IHGC-GAN: influence hypergraph convolutional generative adversarial network for risk prediction of late mild cognitive impairment based on imaging genetic data.

Predicting disease progression in the initial stage to implement early intervention and treatment can effectively prevent the further deterioration of the condition. Traditional methods for medical data analysis usually fail to perform well because of their incapability for mining the correlation pattern of pathogenies. Therefore, many calculation methods have been excavated from the field of deep learning. In this study, we propose a novel method of influence hypergraph convolutional generative adversarial network (IHGC-GAN) for disease risk prediction. First, a hypergraph is constructed with genes and brain regions as nodes. Then, an influence transmission model is built to portray the associations between nodes and the transmission rule of disease information. Third, an IHGC-GAN method is constructed based on this model. This method innovatively combines the graph convolutional network (GCN) and GAN. The GCN is used as the generator in GAN to spread and update the lesion information of nodes in the brain region-gene hypergraph. Finally, the prediction accuracy of the method is improved by the mutual competition and repeated iteration between generator and discriminator. This method can not only capture the evolutionary pattern from early mild cognitive impairment (EMCI) to late MCI (LMCI) but also extract the pathogenic factors and predict the deterioration risk from EMCI to LMCI. The results on the two datasets indicate that the IHGC-GAN method has better prediction performance than the advanced methods in a variety of indicators.

Feature aggregation graph convolutional network based on imaging genetic data for diagnosis and pathogeny identification of Alzheimer's disease.

The roles of brain regions activities and gene expressions in the development of Alzheimer's disease (AD) remain unclear. Existing imaging genetic studies usually has the problem of inefficiency and inadequate fusion of data. This study proposes a novel deep learning method to efficiently capture the development pattern of AD. First, we model the interaction between brain regions and genes as node-to-node feature aggregation in a brain region-gene network. Second, we propose a feature aggregation graph convolutional network (FAGCN) to transmit and update the node feature. Compared with the trivial graph convolutional procedure, we replace the input from the adjacency matrix with a weight matrix based on correlation analysis and consider common neighbor similarity to discover broader associations of nodes. Finally, we use a full-gradient saliency graph mechanism to score and extract the pathogenetic brain regions and risk genes. According to the results, FAGCN achieved the best performance among both traditional and cutting-edge methods and extracted AD-related brain regions and genes, providing theoretical and methodological support for the research of related diseases.

A novel generation adversarial network framework with characteristics aggregation and diffusion for brain disease classification and feature selection.

Imaging genetics provides unique insights into the pathological studies of complex brain diseases by integrating the characteristics of multi-level medical data. However, most current imaging genetics research performs incomplete data fusion. Also, there is a lack of effective deep learning methods to analyze neuroimaging and genetic data jointly. Therefore, this paper first constructs the brain region-gene networks to intuitively represent the association pattern of pathogenetic factors. Second, a novel feature information aggregation model is constructed to accurately describe the information aggregation process among brain region nodes and gene nodes. Finally, a deep learning method called feature information aggregation and diffusion generative adversarial network (FIAD-GAN) is proposed to efficiently classify samples and select features. We focus on improving the generator with the proposed convolution and deconvolution operations, with which the interpretability of the deep learning framework has been dramatically improved. The experimental results indicate that FIAD-GAN can not only achieve superior results in various disease classification tasks but also extract brain regions and genes closely related to AD. This work provides a novel method for intelligent clinical decisions. The relevant biomedical discoveries provide a reliable reference and technical basis for the clinical diagnosis, treatment and pathological analysis of disease.

Morbigenous brain region and gene detection with a genetically evolved random neural network cluster approach in late mild cognitive impairment.

