arXiv subjects

Peter J. Thomas

Publications and source records attributed to Peter J. Thomas.

At least 19 recordsLinked to original sources

arXiv2025

Artificial neural network solver for Fokker-Planck and Koopman eigenfunctions

For a stochastic differential equation (SDE) that is an Itô diffusion or Langevin equation, the Fokker-Planck operator governs the evolution of the probability density, while its adjoint, the infinitesimal generator of the stochastic Koopman operator, governs the evolution of system observables, in the mean. The eigenfunctions of these operators provide a powerful framework to analyze SDEs, and have shown to be particularly useful for systems of stochastic oscillators. However, computing these eigenfunctions typically requires solving high-dimensional PDEs on unbounded domains, which is numerically challenging. Building on previous work, we propose a data-driven artificial neural network solver for Koopman and Fokker-Planck eigenfunctions. Our approach incorporates the differential operator into the loss function, improving accuracy and reducing dependence on large amounts of accurate training data. We demonstrate our approach on several numerical examples in two, three, and four dimensions.

math.NA↗

arXiv2025

$Q$-functions, synchronization, and Arnold tongues for coupled stochastic oscillators

Phase reduction is an effective theoretical and numerical tool for studying synchronization of coupled deterministic oscillators. Stochastic oscillators require new definitions of asymptotic phase. The $Q$-function, i.e. the slowest decaying complex mode of the stochastic Koopman operator (SKO), was proposed as a means of phase reduction for stochastic oscillators. In this paper, we show that the $Q$-function approach also leads to a novel definition of ``synchronization" for coupled stochastic oscillators. A system of coupled oscillators in the synchronous regime may be viewed as a single (higher-dimensional) oscillator. Therefore, we investigate the relation between the $Q$-functions of the uncoupled oscillators and the higher-dimensional $Q$-function for the coupled system. We propose a definition of synchronization between coupled stochastic oscillators in terms of the eigenvalue spectrum of Kolmogorov's backward operator (the generator of the Markov process, or the SKO) of the higher dimensional coupled system. We observe a novel type of bifurcation reflecting (i) the relationship between the leading eigenvalues of the SKO for the coupled system and (ii) qualitative changes in the cross-spectral density of the coupled oscillators. Using our proposed definition, we observe synchronization domains for symmetrically-coupled stochastic oscillators that are analogous to Arnold tongues for coupled deterministic oscillators.

math.PR↗

arXiv2024

Generalized dynamical phase reduction for stochastic oscillators

Phase reduction is an important tool for studying coupled and driven oscillators. The question of how to generalize phase reduction to stochastic oscillators remains actively debated. In this work, we propose a method to derive a self-contained stochastic phase equation of the form $\mathop{}\!\mathrm{d} ϕ= a(ϕ)\mathop{}\!\mathrm{d} t + \sqrt{2D(ϕ)}\,\mathop{}\!\mathrm{d} W(t)$ that is valid not only for noise-perturbed limit cycles, but also for noise-induced oscillations. We show that our reduction captures the asymptotic statistics of qualitatively different stochastic oscillators, and use it to infer their phase-response properties.

math-ph↗

arXiv2024

Phase-Amplitude Description of Stochastic Oscillators: A Parameterization Method Approach

The parameterization method (PM) provides a broad theoretical and numerical foundation for computing invariant manifolds of dynamical systems. PM implements a change of variables in order to represent trajectories of a system of ordinary differential equations ``as simply as possible." In this paper we pursue a similar goal for stochastic oscillator systems. For planar nonlinear stochastic systems that are ``robustly oscillatory", we find a change of variables through which the dynamics are as simple as possible $\textit{in the mean}$. We prove existence and uniqueness of a deterministic vector field, the trajectories of which capture the local mean behavior of the stochastic oscillator. We illustrate the construction of such an ``effective vector field" for several examples, including a limit cycle oscillator perturbed by noise, an excitable system derived from a spiking neuron model, and a spiral sink with noise forcing (2D Ornstein-Uhlenbeck process). The latter examples comprise contingent oscillators that would not sustain rhythmic activity without noise forcing. Finally, we exploit the simplicity of the dynamics after the change of variables to obtain the effective diffusion constant of the resulting phase variable, and the stationary variance of the resulting amplitude (isostable) variable.

