Graph kernel of brain networks considering functional similarity measures.

As a tool of brain network analysis, the graph kernel is often used to assist the diagnosis of neurodegenerative diseases. It is used to judge whether the subject is sick by measuring the similarity between brain networks. Most of the existing graph kernels calculate the similarity of brain networks based on structural similarity, which can better capture the topology of brain networks, but all ignore the functional information including the lobe, centers, left and right brain to which the brain region belongs and functions of brain regions in brain networks. The functional similarities can help more accurately locate the specific brain regions affected by diseases so that we can focus on measuring the similarity of brain networks. Therefore, a multi-attribute graph kernel for the brain network is proposed, which assigns multiple attributes to nodes in the brain network, and computes the graph kernel of the brain network according to Weisfeiler-Lehman color refinement algorithm. In addition, in order to capture the interaction between multiple brain regions, a multi-attribute hypergraph kernel is proposed, which takes into account the functional and structural similarities as well as the higher-order correlation between the nodes of the brain network. Finally, the experiments are conducted on real data sets and the experimental results show that the proposed methods can significantly improve the performance of neurodegenerative disease diagnosis. Besides, the statistical test shows that the proposed methods are significantly different from compared methods.

BIC-LP: A Hybrid Higher-Order Dynamic Bayesian Network Score Function for Gene Regulatory Network Reconstruction.

Reconstructing gene regulatory networks(GRNs) is an increasingly hot topic in bioinformatics. Dynamic Bayesian network(DBN) is a stochastic graph model commonly used as a vital model for GRN reconstruction. But probabilistic characteristics of biological networks and the existence of data noise bring great challenges to GRN reconstruction and always lead to many false positive/negative edges. ScoreLasso is a hybrid DBN score function combining DBN and linear regression with good performance. Its performance is, however, limited by first-order assumption and ignorance of the initial network of DBN. In this article, an integrated model based on higher-order DBN model, higher-order Lasso linear regression model and Pearson correlation model is proposed. Based on this, a hybrid higher-order DBN score function for GRN reconstruction is proposed, namely BIC-LP. BIC-LP score function is constructed by adding terms based on Lasso linear regression coefficients and Pearson correlation coefficients on classical BIC score function. Therefore, it could capture more information from dataset and curb information loss, compared with both many existing Bayesian family score functions and many state-of-the-art methods for GRN reconstruction. Experimental results show that BIC-LP can reasonably eliminate some false positive edges while retaining most true positive edges, so as to achieve better GRN reconstruction performance.

An efficient privacy-preserving blockchain storage method for internet of things environment.

Blockchain is a key technology to realize decentralized trust management. In recent studies, sharding-based blockchain models are proposed and applied to the resource-constrained Internet of Things (IoT) scenario, and machine learning-based models are presented to improve the query efficiency of the sharding-based blockchains by classifying hot data and storing them locally. However, in some scenarios, these presented blockchain models cannot be deployed because the block features used as input in the learning method are privacy. In this paper, we propose an efficient privacy-preserving blockchain storage method for the IoT environment. The new method classifies hot blocks based on the federated extreme learning machine method and saves the hot blocks through one of the sharded blockchain models called ElasticChain. The features of hot blocks will not be read by other nodes in this method, and user privacy is effectively protected. Meanwhile, hot blocks are saved locally, and data query speed is improved. Furthermore, in order to comprehensively evaluate a hot block, five features of hot blocks are defined, including objective feature, historical popularity, potential popularity, storage requirements and training value. Finally, the experimental results on synthetic data demonstrate the accuracy and efficiency of the proposed blockchain storage model.

An Evolving Hypergraph Convolutional Network for the Diagnosis of Alzheimer's Disease.

