Related papers: Biologically Unavoidable Sequences
Biological sequences do not come at random. Instead, they appear with particular frequencies that reflect properties of the associated system or phenomenon. Knowing how biological sequences are distributed in sequence space is thus a…
In this paper we consider a number of natural decision problems involving k-regular sequences. Specifically, they arise from - lower and upper bounds on growth rate; in particular boundedness, - images, - regularity (recognizability by a…
We define and study a few properties of a class of random automata networks. While regular finite one-dimensional cellular automata are defined on periodic lattices, these automata networks, called randomized cellular automata, are defined…
We provide new computations in bounded cohomology: A group is boundedly acyclic if its bounded cohomology with trivial real coefficients is zero in all positive degrees. We show that there exists a continuum of finitely generated…
Well protected human and laboratory animal populations with abundant resources are evolutionary unprecedented. Physical approach, which takes advantage of their extensively quantified mortality, establishes that its dominant fraction yields…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
In principle, all the natural systems such as biological, ecological and economical systems are structure-variable systems (in which some environment parameters are not fixed). In this Letter we show that data sequences from many…
Irreversibility, in which a transient perturbation leaves a system in a new state, is an emergent property in systems of interacting entities. This property has well-established implications in statistical physics but remains underexplored…
The notion of almost periodicity nontrivially generalizes the notion of periodicity. Strongly almost periodic sequences (=uniformly recurrent infinite words) first appeared in the field of symbolic dynamics, but then turned out to be…
A concept of "guessability" is defined for sets of sequences of naturals. Eventually, these sets are thoroughly characterized. To do this, a nonstandard logic is developed, a logic containing symbols for the ellipsis as well as for…
Solomonoff's uncomputable universal prediction scheme $\xi$ allows to predict the next symbol $x_k$ of a sequence $x_1...x_{k-1}$ for any Turing computable, but otherwise unknown, probabilistic environment $\mu$. This scheme will be…
A novel notion of unpredictable strings is revealed and utilized to define deterministic unpredictable sequences on a finite number of symbols. We prove the first law of large strings for random processes in discrete time, which confirms…
Negative avoiding sequences of span $n$ are periodic sequences of elements from $\mathbb{Z}_k$ for some $k$ with the property that no $n$-tuple occurs more than once in a period and if an $n$-tuple does occur then its negative does not.…
Model checking properties are often described by means of finite automata. Any particular such automaton divides the set of infinite trees into finitely many classes, according to which state has an infinite run. Building the full type…
This paper introduces a class of objects called decision rules that map infinite sequences of alternatives to a decision space. These objects can be used to model situations where a decision maker encounters alternatives in a sequence such…
We introduce the $\Sigma_1$-definable universal finite sequence and prove that it exhibits the universal extension property amongst the countable models of set theory under end-extension. That is, (i) the sequence is $\Sigma_1$-definable…
In an automatic search, we found conjectural recurrences for some sequences in the OEIS that were not previously recognized as being D-finite. In some cases, we are able to prove the conjectured recurrence. In some cases, we are not able to…
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works…
The notion of clause set cycle abstracts a family of methods for automated inductive theorem proving based on the detection of cyclic dependencies between clause sets. By discerning the underlying logical features of clause set cycles, we…