Multiple functional connectivity networks fusion for schizophrenia diagnosis

Spatial and frequency domain-based feature fusion for accurate detection of schizophrenia using AI-driven approaches

Schizophrenia is a neuropsychiatric disorder that hampers brain functions and causes hallucinations, delusions, and bizarre behavior. The stigmatization associated with this disabling disorder drives the need to build diagnostic models with impeccable performances. Neuroimaging modality such as structural MRI is coupled with machine learning techniques to perform schizophrenia diagnosis with increased reliability. We investigate the structural aberrations present in the structural MR images using machine learning techniques. In this study, we propose a new hybrid approach using spatial and frequency domain-based features for the early automated detection of schizophrenia using machine learning techniques. The spatial or texture features are extracted using the local binary pattern method, and frequency-based features, including magnitude and phase, are extracted using the fast fourier transform feature extraction technique. Hybrid features, combining spatial and frequency-based features, are utilized for schizophrenia classification using support vector machine, random forest, and k-nearest neighbor with stratified 10-fold cross-validation. The support vector machine and random forest classifiers achieve encouraging detection performances on the hybrid feature set, with 86.5% and 85.1% accuracy, respectively. Among the three classifiers, k-nearest neighbor shows outstanding detection performance with an accuracy of 98.1%. The precision and recall achieved by the k-nearest neighbor classifier are 98.1% and 98.0% respectively, reflecting accurate detection of schizophrenia by the proposed model.

Temporal Dynamic Synchronous Functional Brain Network for Schizophrenia Classification and Lateralization Analysis

Available evidence suggests that dynamic functional connectivity can capture time-varying abnormalities in brain activity in resting-state cerebral functional magnetic resonance imaging (rs-fMRI) data and has a natural advantage in uncovering mechanisms of abnormal brain activity in schizophrenia (SZ) patients. Hence, an advanced dynamic brain network analysis model called the temporal brain category graph convolutional network (Temporal-BCGCN) was employed. Firstly, a unique dynamic brain network analysis module, DSF-BrainNet, was designed to construct dynamic synchronization features. Subsequently, a revolutionary graph convolution method, TemporalConv, was proposed based on the synchronous temporal properties of features. Finally, the first modular test tool for abnormal hemispherical lateralization in deep learning based on rs-fMRI data, named CategoryPool, was proposed. This study was validated on COBRE and UCLA datasets and achieved 83.62% and 89.71% average accuracies, respectively, outperforming the baseline model and other state-of-the-art methods. The ablation results also demonstrate the advantages of TemporalConv over the traditional edge feature graph convolution approach and the improvement of CategoryPool over the classical graph pooling approach. Interestingly, this study showed that the lower-order perceptual system and higher-order network regions in the left hemisphere are more severely dysfunctional than in the right hemisphere in SZ, reaffirmings the importance of the left medial superior frontal gyrus in SZ. Our code was available at: https://github.com/swfen/Temporal-BCGCN.

Intelligent classification of major depressive disorder using rs-fMRI of the posterior cingulate cortex

Major Depressive Disorder (MDD) is a widespread psychiatric condition that affects a significant portion of the global population. The classification and diagnosis of MDD is crucial for effective treatment. Traditional methods, based on clinical assessment, are subjective and rely on healthcare professionals' expertise. Recently, there's growing interest in using Resting-State Functional Magnetic Resonance Imaging (rs-fMRI) to objectively understand MDD's neurobiology, complementing traditional diagnostics. The posterior cingulate cortex (PCC) is a pivotal brain region implicated in MDD which could be used to identify MDD from healthy controls. Thus, this study presents an intelligent approach based on rs-fMRI data to enhance the classification of MDD. Original rs-fMRI data were collected from a cohort of 430 participants, comprising 197 patients and 233 healthy controls. Subsequently, the data underwent preprocessing using DPARSF, and the amplitudes of low-frequency fluctuation values were computed to reduce data dimensionality and feature count. Then data associated with the PCC were extracted. After eliminating redundant features, various types of Support Vector Machines (SVMs) were employed as classifiers for intelligent categorization. Ultimately, we compared the performance of each algorithm, along with its respective optimal classifier, based on classification accuracy, true positive rate, and the area under the receiver operating characteristic curve (AUC-ROC). Upon analyzing the comparison results, we determined that the Random Forest (RF) algorithm, in conjunction with a sophisticated Gaussian SVM classifier, demonstrated the highest performance. Remarkably, this combination achieved a classification accuracy of 81.9 % and a true positive rate of 92.9 %. In conclusion, our study improves the classification of MDD by supplementing traditional methods with rs-fMRI and machine learning techniques, offering deeper neurobiological insights and aiding accuracy, while emphasizing its role as an adjunct to clinical assessment.

