Superstatistical model of bacterial DNA architecture

Superstatistics from a dynamical perspective: Entropy and relaxation

Distributions that deviate from equilibrium predictions are commonly observed across a broad spectrum of systems, ranging from laboratory experiments to astronomical phenomena. These distributions are generally regarded as a manifestation of a quasiequilibrium state and can very often be represented as a superposition of statistics, i.e., superstatistics. The underlying idea in this methodology is that the nonequilibrium system consists of a collection of smaller subsystems that remain infinitely close to equilibrium. This procedure has been effectively implemented in a kinetic setting, but thus far, only in the collisionless regime, limiting its scope of application. In this paper, we address the effect of collisions on the relaxation process and time evolution of superstatistical systems. After confronting the superstatistical distributions with experimental and simulation data, relevant to our analysis, we first study the effect of superstatistics on entropy. We explicitly show that, in the absence of long-range interactions, the extensivity of entropy is preserved, albeit influenced by the specific class of temperature fluctuations. Then, we examine how collisions drive the system towards a global equilibrium state, characterized by a maximum entropy, by employing the relaxation time approximation. This allows us to define a dynamical version of superstatistics, characterized by a singular time-varying parameter q(t), which undergoes a continuous evolution towards equilibrium. We show how this approach enables the determination of the evolution of the underlying temperature distribution under the influence of collisions, which act as stochastic forces, gradually narrowing the temperature distribution over time.

Neural superstatistics for Bayesian estimation of dynamic cognitive models

Mathematical models of cognition are often memoryless and ignore potential fluctuations of their parameters. However, human cognition is inherently dynamic. Thus, we propose to augment mechanistic cognitive models with a temporal dimension and estimate the resulting dynamics from a superstatistics perspective. Such a model entails a hierarchy between a low-level observation model and a high-level transition model. The observation model describes the local behavior of a system, and the transition model specifies how the parameters of the observation model evolve over time. To overcome the estimation challenges resulting from the complexity of superstatistical models, we develop and validate a simulation-based deep learning method for Bayesian inference, which can recover both time-varying and time-invariant parameters. We first benchmark our method against two existing frameworks capable of estimating time-varying parameters. We then apply our method to fit a dynamic version of the diffusion decision model to long time series of human response times data. Our results show that the deep learning approach is very efficient in capturing the temporal dynamics of the model. Furthermore, we show that the erroneous assumption of static or homogeneous parameters will hide important temporal information.

Video-based marker-free tracking and multi-scale analysis of mouse locomotor activity and behavioral aspects in an open field arena: A perspective approach to the quantification of complex gait disturbances associated with Alzheimer's disease

Introduction

Complex gait disturbances represent one of the prominent manifestations of various neurophysiological conditions, including widespread neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Therefore, instrumental measurement techniques and automatic computerized analysis appears essential for the differential diagnostics, as well as for the assessment of treatment effectiveness from experimental animal models to clinical settings.

Methods

Here we present a marker-free instrumental approach to the analysis of gait disturbances in animal models. Our approach is based on the analysis of video recordings obtained with a camera placed underneath an open field arena with transparent floor using the DeeperCut algorithm capable of online tracking of individual animal body parts, such as the snout, the paws and the tail. The extracted trajectories of animal body parts are next analyzed using an original computerized methodology that relies upon a generalized scalable model based on fractional Brownian motion with parameters identified by detrended partial cross-correlation analysis.

Results

We have shown that in a mouse model representative movement patterns are characterized by two asymptotic regimes characterized by integrated 1/f noise at small scales and nearly random displacements at large scales separated by a single crossover. More detailed analysis of gait disturbances revealed that the detrended cross-correlations between the movements of the snout, paws and tail relative to the animal body midpoint exhibit statistically significant discrepancies in the Alzheimer's disease mouse model compared to the control group at scales around the location of the crossover.

Discussion

We expect that the proposed approach, due to its universality, robustness and clear physical interpretation, is a promising direction for the design of applied analysis tools for the diagnostics of various gait disturbances and behavioral aspects in animal models. We further believe that the suggested mathematical models could be relevant as a complementary tool in clinical diagnostics of various neurophysiological conditions associated with movement disorders.

Superstatistical and DNA sequence coding of the human genome

In this work, by considering superstatistics we investigate the short-range correlations (SRCs) and the fluctuations in the distribution of lengths of strings of nucleotides. To this end, a stochastic model provides the distributions of the size of the exons based on the q-Gamma and inverse q-Gamma distributions. Specifically, we define a time series for exon sizes to investigate the SRC and the fluctuations through the superstatistics distributions. To test the model's viability, we use the Project Ensembl database of genes to extract the time evolution of exon sizes, calculated in terms of the number of base pairs (bp) in these biological databases. Our findings show that, depending on the chromosome, both distributions are suitable for describing the length distribution of human DNA for lengths greater than 10 bp. In addition, we used Bayesian statistics to perform a selection model approach, which revealed weak evidence for the inverse q-Gamma distribution for a considerable number of chromosomes.

