Enhancing the feature representation of multi-modal MRI data by combining multi-view information for MCI classification

Detection of mild cognitive impairment based on attention mechanism and parallel dilated convolution

Mild cognitive impairment (MCI) is a precursor to neurodegenerative diseases such as Alzheimer's disease, and an early diagnosis and intervention can delay its progression. However, the brain MRI images of MCI patients have small changes and blurry shapes. At the same time, MRI contains a large amount of redundant information, which leads to the poor performance of current MCI detection methods based on deep learning. This article proposes an MCI detection method that integrates the attention mechanism and parallel dilated convolution. By introducing an attention mechanism, it highlights the relevant information of the lesion area in the image, suppresses irrelevant areas, eliminates redundant information in MRI images, and improves the ability to mine detailed information. Parallel dilated convolution is used to obtain a larger receptive field without downsampling, thereby enhancing the ability to acquire contextual information and improving the accuracy of small target classification while maintaining detailed information on large-scale feature maps. Experimental results on the public dataset ADNI show that the detection accuracy of the method on MCI reaches 81.63%, which is approximately 6.8% higher than the basic model. The method is expected to be used in clinical practice in the future to provide earlier intervention and treatment for MCI patients, thereby improving their quality of life.

Changes in Community Structure of Brain Dynamic Functional Connectivity States in Mild Cognitive Impairment

Recent researches have noted many changes of short-term dynamic modalities in mild cognitive impairment (MCI) patients' brain functional networks. In this study, the dynamic functional brain networks of 82 MCI patients and 85 individuals in the normal control (NC) group were constructed using the sliding window method and Pearson correlation. The window size was determined using single-scale time-dependent (SSTD) method. Subsequently, k-means was applied to cluster all window samples, identifying three dynamic functional connectivity (DFC) states. Collective sparse symmetric non-negative matrix factorization (cssNMF) was then used to perform community detection on these states and quantify differences in brain regions. Finally, metrics such as within-community connectivity strength, community strength, and node diversity were calculated for further analysis. The results indicated high similarity between the two groups in state 2, with no significant differences in optimal community quantity and functional segregation (p < 0.05). However, for state 1 and state 3, the optimal community quantity was smaller in MCI patients compared to the NC group. In state 1, MCI patients had lower within-community connectivity strength and overall strength than the NC group, whereas state 3 showed results opposite to state 1. Brain regions with statistical difference included MFG.L, ORBinf.R, STG.R, IFGtriang.L, CUN.L, CUN.R, LING.R, SOG.L, and PCUN.R. This study on DFC states explores changes in the brain functional networks of patients with MCI from the perspective of alterations in the community structures of DFC states. The findings could provide new insights into the pathological changes in the brains of MCI patients.

Multi-Scale Transformer Network With Edge-Aware Pre-Training for Cross-Modality MR Image Synthesis

Cross-modality magnetic resonance (MR) image synthesis can be used to generate missing modalities from given ones. Existing (supervised learning) methods often require a large number of paired multi-modal data to train an effective synthesis model. However, it is often challenging to obtain sufficient paired data for supervised training. In reality, we often have a small number of paired data while a large number of unpaired data. To take advantage of both paired and unpaired data, in this paper, we propose a Multi-scale Transformer Network (MT-Net) with edge-aware pre-training for cross-modality MR image synthesis. Specifically, an Edge-preserving Masked AutoEncoder (Edge-MAE) is first pre-trained in a self-supervised manner to simultaneously perform 1) image imputation for randomly masked patches in each image and 2) whole edge map estimation, which effectively learns both contextual and structural information. Besides, a novel patch-wise loss is proposed to enhance the performance of Edge-MAE by treating different masked patches differently according to the difficulties of their respective imputations. Based on this proposed pre-training, in the subsequent fine-tuning stage, a Dual-scale Selective Fusion (DSF) module is designed (in our MT-Net) to synthesize missing-modality images by integrating multi-scale features extracted from the encoder of the pre-trained Edge-MAE. Furthermore, this pre-trained encoder is also employed to extract high-level features from the synthesized image and corresponding ground-truth image, which are required to be similar (consistent) in the training. Experimental results show that our MT-Net achieves comparable performance to the competing methods even using 70% of all available paired data. Our code will be released at https://github.com/lyhkevin/MT-Net.

