PageRank Centrality Research Articles

Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia

Biomarkers associated with the progression from gastric intestinal metaplasia (GIM) to gastric adenocarcinoma (GA), i.e., GA-related GIM, could provide valuable insights into identifying patients with increased risk for GA. The aim of this study was to utilize multi-bioinformatics to reveal potential biomarkers for the GA-related GIM and predict potential drug repurposing for GA prevention in patients. The multi-bioinformatics included gene expression matrix (GEM) by microarray gene expression (MGE), ScType (a fully automated and ultra-fast cell-type identification based solely on a given scRNA-seq data), Ingenuity Pathway Analysis, PageRank centrality, GO and MSigDB enrichments, Cytoscape, Human Protein Atlas and molecular docking analysis in combination with immunohistochemistry. To identify GA-related GIM, paired surgical biopsies were collected from 16 GIM-GA patients who underwent gastrectomy, yielding 64 samples (4 biopsies per stomach x 16 patients) for MGE. Co-analysis was performed by including scRNAseq and immunohistochemistry datasets of endoscopic biopsies of 37 patients. The results of the present study showed potential biomarkers for GA-related GIM, including GEM of individual patients, individual genes (such as RBP2 and CD44), signaling pathways, network of molecules, and network of signaling pathways with key topological nodes. Accordingly, potential treatment targets with repurposed drugs were identified including epidermal growth factor receptor, proto-oncogene tyrosine-protein kinase Src, paxillin, transcription factor Jun, breast cancer type 1 susceptibility protein, cellular tumor antigen p53, mouse double minute 2, and CD44.

Higher-order structure based node importance evaluation in directed networks

Evaluating the significance of objects with possible relevant information is a crucial topic in information science. Due to the fact that objects related to each other can often be described using complex networks, this topic also forms a fundamental theme in network science. Most traditional methods for characterizing the importance of nodes in complex networks only utilize the binary relationships between node pairs, neglecting the influence brought by higher-order structures. Considering the specific interaction modes between local nodes in the network, this paper associates the higher-order structural characteristics of the network with the importance of the nodes. It constructs an evaluation framework for the importance of nodes in directed networks based on higher-order structures. Experimental analysis on both artificial data and scientific citation data from the APS dataset has validated the effectiveness of the proposed algorithms. Compared with PageRank and eigenvector centrality, the proposed algorithms demonstrated higher accuracy, revealing the role of higher-order structures in node importance evaluation. Finally, a robustness analysis of several algorithms indicated that the proposed algorithms exhibited good robustness.

Reliability-based ordinal consensus adjustment model for large scale group decision making

In large scale group decision-making (LSGDM), there are the substantial number of decision makers (DMs) with diverse knowledge, backgrounds, and interests related to the decision-making problem, and it is not possible to assure that all DMs are completely reliable. Thus, in order to enhance the quality of decision-making, it is necessary to analyze the reliabilities of DMs in LSGDM. This paper proposes the method to evaluate the reliabilities of DMs, sorts these DMs according to their degree of reliability, and investigates the consensus reaching process based on categories and an ordinal consensus measure. Considering the DMs' trust network, the uncertainty of a DM's evaluation information represented by a fuzzy preference relation (FPR), the deviation between a DM's FPR and those of the other DMs, and additive consistency of FPRs, the reliability of a DM is assessed using four criteria: PageRank centrality, professional competence, collaborative competence, and additive consistency. Following these reliability assessment criteria, ELECTRE-TRI is employed to sort DMs into three ordered categories according to DMs' different levels of reliability under the four assessment criteria. Furthermore, an improved ordinal consensus measure is designed to consider both the importance weights of positions and the deviation of Borda counts of the same alternative in two rankings. As for the consensus reaching process, due to the varied reliabilities of DMs in different categories, we propose a multiple strategies feedback mechanism for DMs in different categories. Finally, a numerical example is provided to illustrate the rationality and validity of the proposed model.

Optimizing Wireless Sensor Networks by Identifying Key Nodes Using Centrality Measures

This study underscores the critical role of graph theory in optimizing the functionality of Wireless Sensor Networks (WSNs). Our research aims to enhance network efficiency by utilizing a variety of centrality metrics, including degree, betweenness, closeness, eigenvector, Katz, PageRank, subgraph, harmonic, and percolation centrality, to identify pivotal nodes. Employing an extended Barabási-Albert model graph of a 50-node network, our methodology focuses on pinpointing nodes crucial for optimal data processing, monitoring, and analysis in WSNs. This comprehensive approach deepens our understanding of sensor networks and significantly boosts operational efficiency by leveraging strategic node functionalities. The findings from our study are poised to revolutionize network management strategies, promoting the development of more robust and efficient WSN operations.