In the diagnosis of Alzheimer's Disease (AD), the brain network analysis method is often used. The traditional network can only reflect the pairwise association between two brain regions, but ignore the higher-order relationship between them. Therefore, a brain network construction method based on hypergraph, called hyperbrain network, is adopted. The brain network constructed by the conventional static hyperbrain network cannot reflect the dynamic changes in brain activity. Based on this, the construction of a dynamic hyperbrain network is proposed. In addition, graph convolutional networks also play a huge role in AD diagnosis. Therefore, an evolving hypergraph convolutional network for the dynamic hyperbrain network is proposed, and the attention mechanism is added to further enhance the ability of representation learning, and then it is used for the aided diagnosis of AD. The experimental results show that the proposed method can effectively improve the accuracy of AD diagnosis up to 99.09%, which is a 0.3 percent improvement over the best existing methods.

The Analysis of Relevant Gene Networks Based on Driver Genes in Breast Cancer.

BACKGROUND: The occurrence and development of breast cancer has a strong correlation with a person's genetics. Therefore, it is important to analyze the genetic factors of breast cancer for future development of potential targeted therapies from the genetic level. METHODS: In this study, we complete an analysis of the relevant protein-protein interaction network relating to breast cancer. This includes three steps, which are breast cancer-relevant genes selection using mutual information method, protein-protein interaction network reconstruction based on the STRING database, and vital genes calculating by nodes centrality analysis. RESULTS: The 230 breast cancer-relevant genes were chosen in gene selection to reconstruct the protein-protein interaction network and some vital genes were calculated by node centrality analyses. Node centrality analyses conducted with the top 10 and top 20 values of each metric found 19 and 39 statistically vital genes, respectively. In order to prove the biological significance of these vital genes, we carried out the survival analysis and DNA methylation analysis, inquired about the prognosis in other cancer tissues and the RNA expression level in breast cancer. The results all proved the validity of the selected genes. CONCLUSIONS: These genes could provide a valuable reference in clinical treatment among breast cancer patients.

Custom 3D fMRI Registration Template Construction Method Based on Time-Series Fusion.

As the brain standard template for medical image registration has only been constructed with an MRI template, there is no three-dimensional fMRI standard template for use, and when the subject's brain structure is quite different from the standard brain structure, the registration to the standard space will lead to large errors. Registration to an individual space can avoid this problem. However, in the current fMRI registration algorithm based on individual space, the reference image is often selected by researchers or randomly selected fMRI images at a certain time point. This makes the quality of the reference image very dependent on the experience and ability of the researchers and has great contingency. Whether the reference image is appropriate and reasonable affects the rationality and accuracy of the registration results to a great extent. Therefore, a method for constructing a 3D custom fMRI template is proposed. First, the data are preprocessed; second, by taking a group of two-dimensional slices corresponding to the same layer of the brain in three-dimensional fMRI images at multiple time points as image sequences, each group of slice sequences are registered and fused; and finally, a group of fused slices corresponding to different layers of the brain are obtained. In the process of registration, in order to make full use of the correlation information between the sequence data, the feature points of each two slices of adjacent time points in the sequence are matched, and then according to the transformation relationship between the adjacent images, they are recursively forwarded and mapped to the same space. Then, the fused slices are stacked in order to form a three-dimensional customized fMRI template with individual pertinence. Finally, in the classic registration algorithm, the difference in the registration accuracy between using a custom fMRI template and different standard spaces is compared, which proves that using a custom template can improve the registration effect to a certain extent.

NDCN-Brain: An Extensible Dynamic Functional Brain Network Model.

As an extension of the static network, the dynamic functional brain network can show continuous changes in the brain's connections. Then, limited by the length of the fMRI signal, it is difficult to show every instantaneous moment in the construction of a dynamic network and there is a lack of effective prediction of the dynamic changes of the network after the signal ends. In this paper, an extensible dynamic brain function network model is proposed. The model utilizes the ability of extracting and predicting the instantaneous state of the dynamic network of neural dynamics on complex networks (NDCN) and constructs a dynamic network model structure that can provide more than the original signal range. Experimental results show that every snapshot in the network obtained by the proposed method has a usable network structure and that it also has a good classification result in the diagnosis of cognitive impairment diseases.

