Scaling of weighted spectral distribution in weighted small-world networks

Many real-world systems can be modeled by weighted small-world networks with high clustering coefficients. Recent studies for rigorously analyzing the weighted spectral distribution（W SD） have focused on unweighted networks with low clustering coefficients. In this paper, we rigorously analyze the W SD in a deterministic weighted scale-free small-world network model and find that the W SD grows sublinearly with increasing network order（i.e., the number of nodes） and provides a sensitive discrimination for each input of this model. This study demonstrates that the scaling feature of the W SD exists in the weighted network model which has high and order-independent clustering coefficients and reasonable power-law exponents.

Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning

Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).

Structural Characteristics and Evolution of a Weighted Sino-US Container Shipping Network

This study selected the Sino-US route data from the top 30 global container liner companies between December 1,2019,and December 29,2019,as the data source utilizing the complex network research methodology.It constructs a Sino-US container shipping network through voyage weighting and analyzes the essential structural characteristics to explore the network’s complex structural fea-tures.The network’s evolution is examined from three perspectives,namely,time,space,and event influence,aiming to comprehens-ively explore the network’s evolution mechanism.The results revealed that:1)the weighted Sino-US container shipping network exhib-its small-world and scale-free properties.Key hub ports in the United States include NEW YORK NY,SAVANNAH GA,LOS ANGELES CA,and OAKLAND CA,whereas SHANGHAI serving as the hub port in China.The geographical distribution of these hub ports is uneven.2)Concerning the evolution of the weighted Sino-US container shipping network,from a temporal perspective,the evolution of the regional structure of the entire Sino-US region and the Inland United States is in a stage of radiative expansion and de-velopment,with a need for further enhancement in competitiveness and development speed.The evolution of the regional structure of southern China and Europe is transitioning from the stage of radiative expansion and development to an advanced equilibrium stage.The shipping development in Northern China,the Western and Eastern United States,and Asia is undergoing significant changes but faces challenges of fierce competition and imbalances.From a spatial perspective,the rationality and effectiveness of the improved weighted Barrat-Barthelemy-Vespignani(BBV)model are confirmed through theoretical derivation.The applicability of the improved evolution model is verified by simulating the evolution of the weighted Sino-US container shipping network.From an event impact per-spective,the Corona Virus Disease 2019(COVID-19)pandemic has not fundamentally affected the spatial pattern of the weighted Sino-US container shipping network but has significantly impacted the network’s connectivity.The network lacks sufficient resilience and stability in emergency situations.3)Based on the analysis of the structural characteristics and evolution of the weighted Sino-US con-tainer shipping network,recommendations for network development are proposed from three aspects:emphasizing the development of hub ports,focusing on the balanced development of the network,and optimizing the layout of Chinese ports.

Exploration of the efficacy and mechanism of treating head wind disease with the combination change of ginger volatile oil and gingerol by using content-weighted network pharmacology technology

Background:Exploring the efficacy,potential components,and mechanism of the combination of ginger essential oil and gingerols in the treatment of head wind disease based on network pharmacology technology with content weight.Methods:The experimental groups were divided into:0:10,1:4,1:2,1:1,2:1,4:1,10:0.The relative content(Ri)of the chemical constituents of ginger's volatile oil was determined using gas chromatography-mass spectrometry(GC-MS).Additionally,the physicochemical and biological property parameters(LogP,MDCK,PPB,MW)of the components were considered.To assess the quantitative effect of the components,a grading score was performed,and the quantitative effect index(Ki)was calculated.Subsequently,the target effect index(Ti)was calculated by combining the component-target matching score(Fit score).Using these calculations,the target effect score A was determined under the influence of multiple components targeting different targets.Key targets with A≥1000 were identified.To predict the targets related to head wind disease,the Comparative Toxicogenomics Database(https://ctdbase.org/),Gene Cards(https://www.genecards.org/),and Disgenet database(https://www.disgenet.org/)were utilized.The key targets,obtained from different proportions of ginger's volatile oil and gingerol,were intersected with the predicted targets.This facilitated network pharmacological analysis and verification of the efficacy.Results:The content of volatile oil in ginger demonstrated an impact on key targets associated with the volatile oil group.Each specific combination of volatile oil consistently activated distinct pathways,with variations stemming from changes in content.Experimental testing revealed that different combinations of ginger's volatile oil and gingerol effectively alleviated migraine symptoms in rats.Conclusion:Through the application of content-weighted network pharmacology technology and pharmacodynamic verification,it was determined that altering the ratio between ginger's volatile oil and gingerol leads to variations in potential targets and pathways,consequently impacting its efficacy.