Multitask Learning for Joint Diagnosis of Multiple Mental Disorders in Resting-State fMRI

Facing the increasing worldwide prevalence of mental disorders, the symptom-based diagnostic criteria struggle to address the urgent public health concern due to the global shortfall in well-qualified professionals. Thanks to the recent advances in neuroimaging techniques, functional magnetic resonance imaging (fMRI) has surfaced as a new solution to characterize neuropathological biomarkers for detecting functional connectivity (FC) anomalies in mental disorders. However, the existing computer-aided diagnosis models for fMRI analysis suffer from unstable performance on large datasets. To address this issue, we propose an efficient multitask learning (MTL) framework for joint diagnosis of multiple mental disorders using resting-state fMRI data. A novel multiobjective evolutionary clustering algorithm is presented to group regions of interests (ROIs) into different clusters for FC pattern analysis. On the optimal clustering solution, the multicluster multigate mixture-of-expert model is used for the final classification by capturing the highly consistent feature patterns among related diagnostic tasks. Extensive simulation experiments demonstrate that the performance of the proposed framework is superior to that of the other state-of-the-art methods. Moreover, the potential for practical application of the framework is also validated in terms of limited computational resources, real-time analysis, and insufficient training data. The proposed model can identify the remarkable interpretative biomarkers associated with specific mental disorders for clinical interpretation analysis.

Attention-Like Multimodality Fusion With Data Augmentation for Diagnosis of Mental Disorders Using MRI

The globally rising prevalence of mental disorders leads to shortfalls in timely diagnosis and therapy to reduce patients' suffering. Facing such an urgent public health problem, professional efforts based on symptom criteria are seriously overstretched. Recently, the successful applications of computer-aided diagnosis approaches have provided timely opportunities to relieve the tension in healthcare services. Particularly, multimodal representation learning gains increasing attention thanks to the high temporal and spatial resolution information extracted from neuroimaging fusion. In this work, we propose an efficient multimodality fusion framework to identify multiple mental disorders based on the combination of functional and structural magnetic resonance imaging. A multioutput conditional generative adversarial network (GAN) is developed to address the scarcity of multimodal data for augmentation. Based on the augmented training data, the multiheaded gating fusion model is proposed for classification by extracting the complementary features across different modalities. The experiments demonstrate that the proposed model can achieve robust accuracies of 75.1 ± 1.5 %, 72.9 ± 1.1 %, and 87.2 ± 1.5 % for autism spectrum disorder (ASD), attention deficit/hyperactivity disorder, and schizophrenia, respectively. In addition, the interpretability of our model is expected to enable the identification of remarkable neuropathology diagnostic biomarkers, leading to well-informed therapeutic decisions.

iDPPIV-SI: identifying dipeptidyl peptidase IV inhibitory peptides by using multiple sequence information

Currently, diabetes has become a great threaten for people's health in the world. Recent study shows that dipeptidyl peptidase IV (DPP-IV) inhibitory peptides may be a potential pharmaceutical agent to treat diabetes. Thus, there is a need to discriminate DPP-IV inhibitory peptides from non-DPP-IV inhibitory peptides. To address this issue, a novel computational model called iDPPIV-SI was developed in this study. In the first, 50 different types of physicochemical (PC) properties were employed to denote the peptide sequences. Three different feature descriptors including the 1-order, 2-order correlation methods and discrete wavelet transform were applied to collect useful information from the PC matrix. Furthermore, the least absolute shrinkage and selection operator (LASSO) algorithm was employed to select these most discriminative features. All of these chosen features were fed into support vector machine (SVM) for identifying DPP-IV inhibitory peptides. The iDPPIV-SI achieved 91.26% and 98.12% classification accuracies on the training and independent dataset, respectively. There is a significantly improvement in the classification performance by the proposed method, as compared with the state-of-the-art predictors. The datasets and MATLAB codes (based on MATLAB2015b) used in current study are available at https://figshare.com/articles/online_resource/iDPPIV-SI/20085878.Communicated by Ramaswamy H. Sarma.