Product network and origin of common equity factor risks

This paper extends the multisector asset pricing model based on production networks, achieving direct pricing of a firm’s equity assets at a more microscopic level within the product network. An Equilibrium-Aligned PageRank (EA-PR) centrality algorithm is proposed, and it is theoretically proven that EA-PR centrality can reflect the relative value of products and further derive the value of firms. A new equity asset pricing factor is constructed based on the EA-PR centrality of firms. The key findings can be summarized as follows: Firstly, the EA-PR centrality of firms shows a significant positive linear predictability for equity returns, and the returns associated with the EA-PR centrality factor cannot be fully explained by the Fama–French 6 (FF6) factors. Secondly, the EA-PR centrality factor demonstrates significant explanatory power for the FF6 factors and, to some extent, exhibits predictive ability for future returns of the FF6 factors. Thirdly, the product network model can effectively reflect the market competitiveness and growth potential of firms, and firms with high EA-PR centrality have stronger value capture capabilities, improving gross profit margin, cash flow, and investment growth in the future. Finally, this study empirically demonstrates the consistency between the product network model and the pricing theory of the q5 model, which incorporates the expected growth factor.

Ictal-onset localization through effective connectivity analysis based on RNN-GC with intracranial EEG signals in patients with epilepsy

Epilepsy is one of the most common clinical diseases of the nervous system. The occurrence of epilepsy will bring many serious consequences, and some patients with epilepsy will develop drug-resistant epilepsy. Surgery is an effective means to treat this kind of patients, and lesion localization can provide a basis for surgery. The purpose of this study was to explore the functional types and connectivity evolution patterns of relevant regions of the brain during seizures. We used intracranial EEG signals from patients with epilepsy as the research object, and the method used was GRU-GC. The role of the corresponding area of each channel in the seizure process was determined by the introduction of group analysis. The importance of each area was analysed by introducing the betweenness centrality and PageRank centrality. The experimental results show that the classification method based on effective connectivity has high accuracy, and the role of the different regions of the brain could also change during the seizures. The relevant methods in this study have played an important role in preoperative assessment and revealing the functional evolution patterns of various relevant regions of the brain during seizures.

Efficacy and Safety of Orally Administered East Asian Herbal Medicine Combined with Narrowband Ultraviolet B against Psoriasis: A Bayesian Network Meta-Analysis and Network Analysis.

Psoriasis is a chronic, immune-mediated inflammatory skin disease with many complications and a poor prognosis that imposes a significant burden on individuals and society. Narrowband ultraviolet B (NB-UVB) represents a cost-effective non-drug therapeutic intervention for psoriasis. East Asian herbal medicine (EAHM) is currently being investigated for its potential as a safe and effective psoriasis treatment. Consequently, it has the potential to be employed as a combination therapy with NB-UVB. The objective was to ascertain the efficacy and safety of the EAHM with NB-UVB combination therapy and to identify important drugs for further research. In this study, randomized controlled trials (RCTs) were retrieved from ten databases in Korea, China, and Japan. All statistical analyses were conducted using R software version 4.3.0. The primary outcomes were the Psoriasis Area and Severity Index (PASI) and the incidence rate of adverse events (AEs), while the secondary outcomes were hematologic markers and the Dermatology Life Quality Index (DLQI), which reflect the immune-mediated inflammatory pathology of psoriasis. The analysis of 40 RCTs, including 3521 participants, demonstrated that EAHM with NB-UVB combination therapy exhibited a statistically significant superiority over NB-UVB monotherapy with respect to primary and secondary outcomes. The Bayesian network meta-analysis revealed that Investigator Presciption 3 and Ziyin Liangxue Decoction exhibited a consistent relative advantage with respect to each PASI-based efficacy metric. The network analysis estimated the potential influence ranking for all individual herbs according to PageRank centrality. The findings of this study suggest that EAHMs co-administered with NB-UVB may provide additional efficacy and safety-related benefits for patients with psoriasis. However, the quality of evidence is still low, and further high-quality trials are needed to reach more definitive conclusions.