Dynamical behaviors in discrete memristor-coupled small-world neuronal networks

The brain is a complex network system in which a large number of neurons are widely connected to each other and transmit signals to each other.The memory characteristic of memristors makes them suitable for simulating neuronal synapses with plasticity.In this paper,a memristor is used to simulate a synapse,a discrete small-world neuronal network is constructed based on Rulkov neurons and its dynamical behavior is explored.We explore the influence of system parameters on the dynamical behaviors of the discrete small-world network,and the system shows a variety of firing patterns such as spiking firing and triangular burst firing when the neuronal parameterαis changed.The results of a numerical simulation based on Matlab show that the network topology can affect the synchronous firing behavior of the neuronal network,and the higher the reconnection probability and number of the nearest neurons,the more significant the synchronization state of the neurons.In addition,by increasing the coupling strength of memristor synapses,synchronization performance is promoted.The results of this paper can boost research into complex neuronal networks coupled with memristor synapses and further promote the development of neuroscience.

Weighted gene co-expression network analysis reveals similarities and differences of molecular features between dilated and ischemic cardiomyopathies

Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different classes of cardiomyopathies remain elusive.This paper aims to describe the similarities and differences in molecular features of dilated cardiomyopathy(DCM)and ischemic cardiomyopathy(ICM).We firstly detected the co-expressed modules using the weighted gene co-expression network analysis(WGCNA).Significant modules associated with DCM/ICM were identified by the Pearson correlation coefficient(PCC)between the modules and the phenotype of DCM/ICM.The differentially expressed genes in the modules were selected to perform functional enrichment.The potential transcription factors(TFs)prediction was conducted for transcription regulation of hub genes.Apoptosis and cardiac conduction were perturbed in DCM and ICM,respectively.TFs demonstrated that the biomarkers and the transcription regulations in DCM and ICM were different,which helps make more accurate discrimination between them at molecular levels.In conclusion,comprehensive analyses of the molecular features may advance our understanding of DCM and ICM causes and progression.Thus,this understanding may promote the development of innovative diagnoses and treatments.

Research on Node Classification Based on Joint Weighted Node Vectors

Node of network has lots of information, such as topology, text and label information. Therefore, node classification is an open issue. Recently, one vector of node is directly connected at the end of another vector. However, this method actually obtains the performance by extending dimensions and considering that the text and structural information are one-to-one, which is obviously unreasonable. Regarding this issue, a method by weighting vectors is proposed in this paper. Three methods, negative logarithm, modulus and sigmoid function are used to weight-trained vectors, then recombine the weighted vectors and put them into the SVM classifier for evaluation output. By comparing three different weighting methods, the results showed that using negative logarithm weighting achieved better results than the other two using modulus and sigmoid function weighting, and was superior to directly concatenating vectors in the same dimension.

Role-Based Network Embedding via Quantum Walk with Weighted Features Fusion

Role-based network embedding aims to embed role-similar nodes into a similar embedding space,which is widely used in graph mining tasks such as role classification and detection.Roles are sets of nodes in graph networks with similar structural patterns and functions.However,the rolesimilar nodes may be far away or even disconnected from each other.Meanwhile,the neighborhood node features and noise also affect the result of the role-based network embedding,which are also challenges of current network embedding work.In this paper,we propose a Role-based network Embedding via Quantum walk with weighted Features fusion(REQF),which simultaneously considers the influence of global and local role information,node features,and noise.Firstly,we capture the global role information of nodes via quantum walk based on its superposition property which emphasizes the local role information via biased quantum walk.Secondly,we utilize the quantum walkweighted characteristic function to extract and fuse features of nodes and their neighborhood by different distributions which contain role information implicitly.Finally,we leverage the Variational Auto-Encoder(VAE)to reduce the effect of noise.We conduct extensive experiments on seven real-world datasets,and the results show that REQF is more effective at capturing role information in the network,which outperforms the best baseline by up to 14.6% in role classification,and 23% in role detection on average.

