The heterogeneity in link weights may decrease the robustness of real-world complex weighted networks

Hyper-brain hyper-frequency network topology dynamics when playing guitar in quartet

Ensemble music performance is a highly coordinated form of social behavior requiring not only precise motor actions but also synchronization of different neural processes both within and between the brains of ensemble players. In previous analyses, which were restricted to within-frequency coupling (WFC), we showed that different frequencies participate in intra- and inter-brain coordination, exhibiting distinct network topology dynamics that underlie coordinated actions and interactions. However, many of the couplings both within and between brains are likely to operate across frequencies. Hence, to obtain a more complete picture of hyper-brain interaction when musicians play the guitar in a quartet, cross-frequency coupling (CFC) has to be considered as well. Furthermore, WFC and CFC can be used to construct hyper-brain hyper-frequency networks (HB-HFNs) integrating all the information flows between different oscillation frequencies, providing important details about ensemble interaction in terms of network topology dynamics (NTD). Here, we reanalyzed EEG (electroencephalogram) data obtained from four guitarists playing together in quartet to explore changes in HB-HFN topology dynamics and their relation to acoustic signals of the music. Our findings demonstrate that low-frequency oscillations (e.g., delta, theta, and alpha) play an integrative or pacemaker role in such complex networks and that HFN topology dynamics are specifically related to the guitar quartet playing dynamics assessed by sound properties. Simulations by link removal showed that the HB-HFN is relatively robust against loss of connections, especially when the strongest connections are preserved and when the loss of connections only affects the brain of one guitarist. We conclude that HB-HFNs capture neural mechanisms that support interpersonally coordinated action and behavioral synchrony.

Community cohesion looseness in gene networks reveals individualized drug targets and resistance

Community cohesion plays a critical role in the determination of an individual's health in social science. Intriguingly, a community structure of gene networks indicates that the concept of community cohesion could be applied between the genes as well to overcome the limitations of single gene-based biomarkers for precision oncology. Here, we develop community cohesion scores which precisely quantify the community ability to retain the interactions between the genes and their cellular functions in each individualized gene network. Using breast cancer as a proof-of-concept study, we measure the community cohesion score profiles of 950 case samples and predict the individualized therapeutic targets in 2-fold. First, we prioritize them by finding druggable genes present in the community with the most and relatively decreased scores in each individual. Then, we pinpoint more individualized therapeutic targets by discovering the genes which greatly contribute to the community cohesion looseness in each individualized gene network. Compared with the previous approaches, the community cohesion scores show at least four times higher performance in predicting effective individualized chemotherapy targets based on drug sensitivity data. Furthermore, the community cohesion scores successfully discover the known breast cancer subtypes and we suggest new targeted therapy targets for triple negative breast cancer (e.g. KIT and GABRP). Lastly, we demonstrate that the community cohesion scores can predict tamoxifen responses in ER+ breast cancer and suggest potential combination therapies (e.g. NAMPT and RXRA inhibitors) to reduce endocrine therapy resistance based on individualized characteristics. Our method opens new perspectives for the biomarker development in precision oncology.

Neural heterogeneity controls computations in spiking neural networks

The brain is composed of complex networks of interacting neurons that express considerable heterogeneity in their physiology and spiking characteristics. How does this neural heterogeneity influence macroscopic neural dynamics, and how might it contribute to neural computation? In this work, we use a mean-field model to investigate computation in heterogeneous neural networks, by studying how the heterogeneity of cell spiking thresholds affects three key computational functions of a neural population: the gating, encoding, and decoding of neural signals. Our results suggest that heterogeneity serves different computational functions in different cell types. In inhibitory interneurons, varying the degree of spike threshold heterogeneity allows them to gate the propagation of neural signals in a reciprocally coupled excitatory population. Whereas homogeneous interneurons impose synchronized dynamics that narrow the dynamic repertoire of the excitatory neurons, heterogeneous interneurons act as an inhibitory offset while preserving excitatory neuron function. Spike threshold heterogeneity also controls the entrainment properties of neural networks to periodic input, thus affecting the temporal gating of synaptic inputs. Among excitatory neurons, heterogeneity increases the dimensionality of neural dynamics, improving the network's capacity to perform decoding tasks. Conversely, homogeneous networks suffer in their capacity for function generation, but excel at encoding signals via multistable dynamic regimes. Drawing from these findings, we propose intra-cell-type heterogeneity as a mechanism for sculpting the computational properties of local circuits of excitatory and inhibitory spiking neurons, permitting the same canonical microcircuit to be tuned for diverse computational tasks.