Network-based diagnostic probability estimation from resting-state functional magnetic resonance imaging

Brain functional connectivity is a useful biomarker for diagnosing brain disorders. Connectivity is measured using resting-state functional magnetic resonance imaging (rs-fMRI). Previous studies have used a sequential application of the graphical model for network estimation and machine learning to construct predictive formulas for determining outcomes (e.g., disease or health) from the estimated network. However, the resulting network had limited utility for diagnosis because it was estimated independent of the outcome. In this study, we proposed a regression method with scores from rs-fMRI based on supervised sparse hierarchical components analysis (SSHCA). SSHCA has a hierarchical structure that consists of a network model (block scores at the individual level) and a scoring model (super scores at the population level). A regression model, such as the multiple logistic regression model with super scores as the predictor, was used to estimate diagnostic probabilities. An advantage of the proposed method was that the outcome-related (supervised) network connections and multiple scores corresponding to the sub-network estimation were helpful for interpreting the results. Our results in the simulation study and application to real data show that it is possible to predict diseases with high accuracy using the constructed model.

Brain disease research based on functional magnetic resonance imaging data and machine learning: a review

Brain diseases, including neurodegenerative diseases and neuropsychiatric diseases, have long plagued the lives of the affected populations and caused a huge burden on public health. Functional magnetic resonance imaging (fMRI) is an excellent neuroimaging technology for measuring brain activity, which provides new insight for clinicians to help diagnose brain diseases. In recent years, machine learning methods have displayed superior performance in diagnosing brain diseases compared to conventional methods, attracting great attention from researchers. This paper reviews the representative research of machine learning methods in brain disease diagnosis based on fMRI data in the recent three years, focusing on the most frequent four active brain disease studies, including Alzheimer's disease/mild cognitive impairment, autism spectrum disorders, schizophrenia, and Parkinson's disease. We summarize these 55 articles from multiple perspectives, including the effect of the size of subjects, extracted features, feature selection methods, classification models, validation methods, and corresponding accuracies. Finally, we analyze these articles and introduce future research directions to provide neuroimaging scientists and researchers in the interdisciplinary fields of computing and medicine with new ideas for AI-aided brain disease diagnosis.

MPS-FFA: A multiplane and multiscale feature fusion attention network for Alzheimer's disease prediction with structural MRI

Structural magnetic resonance imaging (sMRI) is a popular technique that is widely applied in Alzheimer's disease (AD) diagnosis. However, only a few structural atrophy areas in sMRI scans are highly associated with AD. The degree of atrophy in patients' brain tissues and the distribution of lesion areas differ among patients. Therefore, a key challenge in sMRI-based AD diagnosis is identifying discriminating atrophy features. Hence, we propose a multiplane and multiscale feature-level fusion attention (MPS-FFA) model. The model has three components, (1) A feature encoder uses a multiscale feature extractor with hybrid attention layers to simultaneously capture and fuse multiple pathological features in the sagittal, coronal, and axial planes. (2) A global attention classifier combines clinical scores and two global attention layers to evaluate the feature impact scores and balance the relative contributions of different feature blocks. (3) A feature similarity discriminator minimizes the feature similarities among heterogeneous labels to enhance the ability of the network to discriminate atrophy features. The MPS-FFA model provides improved interpretability for identifying discriminating features using feature visualization. The experimental results on the baseline sMRI scans from two databases confirm the effectiveness (e.g., accuracy and generalizability) of our method in locating pathological locations. The source code is available at https://github.com/LiuFei-AHU/MPSFFA.

Orthogonal latent space learning with feature weighting and graph learning for multimodal Alzheimer's disease diagnosis

Recent studies have shown that multimodal neuroimaging data provide complementary information of the brain and latent space-based methods have achieved promising results in fusing multimodal data for Alzheimer's disease (AD) diagnosis. However, most existing methods treat all features equally and adopt nonorthogonal projections to learn the latent space, which cannot retain enough discriminative information in the latent space. Besides, they usually preserve the relationships among subjects in the latent space based on the similarity graph constructed on original features for performance boosting. However, the noises and redundant features significantly corrupt the graph. To address these limitations, we propose an Orthogonal Latent space learning with Feature weighting and Graph learning (OLFG) model for multimodal AD diagnosis. Specifically, we map multiple modalities into a common latent space by orthogonal constrained projection to capture the discriminative information for AD diagnosis. Then, a feature weighting matrix is utilized to sort the importance of features in AD diagnosis adaptively. Besides, we devise a regularization term with learned graph to preserve the local structure of the data in the latent space and integrate the graph construction into the learning processing for accurately encoding the relationships among samples. Instead of constructing a similarity graph for each modality, we learn a joint graph for multiple modalities to capture the correlations among modalities. Finally, the representations in the latent space are projected into the target space to perform AD diagnosis. An alternating optimization algorithm with proved convergence is developed to solve the optimization objective. Extensive experimental results show the effectiveness of the proposed method.

