A bio-inspired methodology of identifying influential nodes in complex networks

Combined bioinformatics technology to explore pivot genes and related clinical prognosis in the development of gastric cancer

To screen the key genes in the development of gastric cancer and their influence on prognosis. The GEO database was used to screen gastric cancer-related gene chips as a training set, and the R packages limma tool was used to analyze the differential genes expressed in gastric cancer tissues compared to normal tissues, and then the selected genes were verified in the validation set. The String database was used to calculate their Protein–protein interaction (PPI) network, using Cytoscape software's Centiscape and other plug-ins to analyze key genes in the PPI network. The DAVID database was used to enrich and annotate gene functions of differential genes and PPI key module genes, and further explore correlation between expression level and clinical stage and prognosis. Based on clinical data and patient samples, differential expression of key node genes was verified by immunohistochemistry. The 63 characteristic differential genes screened had good discrimination between gastric cancer and normal tissues, and are mainly involved in regulating extracellular matrix receptor interactions and the PI3k-AKT signaling pathway. Key nodes in the PPI network regulate tumor proliferation and metastasis. Analysis of the expression levels of key node genes found that relative to normal tissues, the expression of ITGB1 and COL1A2 was significantly increased in gastric cancer tissues, and patients with late clinical stages of tumors had higher expression of ITGB1 and COL1A2 in tumor tissues, and their survival time was longer (P < 0.05). This study found that ITGB1 and COL1A2 are key genes in the development of gastric cancer and can be used as prognostic markers and potential new targets for gastric cancer.

Physarum-Inspired Bicycle Lane Network Design in a Congested Megacity

Improvement of mobility, especially environment-friendly green mobility, is challenging in existing megacities due to road network complexity and space constraints. Endorsing the bicycle lane network (BLN) in congested megacities is a promising option to foster green mobility. This research presents a novel bioinspired network design method that considers various constraints and preferences related to the megacity for designing an optimal BLN. The proposed method is inspired by natural Physarum polycephalum, a brainless, multi-headed single-celled organism, which is capable of developing a reticulated network of complex foraging behaviors in pursuit of food. The mathematical model of Physarum foraging behavior is adapted to maneuver various BLN constraints in megacity contexts in designing the optimal BLN. The Physarum-inspired BLN method is applied to two case studies on the megacity Dhaka for designing BLNs: the first one covers congested central city area, and the second one covers a broader area that includes major locations of the city. The obtained BLNs were evaluated comparing their available routes between different locations with the existing vehicle routes of the city in terms of distance and required travel times in different time periods, and the BLN routes were found to be suitable alternatives for avoiding congested main roads. The expected travel time using BLNs is shorter than other transport (e.g., car and public bus); additionally, at glance, the average travel speed on BLNs is almost double that of public buses in peak hours. Finally, the designed BLNs are promising for environment-friendly and healthy mobility.

Mapping knowledge structures and theme trends of atopic dermatitis: a co-word biclustering and quantitative analysis of the publication between 2015 and 2019

BACKGROUND

Atopic dermatitis (AD) has been a hot research direction of dermatologists for a long time. However, the knowledge structures and theme trends for AD have not yet been studied bibliometrically.

OBJECTIVE

To investigate the distribution pattern and knowledge structure of AD related literatures in PubMed.

METHODS

Bibliographic information was generated by the Bibliographic Item Co-Occurrence Matrix Builder (BICOMB). A visual matrix was created by the gCLUTO software. GraphPad Prism 5 software was used to construct a Strategic diagram analysis. Ucinet 6.0 software and NetDraw 2.084 software were used to generate a social network analysis (SNA).

RESULTS

Among all the extracted MeSH terms and subheadings, 77 MeSH terms/MeSH subheadings with a high-frequency were identified, and hot topics were gathered together into 6 groups. In the strategic diagram, immunology, microbiology, and drug therapy of AD were fully developed. In contrast, prevention, pathology, genetics, metabolism, administration, cost of illness, quality of life therapeutic paradigm, and immunosuppressive agents of AD were considerably immature offering prospective scope for further research.