Integrating Low-Order and High-Order Correlation Information for Identifying Phage Virion Proteins

Phage virion proteins (PVPs) play an important role in the host cell. Fast and accurate identification of PVPs is beneficial for the discovery and development of related drugs. Although wet experimental approaches are the first choice to identify PVPs, they are costly and time-consuming. Thus, researchers have turned their attention to computational models, which can speed up related studies. Therefore, we proposed a novel machine-learning model to identify PVPs in the current study. First, 50 different types of physicochemical properties were used to denote protein sequences. Next, two different approaches, including Pearson's correlation coefficient (PCC) and maximal information coefficient (MIC), were employed to extract discriminative information. Further, to capture the high-order correlation information, we used PCC and MIC once again. After that, we adopted the least absolute shrinkage and selection operator algorithm to select the optimal feature subset. Finally, these chosen features were fed into a support vector machine to discriminate PVPs from phage non-virion proteins. We performed experiments on two different datasets to validate the effectiveness of our proposed method. Experimental results showed a significant improvement in performance compared with state-of-the-art approaches. It indicates that the proposed computational model may become a powerful predictor in identifying PVPs.

Identification of tumor homing peptides by utilizing hybrid feature representation

Cancer is one of the serious diseases, recent studies reported that tumor homing peptides (THPs) play a key role in treatment of cancer. Due to the experimental methods are time-consuming and expensive, it is urgent to develop automatic computational approaches to identify THPs. Hence, in this study, we proposed a novel machine learning methods to distinguish THPs from non-THPs, in which the peptide sequences firstly encoded by pseudo residue pairwise energy content matrix (PseRECM) and pseudo physicochemical property (PsePC). Moreover, the least absolute shrinkage and selection operator (LAASO) was employed to select optimal features from the extracted features. All of these selected features were fed into support vector machine (SVM) for identifying THPs. We achieved 89.02%, 88.49%, and 94.58% classification accuracy on the Main, Small, and Main90 dataset, respectively. Experimental results showed that our proposed method outperforms the existing predictors on the same benchmark datasets. It indicates that the proposed method may be a useful tool in identifying THPs. The datasets and codes used in current study are available at https://figshare.com/articles/online_resource/iTHPs/16778770.Communicated by Ramaswamy H. Sarma.

m7G-DPP: Identifying N7-methylguanosine sites based on dinucleotide physicochemical properties of RNA

N7-methylguanosine (m7G) modification is one of the most common post-transcriptional RNA modifications, which play vital role in the regulation of gene expression. Dysfunction of m7G may result to developmental defects and the appearance of some serious diseases. Thus, it is an urgent task to fast and accurate identifying m7G sites. In view of experimental approaches are costly and time-consuming, researchers focused their attention on computational models. Hence, in current study, we proposed a novel predictor called m7G-DPP to identify m7G sites. In the predictor, the RNA sequences were firstly encoded by physicochemical (PC) properties of dinucleotide. Then, sliding window approach was adopted to divide PC matrix into multiple matrixes, and Pearson's correlation coefficient (PCC), dynamic time warping (DTW), and distance correlation (DC) were employed to extract classification features at each window. Next, the least absolute shrinkage and selection operator (LASSO) algorithm was applied to select discriminative features. Finally, these selected features were fed into support vector machine to identify m7G sites. Experimental results showed that the proposed method is effective, which may play a complementary role in current m7G sites prediction studies. The MATLAB codes and dataset can be obtained from website at https://figshare.com/articles/online_resource/m7G-DPP/15000348.

Brain functional connectivity analysis based on multi-graph fusion

In this paper, we propose a framework for functional connectivity network (FCN) analysis, which conducts the brain disease diagnosis on the resting state functional magnetic resonance imaging (rs-fMRI) data, aiming at reducing the influence of the noise, the inter-subject variability, and the heterogeneity across subjects. To this end, our proposed framework investigates a multi-graph fusion method to explore both the common and the complementary information between two FCNs, i.e., a fully-connected FCN and a 1 nearest neighbor (1NN) FCN, whereas previous methods only focus on conducting FCN analysis from a single FCN. Specifically, our framework first conducts the graph fusion to produce the representation of the rs-fMRI data with high discriminative ability, and then employs the L1SVM to jointly conduct brain region selection and disease diagnosis. We further evaluate the effectiveness of the proposed framework on various data sets of the neuro-diseases, i.e., Fronto-Temporal Dementia (FTD), Obsessive-Compulsive Disorder (OCD), and Alzheimers Disease (AD). The experimental results demonstrate that the proposed framework achieves the best diagnosis performance via selecting reasonable brain regions for the classification tasks, compared to state-of-the-art FCN analysis methods.