Meaningful Infrastructures in Biological Networks: Related Studies, Algorithms and Evaluation Parameters

In network science and big data, the concept of finding meaningful infrastructures in networks has emerged as a method of finding groups of entities with similar properties within very complex systems. The whole concept is generally based on finding subnetworks which have more properties (links) amongst nodes belonging to the same cluster than nodes in other groups (A concept presented by Girvan and Newman, 2002). Today meaningful infrastructure identification is applied in all types of networks from computer networks, to social networks to biological networks. In this article we will look at how meaningful infrastructure identification is applied in biological networks. This concept is important in biological networks as it helps scientist discover patterns in proteins or drugs which helps in solving many medical mysteries. This article will encompass the different algorithms that are used for meaningful infrastructure identification in biological networks. These include Genetic Algorithm, Differential Evolution, Water Cycle Algorithm (WCA), Walktrap Algorithm, Connect Intensity Iteration Algorithm (CIIA), Firefly algorithms and Overlapping Multiple Label Propagation Algorithm. These al-gorithms are compared with using performance measurement parameters such as the Mod-ularity, Normalized Mutual Information, Functional Enrichment, Recall and Precision, Re-dundancy, Purity and Surprise, which we will also discuss here.

Brain CT registration using hybrid supervised convolutional neural network

Background Image registration is an essential step in the automated interpretation of the brain computed tomography (CT) images of patients with acute cerebrovascular disease (ACVD). However, performing brain CT registration accurately and rapidly remains greatly challenging due to the large intersubject anatomical variations, low resolution of soft tissues, and heavy computation costs. To this end, the HSCN-Net, a hybrid supervised convolutional neural network, was developed for precise and fast brain CT registration. Method HSCN-Net generated synthetic deformation fields using a simulator as one supervision for one reference–moving image pair to address the problem of lack of gold standards. Furthermore, the simulator was designed to generate multiscale affine and elastic deformation fields to overcome the registration challenge posed by large intersubject anatomical deformation. Finally, HSCN-Net adopted a hybrid loss function constituted by deformation field and image similarity to improve registration accuracy and generalization capability. In this work, 101 CT images of patients were collected for model construction (57), evaluation (14), and testing (30). HSCN-Net was compared with the classical Demons and VoxelMorph models. Qualitative analysis through the visual evaluation of critical brain tissues and quantitative analysis by determining the endpoint error (EPE) between the predicted sparse deformation vectors and gold-standard sparse deformation vectors, image normalized mutual information (NMI), and the Dice coefficient of the middle cerebral artery (MCA) blood supply area were carried out to assess model performance comprehensively. Results HSCN-Net and Demons had a better visual spatial matching performance than VoxelMorph, and HSCN-Net was more competent for smooth and large intersubject deformations than Demons. The mean EPE of HSCN-Net (3.29 mm) was less than that of Demons (3.47 mm) and VoxelMorph (5.12 mm); the mean Dice of HSCN-Net was 0.96, which was higher than that of Demons (0.90) and VoxelMorph (0.87); and the mean NMI of HSCN-Net (0.83) was slightly lower than that of Demons (0.84), but higher than that of VoxelMorph (0.81). Moreover, the mean registration time of HSCN-Net (17.86 s) was shorter than that of VoxelMorph (18.53 s) and Demons (147.21 s). Conclusion The proposed HSCN-Net could achieve accurate and rapid intersubject brain CT registration.

An efficient scRNA-seq dropout imputation method using graph attention network

Background Single-cell sequencing technology can address the amount of single-cell library data at the same time and display the heterogeneity of different cells. However, analyzing single-cell data is a computationally challenging problem. Because there are low counts in the gene expression region, it has a high chance of recognizing the non-zero entity as zero, which are called dropout events. At present, the mainstream dropout imputation methods cannot effectively recover the true expression of cells from dropout noise such as DCA, MAGIC, scVI, scImpute and SAVER. Results In this paper, we propose an autoencoder structure network, named GNNImpute. GNNImpute uses graph attention convolution to aggregate multi-level similar cell information and implements convolution operations on non-Euclidean space on scRNA-seq data. Distinct from current imputation tools, GNNImpute can accurately and effectively impute the dropout and reduce dropout noise. We use mean square error (MSE), mean absolute error (MAE), Pearson correlation coefficient (PCC) and Cosine similarity (CS) to measure the performance of different methods with GNNImpute. We analyze four real datasets, and our results show that the GNNImpute achieves 3.0130 MSE, 0.6781 MAE, 0.9073 PCC and 0.9134 CS. Furthermore, we use Adjusted rand index (ARI) and Normalized mutual information (NMI) to measure the clustering effect. The GNNImpute achieves 0.8199 (ARI) and 0.8368 (NMI), respectively. Conclusions In this investigation, we propose a single-cell dropout imputation method (GNNImpute), which effectively utilizes shared information for imputing the dropout of scRNA-seq data. We test it with different real datasets and evaluate its effectiveness in MSE, MAE, PCC and CS. The results show that graph attention convolution and autoencoder structure have great potential in single-cell dropout imputation.