Interpretable Model Based on Pyramid Scene Parsing Features for Brain Tumor MRI Image Segmentation.

Due to the black box model nature of convolutional neural networks, computer-aided diagnosis methods based on depth learning are usually poorly interpretable. Therefore, the diagnosis results obtained by these unexplained methods are difficult to gain the trust of patients and doctors, which limits their application in the medical field. To solve this problem, an interpretable depth learning image segmentation framework is proposed in this paper for processing brain tumor magnetic resonance images. A gradient-based class activation mapping method is introduced into the segmentation model based on pyramid structure to visually explain it. The pyramid structure constructs global context information with features after multiple pooling layers to improve image segmentation performance. Therefore, class activation mapping is used to visualize the features concerned by each layer of pyramid structure and realize the interpretation of PSPNet. After training and testing the model on the public dataset BraTS2018, several sets of visualization results were obtained. By analyzing these visualization results, the effectiveness of pyramid structure in brain tumor segmentation task is proved, and some improvements are made to the structure of pyramid model based on the shortcomings of the model shown in the visualization results. In summary, the interpretable brain tumor image segmentation method proposed in this paper can well explain the role of pyramid structure in brain tumor image segmentation, which provides a certain idea for the application of interpretable method in brain tumor segmentation and has certain practical value for the evaluation and optimization of brain tumor segmentation model.

Brain functional network modeling and analysis based on fMRI: a systematic review.

In recent years, the number of patients with neurodegenerative diseases (i.e., Alzheimer's disease, Parkinson's disease, mild cognitive impairment) and mental disorders (i.e., depression, anxiety and schizophrenia) have increased dramatically. Researchers have found that complex network analysis can reveal the topology of brain functional networks, such as small-world, scale-free, etc. In the study of brain diseases, it has been found that these topologies have undergoed abnormal changes in different degrees. Therefore, the research of brain functional networks can not only provide a new perspective for understanding the pathological mechanism of neurological and psychiatric diseases, but also provide assistance for the early diagnosis. Focusing on the study of human brain functional networks, this paper reviews the research results in recent years. First, this paper introduces the background of the study of brain functional networks under complex network theory and the important role of topological properties in the study of brain diseases. Second, the paper describes how to construct a brain functional network using neural image data. Third, the common methods of functional network analysis, including network structure analysis and disease classification, are introduced. Fourth, the role of brain functional networks in pathological study, analysis and diagnosis of brain functional diseases is studied. Finally, the paper summarizes the existing studies of brain functional networks and points out the problems and future research directions.

Breast microcalcifications detection based on fusing features with DTCWT.

BACKGROUND: Breast cancer is a common disease in women. Early detection and early treatment can reduce breast cancer mortality. Studies have shown that breast cancer microcalcifications is one of the important clinical manifestations of early breast cancer, and sometimes even the only manifestation. When the mammography image shows typical malignant microcalcification, it can be diagnosed as breast cancer without any other signs of malignancy. In the aided diagnosis of microcalcifications, it is a crucial step to automatically find and locate regions of interest containing microcalcifications. However, the existing feature extraction method for microcalcifications only extracts features in the time domain or wavelet domain, and does not completely represent all the information of the region of interest. An extraction method based on the combination of Dual-Tree Complex Wavelet Transform (DTCWT) and texture features is proposed in the paper. METHODS: First, the processing operations including denoising, enhancement, and edge detection were performed on mammograms. Sub-image segmentation is then performed. DTCWT features and texture features are extracted for each sub-image.DTCWT features are combined with texture features, and then genetic algorithm is used for feature optimization. The features are classified by the Extreme Learning Machine (ELM) to achieve rapid detection and automatic extraction of ROI with microcalcifications. The experimental results verify that the feature model proposed in this paper has the highest detection rate for ROI regions. The ROI region extracted by the proposed feature model was used as subsequent experimental data. Three different methods were used to detect the microcalcifications, including Top-hat, wavelet transform, and methods combining Top-Hat and wavelet transform. RESULTS: The method was applied to 100 mammograms from the mammograms database of women in Northeast China. In the automatic extraction of ROI, the accuracy, sensitivity, specificity, positive accuracy and negative accuracy of the proposed model combined with DTCWT were 95.92%, 96.71%, 92.20%, 93.65%, 96.33%, respectively. When the Top-hat algorithm was used for microcalcifications detection, the sensitivity reached 89.6%, and the false positive detection rate was 2.6. When the wavelet transform algorithm was used for microcalcifications detection, the sensitivity was 91.1%, and the false positive detection rate was 3.28. When the combined algorithm was used for microcalcifications detection, the sensitivity was 86.7%, and the false positive detection rate decreased to 1.35. CONCLUSIONS: The proposed model combined with DTCWT features achieves better result in the automatic extraction of ROI. Moreover, in the subsequent detection of microcalcifications based on three methods, the three methods achieved better results in sensitivity and false positive detection rate, respectively.

