Related papers: Biologically Unavoidable Sequences
The avoidability, or unavoidability of patterns in words over finite alphabets has been studied extensively. A word (pattern) over a finite set is said to be unavoidable if, for all but finitely many words, there exists a morphism mapping…
We prove that the uniform recurrence of morphic sequences is decidable. For this we show that the number of derived sequences of uniformly recurrent morphic sequences is bounded. As a corollary we obtain that uniformly recurrent morphic…
We review models of biological evolution in which the population frequency changes deterministically with time. If the population is self-replicating, although the equations for simple prototypes can be linearised, nonlinear equations arise…
The predictability of a sequence is defined as the asymptotic performance of the best performing predictor in a given class. The value of the predictability of a sequence will in general depend on the choice of this predictor class. The…
An infinite binary sequence is deemed to be random if it has all definable properties that hold almost surely for the usual probability measure on the set of infinite binary sequences. There are only countably many such properties, so it…
We introduce the notion of unavoidable (complete) sets of word patterns, which is a refinement for that of words, and study certain numerical characteristics for unavoidable sets of patterns. In some cases we employ the graph of pattern…
We show that various aspects of k-automatic sequences -- such as having an unbordered factor of length n -- are both decidable and effectively enumerable. As a consequence it follows that many related sequences are either k-automatic or…
We present a new perfect simulation algorithm for stationary chains having unbounded variable length memory. This is the class of infnite memory chains for which the family of transition probabilities is represented by a probabilistic…
We describe new, simple, recursive methods of construction for orientable sequences over an arbitrary finite alphabet, i.e. periodic sequences in which any sub-sequence of n consecutive elements occurs at most once in a period in either…
In some particular cases we give criteria for morphic sequences to be almost periodic (=uniformly recurrent). Namely, we deal with fixed points of non-erasing morphisms and with automatic sequences. In both cases a polynomial-time algorithm…
An infinite binary sequence A is absolutely undecidable if it is impossible to compute A on a set of positions of positive upper density. Absolute undecidability is a weakening of bi-immunity. Downey, Jockusch and Schupp asked whether,…
We propose a definition of an Euler characteristic for unbounded chain complexes by taking the (usual) Euler characteristics of successively longer parts of the complex, weighted inversely proportional to the length, and passing to the…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
A set X of partial words over a finite alphabet A is called unavoidable if every two-sided infinite word over A has a factor compatible with an element of X. Unlike the case of a set of words without holes, the problem of deciding whether…
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…
Biological approximations, which are universal for diverse species, are well known. With no other experimental data, their invariance to transformations from one species to another yields exact conservation (with respect to biological…
Let p be an odd prime. When n>2, we show that each tensor factor of form E \otimes \Gamma in H(Z,n;Z_p) is an A-infinity bialgebra with non-trivial structure. We give explicit formulas for the structure maps and the quadratic relations…
We describe an algorithm that takes as input a complex sequence $(u_n)$ given by a linear recurrence relation with polynomial coefficients along with initial values, and outputs a simple explicit upper bound $(v_n)$ such that $|u_n| \leq…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
We say that a graph $H$ is planar unavoidable if there is a planar graph $G$ such that any red/blue coloring of the edges of $G$ contains a monochromatic copy of $H$, otherwise we say that $H$ is planar avoidable. I.e., $H$ is planar…