Node Classification of Network Threats Leveraging Graph-Based Characterizations Using Memgraph

This research leverages Memgraph, an open-source graph database, to analyze graph-based network data and apply Graph Neural Networks (GNNs) for a detailed classification of cyberattack tactics categorized by the MITRE ATT&CK framework. As part of graph characterization, the page rank, degree centrality, betweenness centrality, and Katz centrality are presented. Node classification is utilized to categorize network entities based on their role in the traffic. Graph-theoretic features such as in-degree, out-degree, PageRank, and Katz centrality were used in node classification to ensure that the model captures the structure of the graph. The study utilizes the UWF-ZeekDataFall22 dataset, a newly created dataset which consists of labeled network logs from the University of West Florida’s Cyber Range. The uniqueness of this study is that it uses the power of combining graph-based characterization or analysis with machine learning to enhance the understanding and visualization of cyber threats, thereby improving the network security measures.

Water‐controlled ecosystems as complex networks: Evaluation of network‐based approaches to quantify patterns of connectivity

AbstractThis study provides a new perspective on understanding the intricacies of water‐mediated connectivity in ecosystems, bridging landscape ecology and geomorphology through network science. We highlight dryland and river‐floodplain ecosystems as distinct examples of contrasting water‐controlled systems. We (1) discuss central considerations in developing structural connectivity and functional connectivity networks of water‐mediated connectivity; (2) quantify the emergent patterns in these networks; and (3) evaluate the capacity of network science tools for investigating connectivity characteristics. With a focus on strength (weights) and direction, connectivity is quantified using seven parameters at both network and node levels. We find that link density, betweenness centrality and page rank centrality are highly sensitive to directionality; global efficiency and degree centrality are particularly sensitive to weights; and relative node efficiency remains unaffected by weights and directions. Our study underscores how network science approaches can transform how we quantify and understand water‐mediated connectivity, especially in consideration of the role(s) of weights and directionality. This interdisciplinary perspective, linking ecology, hydrology and geomorphology, has implications for both theoretical insights and practical applications in environmental management and conservation efforts.

Application of individual brain connectome in chronic ischemia: mapping symptoms before and after reperfusion.

How brain functions in the distorted ischemic state before and after reperfusion is unclear. It is also uncertain whether there are any indicators within ischemic brain that could predict surgical outcomes. To alleviate these issues, we applied individual brain connectome in chronic steno-occlusive vasculopathy (CSOV) to map both ischemic symptoms and their postbypass changes. A total of 499 bypasses in 455 CSOV patients were collected and followed up for 47.8±20.5 months. Using multimodal parcellation with connectivity-based and pathological distortion-independent approach, areal MR features of brain connectome were generated with three measurements of functional connectivity (FC), structural connectivity, and PageRank centrality at the single-subject level. Thirty-three machine-learning models were then trained with clinical and areal MR features to obtain acceptable classifiers for both ischemic symptoms and their postbypass changes, among which, 11 were deemed acceptable (AUC>0.7). Notably, the FC feature-based model for long-term neurological outcomes performed very well (AUC>0.8). Finally, a Shapley additive explanations plot was adopted to extract important individual features in acceptable models to generate "fingerprints" of brain connectome. This study not only establishes brain connectomic fingerprint databases for brain ischemia with distortion, but also provides informative insights for how brain functions before and after reperfusion.

Portfolio optimization based on network centralities: Which centrality is better for asset selection during global crises?

We construct correlation-based networks linking 86 assets (stock indices, bond indices, foreign exchange rates, commodity futures, and cryptocurrencies) and analyze the impact of asset selection on portfolio optimization using different centrality measures (including degree, eigenvector, eccentricity, betweenness, PageRank, and hybrid centralities). In times of a global crisis, peripheral assets located in cross-market networks are more suitable for investment. By comparing portfolio performance based on different centrality measures, we find that (i) hybrid, eigenvector, and PageRank centralities can best improve portfolio performance; (ii) degree centrality is suitable for larger portfolios; and (iii) eccentricity and betweenness centralities are unsuitable for network optimization portfolios. In response, we explain them based on the construction principle of centrality measures. Additionally, our optimal portfolios suggest that investors pay more attention to the role of emerging countries, which are less exposed to external shocks and whose financial markets are more likely to remain stable.