MOTIVATION: The multimodal data fusion analysis becomes another important field for brain disease detection and increasing researches concentrate on using neural network algorithms to solve a range of problems. However, most current neural network optimizing strategies focus on internal nodes or hidden layer numbers, while ignoring the advantages of external optimization. Additionally, in the multimodal data fusion analysis of brain science, the problems of small sample size and high-dimensional data are often encountered due to the difficulty of data collection and the specialization of brain science data, which may result in the lower generalization performance of neural network. RESULTS: We propose a genetically evolved random neural network cluster (GERNNC) model. Specifically, the fusion characteristics are first constructed to be taken as the input and the best type of neural network is selected as the base classifier to form the initial random neural network cluster. Second, the cluster is adaptively genetically evolved. Based on the GERNNC model, we further construct a multi-tasking framework for the classification of patients with brain disease and the extraction of significant characteristics. In a study of genetic data and functional magnetic resonance imaging data from the Alzheimer's Disease Neuroimaging Initiative, the framework exhibits great classification performance and strong morbigenous factor detection ability. This work demonstrates that how to effectively detect pathogenic components of the brain disease on the high-dimensional medical data and small samples. AVAILABILITY AND IMPLEMENTATION: The Matlab code is available at https://github.com/lizi1234560/GERNNC.git.

Deep Canonical Correlation Fusion Algorithm Based on Denoising Autoencoder for ASD Diagnosis and Pathogenic Brain Region Identification.

Autism Spectrum Disorder (ASD) is defined as a neurodevelopmental condition distinguished by unconventional neural activities. Early intervention is key to managing the progress of ASD, and current research primarily focuses on the use of structural magnetic resonance imaging (sMRI) or resting-state functional magnetic resonance imaging (rs-fMRI) for diagnosis. Moreover, the use of autoencoders for disease classification has not been sufficiently explored. In this study, we introduce a new framework based on autoencoder, the Deep Canonical Correlation Fusion algorithm based on Denoising Autoencoder (DCCF-DAE), which proves to be effective in handling high-dimensional data. This framework involves efficient feature extraction from different types of data with an advanced autoencoder, followed by the fusion of these features through the DCCF model. Then we utilize the fused features for disease classification. DCCF integrates functional and structural data to help accurately diagnose ASD and identify critical Regions of Interest (ROIs) in disease mechanisms. We compare the proposed framework with other methods by the Autism Brain Imaging Data Exchange (ABIDE) database and the results demonstrate its outstanding performance in ASD diagnosis. The superiority of DCCF-DAE highlights its potential as a crucial tool for early ASD diagnosis and monitoring.

Multi-kernel Learning Fusion Algorithm Based on RNN and GRU for ASD Diagnosis and Pathogenic Brain Region Extraction.

Autism spectrum disorder (ASD) is a complex, severe disorder related to brain development. It impairs patient language communication and social behaviors. In recent years, ASD researches have focused on a single-modal neuroimaging data, neglecting the complementarity between multi-modal data. This omission may lead to poor classification. Therefore, it is important to study multi-modal data of ASD for revealing its pathogenesis. Furthermore, recurrent neural network (RNN) and gated recurrent unit (GRU) are effective for sequence data processing. In this paper, we introduce a novel framework for a Multi-Kernel Learning Fusion algorithm based on RNN and GRU (MKLF-RAG). The framework utilizes RNN and GRU to provide feature selection for data of different modalities. Then these features are fused by MKLF algorithm to detect the pathological mechanisms of ASD and extract the most relevant the Regions of Interest (ROIs) for the disease. The MKLF-RAG proposed in this paper has been tested in a variety of experiments with the Autism Brain Imaging Data Exchange (ABIDE) database. Experimental findings indicate that our framework notably enhances the classification accuracy for ASD. Compared with other methods, MKLF-RAG demonstrates superior efficacy across multiple evaluation metrics and could provide valuable insights into the early diagnosis of ASD.

Structure Mapping Generative Adversarial Network for Multi-View Information Mapping Pattern Mining.

Multi-view learning is dedicated to integrating information from different views and improving the generalization performance of models. However, in most current works, learning under different views has significant independency, overlooking common information mapping patterns that exist between these views. This paper proposes a Structure Mapping Generative adversarial network (SM-GAN) framework, which utilizes the consistency and complementarity of multi-view data from the innovative perspective of information mapping. Specifically, based on network-structured multi-view data, a structural information mapping model is proposed to capture hierarchical interaction patterns among views. Subsequently, three different types of graph convolutional operations are designed in SM-GAN based on the model. Compared with regular GAN, we add a structural information mapping module between the encoder and decoder wthin the generator, completing the structural information mapping from the micro-view to the macro-view. This paper conducted sufficient validation experiments using public imaging genetics data in Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. It is shown that SM-GAN outperforms baseline and advanced methods in multi-label classification and evolution prediction tasks.

