Related papers: A Simple Algorithm for the Constrained Sequence Pr…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
An algorithm is proposed, analyzed, and tested for solving continuous nonlinear-equality-constrained optimization problems where the objective and constraint functions are defined by expectations or averages over large, finite numbers of…
The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a…
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…
We consider the general problem of the Longest Common Subsequence (LCS) on weighted sequences. Weighted sequences are an extension of classical strings, where in each position every letter of the alphabet may occur with some probability.…
This paper addresses the Restricted Longest Common Subsequence (RLCS) problem, an extension of the well-known Longest Common Subsequence (LCS) problem. This problem has significant applications in bioinformatics, particularly for…
Longest common subsequence ($\mathsf{LCS}$) is a classic and central problem in combinatorial optimization. While $\mathsf{LCS}$ admits a quadratic time solution, recent evidence suggests that solving the problem may be impossible in truly…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
We investigate the constrained synchronization problem for weakly acyclic, or partially ordered, input automata. We show that, for input automata of this type, the problem is always in NP. Furthermore, we give a full classification of the…
We consider computing a longest palindrome in the streaming model, where the symbols arrive one-by-one and we do not have random access to the input. While computing the answer exactly using sublinear space is not possible in such a…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
In this work we revisit the elementary scheduling problem $1||\sum p_j U_j$. The goal is to select, among $n$ jobs with processing times and due dates, a subset of jobs with maximum total processing time that can be scheduled in sequence…
Given two sequences $A[1..n]$ and $B[1..m]$ over a totally ordered alphabet, the \emph{Longest Common Bitonic Subsequence} (LCBS) problem asks for a longest common subsequence that is strictly increasing up to a single peak element and…
Two important similarity measures between sequences are the longest common subsequence (LCS) and the dynamic time warping distance (DTWD). The computations of these measures for two given sequences are central tasks in a variety of…
Finding a shortest path in a graph is one of the most classic problems in algorithmic and graph theory. While we dispose of quite efficient algorithms for this ordinary problem (like the Dijkstra or Bellman-Ford algorithms), some slight…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
In this work, we obtain the following new results. 1. Given a sequence $D=((h_1,s_1), (h_2,s_2) ..., (h_n,s_n))$ of number pairs, where $s_i>0$ for all $i$, and a number $L_h$, we propose an O(n)-time algorithm for finding an index interval…
In the Longest Common Factor with $k$ Mismatches (LCF$_k$) problem, we are given two strings $X$ and $Y$ of total length $n$, and we are asked to find a pair of maximal-length factors, one of $X$ and the other of $Y$, such that their…
We study dynamic algorithms for the longest increasing subsequence (\textsf{LIS}) problem. A dynamic \textsf{LIS} algorithm maintains a sequence subject to operations of the following form arriving one by one: (i) insert an element, (ii)…
The Longest Common Subsequence (LCS) problem is a very important problem in math- ematics, which has a broad application in scheduling problems, physics and bioinformatics. It is known that the given two random sequences of infinite…