Noninvasive- and invasive mapping reveals similar language network centralities – A function-based connectome analysis

BackgroundFormer comparisons between direct cortical stimulation (DCS) and navigated transcranial magnetic stimulation (nTMS) only focused on cortical mapping. While both can be combined with diffusion tensor imaging, their differences in the visualization of subcortical and even network levels remain unclear. Network centrality is an essential parameter in network analysis to measure the importance of nodes identified by mapping. Those include Degree centrality, Eigenvector centrality, Closeness centrality, Betweenness centrality, and PageRank centrality. While DCS and nTMS have repeatedly been compared on the cortical level, the underlying network identified by both has not been investigated yet. Method27 patients with brain lesions necessitating preoperative nTMS and intraoperative DCS language mapping during awake craniotomy were enrolled. Function-based connectome analysis was performed based on the cortical nodes obtained through the two mapping methods, and language-related network centralities were compared. ResultsCompared with DCS language mapping, the positive predictive value of cortical nTMS language mapping is 74.1%, with good consistency of tractography for the arcuate fascicle and superior longitudinal fascicle. Moreover, network centralities did not differ between the two mapping methods. However, ventral stream tracts can be better traced based on nTMS mappings, demonstrating its strengths in acquiring language-related networks. In addition, it showed lower centralities than other brain areas, with decentralization as an indicator of language function loss. ConclusionThis study deepens the understanding of language-related functional anatomy and proves that non-invasive mapping-based network analysis is comparable to the language network identified via invasive cortical mapping.

Using SNAP to Analyze Policy Measures in e-Learning Roadmaps

Creating policy measures is the final step in the process of e-learning roadmap development. Policy measures can be seen as long-term activities that need to be implemented and constantly upgraded to achieve strategic goals. For resource allocation, it is useful to prioritize policy measures. Prioritization can be implemented using multi-criteria decision-making methods. This paper analyzes policy measures in the Maldives National University’s e-learning roadmap using the social network analysis process (SNAP), which includes the analytic hierarchy process (AHP), the decision-making trial and evaluation laboratory (DEMATEL), and the PageRank centrality. In policy measure evaluation, there were more than 20 participants: persons with managerial functions at the Maldives National University (MNU) (deans, heads of departments) and persons in lecturer and researcher positions. By using the AHP, participants prioritized policy measures with respect to their importance to them. By using the DEMATEL, participants identified and prioritized policy measures with respect to their effect on other measures. Finally, by using the SNAP, it was possible to determine the prioritization list for resource allocation since it aggregates the aspects of the policy measures, their importance, and their effect on other measures.

Non-Centralised Balance Dispatch Strategy in Waked Wind Farms through a Graph Sparsification Partitioning Approach

A novel non-centralised dispatch strategy is presented for wake redirection to optimise large-scale offshore wind farms operation, creating a balanced control between power production and fatigue thrust loads evenly among the wind turbines. This approach is founded on a graph sparsification partitioning strategy that takes into account the impact of wake propagation. More specifically, the breadth-first search algorithm is employed to identify the subgraph based on the connectivity of the wake direction graph, while the PageRank centrality computation algorithm is utilised to determine and rank scores for the shared turbines’ affiliation with the subgraphs. By doing so, the wind farm is divided into smaller subsets of partitioned turbines, resulting in decoupling. The objective function is then formulated by incorporating penalty terms, specifically the standard deviation of fatigue thrust loads, into the maximum power equation. Meanwhile, the non-centralisation sequential quadratic programming optimisation algorithm is subsequently employed within each partition to determine the control actions while considering the objectives of the respective controllers. Finally, the simulation results of case studies prove to reduce computational costs and improve wind farm power production by balancing accumulated fatigue thrust loads over the operational lifetime as much as possible.

Selection of centrality measures using Self-consistency and Bridge axioms

Abstract We consider several families of network centrality measures induced by graph kernels, which include some well-known measures and many new ones. The Self-consistency and Bridge axioms, which appeared earlier in the literature, are closely related to certain kernels and one of the families. We obtain a necessary and sufficient condition for Self-consistency, a sufficient condition for the Bridge axiom, indicate specific measures that satisfy these axioms and show that under some additional conditions they are incompatible. PageRank centrality applied to undirected networks violates most conditions under study and has a property that according to some authors is ‘hard to imagine’ for a centrality measure. We explain this phenomenon. Adopting the Self-consistency or Bridge axiom leads to a drastic reduction in survey time in the culling method designed to select the most appropriate centrality measures.

Can the PageRank centrality be manipulated to obtain any desired ranking?