CONCLUSIONS

The results may potentially aid in describing an all-round grasp of the current research areas and furnish guidelines for the researchers for beginning new projects.

Heatmap centrality: A new measure to identify super-spreader nodes in scale-free networks

The identification of potential super-spreader nodes within a network is a critical part of the study and analysis of real-world networks. Motivated by a new interpretation of the "shortest path" between two nodes, this paper explores the properties of the heatmap centrality by comparing the farness of a node with the average sum of farness of its adjacent nodes in order to identify influential nodes within the network. As many real-world networks are often claimed to be scale-free, numerical experiments based upon both simulated and real-world undirected and unweighted scale-free networks are used to illustrate the effectiveness of the proposed "shortest path" based measure with regards to its CPU run time and ranking of influential nodes.

Compact models for influential nodes identification problem in directed networks

Influential nodes identification problem (INIP) is one of the most important problems in complex networks. Existing methods mainly deal with this problem in undirected networks, while few studies focus on it in directed networks. Moreover, the methods designed for identifying influential nodes in undirected networks do not work for directed networks. Therefore, in this paper, we investigate INIP in directed networks. We first propose a novel metric to assess the influence effect of nodes in directed networks. Then, we formulate a compact model for INIP and prove it to be NP-Complete. Furthermore, we design a novel heuristic algorithm for the proposed model by integrating a 2-opt local search into a greedy framework. The experimental results show that, in most cases, the proposed methods outperform traditional measure-based heuristic methods in terms of accuracy and discrimination.

Research on the Node Importance of a Weighted Network Based on the K-Order Propagation Number Algorithm

To describe both the global and local characteristics of a network more comprehensively, we propose the weighted K-order propagation number (WKPN) algorithm to extract the disease propagation based on the network topology to evaluate the node importance. Each node is set as the source of infection, and the total number of infected nodes is defined as the K-order propagation number after experiencing the propagation time K. The simulation of the symmetric network with bridge nodes indicated that the WKPN algorithm was more effective for evaluation of the algorithm features. A deliberate attack strategy, which indicated an attack on the network according to the node importance from high to low, was employed to evaluate the WKPN algorithm in real networks. Compared with the other methods tested, the results demonstrate the applicability and advancement that a lower number of nodes, with a higher importance calculated by the K-order propagation number algorithm, has to achieve full damage to the network structure.

Benchmarking seeding strategies for spreading processes in social networks: an interplay between influencers, topologies and sizes

The explosion of network science has permitted an understanding of how the structure of social networks affects the dynamics of social contagion. In community-based interventions with spill-over effects, identifying influential spreaders may be harnessed to increase the spreading efficiency of social contagion, in terms of time needed to spread all the largest connected component of the network. Several strategies have been proved to be efficient using only data and simulation-based models in specific network topologies without a consensus of an overall result. Hence, the purpose of this paper is to benchmark the spreading efficiency of seeding strategies related to network structural properties and sizes. We simulate spreading processes on empirical and simulated social networks within a wide range of densities, clustering coefficients, and sizes. We also propose three new decentralized seeding strategies that are structurally different from well-known strategies: community hubs, ambassadors, and random hubs. We observe that the efficiency ranking of strategies varies with the network structure. In general, for sparse networks with community structure, decentralized influencers are suitable for increasing the spreading efficiency. By contrast, when the networks are denser, centralized influencers outperform. These results provide a framework for selecting efficient strategies according to different contexts in which social networks emerge.

Identifying Influential Nodes in Complex Networks Based on Local Effective Distance

With the rapid development of Internet technology, the social network has gradually become an indispensable platform for users to release information, obtain information, and share information. Users are not only receivers of information, but also publishers and disseminators of information. How to select a certain number of users to use their influence to achieve the maximum dissemination of information has become a hot topic at home and abroad. Rapid and accurate identification of influential nodes in the network is of great practical significance, such as the rapid dissemination, suppression of social network information, and the smooth operation of the network. Therefore, from the perspective of improving computational accuracy and efficiency, we propose an influential node identification method based on effective distance, named KDEC. By quantifying the effective distance between nodes and combining the position of the node in the network and its local structure, the influence of the node in the network is obtained, which is used as an indicator to evaluate the influence of the node. Through experimental analysis of a lot of real-world networks, the results show that the method can quickly and accurately identify the influential nodes in the network, and is better than some classical algorithms and some recently proposed algorithms.