DDoS Attack Detection on Internet o Things using Unsupervised Algorithms

The increase in the deployment of IoT networks has improved productivity of humans and organisations. However, IoT networks are increasingly becoming platforms for launching DDoS attacks due to inherent weaker security and resource-constrained nature of IoT devices. This paper focusses on detecting DDoS attack in IoT networks by classifying incoming network packets on the transport layer as either “Suspicious” or “Benign” using unsupervised machine learning algorithms. In this work, two deep learning algorithms and two clustering algorithms were independently trained for mitigating DDoS attacks. We lay emphasis on exploitation based DDOS attacks which include TCP SYN-Flood attacks and UDP-Lag attacks. We use Mirai, BASHLITE and CICDDoS2019 dataset in training the algorithms during the experimentation phase. The accuracy score and normalized-mutual-information score are used to quantify the classification performance of the four algorithms. Our results show that the autoencoder performed overall best with the highest accuracy across all the datasets.

Cluster-Based Memetic Approach of Image Alignment

The paper presents a new memetic, cluster-based methodology for image registration in case of geometric perturbation model involving translation, rotation and scaling. The methodology consists of two stages. First, using the sets of the object pixels belonging to the target image and to the sensed image respectively, the boundaries of the search space are computed. Next, the registration mechanism residing in a hybridization between a version of firefly population-based search procedure and the two membered evolutionary strategy computed on clustered data is applied. In addition, a procedure designed to deal with the premature convergence problem is embedded. The fitness to be maximized by the memetic algorithm is defined by the Dice coefficient, a function implemented to evaluate the similarity between pairs of binary images. The proposed methodology is applied on both binary and monochrome images. In case of monochrome images, a preprocessing step aiming the binarization of the inputs is considered before the registration. The quality of the proposed approach is measured in terms of accuracy and efficiency. The success rate based on Dice coefficient, normalized mutual information measures, and signal-to-noise ratio are used to establish the accuracy of the obtained algorithm, while the efficiency is evaluated by the run time function.

Development of a New Image-Guided Neuronavigation System: Mixed-Reality Projection Mapping Is Accurate and Feasible

BACKGROUND Image-guided systems improve the safety, functional outcome, and overall survival of neurosurgery but require extensive equipment. OBJECTIVE To develop an image-guided surgery system that combines the brain surface photographic texture (BSP-T) captured during surgery with 3-dimensional computer graphics (3DCG) using projection mapping. METHODS Patients who underwent initial surgery with brain tumors were prospectively enrolled. The texture of the 3DCG (3DCG-T) was obtained from 3DCG under similar conditions as those when capturing the brain surface photographs. The position and orientation at the time of 3DCG-T acquisition were used as the reference. The correct position and orientation of the BSP-T were obtained by aligning the BSP-T with the 3DCG-T using normalized mutual information. The BSP-T was combined with and displayed on the 3DCG using projection mapping. This mixed-reality projection mapping (MRPM) was used prospectively in 15 patients (mean age 46.6 yr, 6 males). The difference between the centerlines of surface blood vessels on the BSP-T and 3DCG constituted the target registration error (TRE) and was measured in 16 fields of the craniotomy area. We also measured the time required for image processing. RESULTS The TRE was measured at 158 locations in the 15 patients, with an average of 1.19 ± 0.14 mm (mean ± standard error). The average image processing time was 16.58 min. CONCLUSION Our MRPM method does not require extensive equipment while presenting information of patients’ anatomy together with medical images in the same coordinate system. It has the potential to improve patient safety.

