arXiv subjects

Tobias Galla

Publications and source records attributed to Tobias Galla.

At least 55 records · Page 3Linked to original sources

arXiv2022

Demographic noise in complex ecological communities

We introduce an individual-based model of a complex ecological community with random interactions. The model contains a large number of species, each with a finite population of individuals, subject to discrete reproduction and death events. The interaction coefficients determining the rates of these events is chosen from an ensemble of random matrices, and is kept fixed in time. The set-up is such that the model reduces to the known generalised Lotka-Volterra equations with random interaction coefficients in the limit of an infinite population for each species. Demographic noise in the individual-based model means that species which would survive in the Lotka-Volterra model can become extinct. These noise-driven extinctions are the focus of the paper. We find that, for increasing complexity of interactions, ecological communities generally become less prone to extinctions induced by demographic noise. An exception are systems composed entirely of predator-prey pairs. These systems are known to be stable in deterministic Lotka-Volterra models with random interactions, but, as we show, they are nevertheless particularly vulnerable to fluctuations.

q-bio.PE↗

arXiv2022

Liquid-Hexatic-Solid phases in active and passive Brownian particles determined by stochastic birth and death events

We study the effects of stochastic birth and death processes on the structural phases of systems of active and passive Brownian particles subject to volume exclusion. The total number of particles in the system is a fluctuating quantity, determined by the birth and death parameters, and on the activity of the particles. As the birth and death parameters are varied we find liquid, hexatic and solid phases. For passive particles these phases are found to be spatially homogeneous. For active particles motility-induced phase separation (co-existing hexatic and liquid phases) occurs for large activity and sufficiently small birth rates. We also observe a re-entrant transition to the hexatic phase when the birth rate is increased. This results from a balance of an increasing number of particles filling the system, and a larger number of defects resulting from the birth and death dynamics.

cond-mat.stat-mech↗

arXiv2022

Network Meta-Analysis: A Statistical Physics Perspective

Network meta-analysis (NMA) is a technique used in medical statistics to combine evidence from multiple medical trials. NMA defines an inference and information processing problem on a network of treatment options and trials connecting the treatments. We believe that statistical physics can offer useful ideas and tools for this area, including from the theory of complex networks, stochastic modelling and simulation techniques. The lack of a unique source that would allow physicists to learn about NMA effectively is a barrier to this. In this article we aim to present the `NMA problem' and existing approaches to it coherently and in a language accessible to statistical physicists. We also summarise existing points of contact between statistical physics and NMA, and describe our ideas of how physics might make a difference for NMA in the future. The overall goal of the article is to attract physicists to this interesting, timely and worthwhile field of research.

cond-mat.stat-mech↗

arXiv2021

Sampling rare trajectories using stochastic bridges

The numerical quantification of the statistics of rare events in stochastic processes is a challenging computational problem. We present a sampling method that constructs an ensemble of stochastic trajectories that are constrained to have fixed start and end points (so-called stochastic bridges). We then show that by carefully choosing a set of such bridges and assigning an appropriate statistical weight to each bridge, one can focus more processing power on the rare events of a target stochastic process while faithfully preserving the statistics of these rate trajectories. Further, we also compare the stochastic bridges produced using our method to the Wentzel-Kramers-Brillouin (WKB) optimal paths of the target process, derived in the limit of low noise. We see that the paths produced using our method, encoding the full statistics of the process, collapse onto the WKB optimal path as the level of noise is reduced. We propose that our method can be used to judge the accuracy of the WKB approximation at finite levels of noise.

