Related papers: Entropy and long-range correlations in DNA sequenc…
The evolution of entanglement entropy in quantum circuits composed of Haar-random gates and projective measurements shows versatile behavior, with connections to phase transitions and complexity theory. We reformulate the problem in terms…
Entropic causal inference is a recent framework for learning the causal graph between two variables from observational data by finding the information-theoretically simplest structural explanation of the data, i.e., the model with smallest…
We use the $f-divergence$ also called relative entropy as a measure of diversity between probability densities and review its basic properties. In the sequence we define a few objects which capture relevant information from the sample of a…
In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random…
Motivated by robotic surveillance applications, this paper studies the novel problem of maximizing the return time entropy of a Markov chain, subject to a graph topology with travel times and stationary distribution. The return time entropy…
We study the statistical properties of Ising spin chains with finite (although arbitrary large) range of interaction between the elements. We examine mesoscopic subsystems (fragments of an Ising chain) with the lengths comparable with the…
Two approaches to studying the correlation functions of the binary Markov sequences are considered. The first of them is based on the study of probability of occurring different ''words'' in the sequence. The other one uses recurrence…
A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…
We propose a formal expansion of the transfer entropy to put in evidence irreducible sets of variables which provide information for the future state of each assigned target. Multiplets characterized by a large contribution to the expansion…
We present an alternative derivation of the pair correlation function for simple classical fluids by using a variational approach. That approach involves the conditional probability p(3,..., N /1, 2) of an undefined system of N particles…
We derive a novel chain rule for a family of channel conditional entropies, covering von Neumann and sandwiched R\'{e}nyi entropies. In the process, we show that these channel conditional entropies are equal to their regularized version,…
Transfer entropy is an established method for quantifying directed statistical dependencies in neuroimaging and complex systems datasets. The pairwise (or bivariate) transfer entropy from a source to a target node in a network does not…
RNA molecules are known to form complex secondary structures including pseudoknots. A systematic framework for the enumeration, classification and prediction of secondary structures is critical to determine the biological significance of…
Graphs are widely used for describing systems made up of many interacting components and for understanding the structure of their interactions. Various statistical models exist, which describe this structure as the result of a combination…
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
The entanglement entropy of a subsystem $A$ of a quantum system is expressed, in the replica method, through analytic continuation with respect to n of the trace of the n-th power of the reduced density matrix $\tr\rho_A^n$. We study the…
Entropy is a measure of heterogeneity widely used in applied sciences, often when data are collected over space. Recently, a number of approaches has been proposed to include spatial information in entropy. The aim of entropy is to…