arXiv subjects

Michelle Girvan

Publications and source records attributed to Michelle Girvan.

At least 37 records · Page 2Linked to original sources

arXiv2018

Continuous versus Discontinuous Transitions in the $D$-Dimensional Generalized Kuramoto Model: Odd $D$ is Different

The Kuramoto model, originally proposed to model the dynamics of many interacting oscillators, has been used and generalized for a wide range of applications involving the collective behavior of large heterogeneous groups of dynamical units whose states are characterized by a scalar angle variable. One such application in which we are interested is the alignment of orientation vectors among members of a swarm. Despite being commonly used for this purpose, the Kuramoto model can only describe swarms in 2 dimensions, and hence the results obtained do not apply to the often relevant situation of swarms in 3 dimensions. Partly based on this motivation, as well as on relevance to the classical, mean-field, zero-temperature Heisenberg model with quenched site disorder, in this paper we study the Kuramoto model generalized to $D$ dimensions. We show that in the important case of 3 dimensions, as well as for any odd number of dimensions, the $D$-dimensional generalized Kuramoto model for heterogeneous units has dynamics that are remarkably different from the dynamics in 2 dimensions. In particular, for odd $D$ the transition to coherence occurs discontinuously as the inter-unit coupling constant $K$ is increased through zero, as opposed to the $D=2$ case (and, as we show, also the case of even $D$) for which the transition to coherence occurs continuously as $K$ increases through a positive critical value $K_c$. We also demonstrate the qualitative applicability of our results to related models constructed specifically to capture swarming and flocking dynamics in three dimensions.

nlin.AO↗

arXiv2018

Hybrid Forecasting of Chaotic Processes: Using Machine Learning in Conjunction with a Knowledge-Based Model

A model-based approach to forecasting chaotic dynamical systems utilizes knowledge of the physical processes governing the dynamics to build an approximate mathematical model of the system. In contrast, machine learning techniques have demonstrated promising results for forecasting chaotic systems purely from past time series measurements of system state variables (training data), without prior knowledge of the system dynamics. The motivation for this paper is the potential of machine learning for filling in the gaps in our underlying mechanistic knowledge that cause widely-used knowledge-based models to be inaccurate. Thus we here propose a general method that leverages the advantages of these two approaches by combining a knowledge-based model and a machine learning technique to build a hybrid forecasting scheme. Potential applications for such an approach are numerous (e.g., improving weather forecasting). We demonstrate and test the utility of this approach using a particular illustrative version of a machine learning known as reservoir computing, and we apply the resulting hybrid forecaster to a low-dimensional chaotic system, as well as to a high-dimensional spatiotemporal chaotic system. These tests yield extremely promising results in that our hybrid technique is able to accurately predict for a much longer period of time than either its machine-learning component or its model-based component alone.

cs.LG↗

arXiv2017

Evidence of Herding and Stubbornness in Jury Deliberations

We explore how the mechanics of collective decision-making, especially of jury deliberation, can be inferred from macroscopic statistics. We first hypothesize that the dynamics of competing opinions can leave a "fingerprint" in the joint distribution of final votes and time to reach a decision. We probe this hypothesis by modeling jury datasets from different states collected in different years and identifying which of the models best explains opinion dynamics in juries. In our best-fit model, individual jurors have a "herding" tendency to adopt the majority opinion of the jury, but as the amount of time they have held their current opinion increases, so too does their resistance to changing their opinion (what we call "increasing stubbornness"). By contrast, other models without increasing stubbornness, or without herding, create poorer fits to data. Our findings suggest that both stubbornness and herding play an important role in collective decision-making.

physics.soc-ph↗

arXiv2017

Using Machine Learning to Replicate Chaotic Attractors and Calculate Lyapunov Exponents from Data

