Related papers: An efficient dynamic programming algorithm for the…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
We consider the problem of maintaining a collection of strings while efficiently supporting splits and concatenations on them, as well as comparing two substrings, and computing the longest common prefix between two suffixes. This problem…
We provide a randomized linear time approximation scheme for a generic problem about clustering of binary vectors subject to additional constrains. The new constrained clustering problem encompasses a number of problems and by solving it,…
Integer linear programs $\min\{c^T x : A x = b, x \in \mathbb{Z}^n_{\ge 0}\}$, where $A \in \mathbb{Z}^{m \times n}$, $b \in \mathbb{Z}^m$, and $c \in \mathbb{Z}^n$, can be solved in pseudopolynomial time for any fixed number of constraints…
This paper discusses the odds problem, proposed by Bruss in 2000, and its variants. A recurrence relation called a dynamic programming (DP) equation is used to find an optimal stopping policy of the odds problem and its variants. In 2013,…
The Shortest Superstring Problem (SSP) consists, for a set of strings S = {s_1,...,s_n}, to find a minimum length string that contains all s_i, 1 <= i <= k, as substrings. This problem is proved to be NP-Complete and APX-hard. Guaranteed…
In this paper we present novel algorithms for several multidimensional data processing problems. We consider problems related to the computation of restricted clusters and of the diameter of a set of points using a new distance function. We…
This paper studies parallel algorithms for the longest increasing subsequence (LIS) problem. Let $n$ be the input size and $k$ be the LIS length of the input. Sequentially, LIS is a simple problem that can be solved using dynamic…
Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…
We introduce a parallel machine scheduling problem in which the processing times of jobs are not given in advance but are determined by a system of linear constraints. The objective is to minimize the makespan, i.e., the maximum job…
One of the most fundamental problems in Computer Science is the Knapsack problem. Given a set of n items with different weights and values, it asks to pick the most valuable subset whose total weight is below a capacity threshold T. Despite…
Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…
In this work, we present a plethora of results for the range longest increasing subsequence problem (Range-LIS) and its variants. The input to RLIS is a sequence $S$ of $n$ real numbers and a collection $Q$ of $m$ query ranges, and for each…
Short spanning trees subject to additional constraints are important building blocks in various approximation algorithms. Especially in the context of the Traveling Salesman Problem (TSP), new techniques for finding spanning trees with…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…
Random access to highly compressed strings -- represented by straight-line programs or Lempel-Ziv parses, for example -- is a well-studied topic. Random access to such strings in strongly sublogarithmic time is impossible in the worst case,…