CE-GAN: Community Evolutionary Generative Adversarial Network for Alzheimer's Disease Risk Prediction.

In the studies of neurodegenerative diseases such as Alzheimer's Disease (AD), researchers often focus on the associations among multi-omics pathogeny based on imaging genetics data. However, current studies overlook the communities in brain networks, leading to inaccurate models of disease development. This paper explores the developmental patterns of AD from the perspective of community evolution. We first establish a mathematical model to describe functional degeneration in the brain as the community evolution driven by entropy information propagation. Next, we propose an interpretable Community Evolutionary Generative Adversarial Network (CE-GAN) to predict disease risk. In the generator of CE-GAN, community evolutionary convolutions are designed to capture the evolutionary patterns of AD. The experiments are conducted using functional magnetic resonance imaging (fMRI) data and single nucleotide polymorphism (SNP) data. CE-GAN achieves 91.67% accuracy and 91.83% area under curve (AUC) in AD risk prediction tasks, surpassing advanced methods on the same dataset. In addition, we validated the effectiveness of CE-GAN for pathogeny extraction. The source code of this work is available at https://github.com/fmri123456/CE-GAN.

Community Graph Convolution Neural Network for Alzheimer's Disease Classification and Pathogenetic Factors Identification.

As a complex neural network system, the brain regions and genes collaborate to effectively store and transmit information. We abstract the collaboration correlations as the brain region gene community network (BG-CN) and present a new deep learning approach, such as the community graph convolutional neural network (Com-GCN), for investigating the transmission of information within and between communities. The results can be used for diagnosing and extracting causal factors for Alzheimer's disease (AD). First, an affinity aggregation model for BG-CN is developed to describe intercommunity and intracommunity information transmission. Second, we design the Com-GCN architecture with intercommunity convolution and intracommunity convolution operations based on the affinity aggregation model. Through sufficient experimental validation on the AD neuroimaging initiative (ADNI) dataset, the design of Com-GCN matches the physiological mechanism better and improves the interpretability and classification performance. Furthermore, Com-GCN can identify lesioned brain regions and disease-causing genes, which may assist precision medicine and drug design in AD and serve as a valuable reference for other neurological disorders.

Pathogeny Detection for Mild Cognitive Impairment via Weighted Evolutionary Random Forest With Brain Imaging and Genetic Data.

Medical imaging technology and gene sequencing technology have long been widely used to analyze the pathogenesis and make precise diagnoses of mild cognitive impairment (MCI). However, few studies involve the fusion of radiomics data with genomics data to make full use of the complementarity between different omics to detect pathogenic factors of MCI. This paper performs multimodal fusion analysis based on functional magnetic resonance imaging (fMRI) data and single nucleotide polymorphism (SNP) data of MCI patients. In specific, first, using correlation analysis methods on sequence information of regions of interests (ROIs) and digitalized gene sequences, the fusion features of samples are constructed. Then, introducing weighted evolution strategy into ensemble learning, a novel weighted evolutionary random forest (WERF) model is built to eliminate the inefficient features. Consequently, with the help of WERF, an overall multimodal data analysis framework is established to effectively identify MCI patients and extract pathogenic factors. Based on the data of MCI patients from the ADNI database and compared with some existing popular methods, the superiority in performance of the framework is verified. Our study has great potential to be an effective tool for pathogenic factors detection of MCI.

Hypergraph Structural Information Aggregation Generative Adversarial Networks for Diagnosis and Pathogenetic Factors Identification of Alzheimer's Disease With Imaging Genetic Data.