math.DS↗

arXiv2024

Variational design of sensory feedback for powerstroke-recovery systems

Although the raison d'etre of the brain is the survival of the body, there are relatively few theoretical studies of closed-loop rhythmic motor control systems. In this paper we provide a unified framework, based on variational analysis, for investigating the dual goals of performance and robustness in powerstroke-recovery systems. We augment two previously published closed-loop motor control models by equipping each model with a performance measure based on the rate of progress of the system relative to a spatially extended external substrate -- such as progress relative to the ground for a locomotor task. The sensitivity measure quantifies the ability of the system to maintain performance in response to external perturbations. Motivated by a search for optimal design principles for feedback control achieving the complementary requirements of efficiency and robustness, we discuss the performance-sensitivity patterns of the systems featuring different sensory feedback architectures. In a paradigmatic half-center oscillator (HCO)-motor system, we observe that the excitation-inhibition property of feedback mechanisms determines the sensitivity pattern while the activation-inactivation property determines the performance pattern. Moreover, we show that the nonlinearity of the sigmoid activation of feedback signals allows the existence of optimal combinations of performance and sensitivity. In a detailed hindlimb locomotor system, we find that a force-dependent feedback can simultaneously optimize both performance and robustness, while length-dependent feedback variations result in significant performance-versus-sensitivity tradeoffs. Thus, this work provides an analytical framework for studying feedback control of oscillations in nonlinear dynamical systems, leading to several insights that have the potential to inform the design of control or rehabilitation systems.

q-bio.NC↗

arXiv2023

Sensitivity to control signals in triphasic rhythmic neural systems: a comparative mechanistic analysis via infinitesimal local timing response curves

Similar activity patterns may arise from model neural networks with distinct coupling properties and individual unit dynamics. These similar patterns may, however, respond differently to parameter variations and, specifically, to tuning of inputs that represent control signals. In this work, we analyze the responses resulting from modulation of a localized input in each of three classes of model neural networks that have been recognized in the literature for their capacity to produce robust three-phase rhythms: coupled fast-slow oscillators, near-heteroclinic oscillators, and threshold-linear networks. Triphasic rhythms, in which each phase consists of a prolonged activation of a corresponding subgroup of neurons followed by a fast transition to another phase, represent a fundamental activity pattern observed across a range of central pattern generators underlying behaviors critical to survival, including respiration, locomotion, and feeding. To perform our analysis, we extend the recently developed local timing response curve (lTRC), which allows us to characterize the timing effects due to perturbations, and we complement our lTRC approach with model-specific dynamical systems analysis. Interestingly, we observe disparate effects of similar perturbations across distinct model classes. Thus, this work provides an analytical framework for studying control of oscillations in nonlinear dynamical systems, and may help guide model selection in future efforts to study systems exhibiting triphasic rhythmic activity.

q-bio.NC↗

arXiv2023

Pattern Forming Mechanisms of Color Vision

While our understanding of the way single neurons process chromatic stimuli in the early visual pathway has advanced significantly in recent years, we do not yet know how these cells interact to form stable representations of hue. Drawing on physiological studies, we offer a dynamical model of how the primary visual cortex tunes for color, hinged on intracortical interactions and emergent network effects. After detailing the evolution of network activity through analytical and numerical approaches, we discuss the effects of the model's cortical parameters on the selectivity of the tuning curves. In particular, we explore the role of the model's thresholding nonlinearity in enhancing hue selectivity by expanding the region of stability, allowing for the precise encoding of chromatic stimuli in early vision. Finally, in the absence of a stimulus, the model is capable of explaining hallucinatory color perception via a Turing-like mechanism of biological pattern formation.