Identification of key genes underlying clinical features of hepatocellular carcinoma based on weighted gene co‑expression network analysis and bioinformatics analysis

Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagnosis and treatment. Methods: GSE84598 chip data were downloaded from the GEO database, and module genes closely related to the clinical features of HCC were extracted by comprehensive weighted gene co‑expression network analysis. Hub genes were identified through protein interaction network analysis by the maximum clique centrality (MCC) algorithm;Finally, the expression of hub genes was validated by TCGA database and the Kaplan Meier plotter online database was used to evaluate the prognostic relationship between hub genes and HCC patients. Results: By comparing the gene expression data between HCC tissue samples and normal liver tissue samples, a total of 6 262 differentially expressed genes were obtained, of which 2 207 were upregulated and 4 055 were downregulated. Weighted gene co‑expression network analysis was applied to identify 120 genes of key modules. By intersecting with the differentially expressed genes, 115 candidate hub genes were obtained. The results of enrichment analysis showed that the candidate hub genes were closely related to cell mitosis, p53 signaling pathway and so on. Further application of the MCC algorithm to the protein interaction network of 115 candidate hub genes identified five hub genes, namely NUF2, RRM2, UBE2C, CDC20 and MAD2L1. Validation of hub genes by TCGA database revealed that all five hub genes were significantly upregulated in HCC tissues compared to normal liver tissues;Moreover, survival analysis revealed that high expression of hub genes was closely associated with poor prognosis in HCC patients. Conclusions: This study identifies five hub genes by combining multiple databases, which may provide directions for the clinical diagnosis and treatment of HCC.

Exploring the mechanism of Guizhi decoction’s“Jun-Chen-Zuo-Shi”in treating plant nervous disorders based on weighted network pharmacology and molecular docking techniques

Objective:To explore the mechanism of Guizhi decoction’s“Jun-Chen-Zuo-Shi”in treating plant nervous disorders based on network pharmacology and molecular docking methods.Methods:The main active ingredients of Guizhi decoction were screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP),and plant nervous disorder-related targets were screened from the Gene Cards database,OMIM database,and PharmGKB database.The intersection of the two was obtained.The intersection targets were used to draw a protein interaction network and a“Traditional Chinese Medicine-active ingredient-target”network using the STRING database and Cytoscape 3.9.1.The nodes in the“Traditional Chinese Medicine-active ingredient-target”network were weighted according to the“Jun-Chen-Zuo-Shi”principle.Kyoto Encyclopedia of Genes and Genomes,and gene ontology enrichment analysis were performed on the intersection targets.Molecular docking was used to verify the affinity between core targets and key ingredients.Results:A total of 225 effective components of Guizhi decoction were screened,among which 127 components could bind to 160 common targets and play a therapeutic role.The common targets were mainly enriched in 2785 gene ontology entries and 189 Kyoto Encyclopedia of Genes and Genomes pathways.Molecular docking confirmed that core targets could spontaneously bind to key ingredients.Conclusion:The key targets for the treatment of plant nervous disorders by Guizhi decoction are MAPK1,TP53,RB1,STAT3,MAPK3,MAPK14,etc.,which reflect the characteristics of the synergistic mechanism of traditional Chinese medicine with multiple components,targets,and pathways through the regulation of inflammatory signal pathways and oxidative stress processes.

Study Under AC Stimulation on Excitement Properties of Weighted Small-World Biological Neural Networks with Side-Restrain Mechanism

In this paper, we propose a new model of weighted small-world biological neural networks based on biophysical Hodgkin-Huxley neurons with side-restrain mechanism. Then we study excitement properties of the model under alternating current （AC） stimulation. The study shows that the excitement properties in the networks are preferably consistent with the behavior properties of a brain nervous system under different AC stimuli, such as refractory period and the brain neural excitement response induced by different intensities of noise and coupling. The results of the study have reference worthiness for the brain nerve electrophysiology and epistemological science.

Prediction of Subcellular Localization of Eukaryotic Proteins Using Position-Specific Profiles and Neural Network with Weighted Inputs

Subcellular location is one of the key biological characteristics of proteins. Position-specific profiles （PSP） have been introduced as important characteristics of proteins in this article. In this study, to obtain position-specific profiles, the Position Specific lterative-Basic Local Alignment Search Tool （PSI-BLAST） has been used to search for protein sequences in a database. Position-specific scoring matrices are extracted from the profiles as one class of characteristics. Four-part amino acid compositions and lst-7th order dipeptide compositions have also been calculated as the other two classes of characteristics. Therefore, twelve characteristic vectors are extracted from each of the protein sequences. Next, the characteristic vectors are weighed by a simple weighing function and inputted into a BP neural network predictor named PSP-Weighted Neural Network （PSP-WNN）. The Levenberg-Marquardt algorithm is employed to adjust the weight matrices and thresholds during the network training instead of the error back propagation algorithm. With a jackknife test on the RH2427 dataset, PSP-WNN has achieved a higher overall prediction accuracy of 88.4% rather than the prediction results by the general BP neural network, Markov model, and fuzzy k-nearest neighbors algorithm on this dataset. In addition, the prediction performance of PSP-WNN has been evaluated with a five-fold cross validation test on the PK7579 dataset and the prediction results have been consistently better than those of the previous method on the basis of several support vector machines, using compositions of both amino acids and amino acid pairs. These results indicate that PSP-WNN is a powerful tool for subcellular localization prediction. At the end of the article, influences on prediction accuracy using different weighting proportions among three characteristic vector categories have been discussed. An appropriate proportion is considered by increasing the prediction accuracy.