A similarity measure method fusing deep feature for mammogram retrieval.

BACKGROUND: Breast cancer is one of the most important malignant tumors among women causing a serious impact on women's lives and mammography is one the most important methods for breast examination. When diagnosing the breast disease, radiologists sometimes may consult some previous diagnosis cases as a reference. But there are many previous cases and it is important to find which cases are the similar cases, which is a big project costing lots of time. Medical image retrieval can provide objective reference information for doctors to diagnose disease. The method of fusing deep features can improve the retrieval accuracy, which solves the "semantic gap" problem caused by only using content features and location features. METHODS: A similarity measure method combining deep feature for mammogram retrieval is proposed in this paper. First, the images are pre-processed to extract the low-level features, including content features and location features. Before extracting location features, registration with the standard image is performed. Then, the Convolutional Neural Network, the Stacked Auto-encoder Network, and the Deep Belief Network are built to extract the deep features, which are regarded as high-level features. Next, content similarity and deep similarity are calculated separately using the Euclidean distance between the query image and the dataset images. The location similarity is obtained by calculating the ratio of intersection to union of the mass regions. Finally, content similarity, location similarity, and deep similarity are fused to form the image fusion similarity. According to the similarity, the specified number of the most similar images can be returned. RESULTS: In the experiment, 740 MLO mammograms are used, which are from women in Northeast China. The content similarity, location similarity, and deep similarity are fused by different weight coefficients. When only considering low-level features, the results are better with fusing 60% content feature similarity and 40% lesion location feature similarity. On this basis, CNN deep similarity, DBN deep similarity, and SAE deep similarity are fused separately. The experiments show that when fusing 60% DBN deep feature similarity and 40% low-level feature similarity, the results have obvious advantages. At this time, the precision is 0.745, recall is 0.850, comprehensive evaluation index is 0.794. CONCLUSIONS: We propose a similarity measure method fusing deep feature, content feature, and location feature. The retrieval results show that the precision and recall of this method have obvious advantage, compared with the content-based image retrieval and location-based image retrieval.

Breast mass detection and diagnosis using fused features with density.

BACKGROUND: The morbidity of breast cancer has been increased in these years and ranked the first of all female diseases. Computer-aided diagnosis techniques for mammograms can help radiologists find early breast lesions. In mammograms, the degree of malignancy of the tumor is not only related to its morphology and texture features, but also closely related to the density of the tumor. However, in the current research on breast masses detection and diagnosis, people usually use the fusion feature of morphology and texture but neglect density, or only the density feature is considered. Therefore, this paper proposes a method to detect and diagnose the breast mass using fused features with density. METHODS: In this paper, we first propose a method based on sub-region clustering to detect the breast mass. The breast region is divided into sub-regions of equal size, and each sub-region is extracted based on local density feature, after that, an Unsupervised ELM (US-ELM) is used for clustering to complete the mass detection. Second, the feature model is constructed based on the mass. This model is composed of the mass region density feature, morphology feature and texture feature. And Genetic Algorithm is used for feature selection, and the optimized feature model is formed. Finally, ELM is used to diagnose benign or malignant mass. RESULTS: An experiment on the real dataset of 480 mammograms in Northeast China shows that our proposed method can effectively improve the detection and diagnosis accuracy of breast masses, where we obtained 0.9184 precision in detection of breast masses and 0.911 accuracy in diagnosis of breast masses. CONCLUSIONS: We have proposed a mass detection system, which achieves better detection accuracy performance than the existing state-of-art algorithm. We also propose a mass diagnosis system based on the fused features with density, which is more efficient than other feature model and classifier on the same dataset.