Evaluating Network Threshold Selection for Structural and Functional Brain Connectomes

Structural and functional brain connectomes represent macroscale neurophysical data collected through methods such as magnetic resonance imaging (MRI). Such data may contain noise that contribute to false positive edges, which motivates the use of edge-wise thresholding. Thresholding procedures are useful for reducing network density in graphs to retain only the most informative, non-noisy edges. Nevertheless, limited consensus exists on selecting appropriate threshold levels. We compare existing thresholding methods and introduce a novel thresholding approach in the context of MRI-derived and simulated brain connectomes. Performance is measured using normalized mutual information (NMI), a quantity robust to arbitrary changes in partition labeling, and describes the similarity of community structure between two node-matched networks. We found that the percolation-based threshold and our newly proposed objective function-based threshold exhibited the best performance in terms of NMI. We show an application of these two thresholding methods to real data that showed that both percolation-based and objective function-based thresholding provide statistically similar NMI values between real world FC networks and structural connectivity (SC) counterparts, where shared modular structure is assumed. The two thresholding methods, however, achieve these NMI values at significantly different thresholds (p<0.0001) in both simulated and real networks. Moreover, the threshold obtained from the objective function gives a more accurate estimate of the number of modules present in the network and includes more flexibility in threshold selection, suggesting that this method may represent a useful option for graph thresholding.

Multi-objective NSGA-II based community detection using dynamical evolution social network

Community detection is becoming a highly demanded topic in social networking-based applications. It involves finding the maximum intraconnected and minimum inter-connected sub-graphs in given social networks. Many approaches have been developed for community’s detection and less of them have focused on the dynamical aspect of the social network. The decision of the community has to consider the pattern of changes in the social network and to be smooth enough. This is to enable smooth operation for other community detection dependent application. Unlike dynamical community detection Algorithms, this article presents a non-dominated aware searching Algorithm designated as non-dominated sorting based community detection with dynamical awareness (NDS-CD-DA). The Algorithm uses a non-dominated sorting genetic algorithm NSGA-II with two objectives: modularity and normalized mutual information (NMI). Experimental results on synthetic networks and real-world social network datasets have been compared with classical genetic with a single objective and has been shown to provide superiority in terms of the domination as well as the convergence. NDS-CD-DA has accomplished a domination percentage of 100% over dynamic evolutionary community searching DECS for almost all iterations.

GNN-DBSCAN: A new density-based algorithm using grid and the nearest neighbor

DBSCAN (density-based spatial clustering of applications with noise) is one of the most widely used density-based clustering algorithms, which can find arbitrary shapes of clusters, determine the number of clusters, and identify noise samples automatically. However, the performance of DBSCAN is significantly limited as it is quite sensitive to the parameters of eps and MinPts. Eps represents the eps-neighborhood and MinPts stands for a minimum number of points. Additionally, a dataset with large variations in densities will probably trap the DBSCAN because its parameters are fixed. In order to overcome these limitations, we propose a new density-clustering algorithm called GNN-DBSCAN which uses an adaptive Grid to divide the dataset and defines local core samples by using the Nearest Neighbor. With the help of grid, the dataset space will be divided into a finite number of cells. After that, the nearest neighbor lying in every filled cell and adjacent filled cells are defined as the local core samples. Then, GNN-DBSCAN obtains global core samples by enhancing and screening local core samples. In this way, our algorithm can identify higher-quality core samples than DBSCAN. Lastly, give these global core samples and use dynamic radius based on k-nearest neighbors to cluster the datasets. Dynamic radius can overcome the problems of DBSCAN caused by its fixed parameter eps. Therefore, our method can perform better on dataset with large variations in densities. Experiments on synthetic and real-world datasets were conducted. The results indicate that the average Adjusted Rand Index (ARI), Normalized Mutual Information (NMI), Adjusted Mutual Information (AMI) and V-measure of our proposed algorithm outperform the existing algorithm DBSCAN, DPC, ADBSCAN, and HDBSCAN.

Fault Detection and Diagnosis for Plasticizing Process of Single-Base Gun Propellant Using Mutual Information Weighted MPCA under Limited Batch Samples Modelling

Aiming at the lack of reliable gradual fault detection and abnormal condition alarm and evaluation ability in the plasticizing process of single-base gun propellant, a fault detection and diagnosis method based on normalized mutual information weighted multiway principal component analysis (NMI-WMPCA) under limited batch samples modelling was proposed. In this method, the differences of coupling correlation among multi-dimensional process variables and the coupling characteristics of linear and nonlinear relationships in the process are considered. NMI-WMPCA utilizes the generalization ability of a multi-model to establish an accurate fault detection model in limited batch samples, and adopts fault diagnosis methods based on a multi-model SPE statistic contribution plot to identify the fault source. The experimental results demonstrate that the proposed method is effective, which can realize the rapid detection and diagnosis of multiple faults in the plasticizing process.