Brain Functional Network Based on Small-Worldness and Minimum Spanning Tree for Depression Analysis

Since the outbreak and spread of corona virus disease 2019(COVID-19),the prevalence of mental disorders,such as depression,has continued to increase.To explore the abnormal changes of brain functional connections in patients with depression,this paper proposes a depression analysis method based on brain function network(BFN).To avoid the volume conductor effect,BFN was constructed based on phase lag index(PLI).Then the indicators closely related to depression were selected from weighted BFN based on small-worldness(SW)characteristics and binarization BFN based on the minimum spanning tree(MST).Differences analysis between groups and correlation analysis between these indicators and diagnostic indicators were performed in turn.The resting state electroencephalogram(EEG)data of 24 patients with depression and 29 healthy controls(HC)was used to verify our proposed method.The results showed that compared with HC,the information processing of BFN in patients with depression decreased,and BFN showed a trend of randomization.

Generalized chaos synchronization of a weighted complex network with different nodes

This paper proposes a method of realizing generalized chaos synchronization of a weighted complex network with different nodes. Chaotic systems with diverse structures are taken as the nodes of the complex dynamical network, the nonlinear terms of the systems are taken as coupling functions, and the relations among the nodes are built through weighted connections. The structure of the coupling functions between the connected nodes is obtained based on Lyapunov stability theory. A complex network with nodes of Lorenz system, Coullet system, RSssler system and the New system is taken as an example for simulation study and the results show that generalized chaos synchronization exists in the whole weighted complex network with different nodes when the coupling strength among the nodes is given with any weight value. The method can be used in realizing generalized chaos synchronization of a weighted complex network with different nodes. Furthermore, both the weight value of the coupling strength among the nodes and the number of the nodes have no effect on the stability of synchronization in the whole complex network.

Exploring evolutionary features of directed weighted hazard network in the subway construction

A better understanding of previous accidents is an effective way to reduce the occurrence of similar accidents in the future. In this paper, a complex network approach is adopted to construct a directed weighted hazard network(DWHN) to analyze topological features and evolution of accidents in the subway construction. The nodes are hazards and accidents, the edges are multiple relationships of these nodes and the weight of edges are occurrence times of repetitive relationships. The results indicate that the DWHN possesses the property of small-world with small average path length and large clustering coefficient, indicating that hazards have better connectivity and will spread widely and quickly in the network. Moreover,the DWHN has the property of scale-free network for the cumulative degree distribution follows a power-law distribution.It makes DWHN more vulnerable to target attacks. Controlling key nodes with higher degree, strength and betweenness centrality will destroy the connectivity of DWHN and mitigate the spreading of accidents in the network. This study is helpful for discovering inner relationships and evolutionary features of hazards and accidents in the subway construction.

Weighted Correlation Network Analysis(WGCNA) of Japanese Flounder(Paralichthys olivaceus) Embryo Transcriptome Provides Crucial Gene Sets for Understanding Haploid Syndrome and Rescue by Diploidization

Artificial gynogenesis is of great research value in fish genetics and breeding technology. However, existing studies did not explain the mechanism of some interesting phenomena. Severe developmental defects in gynogenetic haploids can lead to death during hatching. After diploidization of chromosomes, gynogenetic diploids may dispense from the remarkable malformation and restore the viability, although the development time is longer and the survival rate is lower compared with normal diploids. The aim of this study was to reveal key mechanism in haploid syndrome of Japanese flounder, a commercially important marine teleost in East Asia. We measured genome-scale gene expression of flounder haploid, gynogenetic diploid and normal diploid embryos using RNA-Seq, constructed a module-centric co-expression network based on weighted correlation network analysis(WGCNA) and analyzed the biological functions of correlated modules. Module gene content analysis revealed that the formation of gynogenetic haploids was closely related to the abnormality of plasma proteins, and the up-regulation of p53 signaling pathway might rescue gynogenetic embryos from haploid syndrome via regulating cell cycle arrest, apoptosis and DNA repair. Moreover, normal diploid has more robust nervous system. This work provides novel insights into molecular mechanisms in haploid syndrome and the rescue process by gynogenetic diploidization.

