Inferring networks from time series: A neural approach.

Network structures underlie the dynamics of many complex phenomena, from gene regulation and foodwebs to power grids and social media. Yet, as they often cannot be observed directly, their connectivities must be inferred from observations of the dynamics to which they give rise. In this work, we present a powerful computational method to infer large network adjacency matrices from time series data using a neural network, in order to provide uncertainty quantification on the prediction in a manner that reflects both the degree to which the inference problem is underdetermined as well as the noise on the data. This is a feature that other approaches have hitherto been lacking. We demonstrate our method's capabilities by inferring line failure locations in the British power grid from its response to a power cut, providing probability densities on each edge and allowing the use of hypothesis testing to make meaningful probabilistic statements about the location of the cut. Our method is significantly more accurate than both Markov-chain Monte Carlo sampling and least squares regression on noisy data and when the problem is underdetermined, while naturally extending to the case of nonlinear dynamics, which we demonstrate by learning an entire cost matrix for a nonlinear model of economic activity in Greater London. Not having been specifically engineered for network inference, this method in fact represents a general parameter estimation scheme that is applicable to any high-dimensional parameter space.

Path integrals, particular kinds, and strange things.

This paper describes a path integral formulation of the free energy principle. The ensuing account expresses the paths or trajectories that a particle takes as it evolves over time. The main results are a method or principle of least action that can be used to emulate the behaviour of particles in open exchange with their external milieu. Particles are defined by a particular partition, in which internal states are individuated from external states by active and sensory blanket states. The variational principle at hand allows one to interpret internal dynamics-of certain kinds of particles-as inferring external states that are hidden behind blanket states. We consider different kinds of particles, and to what extent they can be imbued with an elementary form of inference or sentience. Specifically, we consider the distinction between dissipative and conservative particles, inert and active particles and, finally, ordinary and strange particles. Strange particles can be described as inferring their own actions, endowing them with apparent autonomy or agency. In short-of the kinds of particles afforded by a particular partition-strange kinds may be apt for describing sentient behaviour.

Neural parameter calibration for large-scale multiagent models.

Computational models have become a powerful tool in the quantitative sciences to understand the behavior of complex systems that evolve in time. However, they often contain a potentially large number of free parameters whose values cannot be obtained from theory but need to be inferred from data. This is especially the case for models in the social sciences, economics, or computational epidemiology. Yet, many current parameter estimation methods are mathematically involved and computationally slow to run. In this paper, we present a computationally simple and fast method to retrieve accurate probability densities for model parameters using neural differential equations. We present a pipeline comprising multiagent models acting as forward solvers for systems of ordinary or stochastic differential equations and a neural network to then extract parameters from the data generated by the model. The two combined create a powerful tool that can quickly estimate densities on model parameters, even for very large systems. We demonstrate the method on synthetic time series data of the SIR model of the spread of infection and perform an in-depth analysis of the Harris-Wilson model of economic activity on a network, representing a nonconvex problem. For the latter, we apply our method both to synthetic data and to data of economic activity across Greater London. We find that our method calibrates the model orders of magnitude more accurately than a previous study of the same dataset using classical techniques, while running between 195 and 390 times faster.

Eigenfunction martingale estimating functions and filtered data for drift estimation of discretely observed multiscale diffusions.

We propose a novel method for drift estimation of multiscale diffusion processes when a sequence of discrete observations is given. For the Langevin dynamics in a two-scale potential, our approach relies on the eigenvalues and the eigenfunctions of the homogenized dynamics. Our first estimator is derived from a martingale estimating function of the generator of the homogenized diffusion process. However, the unbiasedness of the estimator depends on the rate with which the observations are sampled. We therefore introduce a second estimator which relies also on filtering the data, and we prove that it is asymptotically unbiased independently of the sampling rate. A series of numerical experiments illustrate the reliability and efficiency of our different estimators.

Spectroscopy of phase transitions for multiagent systems.

In this paper, we study phase transitions for weakly interacting multiagent systems. By investigating the linear response of a system composed of a finite number of agents, we are able to probe the emergence in the thermodynamic limit of a singular behavior of the susceptibility. We find clear evidence of the loss of analyticity due to a pole crossing the real axis of frequencies. Such behavior has a degree of universality, as it does not depend on either the applied forcing or on the considered observable. We present results relevant for both equilibrium and nonequilibrium phase transitions by studying the Desai-Zwanzig and Bonilla-Casado-Morillo models.

Bayesian mechanics for stationary processes.