q-bio.NC↗

arXiv2023

A Universal Description of Stochastic Oscillators

Many systems in physics, chemistry and biology exhibit oscillations with a pronounced random component. Such stochastic oscillations can emerge via different mechanisms, for example linear dynamics of a stable focus with fluctuations, limit-cycle systems perturbed by noise, or excitable systems in which random inputs lead to a train of pulses. Despite their diverse origins, the phenomenology of random oscillations can be strikingly similar. Here we introduce a nonlinear transformation of stochastic oscillators to a new complex-valued function $Q^*_1(\textbf{x})$ that greatly simplifies and unifies the mathematical description of the oscillator's spontaneous activity, its response to an external time-dependent perturbation, and the correlation statistics of different oscillators that are weakly coupled. The function $Q^*_1(\textbf{x})$ is the eigenfunction of the Kolmogorov backward operator with the least negative (but non-vanishing) eigenvalue $λ_1=μ_1+iω_1$. The resulting power spectrum of the complex-valued function is exactly given by a Lorentz spectrum with peak frequency $ω_1$ and half-width $μ_1$; its susceptibility with respect to a weak external forcing is given by a simple one-pole filter, centered around $ω_1$; and the cross-spectrum between two coupled oscillators can be easily expressed by a combination of the spontaneous power spectra of the uncoupled systems and their susceptibilities. Our approach makes qualitatively different stochastic oscillators comparable, provides simple characteristics for the coherence of the random oscillation, and gives a framework for the description of weakly coupled oscillators.

nlin.AO↗

arXiv2023

Explicitly Solvable Continuous-time Inference for Partially Observed Markov Processes

Many natural and engineered systems can be modeled as discrete state Markov processes. Often, only a subset of states are directly observable. Inferring the conditional probability that a system occupies a particular hidden state, given the partial observation, is a problem with broad application. In this paper, we introduce a continuous-time formulation of the sum-product algorithm, which is a well-known discrete-time method for finding the hidden states' conditional probabilities, given a set of finite, discrete-time observations. From our new formulation, we can explicitly solve for the conditional probability of occupying any state, given the transition rates and observations within a finite time window. We apply our algorithm to a realistic model of the cystic fibrosis transmembrane conductance regulator (CFTR) protein for exact inference of the conditional occupancy probability, given a finite time series of partial observations.

eess.SP↗

arXiv2022

Variational and phase response analysis for limit cycles with hard boundaries, with applications to neuromechanical control problems

Motor systems show an overall robustness, but because they are highly nonlinear, understanding how they achieve robustness is difficult. In many rhythmic systems, robustness against perturbations involves response of both the shape and the timing of the trajectory. This makes the study of robustness even more challenging. To understand how a motor system produces robust behaviors in a variable environment, we consider a neuromechanical model of motor patterns in the feeding apparatus of the marine mollusk \textit{Aplysia californica} \citep{shaw2015,lyttle2017}. We established in \citep{WGCT2021} the tools for studying combined shape and timing responses of limit cycle systems under sustained perturbations and here apply them to study robustness of the neuromechanical model against increased mechanical load during swallowing. Interestingly, we discover that nonlinear biomechanical properties confer resilience by immediately increasing resistance to applied loads. In contrast, the effect of changed sensory feedback signal is significantly delayed by the firing rates' hard boundary properties. Our analysis suggests that sensory feedback contributes to robustness in swallowing primarily by shifting the timing of neural activation involved in the power stroke of the motor cycle (retraction). This effect enables the system to generate stronger retractor muscle forces to compensate for the increased load, and hence achieve strong robustness. The approaches that we are applying to understanding a neuromechanical model in \textit{Aplysia}, and the results that we have obtained, are likely to provide insights into the function of other motor systems that encounter changing mechanical loads and hard boundaries, both due to mechanical and neuronal firing properties.

q-bio.NC↗

arXiv2022

Inferring Density-Dependent Population Dynamics Mechanisms through Rate Disambiguation for Logistic Birth-Death Processes