cond-mat.stat-mech↗

arXiv2021

Retarded kernels for longitudinal survival analysis and dynamic prediction

Predicting patient survival probabilities based on observed covariates is an important assessment in clinical practice. These patient-specific covariates are often measured over multiple follow-up appointments. It is then of interest to predict survival based on the history of these longitudinal measurements, and to update predictions as more observations become available. The standard approaches to these so-called `dynamic prediction' assessments are joint models and landmark analysis. Joint models involve high-dimensional parametrisations, and their computational complexity often prohibits including multiple longitudinal covariates. Landmark analysis is simpler, but discards a proportion of the available data at each `landmark time'. In this work we propose a `retarded kernel' approach to dynamic prediction that sits somewhere in between the two standard methods in terms of complexity. By conditioning hazard rates directly on the covariate measurements over the observation time frame, we define a model that takes into account the full history of covariate measurements but is more practical and parsimonious than joint modelling. Time-dependent association kernels describe the impact of covariate changes at earlier times on the patient's hazard rate at later times. Under the constraints that our model (i) reduces to the standard Cox model for time-independent covariates, and (ii) contains the instantaneous Cox model as a special case, we derive two natural kernel parameterisations. Upon application to three clinical data sets, we find that the predictive accuracy of the retarded kernel approach is comparable to that of the two existing standard methods.

stat.ME↗

arXiv2021

Towards a taxonomy of learning dynamics in 2 x 2 games

Do boundedly rational players learn to choose equilibrium strategies as they play a game repeatedly? A large literature in behavioral game theory has proposed and experimentally tested various learning algorithms, but a comparative analysis of their equilibrium convergence properties is lacking. In this paper we analyze Experience-Weighted Attraction (EWA), which generalizes fictitious play, best-response dynamics, reinforcement learning and also replicator dynamics. Studying $2\times 2$ games for tractability, we recover some well-known results in the limiting cases in which EWA reduces to the learning rules that it generalizes, but also obtain new results for other parameterizations. For example, we show that in coordination games EWA may only converge to the Pareto-efficient equilibrium, never reaching the Pareto-inefficient one; that in Prisoner Dilemma games it may converge to fixed points of mutual cooperation; and that limit cycles or chaotic dynamics may be more likely with longer or shorter memory of previous play.

econ.GN↗

arXiv2021

Network meta-analysis and random walks

Network meta-analysis (NMA) is a central tool for evidence synthesis in clinical research. The results of an NMA depend critically on the quality of evidence being pooled. In assessing the validity of an NMA, it is therefore important to know the proportion contributions of each direct treatment comparison to each network treatment effect. The construction of proportion contributions is based on the observation that each row of the hat matrix represents a so-called 'evidence flow network' for each treatment comparison. However, the existing algorithm used to calculate these values is associated with ambiguity according to the selection of paths. In this work we present a novel analogy between NMA and random walks. We use this analogy to derive closed-form expressions for the proportion contributions. A random walk on a graph is a stochastic process that describes a succession of random 'hops' between vertices which are connected by an edge. The weight of an edge relates to the probability that the walker moves along that edge. We use the graph representation of NMA to construct the transition matrix for a random walk on the network of evidence. We show that the net number of times a walker crosses each edge of the network is related to the evidence flow network. By then defining a random walk on the directed evidence flow network, we derive analytically the matrix of proportion contributions. The random-walk approach, in addition to being computationally more efficient, has none of the associated ambiguity of the existing algorithm.

cs.SI↗

arXiv2020

Beyond the adiabatic limit in systems with fast environments: a $τ$-leaping algorithm

We propose a $τ$-leaping simulation algorithm for stochastic systems subject to fast environmental changes. Similar to conventional $τ$-leaping the algorithm proceeds in discrete time steps, but as a principal addition it captures environmental noise beyond the adiabatic limit. The key idea is to treat the input rates for the $τ$-leaping as (clipped) Gaussian random variables with first and second moments constructed from the environmental process. In this way, each step of the algorithm retains environmental stochasticity to sub-leading order in the time scale separation between system and environment. We test the algorithm on several toy examples with discrete and continuous environmental states, and find good performance in the regime of fast environmental dynamics. At the same time, the algorithm requires significantly less computing time than full simulations of the combined system and environment. In this context we also discuss several methods for the simulation of stochastic population dynamics in time-varying environments with continuous states.

cond-mat.stat-mech↗

arXiv2020

Zealots in multi-state noisy voter models

The noisy voter model is a stylised representation of opinion dynamics. Individuals copy opinions from other individuals, and are subject to spontaneous state changes. In the case of two opinion states this model is known to have a noise-driven transition between a unimodal phase, in which both opinions are present, and a bimodal phase in which one of the opinions dominates. The presence of zealots can remove the unimodal and bimodal phases in the model with two opinion states. Here, we study the effects of zealots in noisy voter models with M>2 opinion states on complete interaction graphs. We find that the phase behaviour diversifies, with up to six possible qualitatively different types of stationary states. The presence of zealots removes some of these phases, but not all. We analyse situations in which zealots affect the entire population, or only a fraction of agents, and show that this situation corresponds to a single-community model with a fractional number of zealots, further enriching the phase diagram. Our study is conducted analytically based on effective birth-death dynamics for the number of individuals holding a given opinion. Results are confirmed in numerical simulations.