This paper develops a Bayesian mechanics for adaptive systems. Firstly, we model the interface between a system and its environment with a Markov blanket. This affords conditions under which states internal to the blanket encode information about external states. Second, we introduce dynamics and represent adaptive systems as Markov blankets at steady state. This allows us to identify a wide class of systems whose internal states appear to infer external states, consistent with variational inference in Bayesian statistics and theoretical neuroscience. Finally, we partition the blanket into sensory and active states. It follows that active states can be seen as performing active inference and well-known forms of stochastic control (such as PID control), which are prominent formulations of adaptive behaviour in theoretical biology and engineering.

Response theory and phase transitions for the thermodynamic limit of interacting identical systems.

We study the response to perturbations in the thermodynamic limit of a network of coupled identical agents undergoing a stochastic evolution which, in general, describes non-equilibrium conditions. All systems are nudged towards the common centre of mass. We derive Kramers-Kronig relations and sum rules for the linear susceptibilities obtained through mean field Fokker-Planck equations and then propose corrections relevant for the macroscopic case, which incorporates in a self-consistent way the effect of the mutual interaction between the systems. Such an interaction creates a memory effect. We are able to derive conditions determining the occurrence of phase transitions specifically due to system-to-system interactions. Such phase transitions exist in the thermodynamic limit and are associated with the divergence of the linear response but are not accompanied by the divergence in the integrated autocorrelation time for a suitably defined observable. We clarify that such endogenous phase transitions are fundamentally different from other pathologies in the linear response that can be framed in the context of critical transitions. Finally, we show how our results can elucidate the properties of the Desai-Zwanzig model and of the Bonilla-Casado-Morillo model, which feature paradigmatic equilibrium and non-equilibrium phase transitions, respectively.

Dynamics of the Desai-Zwanzig model in multiwell and random energy landscapes.

We analyze a variant of the Desai-Zwanzig model [J. Stat. Phys. 19, 1 (1978)JSTPBS0022-471510.1007/BF01020331]. In particular, we study stationary states of the mean field limit for a system of weakly interacting diffusions moving in a multiwell potential energy landscape, coupled via a Curie-Weiss type (quadratic) interaction potential. The location and depth of the local minima of the potential are either deterministic or random. We characterize the structure and nature of bifurcations and phase transitions for this system, by means of extensive numerical simulations and of analytical calculations for an explicitly solvable model. Our numerical experiments are based on Monte Carlo simulations, the numerical solution of the time-dependent nonlinear Fokker-Planck (McKean-Vlasov) equation, the minimization of the free-energy functional, and a continuation algorithm for the stationary solutions.

Instability, Rupture and Fluctuations in Thin Liquid Films: Theory and Computations.

Thin liquid films are ubiquitous in natural phenomena and technological applications. They have been extensively studied via deterministic hydrodynamic equations, but thermal fluctuations often play a crucial role that needs to be understood. An example of this is dewetting, which involves the rupture of a thin liquid film and the formation of droplets. Such a process is thermally activated and requires fluctuations to be taken into account self-consistently. In this work we present an analytical and numerical study of a stochastic thin-film equation derived from first principles. Following a brief review of the derivation, we scrutinise the behaviour of the equation in the limit of perfectly correlated noise along the wall-normal direction, as opposed to the perfectly uncorrelated limit studied by Grün et al. (J Stat Phys 122(6):1261-1291, 2006). We also present a numerical scheme based on a spectral collocation method, which is then utilised to simulate the stochastic thin-film equation. This scheme seems to be very convenient for numerical studies of the stochastic thin-film equation, since it makes it easier to select the frequency modes of the noise (following the spirit of the long-wave approximation). With our numerical scheme we explore the fluctuating dynamics of the thin film and the behaviour of its free energy in the vicinity of rupture. Finally, we study the effect of the noise intensity on the rupture time, using a large number of sample paths as compared to previous studies.

General dynamical density functional theory for classical fluids.

We study the dynamics of a colloidal fluid including inertia and hydrodynamic interactions, two effects which strongly influence the nonequilibrium properties of the system. We derive a general dynamical density functional theory which shows very good agreement with full Langevin dynamics. In suitable limits, we recover existing dynamical density functional theories and a Navier-Stokes-like equation with additional nonlocal terms.

Two-dimensional droplet spreading over random topographical substrates.

We examine theoretically the effects of random topographical substrates on the motion of two-dimensional droplets via statistical approaches, by representing substrate families as stationary random functions. The droplet shift variance at both early times and in the long-time limit is deduced and the droplet footprint is found to be a normal random variable at all times. It is shown that substrate roughness inhibits wetting, illustrating also the tendency of the droplet to slide without spreading as equilibrium is approached. Our theoretical predictions are verified by numerical experiments.