Density dependence is important in the ecology and evolution of microbial and cancer cells. Typically, we can only measure net growth rates, but the underlying density-dependent mechanisms that give rise to the observed dynamics can manifest in birth processes, death processes, or both. Therefore, we utilize the mean and variance of cell number fluctuations to separately identify birth and death rates from time series that follow stochastic birth-death processes with logistic growth. Our method provides a novel perspective on stochastic parameter identifiability, which we validate by analyzing the accuracy in terms of the discretization bin size. We apply our method to the scenario where a homogeneous cell population goes through three stages: (1) grows naturally to its carrying capacity, (2) is treated with a drug that reduces its carrying capacity, and (3) overcomes the drug effect to restore its original carrying capacity. In each stage, we disambiguate whether it happens through the birth process, death process, or some combination of the two, which contributes to understanding drug resistance mechanisms. In the case of limited data sets, we provide an alternative method based on maximum likelihood and solve a constrained nonlinear optimization problem to identify the most likely density dependence parameter for a given cell number time series. Our methods can be applied to other biological systems at different scales to disambiguate density-dependent mechanisms underlying the same net growth rate.

q-bio.PE↗

arXiv2021

Isostables for stochastic oscillators

Thomas and Lindner (2014, Phys.Rev.Lett.) defined an asymptotic phase for stochastic oscillators as the angle in the complex plane made by the eigenfunction, having a complex eigenvalue with a least negative real part, of the backward Kolmogorov (or stochastic Koopman) operator. We complete the phase-amplitude description of noisy oscillators by defining the stochastic isostable coordinate as the eigenfunction with the least negative nontrivial real eigenvalue. Our results suggest a framework for stochastic limit cycle dynamics that encompasses noise-induced oscillations.

math.DS↗

arXiv2021

Heteroclinic cycling and extinction in May-Leonard models with demographic stochasticity

May and Leonard (SIAM J. Appl. Math 1975) introduced a three-species Lotka-Volterra type population model that exhibits heteroclinic cycling. Rather than producing a periodic limit cycle, the trajectory takes longer and longer to complete each "cycle", passing closer and closer to unstable fixed points in which one population dominates and the others approach zero. Aperiodic heteroclinic dynamics have subsequently been studied in ecological systems (side-blotched lizards; colicinogenic E. coli), in the immune system, in neural information processing models ("winnerless competition"), and in models of neural central pattern generators. Yet as May and Leonard observed "Biologically, the behavior (produced by the model) is nonsense. Once it is conceded that the variables represent animals, and therefore cannot fall below unity, it is clear that the system will, after a few cycles, converge on some single population, extinguishing the other two." Here, we explore different ways of introducing discrete stochastic dynamics based on May and Leonard's ODE model, with application to ecological population dynamics, and to a neuromotor central pattern generator system. We study examples of several quantitatively distinct asymptotic behaviors, including total extinction of all species, extinction to a single species, and persistent cyclic dominance with finite mean cycle length.

q-bio.PE↗

arXiv2021

An analytical approach to the Mean--Return-Time~Phase of isotropic stochastic oscillators

One notion of phase for stochastic oscillators is based on the mean return-time (MRT): a set of points represents a certain phase if the mean time to return from any point in this set to this set after one rotation is equal to the mean rotation period of the oscillator (irrespective of the starting point). For this so far only algorithmically defined phase, we derive here analytical expressions for the important class of isotropic stochastic oscillators. This allows us to evaluate cases from the literature explicitly and to study the behavior of the MRT phase in the limits of strong noise. We also use the same formalism to show that lines of constant return time variance (instead of constant mean return time) can be defined, and that they in general differ from the MRT-isochrons.

cond-mat.stat-mech↗

arXiv2021

A factor graph EM algorithm for inference of kinetic microstates from patch clamp measurements

We derive a factor graph EM (FGEM) algorithm, a technique that permits combined parameter estimation and statistical inference, to determine hidden kinetic microstates from patch clamp measurements. Using the cystic fibrosis transmembrane conductance regulator (CFTR) and nicotinic acetylcholine receptor (nAChR) as examples, we perform {\em Monte Carlo} simulations to demonstrate the performance of the algorithm. We show that the performance, measured in terms of the probability of estimation error, approaches the theoretical performance limit of maximum {\em a posteriori} estimation. Moreover, the algorithm provides a reliability score for its estimates, and we demonstrate that the score can be used to further improve the performance of estimation. We use the algorithm to estimate hidden kinetic states in lab-obtained CFTR single channel patch clamp traces.

q-bio.QM↗

arXiv2020

Control for Multifunctionality: Bioinspired Control Based on Feeding in Aplysia californica

