Sampling Properties of the Spectrum and Coherency of Sequences of Action Potentials

The spectrum and coherency are useful quantities for characterizing the temporal correlations and functional relations within and between point processes. This paper begins with a review of these quantities, their interpretation and how they may be estimated. A discussion of how to assess the statistical significance of features in these measures is included. In addition, new work is presented which builds on the framework established in the review section. This work investigates how the estimates and their error bars are modified by finite sample sizes. Finite sample corrections are derived based on a doubly stochastic inhomogeneous Poisson process model in which the rate functions are drawn from a low variance Gaussian process. It is found that, in contrast to continuous processes, the variance of the estimators cannot be reduced by smoothing beyond a scale which is set by the number of point events in the interval. Alternatively, the degrees of freedom of the estimators can be thought of as bounded from above by the expected number of point events in the interval. Further new work describing and illustrating a method for detecting the presence of a line in a point process spectrum is also presented, corresponding to the detection of a periodic modulation of the underlying rate. This work demonstrates that a known statistical test, applicable to continuous processes, applies, with little modification, to point process spectra, and is of utility in studying a point process driven by a continuous stimulus. While the material discussed is of general applicability to point processes attention will be confined to sequences of neuronal action potentials (spike trains) which were the motivation for this work.Comment: 33 pages, 9 figure

Effective phase description of noise-perturbed and noise-induced oscillations

An effective description of a general class of stochastic phase oscillators is presented. For this, the effective phase velocity is defined either by invariant probability density or via first passage times. While the first approach exhibits correct frequency and distribution density, the second one yields proper phase resetting curves. Their discrepancy is most pronounced for noise-induced oscillations and is related to non-monotonicity of the phase fluctuations

Stochastic Effects in Physical Systems

A tutorial review is given of some developments and applications of stochastic processes from the point of view of the practicioner physicist. The index is the following: 1.- Introduction 2.- Stochastic Processes 3.- Transient Stochastic Dynamics 4.- Noise in Dynamical Systems 5.- Noise Effects in Spatially Extended Systems 6.- Fluctuations, Phase Transitions and Noise-Induced Transitions.Comment: 93 pages, 36 figures, LaTeX. To appear in Instabilities and Nonequilibrium Structures VI, E. Tirapegui and W. Zeller,eds. Kluwer Academi

Desynchronization in diluted neural networks

The dynamical behaviour of a weakly diluted fully-inhibitory network of pulse-coupled spiking neurons is investigated. Upon increasing the coupling strength, a transition from regular to stochastic-like regime is observed. In the weak-coupling phase, a periodic dynamics is rapidly approached, with all neurons firing with the same rate and mutually phase-locked. The strong-coupling phase is characterized by an irregular pattern, even though the maximum Lyapunov exponent is negative. The paradox is solved by drawing an analogy with the phenomenon of ``stable chaos'', i.e. by observing that the stochastic-like behaviour is "limited" to a an exponentially long (with the system size) transient. Remarkably, the transient dynamics turns out to be stationary.Comment: 11 pages, 13 figures, submitted to Phys. Rev.

A machine learning framework for data driven acceleration of computations of differential equations

We propose a machine learning framework to accelerate numerical computations of time-dependent ODEs and PDEs. Our method is based on recasting (generalizations of) existing numerical methods as artificial neural networks, with a set of trainable parameters. These parameters are determined in an offline training process by (approximately) minimizing suitable (possibly non-convex) loss functions by (stochastic) gradient descent methods. The proposed algorithm is designed to be always consistent with the underlying differential equation. Numerical experiments involving both linear and non-linear ODE and PDE model problems demonstrate a significant gain in computational efficiency over standard numerical methods

Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics

Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems the inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems, their basic properties allow to understand fundamental dynamical properties of complex biological reaction networks. We analyze the Lyapunov spectrum, determine the probability to find stationary oscillating solutions, demonstrate the effect of the nonlinearity on the effective in- and out-degree of the active interaction network and study how the frequency distributions of oscillatory modes of such system depend on the average connectivity.Comment: 11 pages, 5 figure

Phase transition in protocols minimizing work fluctuations

For two canonical examples of driven mesoscopic systems - a harmonically-trapped Brownian particle and a quantum dot - we numerically determine the finite-time protocols that optimize the compromise between the standard deviation and the mean of the dissipated work. In the case of the oscillator, we observe a collection of protocols that smoothly trade-off between average work and its fluctuations. However, for the quantum dot, we find that as we shift the weight of our optimization objective from average work to work standard deviation, there is an analog of a first-order phase transition in protocol space: two distinct protocols exchange global optimality with mixed protocols akin to phase coexistence. As a result, the two types of protocols possess qualitatively different properties and remain distinct even in the infinite duration limit: optimal-work-fluctuation protocols never coalesce with the minimal work protocols, which therefore never become quasistatic.Comment: 6 pages, 6 figures + SI as ancillary fil