Generalized statistical mechanics of stellar systems

The observed distributions of stellar parameters, in particular, rotational and radial velocities, often depart from the Maxwellian (Gaussian) distribution. In the absence of a consistent statistical framework, these distributions are, in general, accounted for phenomenologically by employing power-law distributions, such as Tsallis or Kaniadakis distributions. Here we argue that the observed distributions correspond to locally Gaussian distributions, whose characteristic width is regarded as a statistical variable, in accordance with common knowledge that this parameter is mass dependent. The distributions arising within this picture correspond to superstatistics-a formalism emerging naturally in the context of self-gravitating media. We discuss in detail the distributions arising within this formalism and confront them with observational data of open clusters. We compute their moments and show that the Chandrasekhar-Münch relation remains invariant in this scenario. We also address the effect of these distributions on the thermalization of a massive body, e.g., a supermassive black hole, immersed in a stellar gas. We further discuss how the superstatistical picture clarifies certain ambiguities while offering a whole family of distributions (of which asymptotic power laws represent a special case), opening possibilities for fitting observational data.

A stochastic model of word occurrences in hierarchically structured written texts

In previous studies, we have treated real written texts as time series data and have tried to investigate dynamic correlations of word occurrences by utilizing autocorrelation functions (ACFs) and also by simulation of pseudo-text synthesis. The results showed that words that appear in written texts can be classified into two groups: a group of words showing dynamic correlations (Type-I words), and a group of words showing no dynamic correlations (Type-II words). In this study, we investigate the characteristics of these two types of words in terms of their waiting time distributions (WTDs) of word occurrences. The results for Type-II words show that the stochastic processes that govern generating Type-II words are superpositions of Poisson point processes with various rate constants. We further propose a model of WTDs for Type-I words in which the hierarchical structure of written texts is considered. The WTDs of Type-I words in real written texts agree well with the predictions of the proposed model, indicating that the hierarchical structure of written texts is important for generating long-range dynamic correlations of words.

Beyond Boltzmann-Gibbs-Shannon in Physics and Elsewhere

The pillars of contemporary theoretical physics are classical mechanics, Maxwell electromagnetism, relativity, quantum mechanics, and Boltzmann–Gibbs (BG) statistical mechanics –including its connection with thermodynamics. The BG theory describes amazingly well the thermal equilibrium of a plethora of so-called simple systems. However, BG statistical mechanics and its basic additive entropy SBG started, in recent decades, to exhibit failures or inadequacies in an increasing number of complex systems. The emergence of such intriguing features became apparent in quantum systems as well, such as black holes and other area-law-like scenarios for the von Neumann entropy. In a different arena, the efficiency of the Shannon entropy—as the BG functional is currently called in engineering and communication theory—started to be perceived as not necessarily optimal in the processing of images (e.g., medical ones) and time series (e.g., economic ones). Such is the case in the presence of generic long-range space correlations, long memory, sub-exponential sensitivity to the initial conditions (hence vanishing largest Lyapunov exponents), and similar features. Finally, we witnessed, during the last two decades, an explosion of asymptotically scale-free complex networks. This wide range of important systems eventually gave support, since 1988, to the generalization of the BG theory. Nonadditive entropies generalizing the BG one and their consequences have been introduced and intensively studied worldwide. The present review focuses on these concepts and their predictions, verifications, and applications in physics and elsewhere. Some selected examples (in quantum information, high- and low-energy physics, low-dimensional nonlinear dynamical systems, earthquakes, turbulence, long-range interacting systems, and scale-free networks) illustrate successful applications. The grounding thermodynamical framework is briefly described as well.

Bayesian model selection for complex dynamic systems

Time series generated by complex systems like financial markets and the earth’s atmosphere often represent superstatistical random walks: on short time scales, the data follow a simple low-level model, but the model parameters are not constant and can fluctuate on longer time scales according to a high-level model. While the low-level model is often dictated by the type of the data, the high-level model, which describes how the parameters change, is unknown in most cases. Here we present a computationally efficient method to infer the time course of the parameter variations from time-series with short-range correlations. Importantly, this method evaluates the model evidence to objectively select between competing high-level models. We apply this method to detect anomalous price movements in financial markets, characterize cancer cell invasiveness, identify historical policies relevant for working safety in coal mines, and compare different climate change scenarios to forecast global warming.

Systematic changes in stock market prices or in the migration behaviour of cancer cells may be hidden behind random fluctuations. Here, Mark et al. describe an empirical approach to identify when and how such real-world systems undergo systematic changes.

First-passage time for superstatistical Fokker-Planck models

The first-passage-time (FPT) problem is studied for superstatistical models assuming that the mesoscopic system dynamics is described by a Fokker-Planck equation. We show that all moments of the random intensive parameter associated to the superstatistical approach can be put in one-to-one correspondence with the moments of the FPT. For systems subjected to an additional uncorrelated external force, the same statistical information is obtained from the dependence of the FPT moments on the external force. These results provide an alternative technique for checking the validity of superstatistical models. As an example, we characterize the mean FPT for a forced Brownian particle.