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A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
While well-known methods to list the intersections of either a list of segments or a complex polygon aim at achieving optimal time-complexity they often do so at the cost of memory comsumption and complex code. Real-life software…
The cornerstone of any algorithm computing all repetitions in a string of length n in O(n) time is the fact that the number of runs (or maximal repetitions) is O(n). We give a simple proof of this result. As a consequence of our approach,…
String attractors [STOC 2018] are combinatorial objects recently introduced to unify all known dictionary compression techniques in a single theory. A set $\Gamma\subseteq [1..n]$ is a $k$-attractor for a string $S\in[1..\sigma]^n$ if and…
The combined universal probability M(D) of strings x in sets D is close to max_{x \in D} M({x}): their ~ logs differ by at most D's information j = I(D:H) about the halting sequence H. Thus if all x have complexity K(x) > k, D carries > i…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
Lately, there is a growing interest in dynamic string matching problems. Specifically, the dynamic Longest Common Factor problem has been researched and some interesting results has been reached. In this paper we examine another classic…
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
The $k$-cardinality assignment problem asks for finding a maximal (minimal) weight of a matching of cardinality $k$ in a weighted bipartite graph $K_{n,n}$, $k \leq n$. The algorithm of Gassner and Klinz from 2010 for the parametric…
The $k$-Means clustering problem on $n$ points is NP-Hard for any dimension $d\ge 2$, however, for the 1D case there exists exact polynomial time algorithms. Previous literature reported an $O(kn^2)$ time dynamic programming algorithm that…
We consider the problem of inferring an edge-labeled graph from the sequence of edge labels seen in a walk of that graph. It has been known that this problem is solvable in $O(n \log n)$ time when the targets are path or cycle graphs. This…
We study the problem of $k$-means clustering in the space of straight-line segments in $\mathbb{R}^{2}$ under the Hausdorff distance. For this problem, we give a $(1+\epsilon)$-approximation algorithm that, for an input of $n$ segments, for…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
We consider a range of simply stated dynamic data structure problems on strings. An update changes one symbol in the input and a query asks us to compute some function of the pattern of length $m$ and a substring of a longer text. We give…
We study the streaming complexity of the membership problem of 1-turn-Dyck2 and Dyck2 when there are a few errors in the input string. 1-turn-Dyck2 with errors: We prove that there exists a randomized one-pass algorithm that given x checks…
Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to…
I present a parallel algorithm for exact probabilistic inference in Bayesian networks. For polytree networks with n variables, the worst-case time complexity is O(log n) on a CREW PRAM (concurrent-read, exclusive-write parallel…
This paper reformulates the problem of finding a longest common increasing subsequence of the two given input sequences in a very succinct way. An extremely simple linear space algorithm based on the new formula can find a longest common…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…