Modelling industry interdependency dynamics in a network context

The analysis of network data is of interest to many disciplines, ranging from sociology to computer science. Recent interest has shifted from static networks to dynamic networks, which evolve over time. A fundamental problem in the analysis of dynamic networks is tracking long-term trends, which are obscured by short-term variations. In this paper, we propose a method for minimum mean-squared error tracking of dynamic networks using a recursive shrinkage estimation framework that accounts for the spatial correlation in the network. Unlike model-based tracking methods such as the Kalman filter, the proposed method does not require knowledge about the network dynamics. We demonstrate that the proposed method is able to track dynamic networks effectively through experiments on simulated and real networks.

Wireless multihop networks are being increasingly used in military and civilian applications. Advanced applications of wireless multihop networks demand better understanding on their properties. Existing research on wireless multihop networks has largely focused on static networks, where the network topology is time-invariant; and there is comparatively a lack of understanding on the properties of dynamic networks with dynamically changing topology. In this paper, we use and extend a recently proposed graph theoretic model, i.e. evolving graphs, to capture the characteristics of such networks. We extend and develop the concepts of route matrix, connectivity matrix and probabilistic connectivity matrix as convenient tools to characterize and investigate the properties of evolving graphs and the associated dynamic networks. The properties of these matrices are established and their relevance to the properties of dynamic wireless multihop networks are introduced.

Despite increased focus on well-being in the psychological sciences in recent years, cross-sectional and group-level methods fall short of capturing the dynamics of individual people’s well-being in daily life. Such an investigation is especially important for young adults who are in a developmental phase in which they are more likely to experience fluctuations in their daily lives. We used ecological momentary assessment over one week in two samples of first-year college students (Sample 1, N = 103, assessments = 2,535; Sample 2, N = 76, assessments = 1,796) and a dynamic network approach (Dynamic Exploratory Graph Analysis). This approach estimates, within each person, how well-being elements fluctuate across days and co-vary with one another, recovering both their differentiation (exclusivity) and their interdependence (connectivity). In this approach, elements of well-being—measured via the PERMA framework—are modeled as a dynamic network to address the following research questions: (1) How do elements of well-being in young adults’ daily life form a dynamic network? (2) Does the structure of well-being hold across all young adults, or is there heterogeneity? (3) Is there synchrony among well-being elements, and do they drive a person’s well-being network? Findings suggest that while group-level dynamic well-being networks align with theoretical models, each person’s individual experiences vary significantly, with each person demonstrating unique well-being network structures and synchronous elements. These findings underscore the importance of considering individual variability in well-being, highlighting the necessity for personalized approaches to understand and promote well-being among young adults.

Background Autism spectrum disorder (ASD) is characterized by aberrant functional brain connectivity and deficits in network dynamics. Transcranial direct current stimulation (tDCS) has emerged as a promising intervention with potential therapeutic effects; however, its effects on both static and dynamic functional brain network organization remained insufficiently understood. Methods A total of 42 children with ASD aged 4–6 years were enrolled and randomly assigned to either active tDCS or sham stimulation groups. Resting-state electroencephalography (EEG) data were acquired before and after the intervention. Low-order functional connectivity (LOFC) and high-order functional connectivity (HOFC) networks were constructed, followed by graph-theoretical analyses to assess clustering coefficient, characteristic path length, global efficiency, and local efficiency. Furthermore, state entropy was employed to evaluate dynamic network transitions between integrated and segregated states. Results Active tDCS was associated with increased LOFC strength in the delta, alpha, and beta bands, and more widespread increases in HOFC across all examined frequency bands. Changes in network topology were primarily observed in HOFC, with reductions in characteristic path length and increases in global and local efficiency, particularly in the delta and theta bands. Dynamic network analysis indicated that tDCS modulated state entropy at specific time scales in both LOFC and HOFC networks. These findings suggest shifts in functional coordination and temporal variability among the recorded regions. Behavioral measures exhibited a trend toward improvement in the active group; however, these changes were not the focus of the present analysis, and their relationship to neural modulation remains to be clarified in future work. Conclusions tDCS modulated functional interaction patterns and dynamic state characteristics among the recorded brain regions in children with ASD. These results provide preliminary neurophysiological evidence regarding the influence of tDCS on both static and dynamic network organization and highlight potential network-based markers to guide future individualized neuromodulation research. Further studies with larger samples and longitudinal follow-ups are needed to clarify the functional and clinical significance of these network-level changes.