Identifying influential nodes in complex networks using a gravity model based on the H-index method

Identifying influential spreaders in complex networks is a widely discussed topic in the field of network science. Numerous methods have been proposed to rank key nodes in the network, and while gravity-based models often perform well, most existing gravity-based methods either rely on node degree, k-shell values, or a combination of both to differentiate node importance without considering the overall impact of neighboring nodes. Relying solely on a node's individual characteristics to identify influential spreaders has proven to be insufficient. To address this issue, we propose a new gravity centrality method called HVGC, based on the H-index. Our approach considers the impact of neighboring nodes, path information between nodes, and the positional information of nodes within the network. Additionally, it is better able to identify nodes with smaller k-shell values that act as bridges between different parts of the network, making it a more reasonable measure compared to previous gravity centrality methods. We conducted several experiments on 10 real networks and observed that our method outperformed previously proposed methods in evaluating the importance of nodes in complex networks.

Robustness of Multi-Project Knowledge Collaboration Network in Open Source Community

Multi-project parallelism is an important feature of open source communities (OSCs), and multi-project collaboration among users is a favorable condition for an OSC's development. This paper studies the robustness of this type of community. Based on the characteristics of knowledge collaboration behavior and the large amount of semantic content generated from user collaboration in open source projects, we construct a directed, weighted, semantic-based multi-project knowledge collaboration network. Using analysis of the KCN's structure and user attributes, nodes are divided into knowledge collaboration nodes and knowledge dissemination nodes that participate in either multi- or single-project collaboration. From the perspectives of user churn and behavior degradation, two types of failure modes are constructed: node failure and edge failure. Based on empirical data from the Local Motors open source vehicle design community, we then carry out a dynamic robustness analysis experiment. Our results show that the robustness of our constructed network varies for different failure modes and different node types: the network has (1) a high robustness to random failure and a low robustness to deliberate failure, (2) a high robustness to edge failure and a low robustness to node failure, and (3) a high robustness to the failure of single-project nodes (or their edges) and a low robustness to the failure of multi-project nodes (or their edges). These findings can be used to provide a more comprehensive and targeted management reference, promoting the efficient development of OSCs.

Complex Network Analysis of Mass Violation, Specifically Mass Killing

News reports in media contain news about society’s social and political conditions. With the help of publicly available digital datasets of events, it is possible to study a complex network of mass violations, i.e., Mass Killings. Multiple approaches have been applied to bring essential insights into the events and involved actors. Power law distribution behavior finds in the tail of actor mention, co-actor mention, and actor degree tells us about the dominant behavior of influential actors that grows their network with time. The United States, France, Israel, and a few other countries have been identified as major players in the propagation of Mass Killing throughout the past 20 years. It is demonstrated that targeting the removal of influential actors may stop the spreading of such conflicting events and help policymakers and organizations. This paper aims to identify and formulate the conflicts with the actor’s perspective at a global level for a period of time. This process is a generalization to be applied to any level of news, i.e., it is not restricted to only the global level.

AIS explorer: Prioritization for watercraft inspections-A decision-support tool for aquatic invasive species management

Invasions of aquatic invasive species have caused significant economic and ecological damage to global aquatic ecosystems. Once an invasive population has established in a new habitat, eradication can be financially and logistically impossible, motivating management strategies to rely heavily upon prevention measures to reduce the introduction and spread. To be productive, on-the-ground management of aquatic invasive species requires effective decision-making surrounding the allocation of limited resources. Watercraft inspections play an important role in managing aquatic invasive species by preventing the overland transport of invasive species between waterbodies and providing education to boaters. In this study, we developed and tested an interactive web-based decision-support tool, AIS Explorer: Prioritization for Watercraft Inspections, to guide AIS managers in developing efficient watercraft inspection plans. The decision-support tool is informed by a network-based algorithm that maximized the number of inspected watercraft that move from AIS infested to uninfested lakes within and between counties in Minnesota, USA. It was iteratively built with stakeholder feedback, including consultations with county managers, beta-testing of the web-based application, and workshops to educate and train end-users. The co-development and implementation of data-driven decision support tools demonstrate how interdisciplinary methods can be used to connect science and management to support decision-making. The AIS Explorer: Prioritization for Watercraft Inspections application makes optimized research outputs accessible in multiple dynamic forms that maintain pace with discovery of new infestations and local needs. In addition, the decision support tool has supported improved and closer communication between AIS managers and researchers on this topic.