Mapping the knowledge structure and trends of epilepsy genetics over the past decade: A co-word analysis based on medical subject headings terms

INTRODUCTION

Over the past 10 years, epilepsy genetics has made dramatic progress. This study aimed to analyze the knowledge structure and the advancement of epilepsy genetics over the past decade based on co-word analysis of medical subject headings (MeSH) terms.

METHODS

Scientific publications focusing on epilepsy genetics from the PubMed database (January 2009-December 2018) were retrieved. Bibliometric information was analyzed quantitatively using Bibliographic Item Co-Occurrence Matrix Builder (BICOMB) software. A knowledge social network analysis and publication trend based on the high-frequency MeSH terms was built using VOSviewer.

RESULTS

According to the search strategy, a total of 5185 papers were included. Among all the extracted MeSH terms, 86 high-frequency MeSH terms were identified. Hot spots were clustered into 5 categories including: "ion channel diseases," "beyond ion channel diseases," "experimental research & epigenetics," "single nucleotide polymorphism & pharmacogenetics," and "genetic techniques". "Epilepsy," "mutation," and "seizures," were located at the center of the knowledge network. "Ion channel diseases" are typically in the most prominent position of epilepsy genetics research. "Beyond ion channel diseases" and "genetic techniques," however, have gradually grown into research cores and trends, such as "intellectual disability," "infantile spasms," "phenotype," "exome," " deoxyribonucleic acid (DNA) copy number variations," and "application of next-generation sequencing." While ion channel genes such as "SCN1A," "KCNQ2," "SCN2A," "SCN8A" accounted for nearly half of epilepsy genes in MeSH terms, a number of additional beyond ion channel genes like "CDKL5," "STXBP1," "PCDH19," "PRRT2," "LGI1," "ALDH7A1," "MECP2," "EPM2A," "ARX," "SLC2A1," and more were becoming increasingly popular. In contrast, gene therapies, treatment outcome, and genotype-phenotype correlations were still in their early stages of research.

CONCLUSION

This co-word analysis provides an overview of epilepsy genetics research over the past decade. The 5 research categories display publication hot spots and trends in epilepsy genetics research which could consequently supply some direction for geneticists and epileptologists when launching new projects.

A Physarum Centrality Measure of the Human Brain Network

The most important goals of brain network analyses are to (a) detect pivotal regions and connections that contribute to disproportionate communication flow, (b) integrate global information, and (c) increase the brain network efficiency. Most centrality measures assume that information propagates in networks with the shortest connection paths, but this assumption is not true for most real networks given that information in the brain propagates through all possible paths. This study presents a methodological pipeline for identifying influential nodes and edges in human brain networks based on the self-regulating biological concept adopted from the Physarum model, thereby allowing the identification of optimal paths that are independent of the stated assumption. Network hubs and bridges were investigated in structural brain networks using the Physarum model. The optimal paths and fluid flow were used to formulate the Physarum centrality measure. Most network hubs and bridges are overlapped to some extent, but those based on Physarum centrality contain local and global information in the superior frontal, anterior cingulate, middle temporal gyrus, and precuneus regions. This approach also reduced individual variation. Our results suggest that the Physarum centrality presents a trade-off between the degree and betweenness centrality measures.

Theme trends and knowledge structure on choroidal neovascularization: a quantitative and co-word analysis

Background

The distribution pattern and knowledge structure of choroidal neovascularization (CNV) was surveyed based on literatures in PubMed.

Methods

Published scientific papers about CNV were retrieved from Jan 1st, 2012 to May 31st, 2017. Extracted MeSH terms were analyzed quantitatively by using Bibliographic Item Co-Occurrence Matrix Builder (BICOMB) and high-frequency MeSH terms were identified. Hierarchical cluster analysis was conducted by SPSS 19.0 according to the MeSH term-source article matrix. High-frequency MeSH terms co-occurrence matrix was constructed to support strategic diagram and social network analysis (SNA).