An Ensemble Hybrid Feature Selection Method for Neuropsychiatric Disorder Classification

Magnetic resonance imagings (MRIs) are providing increased access to neuropsychiatric disorders that can be made available for advanced data analysis. However, the single type of data limits the ability of psychiatrists to distinguish the subclasses of this disease. In this paper, we propose an ensemble hybrid features selection method for the neuropsychiatric disorder classification. The method consists of a 3D DenseNet and a XGBoost, which are used to select the image features from structural MRI images and the phenotypic feature from phenotypic records, respectively. The hybrid feature is composed of image features and phenotypic features. The proposed method is validated in the Consortium for Neuropsychiatric Phenomics (CNP) dataset, where samples are classified into one of the four classes (healthy controls (HC), attention deficit hyperactivity disorder (ADHD), bipolar disorder (BD), and schizophrenia (SD)). Experimental results show that the hybrid feature can improve the performance of classification methods. The best accuracy of binary and multi-class classification can reach 91.22 and 78.62 percent, respectively. We analyze the importance of phenotypic features and image features in different classification tasks. The importance of the structure MRI images is highlighted by incorporating phenotypic features with image features to generate hybrid features. We also visualize the features of three neuropsychiatric disorders and analyze their locations in the brain region.

Prediction of Glioma Grade Using Intratumoral and Peritumoral Radiomic Features From Multiparametric MRI Images

The accurate prediction of glioma grade before surgery is essential for treatment planning and prognosis. Since the gold standard (i.e., biopsy)for grading gliomas is both highly invasive and expensive, and there is a need for a noninvasive and accurate method. In this study, we proposed a novel radiomics-based pipeline by incorporating the intratumoral and peritumoral features extracted from preoperative mpMRI scans to accurately and noninvasively predict glioma grade. To address the unclear peritumoral boundary, we designed an algorithm to capture the peritumoral region with a specified radius. The mpMRI scans of 285 patients derived from a multi-institutional study were adopted. A total of 2153 radiomic features were calculated separately from intratumoral volumes (ITVs)and peritumoral volumes (PTVs)on mpMRI scans, and then refined using LASSO and mRMR feature ranking methods. The top-ranking radiomic features were entered into the classifiers to build radiomic signatures for predicting glioma grade. The prediction performance was evaluated with five-fold cross-validation on a patient-level split. The radiomic signatures utilizing the features of ITV and PTV both show a high accuracy in predicting glioma grade, with AUCs reaching 0.968. By incorporating the features of ITV and PTV, the AUC of IPTV radiomic signature can be increased to 0.975, which outperforms the state-of-the-art methods. Additionally, our proposed method was further demonstrated to have strong generalization performance in an external validation dataset with 65 patients. The source code of our implementation is made publicly available at https://github.com/chengjianhong/glioma_grading.git.

Multi-Modal Feature Selection with Feature Correlation and Feature Structure Fusion for MCI and AD Classification

Feature selection for multiple types of data has been widely applied in mild cognitive impairment (MCI) and Alzheimer's disease (AD) classification research. Combining multi-modal data for classification can better realize the complementarity of valuable information. In order to improve the classification performance of feature selection on multi-modal data, we propose a multi-modal feature selection algorithm using feature correlation and feature structure fusion (FC2FS). First, we construct feature correlation regularization by fusing a similarity matrix between multi-modal feature nodes. Then, based on manifold learning, we employ feature matrix fusion to construct feature structure regularization, and learn the local geometric structure of the feature nodes. Finally, the two regularizations are embedded in a multi-task learning model that introduces low-rank constraint, the multi-modal features are selected, and the final features are linearly fused and input into a support vector machine (SVM) for classification. Different controlled experiments were set to verify the validity of the proposed method, which was applied to MCI and AD classification. The accuracy of normal controls versus Alzheimer's disease, normal controls versus late mild cognitive impairment, normal controls versus early mild cognitive impairment, and early mild cognitive impairment versus late mild cognitive impairment achieve 91.85 ± 1.42%, 85.33 ± 2.22%, 78.29 ± 2.20%, and 77.67 ± 1.65%, respectively. This method makes up for the shortcomings of the traditional multi-modal feature selection based on subjects and fully considers the relationship between feature nodes and the local geometric structure of feature space. Our study not only enhances the interpretation of feature selection but also improves the classification performance, which has certain reference values for the identification of MCI and AD.