We use recent advances in the machine learning area known as 'reservoir computing' to formulate a method for model-free estimation from data of the Lyapunov exponents of a chaotic process. The technique uses a limited time series of measurements as input to a high-dimensional dynamical system called a 'reservoir'. After the reservoir's response to the data is recorded, linear regression is used to learn a large set of parameters, called the 'output weights'. The learned output weights are then used to form a modified autonomous reservoir designed to be capable of producing arbitrarily long time series whose ergodic properties approximate those of the input signal. When successful, we say that the autonomous reservoir reproduces the attractor's 'climate'. Since the reservoir equations and output weights are known, we can compute derivatives needed to determine the Lyapunov exponents of the autonomous reservoir, which we then use as estimates of the Lyapunov exponents for the original input generating system. We illustrate the effectiveness of our technique with two examples, the Lorenz system, and the Kuramoto-Sivashinsky (KS) equation. In particular, we use the Lorenz system to show that achieving climate reproduction may require tuning of the reservoir parameters. For the case of the KS equation, we note that as the system's spatial size is increased, the number of Lyapunov exponents increases, thus yielding a challenging test of our method, which we find the method successfully passes.

nlin.CD↗

arXiv2017

Modeling the Network Dynamics of Pulse-Coupled Neurons

We derive a mean-field approximation for the macroscopic dynamics of large networks of pulse-coupled theta neurons in order to study the effects of different network degree distributions, as well as degree correlations (assortativity). Using the ansatz of Ott and Antonsen (Chaos, 19 (2008) 037113), we obtain a reduced system of ordinary differential equations describing the mean-field dynamics, with significantly lower dimensionality compared with the complete set of dynamical equations for the system. We find that, for sufficiently large networks and degrees, the dynamical behavior of the reduced system agrees well with that of the full network. This dimensional reduction allows for an efficient characterization of system phase transitions and attractors. For networks with tightly peaked degree distributions, the macroscopic behavior closely resembles that of fully connected networks previously studied by others. In contrast, networks with scale-free degree distributions exhibit different macroscopic dynamics due to the emergence of degree dependent behavior of different oscillators. For nonassortative networks (i.e., networks without degree correlations) we observe the presence of a synchronously firing phase that can be suppressed by the presence of either assortativity or disassortativity in the network. We show that the results derived here can be used to analyze the effects of network topology on macroscopic behavior in neuronal networks in a computationally efficient fashion.

nlin.CD↗

arXiv2016

Competing opinions and stubbornness: connecting models to data

We introduce a general contagion-like model for competing opinions that includes dynamic resistance to alternative opinions. We show that this model can describe candidate vote distributions, spatial vote correlations, and a slow approach to opinion consensus with sensible parameter values. These empirical properties of large group dynamics, previously understood using distinct models, may be different aspects of human behavior that can be captured by a more unified model, such as the one introduced in this paper.

physics.soc-ph↗

arXiv2016

The Myopia of Crowds: A Study of Collective Evaluation on Stack Exchange

Crowds can often make better decisions than individuals or small groups of experts by leveraging their ability to aggregate diverse information. Question answering sites, such as Stack Exchange, rely on the "wisdom of crowds" effect to identify the best answers to questions asked by users. We analyze data from 250 communities on the Stack Exchange network to pinpoint factors affecting which answers are chosen as the best answers. Our results suggest that, rather than evaluate all available answers to a question, users rely on simple cognitive heuristics to choose an answer to vote for or accept. These cognitive heuristics are linked to an answer's salience, such as the order in which it is listed and how much screen space it occupies. While askers appear to depend more on heuristics, compared to voting users, when choosing an answer to accept as the most helpful one, voters use acceptance itself as a heuristic: they are more likely to choose the answer after it is accepted than before that very same answer was accepted. These heuristics become more important in explaining and predicting behavior as the number of available answers increases. Our findings suggest that crowd judgments may become less reliable as the number of answers grow.

cs.HC↗

arXiv2014

Dynamical Transitions in Large Systems of Mean Field-Coupled Landau-Stuart Oscillators: Extensive Chaos and Clumped States