Identifying influential spreaders by gravity model considering multi-characteristics of nodes

How to identify influential spreaders in complex networks is a topic of general interest in the field of network science. Therefore, it wins an increasing attention and many influential spreaders identification methods have been proposed so far. A significant number of experiments indicate that depending on a single characteristic of nodes to reliably identify influential spreaders is inadequate. As a result, a series of methods integrating multi-characteristics of nodes have been proposed. In this paper, we propose a gravity model that effectively integrates multi-characteristics of nodes. The number of neighbors, the influence of neighbors, the location of nodes, and the path information between nodes are all taken into consideration in our model. Compared with well-known state-of-the-art methods, empirical analyses of the Susceptible-Infected-Recovered (SIR) spreading dynamics on ten real networks suggest that our model generally performs best. Furthermore, the empirical results suggest that even if our model only considers the second-order neighborhood of nodes, it still performs very competitively.

Identifying influential spreaders in complex networks by an improved gravity model

Identification of influential spreaders is still a challenging issue in network science. Therefore, it attracts increasing attention from both computer science and physical societies, and many algorithms to identify influential spreaders have been proposed so far. Degree centrality, as the most widely used neighborhood-based centrality, was introduced into the network world to evaluate the spreading ability of nodes. However, degree centrality always assigns too many nodes with the same value, so it leads to the problem of resolution limitation in distinguishing the real influences of these nodes, which further affects the ranking efficiency of the algorithm. The k-shell decomposition method also faces the same problem. In order to solve the resolution limit problem, we propose a high-resolution index combining both degree centrality and the k-shell decomposition method. Furthermore, based on the proposed index and the well-known gravity law, we propose an improved gravity model to measure the importance of nodes in propagation dynamics. Experiments on ten real networks show that our model outperforms most of the state-of-the-art methods. It has a better performance in terms of ranking performance as measured by the Kendall's rank correlation, and in terms of ranking efficiency as measured by the monotonicity value.

Dynamic Robustness of Open-Source Project Knowledge Collaborative Network Based on Opinion Leader Identification

A large amount of semantic content is generated during designer collaboration in open-source projects (OSPs). Based on the characteristics of knowledge collaboration behavior in OSPs, we constructed a directed, weighted, semantic-based knowledge collaborative network. Four social network analysis indexes were created to identify the key opinion leader nodes in the network using the entropy weight and TOPSIS method. Further, three degradation modes were designed for (1) the collaborative behavior of opinion leaders, (2) main knowledge dissemination behavior, and (3) main knowledge contribution behavior. Regarding the degradation model of the collaborative behavior of opinion leaders, we considered the propagation characteristics of opinion leaders to other nodes, and we created a susceptible–infected–removed (SIR) propagation model of the influence of opinion leaders’ behaviors. Finally, based on empirical data from the Local Motors open-source vehicle design community, a dynamic robustness analysis experiment was carried out. The results showed that the robustness of our constructed network varied for different degradation modes: the degradation of the opinion leaders’ collaborative behavior had the lowest robustness; this was followed by the main knowledge dissemination behavior and the main knowledge contribution behavior; the degradation of random behavior had the highest robustness. Our method revealed the influence of the degradation of collaborative behavior of different types of nodes on the robustness of the network. This could be used to formulate the management strategy of the open-source design community, thus promoting the stable development of OSPs.

