arXiv subjects

Naoki Masuda

Publications and source records attributed to Naoki Masuda.

At least 37 records · Page 2Linked to original sources

arXiv2025

Spline tie-decay temporal networks

Increasing amounts of data are available on temporal, or time-varying, networks. There have been various representations of temporal network data each of which has different advantages for downstream tasks such as mathematical analysis, visualizations, agent-based and other dynamical simulations on the temporal network, and discovery of useful structure. The tie-decay network is a representation of temporal networks whose advantages include the capability of generating continuous-time networks from discrete time-stamped contact event data with mathematical tractability and a low computational cost. However, the current framework of tie-decay networks is limited in terms of how each discrete contact event can affect the time-dependent tie strength (which we call the kernel). Here we extend the tie-decay network model in terms of the kernel. Specifically, we use a cubic spline function for modeling short-term behavior of the kernel and an exponential decay function for long-term behavior, and graft them together. This spline version of tie-decay network enables delayed and $C^1$-continuous interaction rates between two nodes while it only marginally increases the computational and memory burden relative to the conventional tie-decay network. We show mathematical properties of the spline tie-decay network and numerically showcase it with three tasks: network embedding, a deterministic opinion dynamics model, and a stochastic epidemic spreading model.

physics.soc-ph↗

arXiv2024

Global and local synchrony of coupled neurons in small-world networks

Synchronous firing of neurons is thought to play important functional roles such as feature binding and switching of cognitive states. Although synchronization has mainly been investigated using model neurons with simple connection topology so far, real neural networks have more complex structures. Here we examine behavior of pulse-coupled leaky integrate-and-fire neurons with various network structures. We first show that the dispersion of the number of connections for neurons influences dynamical behavior even if other major topological statistics are kept fixed. The rewiring probability parameter representing the randomness of networks bridges two spatially opposite frameworks: precise local synchrony and rough global synchrony. Finally, cooperation of the global connections and the local clustering property, which is prominent in small-world networks, reinforces synchrony of distant neuronal groups receiving coherent inputs.

q-bio.NC↗

arXiv2024

Filtered interspike interval encoding by class II neurons

Dynamics of class II neurons, firing frequencies of which are strongly regulated by the inherent neuronal property, have been extensively studied since the formulation of the Hodgkin--Huxley model in 1952. However, how class II neurons process stimulus information and what kind of external information and internal structure firing patterns of neurons represent are vaguely understood in contrast to firing rate coding by class I neurons. Here we show that the FitzHugh--Nagumo class II neuron simultaneously filters inputs based on the input frequency and represent the signal strength by interspike intervals. In this sense, the class II neuron works as an AM processor that passes the information on the carrier and on the temporal waveform of signals.

cond-mat.dis-nn↗

arXiv2024

A Parrondo paradox in susceptible-infectious-susceptible dynamics over periodic temporal networks

Many social and biological networks periodically change over time with daily, weekly, and other cycles. Thus motivated, we formulate and analyze susceptible-infectious-susceptible (SIS) epidemic models over temporal networks with periodic schedules. More specifically, we assume that the temporal network consists of a cycle of alternately used static networks, each with a given duration. We observe a phenomenon in which two static networks are individually above the epidemic threshold but the alternating network composed of them renders the dynamics below the epidemic threshold, which we refer to as a Parrondo paradox for epidemics. We find that network structure plays an important role in shaping this phenomenon, and we study its dependence on the connectivity between and number of subpopulations in the network. We associate such paradoxical behavior with anti-phase oscillatory dynamics of the number of infectious individuals in different subpopulations.

physics.soc-ph↗

arXiv2024

Spatial prisoner's dilemma optimally played in small-world networks

Cooperation is commonly found in ecological and social systems even when it apparently seems that individuals can benefit from selfish behavior. We investigate how cooperation emerges with the spatial prisoner's dilemma played in a class of networks ranging from regular lattices to random networks. We find that, among these networks, small-world topology is the optimal structure when we take into account the speed at which cooperative behavior propagates. Our results may explain why the small-world properties are self-organized in real networks.