Voxelwise-based Brain Function Network using Multi-Graph Model.

In the research of the fMRI based brain functional network, the pairwise correlation between vertices usually means the similarity between BOLD signals. Our analysis found that the low (0:01-0:06 Hz), intermediate (0:06-0:15 Hz), and high (0:15-0:2 Hz) bands of the BOLD signal are not synchronous. Therefore, this paper presents a voxelwise based multi-frequency band brain functional network model, called Multi-graph brain functional network. First, our analysis found the low-frequency information on the BOLD signal of the brain functional network obscures the other information because of its high intensity. Then, a low-, intermediate-, and high-band brain functional networks were constructed by dividing the BOLD signals. After that, using complex network analysis, we found that different frequency bands have different properties; the modulation in low-frequency is higher than that of the intermediate and high frequency. The power distributions of different frequency bands were also significantly different, and the 'hub' vertices under all frequency bands are evenly distributed. Compared to a full-frequency network, the multi-graph model enhances the accuracy of the classification of Alzheimer's disease.

Improvements to the gastric cancer tumor-node-metastasis staging system based on computer-aided unsupervised clustering.

BACKGROUND: The Union for International Cancer Control (UICC) tumor-node-metastasis (TNM) classification is a key gastric cancer prognosis system. This study aimed to create a new TNM system to provide a reference for the clinical diagnosis and treatment of gastric cancer. METHODS: A review of gastric cancer patients' records was conducted in The First Hospital of China Medical University and the Liaoning Cancer Hospital and Institute. Based on patients' prognoses data, computer-aided unsupervised clustering was performed for all possible TNM staging situations to create a new staging division system. RESULTS: The primary outcome measure was 5-year survival, analyzed according to TNM classifications. Computer-aided unsupervised clustering for all TNM staging situations was used to create TNM division criteria that were more consistent with clinical situations. Furthermore, unsupervised clustering for the number of lymph node metastasis in the N stage led to the formulation of a classification method that differs from the existing N stage criteria, and unsupervised clustering for tumor size provided an additional reference for prognosis estimates. CONCLUSIONS: Finally, we developed a TNM staging system based on the computer-aided unsupervised clustering method; this system was more in line with clinical prognosis data when compared with the 7th edition of UICC gastric cancer TNM classification.

Improved lung nodule diagnosis accuracy using lung CT images with uncertain class.

BACKGROUND AND OBJECTIVE: Among all malignant tumors, lung cancer ranks in the top in mortality rate. Pulmonary nodule is the early manifestation of lung cancer, and plays an important role in its discovery, diagnosis and treatment. The technology of medical imaging has encountered a rapid development in recent years, thus the amount of pulmonary nodules can be discovered are on the raise, which means even tiny or minor changes in lung can be recorded by the CT images. This paper proposes a pulmonary nodule computer aided diagnosis (CAD) based on semi-supervised extreme learning machine(SS-ELM). METHODS: First, the feature model based on the pulmonary nodules regions of lung CT images is established. After that, the same feature data sets have been put into ELM, support vector machine (SVM) methods, probabilistic neural network (PNN) and multilayer perceptron (MLP) so as to compare the performance of the methods. ELM turned out to have better performance in training time and testing accuracy compared with SVM, PNN and MLP. Then, we propose a pulmonary nodules computer aided diagnosis algorithm based on semi-supervised ELM (SS-ELM), which enables both certain class feature sets with labels and unlabeled feature sets to be input for training and computer aided diagnosing. This algorithm has provided a solution for the using of uncertain class data and improve the testing accuracy of benign and malignant diagnosis. RESULTS: 1018 sets of thoracic CT images from the Lung Database Consortium and Image Database Resource Initiative (LIDC-IDRI) have been used in experiment in order to test the effectiveness of the algorithm. Compared with ELM, the pulmonary nodules CAD based on SS-ELM has better testing accuracy performance. CONCLUSIONS: We have proposed a pulmonary nodule CAD system based on SS-ELM, which achieving better generalization performance at faster learning speed and higher testing accuracy than ELM, SVM, PNN and MLP. The SS-ELM based pulmonary nodules CAD has been proposed to solve the problem of uncertain class data using.