Diagnosis of Alzheimer’s Disease Based on the Modified Tresnet

In the medical field, Alzheimer’s disease (AD), as a neurodegenerative brain disease which is very difficult to diagnose, can cause cognitive impairment and memory decline. Many existing works include a variety of clinical neurological and psychological examinations, especially computer-aided diagnosis (CAD) methods based on electroencephalographic (EEG) recording or MRI images by using machine learning (ML) combined with different preprocessing steps such as hippocampus shape analysis, fusion of embedded features, and so on, where EEG dataset used for AD diagnosis is usually is large and complex, requiring extraction of a series of features like entropy features, spectral feature, etc., and it has seldom been applied in the AD detection based on deep learning (DL), while MRI images were suitable for both ML and DL. In terms of the structural MRI brain images, few differences could be found in brain atrophy among the three situations: AD, mild cognitive impairment (MCI), and Normal Control (NC). On the other hand, DL methods have been used to diagnose AD incorporating MRI images in recent years, but there have not yet been many selective models with very deep layers. In this article, the Gray Matter (GM) Magnetic Resonance Imaging (MRI) is automatically extracted, which could better distinguish among the three types of situations like AD, MCI, and NC, compared with Cerebro Spinal Fluid (CSF) and White Matter (WM). Firstly, FMRIB Software Library (FSL) software is utilized for batch processing to remove the skull, cerebellum and register the heterogeneous images, and the SPM + cat12 tool kits in MATLAB is used to segment MRI images for obtaining the standard GM MRI images. Next, the GM MRI images are trained by some new neural networks. The characteristics of the training process are as follows: (1) The Tresnet, as the network that achieves the best classification effect among several new networks in the experiment, is selected as the basic network. (2) A multi-receptive-field mechanism is integrated into the network, which is inspired by neurons that can dynamically adjust the receptive fields according to different stimuli. (3) The whole network is realized by adding multiple channels to the convolutional layer, and the size of the convolution kernel of each channel can be dynamically adjusted. (4) Transfer learning method is used to train the model for speeding up the learning and optimizing the learning efficiency. Finally, we achieve the accuracies of 86.9% for AD vs. NC, 63.2% for AD vs. MCI vs. NC respectively, which outperform the previous approaches. The results demonstrate the effectiveness of our approach.

RFCell: A Gene Selection Approach for scRNA-seq Clustering Based on Permutation and Random Forest

In recent years, the application of single cell RNA-seq (scRNA-seq) has become more and more popular in fields such as biology and medical research. Analyzing scRNA-seq data can discover complex cell populations and infer single-cell trajectories in cell development. Clustering is one of the most important methods to analyze scRNA-seq data. In this paper, we focus on improving scRNA-seq clustering through gene selection, which also reduces the dimensionality of scRNA-seq data. Studies have shown that gene selection for scRNA-seq data can improve clustering accuracy. Therefore, it is important to select genes with cell type specificity. Gene selection not only helps to reduce the dimensionality of scRNA-seq data, but also can improve cell type identification in combination with clustering methods. Here, we proposed RFCell, a supervised gene selection method, which is based on permutation and random forest classification. We first use RFCell and three existing gene selection methods to select gene sets on 10 scRNA-seq data sets. Then, three classical clustering algorithms are used to cluster the cells obtained by these gene selection methods. We found that the gene selection performance of RFCell was better than other gene selection methods.