Alzheimer's disease (AD) is a neurodegenerative disease with profound pathogenetic causes. Imaging genetic data analysis can provide comprehensive insights into its causes. To fully utilize the multi-level information in the data, this article proposes a hypergraph structural information aggregation model, and constructs a novel deep learning method named hypergraph structural information aggregation generative adversarial networks (HSIA-GANs) for the automatic sample classification and accurate feature extraction. Specifically, HSIA-GAN is composed of generator and discriminator. The generator has three main functions. First, vertex graph and edge graph are constructed based on the input hypergraph to present the low-order relations. Second, the low-order structural information of hypergraph is extracted by the designed vertex convolution layers and edge convolution layers. Finally, the synthetic hypergraph is generated as the input of the discriminator. The discriminator can extract the high-order structural information directly from hypergraph through vertex-edge convolution, fuse the high and low-order structural information, and finalize the results through the full connection (FC) layers. Based on the data acquired from AD neuroimaging initiative, HSIA-GAN shows significant advantages in three classification tasks, and extracts discriminant features conducive to better disease classification.

Detecting Risk Gene and Pathogenic Brain Region in EMCI Using a Novel GERF Algorithm Based on Brain Imaging and Genetic Data.

Fusion analysis of disease-related multi-modal data is becoming increasingly important to illuminate the pathogenesis of complex brain diseases. However, owing to the small amount and high dimension of multi-modal data, current machine learning methods do not fully achieve the high veracity and reliability of fusion feature selection. In this paper, we propose a genetic-evolutionary random forest (GERF) algorithm to discover the risk genes and disease-related brain regions of early mild cognitive impairment (EMCI) based on the genetic data and resting-state functional magnetic resonance imaging (rs-fMRI) data. Classical correlation analysis method is used to explore the association between brain regions and genes, and fusion features are constructed. The genetic-evolutionary idea is introduced to enhance the classification performance, and to extract the optimal features effectively. The proposed GERF algorithm is evaluated by the public Alzheimer's Disease Neuroimaging Initiative (ADNI) database, and the results show that the algorithm achieves satisfactory classification accuracy in small sample learning. Moreover, we compare the GERF algorithm with other methods to prove its superiority. Furthermore, we propose the overall framework of detecting pathogenic factors, which can be accurately and efficiently applied to the multi-modal data analysis of EMCI and be able to extend to other diseases. This work provides a novel insight for early diagnosis and clinicopathologic analysis of EMCI, which facilitates clinical medicine to control further deterioration of diseases and is good for the accurate electric shock using transcranial magnetic stimulation.

Pathogenic Factors Identification of Brain Imaging and Gene in Late Mild Cognitive Impairment.

Mild cognitive impairment (MCI) is a dangerous signal of severe cognitive decline. It can be separated into two steps: early MCI (EMCI) and late MCI (LMCI). As the post-state of MCI and pre-state of Alzheimer's disease (AD), LMCI receives insufficient attention in the field of brain science, causing the internal mechanism of LMCI has not been well understood. To better explore the focus and pathological mechanism of LMCI, a method called genetic evolved random forest (GERF) is applied. Resting functional magnetic resonance imaging (rfMRI) and gene data are obtained from 62 subjects (36 LMCI and 26 normal controls), and Pearson correlation analysis is adopted to perform the multimodal fusion of two types of data to construct fusion features. We identified pathogenic brain regions and genes that are highly related to LMCI using GERF and achieves a good effect. Compared with the normal control (NC) group, the abnormal brain regions of LMCI are PUT.L, PreCG.L, IFGtriang.R, REC.R, DCG.R, PoCG.L, and HES.L, and the pathogenic genes are FHIT, RF00019, FRMD4A, PTPRD, and RBFOX1. More importantly, most of these risk genes and abnormal brain regions have been confirmed to be related to AD and MCI in previous studies. In this study, we mapped them to LMCI with higher accuracies, so as to provide a more robust understanding of the physiological mechanism of MCI.

A novel CERNNE approach for predicting Parkinson's Disease-associated genes and brain regions based on multimodal imaging genetics data.

