Related papers: Biologically Unavoidable Sequences
It has been known for nearly a decade that deterministically modeled reaction networks that are weakly reversible and consist of a single linkage class have trajectories that are bounded from both above and below by positive constants (so…
This paper is composed of two main results concerning chains of infinite order which are not necessarily continuous. The first one is a decomposition of the transition probability kernel as a countable mixture of unbounded probabilistic…
We present a family of avoidable formulas with reversal whose avoidability index is unbounded. We also complete the determination of the avoidability index of the formulas with reversal in the 3-avoidance basis.
We implement a decision procedure for answering questions about a class of infinite words that might be called (for lack of a better name) "Fibonacci-automatic". This class includes, for example, the famous Fibonacci word f = 01001010...,…
A graph property is elusive (or evasive) if any algorithm testing it by asking questions of the form ''Is there an edge between vertices x and y?'' must, in the worst case, examine all pairs of vertices. Elusiveness for infinite vertex sets…
We show that all--instances termination of chase is undecidable. More precisely, there is no algorithm deciding, for a given set $\cal T$ consisting of Tuple Generating Dependencies (a.k.a. Datalog$^\exists$ program), whether the $\cal…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
We explore a family of nested recurrence relations with arbitrary levels of nesting, which have an interpretation in terms of fixed points of morphisms over a countably infinite alphabet. Recurrences in this family are related to a number…
We consider character sequences evolving on a phylogenetic tree under the TKF91 model. We show that as the sequence lengths tend to infinity the the topology of the phylogenetic tree and the edge lengths are determined by any one of (a) the…
Assume that for some $\alpha<1$ and for all nutural $n$ a set $F_n$ of at most $2^{\alpha n}$ "forbidden" binary strings of length $n$ is fixed. Then there exists an infinite binary sequence $\omega$ that does not have (long) forbidden…
The asynchronous systems are the non-deterministic real time-binary models of the asynchronous circuits from electrical engineering. Autonomy means that the circuits and their models have no input. Regularity means analogies with the…
We study proportions of consecutive occurrences of permutations of a given size. Specifically, the feasible limits of such proportions on large permutations form a region, called feasible region. We show that this feasible region is a…
Causal Graph Dynamics extend Cellular Automata to arbitrary, bounded-degree, time-varying graphs. The whole graph evolves in discrete time steps, and this global evolution is required to have a number of physics-like symmetries:…
Rooted binary perfect phylogenies provide a generalization of rooted binary unlabeled trees in which each leaf is assigned a positive integer value that corresponds in a biological setting to the count of the number of indistinguishable…
This article considers a model of genealogy corresponding to a regular exchangeable coalescent (also known as Xi-coalescent) started from a large finite configuration, and undergoing neutral mutations. Asymptotic expressions for the number…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
For several classes of bounded sets $A$, the limit of a one-dimensional L\'{e}vy process conditioned to avoid $A$ up to a parametrized random time which tends to infinity. For $A$ we take the set of finite points with several clocks and a…
We consider the arithmetic complexity of index sets of uniformly computably enumerable families learnable under different learning criteria. We determine the exact complexity of these sets for the standard notions of finite learning,…