A similarity measure method combining location feature for mammogram retrieval.

BACKGROUND: Breast cancer, the most common malignancy among women, has a high mortality rate in clinical practice. Early detection, diagnosis and treatment can reduce the mortalities of breast cancer greatly. The method of mammogram retrieval can help doctors to find the early breast lesions effectively and determine a reasonable feature set for image similarity measure. This will improve the accuracy effectively for mammogram retrieval. METHODS: This paper proposes a similarity measure method combining location feature for mammogram retrieval. Firstly, the images are pre-processed, the regions of interest are detected and the lesions are segmented in order to get the center point and radius of the lesions. Then, the method, namely Coherent Point Drift, is used for image registration with the pre-defined standard image. The center point and radius of the lesions after registration are obtained and the standard location feature of the image is constructed. This standard location feature can help figure out the location similarity between the image pair from the query image to each dataset image in the database. Next, the content feature of the image is extracted, including the Histogram of Oriented Gradients, the Edge Direction Histogram, the Local Binary Pattern and the Gray Level Histogram, and the image pair content similarity can be calculated using the Earth Mover's Distance. Finally, the location similarity and content similarity are fused to form the image fusion similarity, and the specified number of the most similar images can be returned according to it. RESULTS: In the experiment, 440 mammograms, which are from Chinese women in Northeast China, are used as the database. When fusing 40% lesion location feature similarity and 60% content feature similarity, the results have obvious advantages. At this time, precision is 0.83, recall is 0.76, comprehensive indicator is 0.79, satisfaction is 96.0%, mean is 4.2 and variance is 17.7. CONCLUSIONS: The results show that the precision and recall of this method have obvious advantage, compared with the content-based image retrieval.

Single NMR image super-resolution based on extreme learning machine.

INTRODUCTION: The performance limitation of MRI equipment and higher resolution demand of NMR images from radiologists have formed a strong contrast. Therefore, it is important to study the super resolution algorithm suitable for NMR images, using low costs software to replace the expensive equipment-updating. METHODS AND MATERIALS: Firstly, a series of NMR images are obtained from original NMR images with original noise to the lowest resolution images with the highest noise. Then, based on extreme learning machine, the mapping relation model is constructed from lower resolution NMR images with higher noise to higher resolution NMR images with lower noise in each pair of adjacent images in the obtained image sequence. Finally, the optimal mapping model is established by the ensemble way to reconstruct the higher resolution NMR images with lower noise on the basis of original resolution NMR images with original noise. Experiments are carried out by 990111 NMR brain images in datasets NITRC, REMBRANDT, RIDER NEURO MRI, TCGA-GBM and TCGA-LGG. RESULTS: The performance of proposed method is compared with three approaches through 7 indexes, and the experimental results show that our proposed method has a significant improvement. DISCUSSION: Since our method considers the influence of the noise, it has 20% higher in Peak-Signal-to-Noise-Ratio comparison. As our method is sensitive to details, and has a better characteristic retention, it has higher image quality upgrade of 15% in the additional evaluation. Finally, since extreme learning machine has a celerity learning speed, our method is 46.1% faster.