The rational search for allosteric modulators and the allosteric mechanisms of these modulators in the presence of evolutionary mutations, including resistant ones, is a relatively unexplored field. Here, we established novel in silico approaches and applied to SARS-CoV-2 main protease (Mpro). First, we identified six potential allosteric modulators (SANC00302, SANC00303, SANC00467, SANC00468, SANC00469, SANC00630) from the South African Natural Compounds Database (SANCDB) bound to the allosteric pocket of Mpro that we determined in our previous work. We also checked the stability of these compounds against Mpro of laboratory strain HCoV-OC43 and identified differences due to residue changes between the two proteins. Next, we focused on understanding the allosteric effects of these modulators on each protomer of the reference Mpro protein, while incorporating the symmetry problem in the functional homodimer. In general, asymmetric behavior of multimeric proteins is not commonly considered in computational analysis. We introduced a novel combinatorial approach and dynamic residue network (DRN) analysis algorithms to examine patterns of change and conservation of critical nodes, according to five independent criteria of network centrality (betweenness centrality (BC), closeness centrality (CC), degree centrality (DC), eigencentrality (EC) and katz centrality (KC)). The relationships and effectiveness of each metric in characterizing allosteric behavior were also investigated. We observed highly conserved network hubs for each averaged DRN metric on the basis of their existence in both protomers in the absence and presence of all ligands, and we called them persistent hubs (residues 17, 111, 112 and 128 for averaged BC; 6, 7, 113, 114, 115, 124, 125, 126, 127 and 128 for averaged CC; 36, 91, 146, 150 and 206 for averaged DC; 7, 115 and 125 for EC; 36, 125 and 146 for KC). We also detected ligand specific signal changes some of which were in or around functional residues (i.e. chameleon switch PHE140). Using EC persistent hubs and ligand introduced hubs we identified a residue communication path between allosteric binding site and catalytic site. Finally, we examined the effects of the mutations on the behavior of the protein in the presence of selected potential allosteric modulators and investigated the ligand stability. The hit compounds showed various levels of stability in the presence of SARS-CoV-2 Mpro mutations, being most stable in A173V, N274D and R279C, and least stable in R60C, N151D V157I, C160S and A255V. SANC00468 was the most stable compound in the 43 mutant protein systems. We further used DRN metric analysis to define cold spots as being those regions that are least impacted, or not impacted, by mutations. One crucial outcome of this study was to show that EC centrality hubs form an allosteric communication path between the allosteric ligand binding site to the active site going through the interface residues of Domain I and II; and this path was either weakened or lost in the presence of some of the mutations. Overall, the results of this study revealed crucial aspects that need to be considered in drug discovery in COVID-19 specifically and in general for rational computational drug design purposes.

Advances in exponential random graph ( p*) models applied to a large social network

The Limits of Diversification and the Pricing of Tail Risk

BackgroundPancreatic ductal adenocarcinoma (PDAC) is one of the deadliest solid tumors. The rapid progression of PDAC results in an advanced stage of patients when diagnosed. However, the dynamic molecular mechanism underlying PDAC progression remains far from clear.MethodsThe microarray GSE62165 containing PDAC staging samples was obtained from Gene Expression Omnibus and the differentially expressed genes (DEGs) between normal tissue and PDAC of different stages were profiled using R software, respectively. The software program Short Time-series Expression Miner was applied to cluster, compare, and visualize gene expression differences between PDAC stages. Then, function annotation and pathway enrichment of DEGs were conducted by Database for Annotation Visualization and Integrated Discovery. Further, the Cytoscape plugin DyNetViewer was applied to construct the dynamic protein–protein interaction networks and to analyze different topological variation of nodes and clusters over time. The phosphosite markers of stage-specific protein kinases were predicted by PhosphoSitePlus database. Moreover, survival analysis of candidate genes and pathways was performed by Kaplan–Meier plotter. Finally, candidate genes were validated by immunohistochemistry in PDAC tissues.ResultsCompared with normal tissues, the total DEGs number for each PDAC stage were 994 (stage I), 967 (stage IIa), 965 (stage IIb), 1027 (stage III), 925 (stage IV), respectively. The stage-course gene expression analysis showed that 30 distinct expressional models were clustered. Kyoto Encyclopedia of Genes and Genomes analysis indicated that the up-regulated DEGs were commonly enriched in five fundamental pathways throughout five stages, including pathways in cancer, small cell lung cancer, ECM-receptor interaction, amoebiasis, focal adhesion. Except for amoebiasis, these pathways were associated with poor PDAC overall survival. Meanwhile, LAMA3, LAMB3, LAMC2, COL4A1 and FN1 were commonly shared by these five pathways and were unfavorable factors for prognosis. Furthermore, by constructing the stage-course dynamic protein interaction network, 45 functional molecular modules and 19 nodes were identified as featured regulators for all PDAC stages, among which the collagen family and integrins were considered as two main regulators for facilitating aggressive progression. Additionally, the clinical relevance analysis suggested that the stage IV featured nodes MLF1IP and ITGB4 were significantly correlated with shorter overall survival. Moreover, 15 stage-specific protein kinases were identified from the dynamic network and CHEK1 was particularly activated at stage IV. Experimental validation showed that MLF1IP, LAMA3 and LAMB3 were progressively increased from tumor initiation to progression.ConclusionsOur study provided a view for a better understanding of the dynamic landscape of molecular interaction networks during PDAC progression and offered potential targets for therapeutic intervention.