physics.soc-ph↗

arXiv2024

Online landmark replacement for out-of-sample dimensionality reduction methods

A strategy to assist visualization and analysis of large and complex data sets is dimensionality reduction, with which one maps each data point into a low-dimensional manifold. However, various dimensionality reduction techniques are computationally infeasible for large data. Out-of-sample techniques aim to resolve this difficulty; they only apply the dimensionality reduction technique on a small portion of data, referred to as landmarks, and determine the embedding coordinates of the other points using landmarks as references. Out-of-sample techniques have been applied to online settings, or when data arrive as time series. However, existing online out-of-sample techniques use either all the previous data points as landmarks or the fixed set of landmarks and therefore are potentially not good at capturing the geometry of the entire data set when the time series is non-stationary. To address this problem, we propose an online landmark replacement algorithm for out-of-sample techniques using geometric graphs and the minimal dominating set on them. We mathematically analyze some properties of the proposed algorithm, particularly focusing on the case of landmark multidimensional scaling as the out-of-sample technique, and test its performance on synthetic and empirical time series data.

physics.soc-ph↗

arXiv2024

Fixation dynamics on multilayer networks

Network structure has a large impact on constant-selection evolutionary dynamics, with which multiple types of fitness (i.e., strength) compete on the network. Here we study constant-selection dynamics on two-layer networks in which the fitness of a node in one layer affects that in the other layer, under birth-death processes and uniform initialization, which are commonly assumed. We show mathematically and numerically that two-layer networks are suppressors of selection, which means that they suppress the effects of the different fitness values among the different types on the final outcomes of the evolutionary dynamics (called fixation probability) relative to the constituent one-layer networks. In fact, many two-layer networks are suppressors of selection relative to the most basic baseline, the Moran process. This result is in stark contrast with the results for conventional one-layer networks for which most networks are amplifiers of selection.

physics.soc-ph↗

arXiv2024

Autocorrelation properties of temporal networks governed by dynamic node variables

We study synthetic temporal networks whose evolution is determined by stochastically evolving node variables - synthetic analogues of, e.g., temporal proximity networks of mobile agents. We quantify the long-timescale correlations of these evolving networks by an autocorrelative measure of edge persistence. Several distinct patterns of autocorrelation arise, including power-law decay and exponential decay, depending on the choice of node-variable dynamics and connection probability function. Our methods are also applicable in wider contexts; our temporal network models are tractable mathematically and in simulation, and our long-term memory quantification is analytically tractable and straightforwardly computable from temporal network data.

physics.soc-ph↗

arXiv2024

Constant-selection evolutionary dynamics on weighted networks

The population structure often impacts evolutionary dynamics. In constant-selection evolutionary dynamics between two types, amplifiers of selection are networks that promote the fitter mutant to take over the entire population, and suppressors of selection do the opposite. It has been shown that most undirected and unweighted networks are amplifiers of selection under a common updating rule and initial condition. Here, we extensively investigate how edge weights influence selection on undirected networks. We show that random edge weights make small networks less amplifying than the corresponding unweighted networks in a majority of cases and also make them suppressors of selection (i.e., less amplifying than the complete graph, or equivalently, the Moran process) in many cases. Qualitatively, the same result holds true for larger empirical networks. These results suggest that amplifiers of selection are not as common for weighted networks as for unweighted counterparts.

physics.soc-ph↗

arXiv2024

Reliability of energy landscape analysis of resting-state functional MRI data

Energy landscape analysis is a data-driven method to analyze multidimensional time series, including functional magnetic resonance imaging (fMRI) data. It has been shown to be a useful characterization of fMRI data in health and disease. It fits an Ising model to the data and captures the dynamics of the data as movement of a noisy ball constrained on the energy landscape derived from the estimated Ising model. In the present study, we examine test-retest reliability of the energy landscape analysis. To this end, we construct a permutation test that assesses whether or not indices characterizing the energy landscape are more consistent across different sets of scanning sessions from the same participant (i.e., within-participant reliability) than across different sets of sessions from different participants (i.e., between-participant reliability). We show that the energy landscape analysis has significantly higher within-participant than between-participant test-retest reliability with respect to four commonly used indices. We also show that a variational Bayesian method, which enables us to estimate energy landscapes tailored to each participant, displays comparable test-retest reliability to that using the conventional likelihood maximization method. The proposed methodology paves the way to perform individual-level energy landscape analysis for given data sets with a statistically controlled reliability.