In this paper, we study dynamical systems in which a large number $N$ of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors including clumped states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as situations in which all oscillators have different states and the macroscopic dynamics of the mean field is chaotic. We argue that this second type of behavior is $^{\backprime}$extensive$^{\prime}$ in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with $N$ and that the number of positive Lyapunov exponents of the attractor also scales with linearly $N$. An important focus of this paper is the transition between clumped states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe explosive (i.e., discontinuous) transitions between the clumped states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the clumped state, as the system approaches the explosive transition to extensive chaos, we find that the oscillator population distribution between the clumps continually evolves so that the clumped state is always marginally stable. This behavior is used to reveal the mechanism of the explosive transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.

nlin.CD↗

arXiv2014

The Impact of Imperfect Information on Network Attack

This paper explores the effectiveness of network attack when the attacker has imperfect information about the network. For Erdős-Rényi networks, we observe that dynamical importance and betweenness centrality-based attacks are surprisingly robust to the presence of a moderate amount of imperfect information and are more effective compared with simpler degree-based attacks even at moderate levels of network information error. In contrast, for scale-free networks the effectiveness of attack is much less degraded by a moderate level of information error. Furthermore, in the Erdőos-Rényi case the effectiveness of network attack is much more degraded by missing links as compared with the same number of false links.

physics.soc-ph↗

arXiv2013

Spatially embedded growing small-world networks

Networks in nature are often formed within a spatial domain in a dynamical manner, gaining links and nodes as they develop over time. We propose a class of spatially-based growing network models and investigate the relationship between the resulting statistical network properties and the dimension and topology of the space in which the networks are embedded. In particular, we consider models in which nodes are placed one by one in random locations in space, with each such placement followed by configuration relaxation toward uniform node density, and connection of the new node with spatially nearby nodes. We find that such growth processes naturally result in networks with small-world features, including a short characteristic path length and nonzero clustering. These properties do not appear to depend strongly on the topology of the embedding space, but do depend strongly on its dimension; higher-dimensional spaces result in shorter path lengths but less clustering.

physics.soc-ph↗

arXiv2013

Stability of Boolean networks: The joint effects of topology and update rules

We study the stability of orbits in large Boolean networks with given complex topology. We impose no restrictions on the form of the update rules, which may be correlated with local topological properties of the network. While recent past work has addressed the separate effects of nontrivial network topology and certain special classes of update rules on stability, only crude results exist about how these effects interact. We present a widely applicable solution to this problem. Numerical experiments confirm our theory and show that local correlations between topology and update rules can have profound effects on the qualitative behavior of these systems.

physics.soc-ph↗

arXiv2013

Robustness of Network Measures to Link Errors

In various applications involving complex networks, network measures are employed to assess the relative importance of network nodes. However, the robustness of such measures in the presence of link inaccuracies has not been well characterized. Here we present two simple stochastic models of false and missing links and study the effect of link errors on three commonly used node centrality measures: degree centrality, betweenness centrality, and dynamical importance. We perform numerical simulations to assess robustness of these three centrality measures. We also develop an analytical theory, which we compare with our simulations, obtaining very good agreement.

physics.soc-ph↗

arXiv2013

Understanding the Predictive Power of Computational Mechanics and Echo State Networks in Social Media

There is a large amount of interest in understanding users of social media in order to predict their behavior in this space. Despite this interest, user predictability in social media is not well-understood. To examine this question, we consider a network of fifteen thousand users on Twitter over a seven week period. We apply two contrasting modeling paradigms: computational mechanics and echo state networks. Both methods attempt to model the behavior of users on the basis of their past behavior. We demonstrate that the behavior of users on Twitter can be well-modeled as processes with self-feedback. We find that the two modeling approaches perform very similarly for most users, but that they differ in performance on a small subset of the users. By exploring the properties of these performance-differentiated users, we highlight the challenges faced in applying predictive models to dynamic social data.