The significance of the PageRank algorithm in shaping the modern Internet cannot be overstated, and its complex network theory foundations continue to be a subject of research. In this article, we carry out a systematic study of the structural and parametric controllability of PageRank’s outcomes, translating a spectral graph theory problem into a geometric one, where a natural characterization of its rankings emerges. Furthermore, we show that the change of perspective employed can be applied to the biplex PageRank proposal, performing numerical computations on both real and synthetic network datasets to compare centrality measures used.

PageRank centrality with non-local random walk-based teleportation

Abstract PageRank is a popular measure of centrality that is often applied to rank nodes in real-world networks. However, in many cases, the notion of teleportation is counterintuitive because it implies that whatever is moving around the network will jump or ‘teleport’ directly from one node to any other, without considering how far apart the nodes are. To overcome this issue, we propose here a general measure of PageRank centrality whereby the teleportation probabilities depend, in some way, on the distance separating the nodes. We accomplish this by drawing upon recent advances in non-local random walks, which allow the proposed measure to be tailored for various real-world networks and applications. To illustrate the flexibility of the proposed measure and to demonstrate how it differs from PageRank centrality, we present and discuss experimental results for a selection of real-world spatial and social networks, including an air transportation network, a collaboration network and an urban street network.

Benchmarking Optimization Algorithms for Auto-Tuning GPU Kernels

Recent years have witnessed phenomenal growth in the application, and capabilities of Graphical Processing Units (GPUs) due to their high parallel computation power at relatively low cost. However, writing a computationally efficient GPU program (kernel) is challenging, and generally only certain specific kernel configurations lead to significant increases in performance. Auto-tuning is the process of automatically optimizing software for highly-efficient execution on a target hardware platform. Auto-tuning is particularly useful for GPU programming, as a single kernel requires re-tuning after code changes, for different input data, and for different architectures. However, the discrete, and non-convex nature of the search space creates a challenging optimization problem. In this work, we investigate which algorithm produces the fastest kernels if the time-budget for the tuning task is varied. We conduct a survey by performing experiments on 26 different kernel spaces, from 9 different GPUs, for 16 different evolutionary black-box optimization algorithms. We then analyze these results and introduce a novel metric based on the PageRank centrality concept as a tool for gaining insight into the difficulty of the optimization problem. We demonstrate that our metric correlates strongly with observed tuning performance.

Unveiling technological innovation in hospitality and tourism through patent data: Development perspective and competition landscaping

This study fills a gap in the literature by focusing on hospitality and tourism technology development (supply-side perspective) rather than technological adoption (demand-side perspective). Drawing on US patent data, we focus on three main technology areas: travel agencies, hotels and restaurants, and online reservations. With a dataset of 88,344 patents granted to 13,696 assignees since 1966, we study hospitality and tourism-related technologies under the three fields. Using the machine learning-based text analytics, we analyze the classes of patents invented in each sector. We also map technological competition landscapes in the three domains in terms of innovation quality (PageRank centrality) and quantity (patent volume) and discover leading/following firms.

Functional connectivity of the language area in migraine: a preliminary classification model

BackgroundMigraine is a complex disorder characterized by debilitating headaches. Despite its prevalence, its pathophysiology remains unknown, with subsequent gaps in diagnosis and treatment. We combined machine learning with connectivity analysis and applied a whole-brain network approach to identify potential targets for migraine diagnosis and treatment.MethodsBaseline anatomical T1 magnetic resonance imaging (MRI), resting-state functional MRI(rfMRI), and diffusion weighted scans were obtained from 31 patients with migraine, and 17 controls. A recently developed machine learning technique, Hollow Tree Super (HoTS) was used to classify subjects into diagnostic groups based on functional connectivity (FC) and derive networks and parcels contributing to the model. PageRank centrality analysis was also performed on the structural connectome to identify changes in hubness.ResultsOur model attained an area under the receiver operating characteristic curve (AUC-ROC) of 0.68, which rose to 0.86 following hyperparameter tuning. FC of the language network was most predictive of the model’s classification, though patients with migraine also demonstrated differences in the accessory language, visual and medial temporal regions. Several analogous regions in the right hemisphere demonstrated changes in PageRank centrality, suggesting possible compensation.ConclusionsAlthough our small sample size demands caution, our preliminary findings demonstrate the utility of our method in providing a network-based perspective to diagnosis and treatment of migraine.