physics.soc-ph↗

arXiv2020

Ecological communities from random generalised Lotka-Volterra dynamics with non-linear feedback

We investigate the outcome of generalised Lotka-Volterra dynamics of ecological communities with random interaction coefficients and non-linear feedback. We show in simulations that the saturation of non-linear feedback stabilises the dynamics. This is confirmed in an analytical generating-functional approach to generalised Lotka-Volterra equations with piecewise linear saturating response. For such systems we are able to derive self-consistent relations governing the stable fixed-point phase, and to carry out a linear stability analysis to predict the onset of unstable behaviour. We investigate in detail the combined effects of the mean, variance and co-variance of the random interaction coefficients, and the saturation value of the non-linear response. We find that stability and diversity increases with the introduction of non-linear feedback, where decreasing the saturation value has a similar effect to decreasing the co-variance. We also find co-operation to no longer have a detrimental effect on stability with non-linear feedback, and the order parameters mean abundance and diversity to be less dependent on the symmetry of interactions with stronger saturation.

q-bio.PE↗

arXiv2020

Degree irregularity and rank probability bias in network meta-analysis

Network meta-analysis (NMA) is a statistical technique for the comparison of treatment options. The nodes of the network are the competing treatments and edges represent comparisons of treatments in trials. Outcomes of Bayesian NMA include estimates of treatment effects, and the probabilities that each treatment is ranked best, second best and so on. How exactly network geometry affects the accuracy and precision of these outcomes is not fully understood. Here we carry out a simulation study and find that disparity in the number of trials involving different treatments leads to a systematic bias in estimated rank probabilities. This bias is associated with an increased variation in the precision of treatment effect estimates. Using ideas from the theory of complex networks, we define a measure of `degree irregularity' to quantify asymmetry in the number of studies involving each treatment. Our simulations indicate that more regular networks have more precise treatment effect estimates and smaller bias of rank probabilities. We also find that degree regularity is a better indicator of NMA quality than both the total number of studies in a network and the disparity in the number of trials per comparison. These results have implications for planning future trials. We demonstrate that choosing trials which reduce the network's irregularity can improve the precision and accuracy of NMA outcomes.

stat.ME↗

arXiv2020

Effective diffusion coefficients in reaction-diffusion systems with anomalous transport

We show that the Turing patterns in reaction systems with subdiffusion can be replicated in an effective system with Markovian cross-diffusion. The effective system has the same Turing instability as the original system, and the same patterns. If particles are short-lived, the transient dynamics are captured as well. We use the cross-diffusive system to define effective diffusion coefficients for the system with anomalous transport, and we show how they can be used to efficiently describe the Turing instability. We also demonstrate that the mean squared displacement of a suitably defined ensemble of subdiffusing particles grows linearly with time, with a diffusion coefficient which agrees with our earlier calculations. We verify these deductions by numerically integrating both the fractional reaction-diffusion equation and its normally diffusing counterpart. Our findings suggest that cross-diffusive behaviour can come about as a result of anomalous transport.

nlin.PS↗

arXiv2019

Intrinsic noise, Delta-Notch signalling and delayed reactions promote sustained, coherent, synchronised oscillations in the presomitic mesoderm

Using a stochastic individual-based modelling approach, we examine the role that Delta-Notch signalling plays in the regulation of a robust and reliable somite segmentation clock. We find that not only can Delta-Notch signalling synchronise noisy cycles of gene expression in adjacent cells in the presomitic mesoderm (as is known), but it can also amplify and increase the coherence of these cycles. We examine some of the shortcomings of deterministic approaches to modelling these cycles and demonstrate how intrinsic noise can play an active role in promoting sustained oscillations, giving rise to noise-induced quasi-cycles. Finally, we explore how translational/transcriptional delays can result in the cycles in neighbouring cells oscillating in anti-phase and we study how this effect relates to the propagation of noise-induced stochastic waves.

