for the multimodal nature of the disorder. Structural MRI and resting‐state functional MRI data were acquired from a total of 295 patients with schizophrenia and 452 healthy controls at five research centers. We extracted features from the data including gray matter volume, white matter volume, amplitude of low‐frequency fluctuation, regional homogeneity and two connectome‐wide based metrics: structural covariance matrices and functional connectivity matrices. A support vector machine classifier was trained on each dataset separately to distinguish the subjects at individual level using each of the single feature as well as their combination, and 10‐fold cross‐validation was used to assess the performance of the model. Functional data allow higher accuracy of classification than structural data (mean 82.75% vs. 75.84%). Within each modality, the combination of images and matrices improves performance, resulting in mean accuracies of 81.63% for structural data and 87.59% for functional data. The use of all combined structural and functional measures allows the highest accuracy of classification (90.83%). We conclude that combining multimodal measures within a single model is a promising direction for developing biologically informed diagnostic tools in schizophrenia.

Brain Connectivity Based Prediction of Alzheimer's Disease in Patients With Mild Cognitive Impairment Based on Multi-Modal Images

Structural and metabolic connectivity are advanced features that facilitate the diagnosis of patients with Alzheimer’s disease (AD) and mild cognitive impairment (MCI). Connectivity from a single imaging modality, however, did not show evident discriminative value in predicting MCI-to-AD conversion, possibly because the inter-modal information was not considered when quantifying the relationship between brain regions. Here we introduce a novel approach that extracts connectivity based on both structural and metabolic information to improve AD early diagnosis. Principal component analysis was performed on each imaging modality to extract the key discriminative patterns of each brain region in an independent auxiliary domain composed of AD and normal control (NC) subjects, which were then used to project the two subtypes of MCI to the low-dimensional space. The connectivity between each target brain region and all other regions was quantified via a multi-task regression model using the projected data. The prediction performance was evaluated in 75 stable MCI (sMCI) patients and 51 progressive MCI (pMCI) patients who converted to AD within 3 years. We achieved 79.37% accuracy, with 74.51% sensitivity and 82.67% specificity, in predicting MCI-to-AD progression, superior to other existing algorithms using either structural and metabolic connectivities alone or a combination thereof. Our results demonstrate the effectiveness of multi-modal connectivity, serving as robust biomarker for early AD diagnosis.

An Amyloid-β Targeting Chemical Exchange Saturation Transfer Probe for In Vivo Detection of Alzheimer's Disease

A reliable and reproducible detection of Aβ deposits would be beneficial for the early diagnosis of Alzheimer's disease (AD). In the present study, the feasibility of applying chemical exchange saturation transfer (CEST) for Aβ deposit detection using angiopep-2 as a probe was evaluated, and it was demonstrated that CEST could detect angiopep-2 and Aβ-angiopep-2 aggregates in vitro. Furthermore, APP/PS1 mice injected with angiopep-2 exhibited a significantly higher in vivo CEST effect when compared with controls. The distribution of Aβ deposits detected by CEST imaging was consistent with the histological staining results. The present study is the first to report a reliable exogenous CEST probe to noninvasively evaluate Aβ deposits in APP/PS1 mice. Furthermore, these results demonstrate the potential for clinical AD diagnosis and Aβ-targeted drug therapy assessment using CEST imaging with the angiopep-2 probe.