q-bio.NC↗

arXiv2024

Network Analysis of U.S. Non-Fatal Opioid-Involved Overdose Journeys, 2018-2023

We present a nation-wide network analysis of non-fatal opioid-involved overdose journeys in the United States. Leveraging a unique proprietary dataset of Emergency Medical Services incidents, we construct a journey-to-overdose geospatial network capturing nearly half a million opioid-involved overdose events spanning 2018-2023. We analyze the structure and sociological profiles of the nodes, which are counties or their equivalents, characterize the distribution of overdose journey lengths, and investigate changes in the journey network between 2018 and 2023. Our findings include that authority and hub nodes identified by the HITS algorithm tend to be located in urban areas and involved in overdose journeys with particularly long geographical distances.

cs.SI↗

arXiv2024

Evolutionary game dynamics with environmental feedback in a network with two communities

Recent developments of eco-evolutionary models have shown that evolving feedbacks between behavioral strategies and the environment of game interactions, leading to changes in the underlying payoff matrix, can impact the underlying population dynamics in various manners. We propose and analyze an eco-evolutionary game dynamics model on a network with two communities such that players interact with other players in the same community and those in the opposite community at different rates. In our model, we consider two-person matrix games with pairwise interactions occurring on individual edges and assume that the environmental state depends on edges rather than on nodes or being globally shared in the population. We analytically determine the equilibria and their stability under a symmetric population structure assumption, and we also numerically study the replicator dynamics of the general model. The model shows rich dynamical behavior, such as multiple transcritical bifurcations, multistability, and anti-synchronous oscillations. Our work offers insights into understanding how the presence of community structure impacts the eco-evolutionary dynamics within and between niches.

physics.soc-ph↗

arXiv2024

Effects of concurrency on epidemic spreading in Markovian temporal networks

The concurrency of edges, quantified by the number of edges that share a common node at a given time point, may be an important determinant of epidemic processes in temporal networks. We propose theoretically tractable Markovian temporal network models in which each edge flips between the active and inactive states in continuous time. The different models have different amounts of concurrency while we can tune the models to share the same statistics of edge activation and deactivation (and hence the fraction of time for which each edge is active) and the structure of the aggregate (i.e., static) network. We analytically calculate the amount of concurrency of edges sharing a node for each model. We then numerically study effects of concurrency on epidemic spreading in the stochastic susceptible-infectious-susceptible and susceptible-infectious-recovered dynamics on the proposed temporal network models. We find that the concurrency enhances epidemic spreading near the epidemic threshold while this effect is small in many cases. Furthermore, when the infection rate is substantially larger than the epidemic threshold, the concurrency suppresses epidemic spreading in a majority of cases. In sum, our numerical simulations suggest that the impact of concurrency on enhancing epidemic spreading within our model is consistently present near the epidemic threshold but modest. The proposed temporal network models are expected to be useful for investigating effects of concurrency on various collective dynamics on networks including both infectious and other dynamics.

physics.soc-ph↗

arXiv2024

Temporal scaling theory for bursty time series with clusters of arbitrarily many events

Long-term temporal correlations in time series in a form of an event sequence have been characterized using an autocorrelation function (ACF) that often shows a power-law decaying behavior. Such scaling behavior has been mainly accounted for by the heavy-tailed distribution of interevent times (IETs), i.e., the time interval between two consecutive events. Yet little is known about how correlations between consecutive IETs systematically affect the decaying behavior of the ACF. Empirical distributions of the burst size, which is the number of events in a cluster of events occurring in a short time window, often show heavy tails, implying that arbitrarily many consecutive IETs may be correlated with each other. In the present study, we propose a model for generating a time series with arbitrary functional forms of IET and burst size distributions. Then, we analytically derive the ACF for the model time series. In particular, by assuming that the IET and burst size are power-law distributed, we derive scaling relations between power-law exponents of the ACF decay, IET distribution, and burst size distribution. These analytical results are confirmed by numerical simulations. Our approach helps to rigorously and analytically understand the effects of correlations between arbitrarily many consecutive IETs on the decaying behavior of the ACF.

physics.data-an↗

arXiv2024

State-transition dynamics of resting-state functional magnetic resonance imaging data: Model comparison and test-to-retest analysis