q-bio.SC↗

arXiv2019

Stochastic fluctuations and quasi-pattern formation in reaction-diffusion systems with anomalous transport

Many approaches to modelling reaction-diffusion systems with anomalous transport rely on deterministic equations and ignore fluctuations arising due to finite particle numbers. Starting from an individual-based model we use a generating-functional approach to derive a Gaussian approximation for this intrinsic noise in subdiffusive systems. This results in corrections to the deterministic fractional reaction-diffusion equations. Using this analytical approach, we study the onset of noise-driven quasi-patterns in reaction-subdiffusion systems. We find that subdiffusion can be conducive to the formation of both deterministic and stochastic patterns. Our analysis shows that the combination of subdiffusion and intrinsic stochasticity can reduce the threshold ratio of the effective diffusion coefficients required for pattern formation to a greater degree than either effect on its own.

cond-mat.stat-mech↗

arXiv2019

Consensus and diversity in multi-state noisy voter models

We study a variant of the voter model with multiple opinions; individuals can imitate each other and also change their opinion randomly in mutation events. We focus on the case of a population with all-to-all interaction. A noise-driven transition between regimes with multi-modal and unimodal stationary distributions is observed. In the former, the population is mostly in consensus states; in the latter opinions are mixed. We derive an effective death-birth process, describing the dynamics from the perspective of one of the opinions, and use it to analytically compute marginals of the stationary distribution. These calculations are exact for models with homogeneous imitation and mutation rates, and an approximation if rates are heterogeneous. Our approach can be used to characterize the noise-driven transition and to obtain mean switching times between consensus states.

physics.soc-ph↗

arXiv2019

Motion, fixation probability and the choice of an evolutionary process

Different evolutionary models are known to make disparate predictions for the success of an invading mutant in some situations. For example, some evolutionary mechanics lead to amplification of selection in structured populations, while others suppress it. Here, we use computer simulations to study evolutionary populations moved by flows, and show how the speed of this motion impacts the fixation probability of an invading mutant. Flows of different speeds interpolate between evolutionary dynamics on fixed heterogeneous graphs and in well-stirred populations. We find that the motion has an active role in amplifying or suppressing selection, accomplished by fragmenting and reconnecting the interaction graph. While increasing flow speeds suppress selection for most evolutionary models, we identify characteristic responses to flow for the different update rules we test. We suggest these responses as a potential aid for choosing the most suitable update rule for a given biological system.

q-bio.PE↗

arXiv2018

Dynamically evolved community size and stability of random Lotka-Volterra ecosystems

We use dynamical generating functionals to study the stability and size of communities evolving in Lotka-Volterra systems with random interaction coefficients. The size of the eco-system is not set from the beginning. Instead, we start from a set of possible species, which may undergo extinction. How many species survive depends on the properties of the interaction matrix; the size of the resulting food web at stationarity is a property of the system itself in our model, and not a control parameter as in most studies based on random matrix theory. We find that prey-predator relations enhance stability, and that variability of species interactions promotes instability. Complexity of inter-species couplings leads to reduced sizes of ecological communities. Dynamically evolved community size and stability are hence positively correlated.

q-bio.PE↗

arXiv2018

Calculating normal tissue complication probabilities and probabilities of complication-free tumour control from stochastic models of population dynamics

We use a stochastic birth-death model for a population of cells to estimate the normal tissue complication probability (NTCP) under a particular radiotherapy protocol. We specifically allow for interaction between cells, via a nonlinear logistic growth model. To capture some of the effects of intrinsic noise in the population we develop several approximations of NTCP, using Kramers-Moyal expansion techniques. These approaches provide an approximation to the first and second moments of a general first-passage time problem in the limit of large, but finite populations. We use this method to study NTCP in a simple model of normal cells and in a model of normal and damaged cells. We also study a combined model of normal tissue cells and tumour cells. Based on existing methods to calculate tumour control probabilities, and our procedure to approximate NTCP, we estimate the probability of complication free tumour control.

q-bio.PE↗