Results

According to the searching strategy, all together 2366 papers were included, and the number of annual papers changed slightly from Jan 1st, 2012 to May 31st, 2017. Among all the extracted MeSH terms, 44 high-frequency MeSH terms were identified and hotspots were clustered into 6 categories. In the strategic diagram, clinical drug therapy, pathology and diagnosis related researches of CNV were well developed. In contrast, the metabolism, etiology, complications, prevention and control of CNV in animal models, and genetics related researches of CNV were relatively immature, which offers potential research space for future study. As for the SNA result, the position status of each component was described by the centrality values.

Conclusions

The studies on CNV are relatively divergent and the 6 research categories concluded from this study could reflect the publication trends on CNV to some extent. By providing a quantitative bibliometric research across a 5-year span, it could help to depict an overall command of the latest topics and provide some hints for researchers when launching new projects.

A study of structural properties of gene network graphs for mathematical modeling of integrated mosaic gene networks

Gene network modeling is one of the widely used approaches in systems biology. It allows for the study of complex genetic systems function, including so-called mosaic gene networks, which consist of functionally interacting subnetworks. We conducted a study of a mosaic gene networks modeling method based on integration of models of gene subnetworks by linear control functionals. An automatic modeling of 10,000 synthetic mosaic gene regulatory networks was carried out using computer experiments on gene knockdowns/knockouts. Structural analysis of graphs of generated mosaic gene regulatory networks has revealed that the most important factor for building accurate integrated mathematical models, among those analyzed in the study, is data on expression of genes corresponding to the vertices with high properties of centrality.

A, Kumar KS. Learning from Bees: An Approach for Influence Maximization on Viral Campaigns

Maximisation of influence propagation is a key ingredient to any viral marketing or socio-political campaigns. However, it is an NP-hard problem, and various approximate algorithms have been suggested to address the issue, though not largely successful. In this paper, we propose a bio-inspired approach to select the initial set of nodes which is significant in rapid convergence towards a sub-optimal solution in minimal runtime. The performance of the algorithm is evaluated using the re-tweet network of the hashtag #KissofLove on Twitter associated with the non-violent protest against the moral policing spread to many parts of India. Comparison with existing centrality based node ranking process the proposed method significant improvement on influence propagation. The proposed algorithm is one of the hardly few bio-inspired algorithms in network theory. We also report the results of the exploratory analysis of the network kiss of love campaign.

Identification of important nodes in directed biological networks: a network motif approach

Identification of important nodes in complex networks has attracted an increasing attention over the last decade. Various measures have been proposed to characterize the importance of nodes in complex networks, such as the degree, betweenness and PageRank. Different measures consider different aspects of complex networks. Although there are numerous results reported on undirected complex networks, few results have been reported on directed biological networks. Based on network motifs and principal component analysis (PCA), this paper aims at introducing a new measure to characterize node importance in directed biological networks. Investigations on five real-world biological networks indicate that the proposed method can robustly identify actually important nodes in different networks, such as finding command interneurons, global regulators and non-hub but evolutionary conserved actually important nodes in biological networks. Receiver Operating Characteristic (ROC) curves for the five networks indicate remarkable prediction accuracy of the proposed measure. The proposed index provides an alternative complex network metric. Potential implications of the related investigations include identifying network control and regulation targets, biological networks modeling and analysis, as well as networked medicine.

A bio-inspired method for the constrained shortest path problem

The constrained shortest path (CSP) problem has been widely used in transportation optimization, crew scheduling, network routing and so on. It is an open issue since it is a NP-hard problem. In this paper, we propose an innovative method which is based on the internal mechanism of the adaptive amoeba algorithm. The proposed method is divided into two parts. In the first part, we employ the original amoeba algorithm to solve the shortest path problem in directed networks. In the second part, we combine the Physarum algorithm with a bio-inspired rule to deal with the CSP. Finally, by comparing the results with other method using an examples in DCLC problem, we demonstrate the accuracy of the proposed method.