The detection and pathogenic factors analysis of Parkinson's disease (PD) has a practical significance for its diagnosis and treatment. However, the traditional research paradigms are commonly based on single neural imaging data, which is easy to ignore the complementarity between multimodal imaging genetics data. The existing researches also pay little attention to the comprehensive framework of patient detection and pathogenic factors analysis for PD. Based on functional magnetic resonance imaging (fMRI) data and single nucleotide polymorphism (SNP) data, a novel brain disease multimodal data analysis model is proposed in this paper. Firstly, according to the complementarity between the two types of data, the classical correlation analysis method is used to construct the fusion feature of subjects. Secondly, based on the artificial neural network, the fusion feature analysis tool named clustering evolutionary random neural network ensemble (CERNNE) is designed. This method integrates multiple neural networks constructed randomly, and uses clustering evolution strategy to optimize the ensemble learner by adaptive selective integration, selecting the discriminative features for PD analysis and ensuring the generalization performance of the ensemble model. By combining with data fusion scheme, the CERNNE is applied to forming a multi-task analysis framework, recognizing PD patients and predicting PD-associated brain regions and genes. In the multimodal data experiment, the proposed framework shows better classification performance and pathogenic factors predicting ability, which provides a new perspective for the diagnosis of PD.

The exploration of Parkinson's disease: a multi-modal data analysis of resting functional magnetic resonance imaging and gene data.

Parkinson's disease (PD) is the most universal chronic degenerative neurological dyskinesia and an important threat to elderly health. At present, the researches of PD are mainly based on single-modal data analysis, while the fusion research of multi-modal data may provide more meaningful information in the aspect of comprehending the pathogenesis of PD. In this paper, 104 samples having resting functional magnetic resonance imaging (rfMRI) and gene data are from Parkinson's Progression Markers Initiative (PPMI) and Alzheimer's Disease Neuroimaging Initiative (ADNI) database to predict pathological brain areas and risk genes related to PD. In the experiment, Pearson correlation analysis is adopted to conduct fusion analysis from the data of genes and brain areas as multi-modal sample characteristics, and the clustering evolution random forest (CERF) method is applied to detect the discriminative genes and brain areas. The experimental results indicate that compared with several existing advanced methods, the CERF method can further improve the diagnosis of PD and healthy control, and can achieve a significant effect. More importantly, we find that there are some interesting associations between brain areas and genes in PD patients. Based on these associations, we notice that PD-related brain areas include angular gyrus, thalamus, posterior cingulate gyrus and paracentral lobule, and risk genes mainly include C6orf10, HLA-DPB1 and HLA-DOA. These discoveries have a significant contribution to the early prevention and clinical treatments of PD.

Multimodal Data Analysis of Alzheimer's Disease Based on Clustering Evolutionary Random Forest.

Alzheimer's disease (AD) has become a severe medical challenge. Advances in technologies produced high-dimensional data of different modalities including functional magnetic resonance imaging (fMRI) and single nucleotide polymorphism (SNP). Understanding the complex association patterns among these heterogeneous and complementary data is of benefit to the diagnosis and prevention of AD. In this paper, we apply the appropriate correlation analysis method to detect the relationships between brain regions and genes, and propose "brain region-gene pairs" as the multimodal features of the sample. In addition, we put forward a novel data analysis method from technology aspect, cluster evolutionary random forest (CERF), which is suitable for "brain region-gene pairs". The idea of clustering evolution is introduced to improve the generalization performance of random forest which is constructed by randomly selecting samples and sample features. Through hierarchical clustering of decision trees in random forest, the decision trees with higher similarity are clustered into one class, and the decision trees with the best performance are retained to enhance the diversity between decision trees. Furthermore, based on CERF, we integrate feature construction, feature selection and sample classification to find the optimal combination of different methods, and design a comprehensive diagnostic framework for AD. The framework is validated by the samples with both fMRI and SNP data from ADNI. The results show that we can effectively identify AD patients and discover some brain regions and genes associated with AD significantly based on this framework. These findings are conducive to the clinical treatment and prevention of AD.

Effective Diagnosis of Alzheimer's Disease via Multimodal Fusion Analysis Framework.