Multimodal Disentangled Variational Autoencoder with Game Theoretic Interpretability for Glioma grading

Effective fusion of multimodal magnetic resonance imaging (MRI) is of great significance to boost the accuracy of glioma grading thanks to the complementary information provided by different imaging modalities. However, how to extract the common and distinctive information from MRI to achieve complementarity is still an open problem in information fusion research. In this study, we propose a deep neural network model termed as multimodal disentangled variational autoencoder (MMD-VAE) for glioma grading based on radiomics features extracted from preoperative multimodal MRI images. Specifically, the radiomics features are quantized and extracted from the region of interest for each modality. Then, the latent representations of variational autoencoder for these features are disentangled into common and distinctive representations to obtain the shared and complementary data among modalities. Afterward, cross-modality reconstruction loss and common-distinctive loss are designed to ensure the effectiveness of the disentangled representations. Finally, the disentangled common and distinctive representations are fused to predict the glioma grades, and SHapley Additive exPlanations (SHAP) is adopted to quantitatively interpret and analyze the contribution of the important features to grading. Experimental results on two benchmark datasets demonstrate that the proposed MMD-VAE model achieves encouraging predictive performance (AUC:0.9939) on a public dataset, and good generalization performance (AUC:0.9611) on a cross-institutional private dataset. These quantitative results and interpretations may help radiologists understand gliomas better and make better treatment decisions for improving clinical outcomes.

ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets

Clustering analysis of gene expression data is essential for understanding complex biological data, and is widely used in important biological applications such as the identification of cell subpopulations and disease subtypes. In commonly used methods such as hierarchical clustering (HC) and consensus clustering (CC), holistic expression profiles of all genes are often used to assess the similarity between samples for clustering. While these methods have been proven successful in identifying sample clusters in many areas, they do not provide information about which gene sets (functions) contribute most to the clustering, thus limiting the interpretability of the resulting cluster. We hypothesize that integrating prior knowledge of annotated gene sets would not only achieve satisfactory clustering performance but also, more importantly, enable potential biological interpretation of clusters. Here we report ClusterMine, an approach that identifies clusters by assessing functional similarity between samples through integrating known annotated gene sets in functional annotation databases such as Gene Ontology. In addition to the cluster membership of each sample as provided by conventional approaches, it also outputs gene sets that most likely contribute to the clustering, thus facilitating biological interpretation. We compare ClusterMine with conventional approaches on nine real-world experimental datasets that represent different application scenarios in biology. We find that ClusterMine achieves better performances and that the gene sets prioritized by our method are biologically meaningful. ClusterMine is implemented as an R package and is freely available at: www.genemine.org/clustermine.php.

IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation

MOTIVATION

High resolution annotation of gene functions is a central goal in functional genomics. A single gene may produce multiple isoforms with different functions through alternative splicing. Conventional approaches, however, consider a gene as a single entity without differentiating these functionally different isoforms. Towards understanding gene functions at higher resolution, recent efforts have focused on predicting the functions of isoforms. However, the performance of existing methods is far from satisfactory mainly because of the lack of isoform-level functional annotation.

RESULTS

We present IsoResolve, a novel approach for isoform function prediction, which leverages the information from gene function prediction models with domain adaptation (DA). IsoResolve treats gene-level and isoform-level features as source and target domains, respectively. It uses DA to project the two domains into a latent variable space in such a way that the latent variables from the two domains have similar distribution, which enables the gene domain information to be leveraged for isoform function prediction. We systematically evaluated the performance of IsoResolve in predicting functions. Compared with five state-of-the-art methods, IsoResolve achieved significantly better performance. IsoResolve was further validated by case studies of genes with isoform-level functional annotation.

AVAILABILITY AND IMPLEMENTATION

IsoResolve is freely available at https://github.com/genemine/IsoResolve.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Diagnostic power of resting-state fMRI for detection of network connectivity in Alzheimer's disease and mild cognitive impairment: A systematic review

Resting‐state fMRI (rs‐fMRI) detects functional connectivity (FC) abnormalities that occur in the brains of patients with Alzheimer's disease (AD) and mild cognitive impairment (MCI). FC of the default mode network (DMN) is commonly impaired in AD and MCI. We conducted a systematic review aimed at determining the diagnostic power of rs‐fMRI to identify FC abnormalities in the DMN of patients with AD or MCI compared with healthy controls (HCs) using machine learning (ML) methods. Multimodal support vector machine (SVM) algorithm was the commonest form of ML method utilized. Multiple kernel approach can be utilized to aid in the classification by incorporating various discriminating features, such as FC graphs based on “nodes” and “edges” together with structural MRI‐based regional cortical thickness and gray matter volume. Other multimodal features include neuropsychiatric testing scores, DTI features, and regional cerebral blood flow. Among AD patients, the posterior cingulate cortex (PCC)/Precuneus was noted to be a highly affected hub of the DMN that demonstrated overall reduced FC. Whereas reduced DMN FC between the PCC and anterior cingulate cortex (ACC) was observed in MCI patients. Evidence indicates that the nodes of the DMN can offer moderate to high diagnostic power to distinguish AD and MCI patients. Nevertheless, various concerns over the homogeneity of data based on patient selection, scanner effects, and the variable usage of classifiers and algorithms pose a challenge for ML‐based image interpretation of rs‐fMRI datasets to become a mainstream option for diagnosing AD and predicting the conversion of HC/MCI to AD.

