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Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
Wheeler nondeterministic finite automata (WNFAs) were introduced as a generalization of prefix sorting from strings to labeled graphs. WNFAs admit optimal solutions to classic hard problems on labeled graphs and languages. The problem of…
Partially ordered nondeterminsitic finite automata (poNFAs) are NFAs whose transition relation induces a partial order on states, that is, for which cycles occur only in the form of self-loops on a single state. A poNFA is universal if it…
A tower is a sequence of words alternating between two languages in such a way that every word is a subsequence of the following word. The height of the tower is the number of words in the sequence. If there is no infinite tower (a tower of…
Let $NFA_b(q)$ denote the set of languages accepted by nondeterministic finite automata with $q$ states over an alphabet with $b$ letters. Let $B_n$ denote the set of words of length $n$. We give a quadratic lower bound on the VC dimension…
We investigate the descriptional complexity of different variants of 1-limited automata (1-las), an extension of two-way finite automata (2nfas) characterizing regular languages. In particular, we consider 2nfas with common-guess…
We use results from communication complexity, both new and old ones, to prove lower bounds for unambiguous finite automata (UFAs). We show three results. $\textit{Complement:}$ There is a language $L$ recognised by an $n$-state UFA such…
Consider the finite regular language L_n = {w0 : w \in {0,1}^*, |w| \le n}. It was shown by Ambainis, Nayak, Ta-Shma and Vazirani that while this language is accepted by a deterministic finite automaton of size O(n), any one-way quantum…
In this paper we consider the following problems: how many different subsets of Sigma^n can occur as set of all length-n factors of a finite word? If a subset is representable, how long a word do we need to represent it? How many such…
It is well known that computing a minimum DFA consistent with a given set of positive and negative examples is NP-hard. Previous work has identified conditions on the input sample under which the problem becomes tractable or remains hard.…
We pose the fine-grained hardness hypothesis that the textbook algorithm for the NFA Acceptance problem is optimal up to subpolynomial factors, even for dense NFAs and fixed alphabets. We show that this barrier appears in many variations…
Consider words of length $n$. The set of all periods of a word of length $n$ is a subset of $\{0,1,2,\ldots,n-1\}$. However, any subset of $\{0,1,2,\ldots,n-1\}$ is not necessarily a valid set of periods. In a seminal paper in 1981, Guibas…
The \v{C}ern\'y's conjecture states that for every synchronizing automaton with n states there exists a reset word of length not exceeding (n-11)^2. We prove this conjecture for a class of automata preserving certain properties of intervals…
We consider the problem {\sc Max Sync Set} of finding a maximum synchronizing set of states in a given automaton. We show that the decision version of this problem is PSPACE-complete and investigate the approximability of {\sc Max Sync Set}…
We investigate the shuffle operation on regular languages represented by complete deterministic finite automata. We prove that $f(m,n)=2^{mn-1} + 2^{(m-1)(n-1)}(2^{m-1}-1)(2^{n-1}-1)$ is an upper bound on the state complexity of the shuffle…
The permutation language $P_n$ consists of all words that are permutations of a fixed alphabet of size $n$. Using divide-and-conquer, we construct a regular expression $R_n$ that specifies $P_n$. We then give explicit bounds for the length…
The single shortest path algorithm is undefined for weighted finite-state automata over non-idempotent semirings because such semirings do not guarantee the existence of a shortest path. However, in non-idempotent semirings admitting an…
Twins in a finite word are formed by a pair of identical subwords placed at disjoint sets of positions. We investigate the maximum length of twins in a random word over a $k$-letter alphabet. The obtained lower bounds for small values of…
Factor Analysis (FA) is a technique of fundamental importance that is widely used in classical and modern multivariate statistics, psychometrics and econometrics. In this paper, we revisit the classical rank-constrained FA problem, which…
The relationship between the length of a word and the maximum length of its unbordered factors is investigated in this paper. Consider a finite word w of length n. We call a word bordered, if it has a proper prefix which is also a suffix of…