Alzheimer's disease (AD) is a complex neurodegenerative disease involving a variety of pathogenic factors, and the etiology detection of this disease has been a major concern of researchers. Neuroimaging is a basic and important means to explore the problem. It is the main current scientific research direction for combining neuroimaging with other modal data to dig deep into the potential information of AD through the complementarities among multiple data points. Machine learning methods possess great potentiality and have reached some achievements in this research area. A few studies have proposed some solutions to the effects of multimodal data fusion, however, the overall analytical framework for data fusion and fusion result analysis has thus far been ignored. In this paper, we first put forward a novel multimodal data fusion method, and further present a new machine learning framework of data fusion, classification, feature selection, and disease-causing factor extraction. The real dataset of 37 AD patients and 35 normal controls (NC) with functional magnetic resonance imaging (fMRI) and genetic data was used to verify the effectiveness of the framework, which was more accurate in classification and optimal feature extraction than other methods. Furthermore, we revealed disease-causing brain regions and genes, such as the olfactory cortex, insula, posterior cingulate gyrus, lingual gyrus, CNTNAP2, LRP1B, FRMD4A, and DAB1. The results show that the machine learning framework could effectively perform multimodal data fusion analysis, providing new insights and perspectives for the diagnosis of Alzheimer's disease.

Random support vector machine cluster analysis of resting-state fMRI in Alzheimer's disease.

Early diagnosis is critical for individuals with Alzheimer's disease (AD) in clinical practice because its progress is irreversible. In the existing literature, support vector machine (SVM) has always been applied to distinguish between AD and healthy controls (HC) based on neuroimaging data. But previous studies have only used a single SVM to classify AD and HC, and the accuracy is not very high and generally less than 90%. The method of random support vector machine cluster was proposed to classify AD and HC in this paper. From the Alzheimer's Disease Neuroimaging Initiative database, the subjects including 25 AD individuals and 35 HC individuals were obtained. The classification accuracy could reach to 94.44% in the results. Furthermore, the method could also be used for feature selection and the accuracy could be maintained at the level of 94.44%. In addition, we could also find out abnormal brain regions (inferior frontal gyrus, superior frontal gyrus, precentral gyrus and cingulate cortex). It is worth noting that the proposed random support vector machine cluster could be a new insight to help the diagnosis of AD.

The Diagnosis of Autism Spectrum Disorder Based on the Random Neural Network Cluster.

As the autism spectrum disorder (ASD) is highly heritable, pervasive and prevalent, the clinical diagnosis of ASD is vital. In the existing literature, a single neural network (NN) is generally used to classify ASD patients from typical controls (TC) based on functional MRI data and the accuracy is not very high. Thus, the new method named as the random NN cluster, which consists of multiple NNs was proposed to classify ASD patients and TC in this article. Fifty ASD patients and 42 TC were selected from autism brain imaging data exchange (ABIDE) database. First, five different NNs were applied to build five types of random NN clusters. Second, the accuracies of the five types of random NN clusters were compared to select the highest one. The random Elman NN cluster had the highest accuracy, thus Elman NN was selected as the best base classifier. Then, we used the significant features between ASD patients and TC to find out abnormal brain regions which include the supplementary motor area, the median cingulate and paracingulate gyri, the fusiform gyrus (FG) and the insula (INS). The proposed method provides a new perspective to improve classification performance and it is meaningful for the diagnosis of ASD.

Analysis of Asperger Syndrome Using Genetic-Evolutionary Random Support Vector Machine Cluster.

Asperger syndrome (AS) is subtype of autism spectrum disorder (ASD). Diagnosis and pathological analysis of AS through resting-state fMRI data is one of the hot topics in brain science. We employed a new model called the genetic-evolutionary random Support Vector Machine cluster (GE-RSVMC) to classify AS and normal people, and search for lesions. The model innovatively integrates the methods of the cluster and genetic evolution to improve the performance of the model. We randomly selected samples and sample features to construct GE-RSVMC, and then used the cluster to classify and extract lesions according to classification results. The model was validated by data of 157 participants (86 AS and 71 health controls) in ABIDE database. The classification accuracy of the model reached to 97.5% and we discovered the brain regions with significant differences, such as the Angular gyrus (ANG.R), Precuneus (PCUN.R), Caudate nucleus (CAU.R), Cuneus (CUN.R) and so on. Our method provides a new perspective for the diagnosis and treatment of AS, and a universal framework for other brain science research as the model has excellent generalization performance.