Improving Loanword Identification in Low-Resource Language with Data Augmentation and Multiple Feature Fusion

Loanword identification is studied in recent years to alleviate data sparseness in several natural language processing (NLP) tasks, such as machine translation, cross-lingual information retrieval, and so on. However, recent studies on this topic usually put efforts on high-resource languages (such as Chinese, English, and Russian); for low-resource languages, such as Uyghur and Mongolian, due to the limitation of resources and lack of annotated data, loanword identification on these languages tends to have lower performance. To overcome this problem, we first propose a lexical constraint-based data augmentation method to generate training data for low-resource language loanword identification; then, a loanword identification model based on a log-linear RNN is introduced to improve the performance of low-resource loanword identification by incorporating features such as word-level embeddings, character-level embeddings, pronunciation similarity, and part-of-speech (POS) into one model. Experimental results on loanword identification in Uyghur (in this study, we mainly focus on Arabic, Chinese, Russian, and Turkish loanwords in Uyghur) showed that our proposed method achieves best performance compared with several strong baseline systems.

Diagnosis of Mild Cognitive Impairment Using Cognitive Tasks: A Functional Near-Infrared Spectroscopy Study

BACKGROUND

Early diagnosis of Alzheimer's disease (AD) is essential in preventing its progression to dementia. Mild cognitive impairment (MCI) can be indicative of early-stage AD. In this study, we propose a channel-wise feature extraction method of functional near-infrared spectroscopy (fNIRS) data to diagnose MCI when performing cognitive tasks, including two-back, Stroop, and semantic verbal fluency tasks (SVFT).

METHODS

A new channel-wise feature extraction method is proposed as follows: A region-of-interest (ROI) channel is defined as such channel having a statistical difference (p < 0.05) in t-values between two groups. For each ROI channel, features (the mean, slope, skewness, kurtosis, and peak value of oxy- and deoxy-hemoglobin) are extracted. The extracted features for the two classes (MCI, HC) are classified using the linear discriminant analysis (LDA) and support vector machine (SVM). Finally, the classifiers are validated using the area under curve (AUC) of the receiver operating characteristics. Furthermore, the suggested feature extraction method is compared with the conventional approach. Fifteen MCI patients and fifteen healthy controls (HCs) participated in the study.

RESULTS

In the two-back and Stroop tasks, HCs showed activation in the ventrolateral prefrontal cortex (VLPFC). However, in the case of MCI, the VLPFC was not activated. Instead, Ch. 30 was activated. In the SVFT task, the PFC was activated in both groups, but the t-values of HCs were higher than those of MCI. For the SVFT, the classification accuracies using the proposed feature extraction method were 80.77% (LDA) and 83.33% (SVM), showing the highest among the three tasks; for the Stroop task, 79.49% (LDA) and 73.08% (SVM); and for the two-back task, 73.08% (LDA) and 69.23% (SVM).

CONCLUSION

The cognitive disparities between the MCI and HC groups were detected in the ventrolateral prefrontal cortex using fNIRS. The proposed feature extraction method has shown an improvement in the classification accuracies, see Subsection 3.3. Most of all, the suggested method contains a groupdistinction information per cognitive task. The obtained results successfully discriminated MCI patients from HCs, which reflects that the proposed method is an efficient tool to extract features in fNIRS signals.