Weighted average consensus problem in networks of agents with diverse time-delays

This paper studies the weighted average consensus problem for networks of agents with fixed directed asymmetric unbalance information exchange topology. We suppose that the classical distributed consensus protocol is destroyed by diverse time-delays which include communication time-delay and self time-delay. Based on the generalized Nyquist stability criterion and the Gerschgorin disk theorem, some sufficient conditions for the consensus of multi-agent systems are obtained. And we give the expression of the weighted average consensus value for our consensus protocol. Finally, numerical examples are presented to illustrate the theoretical results.

FEW-NNN: A Fuzzy Entropy Weighted Natural Nearest Neighbor Method for Flow-Based Network Traffic Attack Detection

Attacks such as APT usually hide communication data in massive legitimate network traffic, and mining structurally complex and latent relationships among flow-based network traffic to detect attacks has become the focus of many initiatives. Effectively analyzing massive network security data with high dimensions for suspicious flow diagnosis is a huge challenge. In addition, the uneven distribution of network traffic does not fully reflect the differences of class sample features, resulting in the low accuracy of attack detection. To solve these problems, a novel approach called the fuzzy entropy weighted natural nearest neighbor(FEW-NNN) method is proposed to enhance the accuracy and efficiency of flowbased network traffic attack detection. First, the FEW-NNN method uses the Fisher score and deep graph feature learning algorithm to remove unimportant features and reduce the data dimension. Then, according to the proposed natural nearest neighbor searching algorithm(NNN_Searching), the density of data points, each class center and the smallest enclosing sphere radius are determined correspondingly. Finally, a fuzzy entropy weighted KNN classification method based on affinity is proposed, which mainly includes the following three steps: 1、 the feature weights of samples are calculated based on fuzzy entropy values, 2、 the fuzzy memberships of samples are determined based on affinity among samples, and 3、 K-neighbors are selected according to the class-conditional weighted Euclidean distance, the fuzzy membership value of the testing sample is calculated based on the membership of k-neighbors, and then all testing samples are classified according to the fuzzy membership value of the samples belonging to each class;that is, the attack type is determined. The method has been applied to the problem of attack detection and validated based on the famous KDD99 and CICIDS-2017 datasets. From the experimental results shown in this paper, it is observed that the FEW-NNN method improves the accuracy and efficiency of flow-based network traffic attack detection.

Comparison of Artificial Neural Networks,Geographically Weighted Regression and Cokriging Methods for Predicting the Spatial Distribution of Soil Macronutrients(N,P,and K)

Soil macronutrients(i.e. nitrogen(N), phosphorus(P), and potassium(K)) are important soils components and knowing the spatial distribution of these parameters are necessary at precision agriculture. The purpose of this study was to evaluate the feasibility of different methods such as artificial neural networks(ANN) and two geostatistical methods(geographically weighted regression(GWR) and cokriging(CK)) to estimate N, P and K contents. For this purpose, soil samples were taken from topsoil(0–30 cm) at 106 points and analyzed for their chemical and physical parameters. These data were divided into calibration(n = 84) and validation(n = 22). Chemical and physical variables including clay, p H and organic carbon(OC) were used as auxiliary soil variables to estimate the N, P and K contents. Results showed that the ANN model(with coefficient of determination R^2 = 0.922 and root mean square error RMSE = 0.0079%) was more accurate compared to the CK model(with R^2 = 0.612 and RMSE = 0.0094%), and the GWR model(with R^2 = 0.872 and RMSE = 0.0089%) to estimate the N variable. The ANN model estimated the P with the RMSE of 3.630 ppm, which was respectively 28.93% and 20.00% less than the RMSE of 4.680 ppm and 4.357 ppm from the CK and GWR models. The estimated K by CK, GWR and ANN models have the RMSE of 76.794 ppm, 75.790 ppm and 52.484 ppm. Results indicated that the performance of the CK model for estimation of macro nutrients(N, P and K) was slightly lower than the GWR model. Also, the accuracy of the ANN model was higher than CK and GWR models, which proved to be more effective and reliable methods for estimating macro nutrients.

Entropy-based link prediction in weighted networks

Information entropy has been proved to be an effective tool to quantify the structural importance of complex networks.In a previous work [Xu et al. Physica A, 456 294（2016）], we measure the contribution of a path in link prediction with information entropy. In this paper, we further quantify the contribution of a path with both path entropy and path weight,and propose a weighted prediction index based on the contributions of paths, namely weighted path entropy（WPE）, to improve the prediction accuracy in weighted networks. Empirical experiments on six weighted real-world networks show that WPE achieves higher prediction accuracy than three other typical weighted indices.