Network Theory and Switching Behaviors: A User Guide for Analyzing Electronic Records Databases

As part of studies that employ health electronic records databases, this paper advocates the employment of graph theory for investigating drug-switching behaviors. Unlike the shared approach in this field (comparing groups that have switched with control groups), network theory can provide information about actual switching behavior patterns. After a brief and simple introduction to fundamental concepts of network theory, here we present (i) a Python script to obtain an adjacency matrix from a records database and (ii) an illustrative example of the application of network theory basic concepts to investigate drug-switching behaviors. Further potentialities of network theory (weighted matrices and the use of clustering algorithms), along with the generalization of these methods to other kinds of switching behaviors beyond drug switching, are discussed.

Adaptive Rewiring in Weighted Networks Shows Specificity, Robustness, and Flexibility

Brain network connections rewire adaptively in response to neural activity. Adaptive rewiring may be understood as a process which, at its every step, is aimed at optimizing the efficiency of signal diffusion. In evolving model networks, this amounts to creating shortcut connections in regions with high diffusion and pruning where diffusion is low. Adaptive rewiring leads over time to topologies akin to brain anatomy: small worlds with rich club and modular or centralized structures. We continue our investigation of adaptive rewiring by focusing on three desiderata: specificity of evolving model network architectures, robustness of dynamically maintained architectures, and flexibility of network evolution to stochastically deviate from specificity and robustness. Our adaptive rewiring model simulations show that specificity and robustness characterize alternative modes of network operation, controlled by a single parameter, the rewiring interval. Small control parameter shifts across a critical transition zone allow switching between the two modes. Adaptive rewiring exhibits greater flexibility for skewed, lognormal connection weight distributions than for normally distributed ones. The results qualify adaptive rewiring as a key principle of self-organized complexity in network architectures, in particular of those that characterize the variety of functional architectures in the brain.

Modelling photosystem I as a complex interacting network

In this paper, we model the excitation energy transfer (EET) of photosystem I (PSI) of the common pea plant Pisum sativum as a complex interacting network. The magnitude of the link energy transfer between nodes/chromophores is computed by Forster resonant energy transfer (FRET) using the pairwise physical distances between chromophores from the PDB 5L8R (Protein Data Bank). We measure the global PSI network EET efficiency adopting well-known network theory indicators: the network efficiency (Eff) and the largest connected component (LCC). We also account the number of connected nodes/chromophores to P700 (CN), a new ad hoc measure we introduce here to indicate how many nodes in the network can actually transfer energy to the P700 reaction centre. We find that when progressively removing the weak links of lower EET, the Eff decreases, while the EET paths integrity (LCC and CN) is still preserved. This finding would show that the PSI is a resilient system owning a large window of functioning feasibility and it is completely impaired only when removing most of the network links. From the study of different types of chromophore, we propose different primary functions within the PSI system: chlorophyll a (CLA) molecules are the central nodes in the EET process, while other chromophore types have different primary functions. Furthermore, we perform nodes removal simulations to understand how the nodes/chromophores malfunctioning may affect PSI functioning. We discover that the removal of the CLA triggers the fastest decrease in the Eff, confirming that CAL is the main contributors to the high EET efficiency. Our outcomes open new perspectives of research, such comparing the PSI energy transfer efficiency of different natural and agricultural plant species and investigating the light-harvesting mechanisms of artificial photosynthesis both in plant agriculture and in the field of solar energy applications.

A comparative analysis of link removal strategies in real complex weighted networks

In this report we offer the widest comparison of links removal (attack) strategies efficacy in impairing the robustness of six real-world complex weighted networks. We test eleven different link removal strategies by computing their impact on network robustness by means of using three different measures, i.e. the largest connected cluster (LCC), the efficiency (Eff) and the total flow (TF). We find that, in most of cases, the removal strategy based on the binary betweenness centrality of the links is the most efficient to disrupt the LCC. The link removal strategies based on binary-topological network features are less efficient in decreasing the weighted measures of the network robustness (e.g. Eff and TF). Removing highest weight links first is the best strategy to decrease the efficiency (Eff) in most of the networks. Last, we found that the removal of a very small fraction of links connecting higher strength nodes or of highest weight does not affect the LCC but it determines a rapid collapse of the network efficiency Eff and the total flow TF. This last outcome raises the importance of both to adopt weighted measures of network robustness and to focus the analyses on network response to few link removals.