Wilson disease tissue classification and characterization using seven artificial intelligence models embedded with 3D optimization paradigm on a weak training brain magnetic resonance imaging datasets: a supercomputer application

Wilson's disease (WD) is caused by copper accumulation in the brain and liver, and if not treated early, can lead to severe disability and death. WD has shown white matter hyperintensity (WMH) in the brain magnetic resonance scans (MRI) scans, but the diagnosis is challenging due to (i) subtle intensity changes and (ii) weak training MRI when using artificial intelligence (AI). Design and validate seven types of high-performing AI-based computer-aided design (CADx) systems consisting of 3D optimized classification, and characterization of WD against controls. We propose a "conventional deep convolution neural network" (cDCNN) and an "improved DCNN" (iDCNN) where rectified linear unit (ReLU) activation function was modified ensuring "differentiable at zero." Three-dimensional optimization was achieved by recording accuracy while changing the CNN layers and augmentation by several folds. WD was characterized using (i) CNN-based feature map strength and (ii) Bispectrum strengths of pixels having higher probabilities of WD. We further computed the (a) area under the curve (AUC), (b) diagnostic odds ratio (DOR), (c) reliability, and (d) stability and (e) benchmarking. Optimal results were achieved using 9 layers of CNN, with 4-fold augmentation. iDCNN yields superior performance compared to cDCNN with accuracy and AUC of 98.28 ± 1.55, 0.99 (p < 0.0001), and 97.19 ± 2.53%, 0.984 (p < 0.0001), respectively. DOR of iDCNN outperformed cDCNN fourfold. iDCNN also outperformed (a) transfer learning-based "Inception V3" paradigm by 11.92% and (b) four types of "conventional machine learning-based systems": k-NN, decision tree, support vector machine, and random forest by 55.13%, 28.36%, 15.35%, and 14.11%, respectively. The AI-based systems can potentially be useful in the early WD diagnosis. Graphical Abstract.

Gray Matter Deterioration Pattern During Alzheimer's Disease Progression: A Regions-of-Interest Based Surface Morphometry Study

Accurate detection of the regions of Alzheimer's disease (AD) lesions is critical for early intervention to effectively slow down the progression of the disease. Although gray matter volumetric abnormalities are commonly detected in patients with mild cognition impairment (MCI) and patients with AD, the gray matter surface-based deterioration pattern associated with the progression of the disease from MCI to AD stages is largely unknown. To identify group differences in gray matter surface morphometry, including cortical thickness, the gyrification index (GI), and the sulcus depth, 80 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database were split into healthy controls (HCs; N = 20), early MCIs (EMCI; N = 20), late MCIs (LMCI; N = 20), and ADs (N = 20). Regions-of-interest (ROI)-based surface morphometry was subsequently studied and compared across the four stage groups to characterize the gray matter deterioration during AD progression. Co-alteration patterns (Spearman's correlation coefficient) across the whole brain were also examined. Results showed that patients with MCI and AD exhibited a significant reduction in cortical thickness (p < 0.001) mainly in the cingulate region (four subregions) and in the temporal (thirteen subregions), parietal (five subregions), and frontal (six subregions) lobes compared to HCs. The sulcus depth of the eight temporal, four frontal, four occipital, and eight parietal subregions were also significantly affected (p < 0.001) by the progression of AD. The GI was shown to be insensitive to AD progression (only three subregions were detected with a significant difference, p < 0.001). Moreover, Spearman's correlation analysis confirmed that the co-alteration pattern of the cortical thickness and sulcus depth indices is predominant during AD progression. The findings highlight the relevance between gray matter surface morphometry and the stages of AD, laying the foundation for in vivo tracking of AD progression. The co-alteration pattern of surface-based morphometry would improve the researchers' knowledge of the underlying pathologic mechanisms in AD.

Multi-View Based Multi-Model Learning for MCI Diagnosis

Mild cognitive impairment (MCI) is the early stage of Alzheimer’s disease (AD). Automatic diagnosis of MCI by magnetic resonance imaging (MRI) images has been the focus of research in recent years. Furthermore, deep learning models based on 2D view and 3D view have been widely used in the diagnosis of MCI. The deep learning architecture can capture anatomical changes in the brain from MRI scans to extract the underlying features of brain disease. In this paper, we propose a multi-view based multi-model (MVMM) learning framework, which effectively combines the local information of 2D images with the global information of 3D images. First, we select some 2D slices from MRI images and extract the features representing 2D local information. Then, we combine them with the features representing 3D global information learned from 3D images to train the MVMM learning framework. We evaluate our model on the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. The experimental results show that our proposed model can effectively recognize MCI through MRI images (accuracy of 87.50% for MCI/HC and accuracy of 83.18% for MCI/AD).