arXiv subjects
Publications and source records attributed to Robert Mercas.
Fici and Saarela ([2]) conjectured that a binary word of length n contains at least $\lfloor n/4 \rfloor$ abelian squares. We slightly extend this conjecture and show that it holds in some special cases. In all other cases we have the following: given a Parikh vector over a two letter alphabet we produce a word with that Parikh vector which we conjecture contains the least possible number of abelian squares.
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free techniques, which are based on measures referring to the composition of sequences in terms of their constituent patterns. These measures, such as $q$-gram distance, are usually computed in time linear with respect to the length of the sequences. In this paper, we focus on the complementary idea: how two sequences can be efficiently compared based on information that does not occur in the sequences. A word is an {\em absent word} of some sequence if it does not occur in the sequence. An absent word is {\em minimal} if all its proper factors occur in the sequence. Here we present the first linear-time and linear-space algorithm to compare two sequences by considering {\em all} their minimal absent words. In the process, we present results of combinatorial interest, and also extend the proposed techniques to compare circular sequences. We also present an algorithm that, given a word $x$ of length $n$, computes the largest integer for which all factors of $x$ of that length occur in some minimal absent word of $x$ in time and space $\cO(n)$. Finally, we show that the known asymptotic upper bound on the number of minimal absent words of a word is tight.
The work takes another look at the number of runs that a string might contain and provides an alternative proof for the bound. We also propose another stronger conjecture that states that, for a fixed order on the alphabet, within every factor of a word there are at most as many occurrences of Lyndon roots corresponding to runs in a word as the length of the factor (only first such occurrences for each run are considered).
The avoidability of binary patterns by binary cube-free words is investigated and the exact bound between unavoidable and avoidable patterns is found. All avoidable patterns are shown to be D0L-avoidable. For avoidable patterns, the growth rates of the avoiding languages are studied. All such languages, except for the overlap-free language, are proved to have exponential growth. The exact growth rates of languages avoiding minimal avoidable patterns are approximated through computer-assisted upper bounds. Finally, a new example of a pattern-avoiding language of polynomial growth is given.