The relevance of nodes with respect to the position they have in a network is often investigated with centrality measures. In particular, in cases where it is specifically meaningful to consider nodes’ ability to cumulate and convey information, like in economic systems, betweenness centrality is one of the most pertinent options because of its underlying concept. However, this statistic presents two limitations. First, as it relies on the computation of shortest paths, it is grounded on a binary topological evaluation: every time a node is not located in the shortest path between two other nodes, it gains no score at all in its centrality (even if it is located on a path just one step longer). Second, betweenness centrality does not allow the direct analysis of multi-dimensional and dynamic networks: it has to be computed one dimension and one instant at a time, and this causes problems of comparability in case of weighted connections. The scope and the originality of this work is to design a network model that makes it possible to solve these issues. The proposed Dynamic Multi-Layer Network (DMLN) allows the structural representation of the multi-dimensional and dynamic properties of nodes’ interactions. Then, this allows the computation of a metric that, based on Infomap random walks, assesses the level of information cumulated and conveyed by nodes in any moment and in any dimension of interaction. Importantly, this is performed without relying on a binary evaluation, and by jointly taking into account what occurred in all the dimensions and during the entire period, in which the system is observed. We present and discuss an implementation based on ICT worldwide trade of goods and services in the period 2004–2014.

Anomaly analysis and visualization for dynamic networks through spatiotemporal graph segmentations

Access to resources depends on an individual's position within the environment. This is particularly important to animals that invest heavily in nest construction, such as social insects. Many ant species have a polydomous nesting strategy: a single colony inhabits several spatially separated nests, often exchanging resources between the nests. Different nests in a polydomous colony potentially have differential access to resources, but the ecological consequences of this are unclear. In this study, we investigate how nest survival and budding in polydomous wood ant (Formica lugubris) colonies are affected by being part of a multi‐nest system. Using field data and novel analytical approaches combining survival models with dynamic network analysis, we show that the survival and budding of nests within a polydomous colony are affected by their position in the nest network structure. Specifically, we find that the flow of resources through a nest, which is based on its position within the wider nest network, determines a nest's likelihood of surviving and of founding new nests. Our results highlight how apparently disparate entities in a biological system can be integrated into a functional ecological unit. We also demonstrate how position within a dynamic network structure can have important ecological consequences.

BackgroundDespite impressive dissemination programs of best-practice therapies, clinical psychology faces obstacles in developing more efficacious treatments for mental disorders. In contrast to other medical disciplines, psychotherapy has made only slow progress in improving treatment outcomes. Improvements in the classification of mental disorders could enhance the tailoring of treatments to improve effectiveness. We introduce a multimodal dynamical network approach, to address some of the challenges faced by clinical research. These challenges include the absence of a comprehensive meta-theory, comorbidity, substantial diagnostic heterogeneity, violations of ergodicity assumptions, and a limited understanding of causal processes.MethodsThrough the application of multimodal dynamical network analysis, we describe how to advance clinical research by addressing central problems in the field. By utilizing dynamic network analysis techniques (e.g., Group Iterative Multiple Model Estimation, multivariate Granger causality), multimodal measurements (i.e., psychological, psychopathological, and neurobiological data), intensive longitudinal data collection (e.g., Ecological Momentary Assessment), and causal inference methods (e.g., GIMME), our approach could improve the comprehension and treatment of mental disorders. Under the umbrella of the systems approach and utilizing e.g., graph theory and control theory, we aim to integrate data from longitudinal, multimodal measurements.ResultsThe multimodal dynamical network approach enables a comprehensive understanding of mental disorders as dynamic networks of interconnected symptoms. It dismantles artificial diagnostic boundaries, facilitating a transdiagnostic view of psychopathology. The integration of longitudinal data and causal inference techniques enhances our ability to identify influential nodes, prioritize interventions, and predict the impact of therapeutic strategies.ConclusionThe proposed approach could improve psychological treatment by providing individualized models of psychopathology and by suggesting individual treatment angles.

Brain networks are commonly used to identify cognitive neurobehavioral and brain conscious disorders. Most of the studies on state networks focus on the characterization and expression of resting-state brain networks, but there are few studies on dynamic brain networks. In fact, the analysis of dynamic brain networks can find more valuable information, because it can dynamically depict the dynamic characteristics of brain networks from the time dimension. However, too much consideration of the expression of dynamic networks will naturally hide many of its static characteristics. Therefore, this study proposes a tense-based multi-view fusion fuzzy learning model (TM-FL) to identify dynamic brain networks. TM-FL relearns the features of adjacent networks in high-dimensional space, mining the dynamic features between adjacent brain networks. Best of all, TM-FL can also capture resting information in the brain network at different times in the source space. The fuzzy TSK-based TM-FL also possesses the strong interpretability inherent in fuzzy systems. In this study, a fusion mechanism is designed to effectively integrate decision support under dynamic and static features, and enhance the classification and generalization performance of the proposed fuzzy classification model. For the proposed fusion fuzzy mechanism, Simon entropy is cleverly set as the regular term of the objective function, which not only constrains the decision weight, but also avoids the embarrassment of making mistakes in a leading decision. Experimental results show that TM-FL has good classification, generalization and interpretable capabilities in recognition of multi-channel epileptic electroencephalographic (EEG) signals.

Network dynamics of positive and negative affect in bipolar disorder

Exploring dynamic network signatures of stability and activity in Bacillus subtilis Lipase A.