cs.SI↗

arXiv2013

A hierarchical network heuristic for solving the orientation problem in genome assembly

In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves building ordered and oriented linear collections of contigs (continuous overlapping sequence reads) called scaffolds and relies on the use of mate pair data. A mate pair is a set of two reads that are sequenced from the ends of a single fragment of DNA, and therefore have opposite mutual orientations. When two reads of a mate-pair are placed into two different contigs, one can infer the mutual orientation of these contigs. While several orientation algorithms exist as part of assembly programs, all encounter challenges while solving the orientation problem due to errors from mis-assemblies in contigs or errors in read placements. In this paper we present an algorithm based on hierarchical clustering that independently solves the orientation problem and is robust to errors. We show that our algorithm can correctly solve the orientation problem for both faux (generated) assembly data and real assembly data for {\em R. sphaeroides bacteria}. We demonstrate that our algorithm is stable to both changes in the initial orientations as well as noise in the data, making it advantageous compared to traditional approaches.

q-bio.GN↗

arXiv2013

Weakly Explosive Percolation in Directed Networks

Percolation, the formation of a macroscopic connected component, is a key feature in the description of complex networks. The dynamical properties of a variety of systems can be understood in terms of percolation, including the robustness of power grids and information networks, the spreading of epidemics and forest fires, and the stability of gene regulatory networks. Recent studies have shown that if network edges are added "competitively" in undirected networks, the onset of percolation is abrupt or "explosive." The unusual qualitative features of this phase transition have been the subject of much recent attention. Here we generalize this previously studied network growth process from undirected networks to directed networks and use finite-size scaling theory to find several scaling exponents. We find that this process is also characterized by a very rapid growth in the giant component, but that this growth is not as sudden as in undirected networks.

cond-mat.stat-mech↗

arXiv2013

Modeling the dynamics of bivalent histone modifications

Epigenetic modifications to histones may promote either activation or repression of the transcription of nearby genes. Recent experimental studies show that the promoters of many lineage-control genes in stem cells have "bivalent domains" in which the nucleosomes contain both active (H3K4me3) and repressive (H3K27me3) marks. It is generally agreed that bivalent domains play an important role in stem cell differentiation, but the underlying mechanisms remain unclear. Here we formulate a mathematical model to investigate the dynamic properties of histone modification patterns. We then illustrate that our modeling framework can be used to capture key features of experimentally observed combinatorial chromatin states.

q-bio.GN↗

arXiv2013

Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets

Gene annotation databases (compendiums maintained by the scientific community that describe the biological functions performed by individual genes) are commonly used to evaluate the functional properties of experimentally derived gene sets. Overlap statistics, such as Fisher's Exact Test (FET), are often employed to assess these associations, but don't account for non-uniformity in the number of genes annotated to individual functions or the number of functions associated with individual genes. We find FET is strongly biased toward over-estimating overlap significance if a gene set has an unusually high number of annotations. To correct for these biases, we develop Annotation Enrichment Analysis (AEA), which properly accounts for the non-uniformity of annotations. We show that AEA is able to identify biologically meaningful functional enrichments that are obscured by numerous false-positive enrichment scores in FET, and we therefore suggest it be used to more accurately assess the biological properties of gene sets.

q-bio.QM↗

arXiv2013

Finding New Order in Biological Functions from the Network Structure of Gene Annotations

The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to each other. These term-term relationships encode how scientists conceive the organization of biological functions, and they take the form of a directed acyclic graph (DAG). Here, we propose that the network structure of gene-term annotations made using GO can be employed to establish an alternate natural way to group the functional terms which is different from the hierarchical structure established in the GO DAG. Instead of relying on an externally defined organization for biological functions, our method connects biological functions together if they are performed by the same genes, as indicated in a compendium of gene annotation data from numerous different experiments. We show that grouping terms by this alternate scheme is distinct from term relationships defined in the ontological structure and provides a new framework with which to describe and predict the functions of experimentally identified sets of genes.

q-bio.QM↗