Related papers: Using biochemical circuits to approximately comput…

The discovery of transition pathways to unravel distinct reaction mechanisms and, in general, rare events that occur in molecular systems is still a challenge. Recent advances have focused on analyzing the transition path ensemble using the…

Biomedical signals carry signature rhythms of complex physiological processes that control our daily bodily activity. The properties of these rhythms indicate the nature of interaction dynamics among physiological processes that maintain a…

A continuously measured quantum system with multiple jump channels gives rise to a stochastic process described by random jump times and random emitted symbols, representing each jump channel. While much is known about the waiting time…

Stochastic finite automata arise naturally in many language and speech processing tasks. They include stochastic acceptors, which represent certain probability distributions over random strings. We consider the problem of efficient…

The online estimation of the derivative of an input signal is widespread in control theory and engineering. In the realm of chemical reaction networks (CRN), this raises however a number of specific issues on the different ways to achieve…

Estimating density ratios between pairs of intractable data distributions is a core problem in probabilistic modeling, enabling principled comparisons of sample likelihoods under different data-generating processes across conditions and…

Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…

The Ge:Ga detectors used in the PACS spectrograph onboard the Herschel space telescope react to changes of the incident flux with a certain delay. This generates transient effects on the resulting signal which can be important and last for…

We develop a method for calculation of charge transfer statistics of persistent current in nanostructures in terms of the cumulant generating function (CGF) of transferred charge. We consider a simply connected one-dimensional system (a…

Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…

The statistics of persistent events, recently introduced in the context of phase ordering dynamics, is investigated in the case of the 1D lattice random walk in discrete time. We determine the survival probability of the random walker in…

Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…

Persistent homology provides information about the lifetime of homology classes along a filtration of cell complexes. Persistence barcode is a graphical representation of such information. A filtration might be determined by time in a set…

In this paper, we are concerned with the detection of progressive dynamic saliency from video sequences. More precisely, we are interested in saliency related to motion and likely to appear progressively over time. It can be relevant to…

Background: In addition to known protein-coding genes, large amount of apparently non-coding sequence are conserved between the human and mouse genomes. It seems reasonable to assume that these conserved regions are more likely to contain…

Long term behavior of nonlinear deterministic continuous time signals can be studied in terms of their reconstructed attractors. Reconstructed attractors of a continuous signal are meant to be topologically equivalent representations of the…

In this paper we survey recent work on the use of statistical model checking techniques for biological applications. We begin with an overview of the basic modelling techniques for biochemical reactions and their corresponding stochastic…

The use of machine learning algorithms is an attractive way to produce very fast detector simulations for scattering reactions that can otherwise be computationally expensive. Here we develop a factorised approach where we deal with each…

The paper proposes a numerically stable recursive algorithm for the exact computation of the linear-chain conditional random field gradient. It operates as a forward algorithm over the log-domain expectation semiring and has the purpose of…

The genetic repressilator circuit consists of three transcription factors, or repressors, which negatively regulate each other in a cyclic manner. This circuit was synthetically constructed on plasmids in {\it Escherichia coli} and was…