Related papers: Algorithmical Aspects of Some Bio Inspired Operati…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
Word-vector representations associate a high dimensional real-vector to every word from a corpus. Recently, neural-network based methods have been proposed for learning this representation from large corpora. This type of word-to-vector…
In this paper, we investigate the combinatorial and density properties of infinite words generated by Fibonacci-type morphisms, focusing on their subword structure, palindrome density, and extremal statistical behaviors. Using the morphism…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
Recent developments in theoretical linguistics have lead to a widespread acceptance of constraint-based analyses of prosodic morphology phenomena such as truncation, infixation, floating morphemes and reduplication. Of these, reduplication…
In this paper we introduce and study a new property of infinite words: An infinite word $x\in A^\mathbb{N}$, with values in a finite set $A$, is said to be $k$-self-shuffling $(k\geq 2)$ if $x$ admits factorizations: $x=\prod_{i=0}^\infty…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
In this paper we study several variations of the \emph{pancake flipping problem}, which is also well known as the problem of \emph{sorting by prefix reversals}. We consider the variations in the sorting process by adding with prefix…
We consider questions related to the structure of infinite words (over an integer alphabet) with bounded additive complexity, i.e., words with the property that the number of distinct sums exhibited by factors of the same length is bounded…
A word is closed if it contains a proper factor that occurs both as a prefix and as a suffix but does not have internal occurrences, otherwise it is open. We deal with the sequence of open and closed prefixes of Sturmian words and prove…
We study words that barely avoid repetitions, for several senses of "barely". A squarefree (respectively, overlap-free, cubefree) word is irreducible if removing any one of its interior letters creates a square (respectively, overlap,…
A net occurrence of a repeated string in a text is an occurrence with unique left and right extensions, and the net frequency of the string is the number of its net occurrences in the text. Originally introduced for applications in Natural…
Several insertion operations are studied applied to languages accepted by one-way and two-way deterministic reversal-bounded multicounter machines. These operations are defined by the ideals obtained from relations such as the prefix,…
A language L is prefix-free if, whenever words u and v are in L and u is a prefix of v, then u=v. Suffix-, factor-, and subword-free languages are defined similarly, where "subword" means "subsequence". A language is bifix-free if it is…
We develop faultless, fixed-depth, string-based, prefix and postfix symbolic regression grammars, capable of producing \emph{any} expression from a set of operands, unary operators and/or binary operators. Using these grammars, we outline…
In this work, we investigate novel algorithmic growth processes. In particular, we propose three growth operations, full doubling, RC doubling and doubling, and explore the algorithmic and structural properties of their resulting processes…
We show that the number of length-n words over a k-letter alphabet having no even palindromic prefix is the same as the number of length-n unbordered words, by constructing an explicit bijection between the two sets. A slightly different…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…
We present a construction of a certain infinite complete partial order (CPO) that differs from the standard construction used in Scott's denotational semantics. In addition, we construct several other infinite CPO's. For some of those, we…