Related papers: Topological Entropy of DNA Sequences
Topological and metric entropies of the DNA sequences from different organisms were calculated. Obtained results were compared each other and with ones of corresponding artificial sequences. For all envisaged DNA sequences there is a…
The entropy of a hierarchical network topology in an ensemble of sparse random networks with "hidden variables" associated to its nodes, is the log-likelihood that a given network topology is present in the chosen ensemble.We obtain a…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…
Shannon entropy is widely used to measure the complexity of DNA sequences but suffers from saturation effects that limit its discriminative power for long uniform segments. We introduce a novel metric, the entropy rank ratio R, which…
A convenient measure of a map or flow's chaotic action is the topological entropy. In many cases, the entropy has a homological origin: it is forced by the topology of the space. For example, in simple toral maps, the topological entropy is…
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
Topological entropy is a widely studied indicator of chaos in topological dynamics. Here we give a generalized definition of topological entropy which may be applied to set-valued functions. We demonstrate that some of the well-known…
Bounds on the entropy of patterns of sequences generated by independently identically distributed (i.i.d.) sources are derived. A pattern is a sequence of indices that contains all consecutive integer indices in increasing order of first…
Motivated by the notion of intermediate dimensions introduced by Falconer et al., we introduce a continuum of topological entropies that are intermediate between the (Bowen) topological entropy and the lower and upper capacity topological…
A general upper bound for topological entropy of switched nonlinear systems is constructed, using an asymptotic average of upper limits of the matrix measures of Jacobian matrices of strongly persistent individual modes, weighted by their…
We evaluate the entanglement entropy of exactly solvable Hamiltonians corresponding to general families of three-dimensional topological models. We show that the modification to the entropic area law due to three-dimensional topological…
Entropy rate is a real valued functional on the space of discrete random sources which lacks a closed formula even for subclasses of sources which have intuitive parameterizations. A good way to overcome this problem is to examine its…
In this note a notion of generalized topological entropy for arbitrary subsets of the space of all sequences in a compact topological space is introduced. It is shown that for a continuous map on a compact space the generalized topological…
Autoencoders have been proposed as a powerful tool for model-independent anomaly detection in high-energy physics. The operating principle is that events which do not belong to the space of training data will be reconstructed poorly, thus…
In a genetic algorithm, fluctuations of the entropy of a genome over time are interpreted as fluctuations of the information that the genome's organism is storing about its environment, being this reflected in more complex organisms. The…
We generalize the topological entanglement entropy to a family of topological Renyi entropies parametrized by a parameter alpha, in an attempt to find new invariants for distinguishing topologically ordered phases. We show that,…
We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through…
In this paper, we mainly revisit a nice theory for topological entropy of weakly equivalent flows, which was originally investigated by Ohno in 1980. We will develop a new approach, being more straightforward and elementary than the…