Animals exhibit remarkable feats of behavioral flexibility and multifunctional control that remain challenging for robotic systems. The neural and morphological basis of multifunctionality in animals can provide a source of bio-inspiration for robotic controllers. However, many existing approaches to modeling biological neural networks rely on computationally expensive models and tend to focus solely on the nervous system, often neglecting the biomechanics of the periphery. As a consequence, while these models are excellent tools for neuroscience, they fail to predict functional behavior in real time, which is a critical capability for robotic control. To meet the need for real-time multifunctional control, we have developed a hybrid Boolean model framework capable of modeling neural bursting activity and simple biomechanics at speeds faster than real time. Using this approach, we present a multifunctional model of Aplysia californica feeding that qualitatively reproduces three key feeding behaviors (biting, swallowing, and rejection), demonstrates behavioral switching in response to external sensory cues, and incorporates both known neural connectivity and a simple bioinspired mechanical model of the feeding apparatus. We demonstrate that the model can be used for formulating testable hypotheses and discuss the implications of this approach for robotic control and neuroscience.

q-bio.NC↗

arXiv2020

Resolving Molecular Contributions of Ion Channel Noise to Interspike Interval Variability through Stochastic Shielding

The contributions of independent noise sources to the variability of action potential timing has not previously been studied at the level of individual directed molecular transitions within a conductance-based model ion-state graph. The underlying connection provides an important example of how mathematics can be applied to study the effects of unobservable microscopic fluctuations to macroscopically observable quantities. We study a stochastic Langevin model and show how to resolve the individual contributions that each transition in the ion channel graph makes to the variance of the interspike interval (ISI). We extend the mean--return-time (MRT) phase reduction developed in (Cao et al. 2020, SIAM J. Appl. Math) to the second moment of the return time from an MRT isochron to itself. Because fixed-voltage spike-detection triggers do not correspond to MRT isochrons, the inter-phase interval (IPI) variance only approximates the ISI variance. We find the IPI variance and ISI variance agree to within a few percent when both can be computed. Moreover, we prove rigorously, and show numerically, that our expression for the IPI variance is accurate in the small noise (large system size) regime; our theory is exact in the limit of small noise. By selectively including the noise associated with only those few transitions responsible for most of the ISI variance, our analysis extends the stochastic shielding (SS) paradigm (Schmandt et al. 2012, Phys. Rev. Lett.) from the stationary voltage-clamp case to the current-clamp case. We show numerically that the SS approximation has a high degree of accuracy even for larger, physiologically relevant noise levels. We show that the ISI variance is not an unambiguously defined quantity, but depends on the choice of voltage level set as the spike-detection threshold, both in vitro and in silico.

q-bio.NC↗

arXiv2020

The Network HHD: Quantifying Cyclic Competition in Trait-Performance Models of Tournaments

Competitive tournaments appear in sports, politics, population ecology, and animal behavior. All of these fields have developed methods for rating competitors and ranking them accordingly. A tournament is intransitive if it is not consistent with any ranking. Intransitive tournaments contain rock-paper-scissor type cycles. The discrete Helmholtz-Hodge decomposition (HHD) is well adapted to describing intransitive tournaments. It separates a tournament into perfectly transitive and perfectly cyclic components, where the perfectly transitive component is associated with a set of ratings. The size of the cyclic component can be used as a measure of intransitivity. Here we show that the HHD arises naturally from two classes of tournaments with simple statistical interpretations. We then discuss six different sets of assumptions that define equivalent decompositions. This analysis motivates the choice to use the HHD among other existing methods. Success in competition is typically mediated by the traits of the competitors. A trait-performance model assumes that the probability that one competitor beats another can be expressed as a function of their traits. We show that, if the traits of each competitor are drawn independently and identically from a trait distribution then the expected degree of intransitivity in the network can be computed explicitly. Using this result we show that increasing the number of pairs of competitors who could compete promotes cyclic competition, and that increasing the correlation in the performance of $A$ against $B$ with the performance of $A$ against $C$ promotes transitive competition. The expected size of cyclic competition can thus be understood by analyzing this correlation. An illustrative example is provided.

physics.soc-ph↗