Electroencephalogram (EEG) microstate analysis entails finding dynamics of quasi-stable and generally recurrent discrete states in multichannel EEG time series data and relating properties of the estimated state-transition dynamics to observables such as cognition and behavior. While microstate analysis has been widely employed to analyze EEG data, its use remains less prevalent in functional magnetic resonance imaging (fMRI) data, largely due to the slower timescale of such data. In the present study, we extend various data clustering methods used in EEG microstate analysis to resting-state fMRI data from healthy humans to extract their state-transition dynamics. We show that the quality of clustering is on par with that for various microstate analyses of EEG data. We then develop a method for examining test-retest reliability of the discrete-state transition dynamics between fMRI sessions and show that the within-participant test-retest reliability is higher than between-participant test-retest reliability for different indices of state-transition dynamics, different networks, and different data sets. This result suggests that state-transition dynamics analysis of fMRI data could discriminate between different individuals and is a promising tool for performing fingerprinting analysis of individuals.

q-bio.NC↗

arXiv2024

Cooperation and the social brain hypothesis in primate social networks

The social brain hypothesis states that the relative size of the neocortex is larger for species with higher social complexity as a result of evolution. Various lines of empirical evidence have supported the social brain hypothesis, including evidence from the structure of social networks. Social complexity may itself positively impact cooperation among individuals, which occurs across different animal taxa and is a key behavior for successful group living. Theoretical research has shown that particular structures of social networks foster cooperation more easily than others. Therefore, we hypothesized that species with a relatively large neocortex tend to form social networks that better enable cooperation. In the present study, we combine data on brain and body mass, data on social networks, and theory on the evolution of cooperation on networks to test this hypothesis in primates. We have found a positive effect of brain size on cooperation in social networks even after controlling for the effect of other structural properties of networks that are known to promote cooperation.

physics.soc-ph↗

arXiv2023

Gene communities in co-expression networks across different tissues

With the recent availability of tissue-specific gene expression data, e.g., provided by the GTEx Consortium, there is interest in comparing gene co-expression patterns across tissues. One promising approach to this problem is to use a multilayer network analysis framework and perform multilayer community detection. Communities in gene co-expression networks reveal groups of genes similarly expressed across individuals, potentially involved in related biological processes responding to specific environmental stimuli or sharing common regulatory variations. We construct a multilayer network in which each of the four layers is an exocrine gland tissue-specific gene co-expression network. We develop methods for multilayer community detection with correlation matrix input and an appropriate null model. Our correlation matrix input method identifies five groups of genes that are similarly co-expressed in multiple tissues (a community that spans multiple layers, which we call a generalist community) and two groups of genes that are co-expressed in just one tissue (a community that lies primarily within just one layer, which we call a specialist community). We further found gene co-expression communities where the genes physically cluster across the genome significantly more than expected by chance (on chromosomes 1 and 11). This clustering hints at underlying regulatory elements determining similar expression patterns across individuals and cell types. We suggest that KRTAP3-1, KRTAP3-3, and KRTAP3-5 share regulatory elements in skin and pancreas. Furthermore, we find that CELA3A and CELA3B share associated expression quantitative trait loci in the pancreas. The results indicate that our multilayer community detection method for correlation matrix input extracts biologically interesting communities of genes.

q-bio.MN↗

arXiv2023

Quantifying gender imbalance in East Asian academia: Research career and citation practice

Gender imbalance in academia has been confirmed in terms of a variety of indicators, and its magnitude often varies from country to country. Europe and North America, which cover a large fraction of research workforce in the world, have been the main geographical regions for research on gender imbalance in academia. However, the academia in East Asia, which accounts for a substantial fraction of research, may be exposed to strong gender imbalance because Asia has been facing persistent and stronger gender imbalance in society at large than Europe and North America. Here we use publication data between 1950 and 2020 to analyze gender imbalance in academia in China, Japan, and South Korea in terms of the number of researchers, their career, and citation practice. We found that, compared to the average of the other countries, gender imbalance is larger in these three East Asian countries in terms of the number of researchers and their citation practice and additionally in Japan in terms of research career. Moreover, we found that Japan has been exposed to the larger gender imbalance than China and South Korea in terms of research career and citation practice.

cs.DL↗