Related papers: Space-Efficient Algorithms for Longest Increasing …

The use of Hirschberg algorithm reduces the spatial cost of recovering the Longest Common Subsequence to linear space. The same technique can be applied to similar problems like Sequence Alignment. However, the price to pay is a duplication…

Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…

The distinct elements problem is one of the fundamental problems in streaming algorithms --- given a stream of integers in the range $\{1,\ldots,n\}$, we wish to provide a $(1+\varepsilon)$ approximation to the number of distinct elements…

The suffix array and the suffix tree are the two most fundamental data structures for string processing. For a length-$n$ text, however, they use $\Theta(n \log n)$ bits of space, which is often too costly. To address this, Grossi and…

We present the first in-place algorithm for sorting an array of size n that performs, in the worst case, at most O(n log n) element comparisons and O(n) element transports. This solves a long-standing open problem, stated explicitly, e.g.,…

Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…

Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…

We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…

We investigate adaptive sublinear algorithms for detecting monotone patterns in an array. Given fixed $2 \leq k \in \mathbb{N}$ and $\varepsilon > 0$, consider the problem of finding a length-$k$ increasing subsequence in an array $f \colon…

In the classical longest palindromic substring (LPS) problem, we are given a string $S$ of length $n$, and the task is to output a longest palindromic substring in $S$. Gilbert, Hajiaghayi, Saleh, and Seddighin [SPAA 2023] showed how to…

We solve the problems of detecting and counting various forms of regularities in a string represented as a Straight Line Program (SLP). Given an SLP of size $n$ that represents a string $s$ of length $N$, our algorithm compute all runs and…

We consider the problem of augmenting an n-vertex graph embedded in a metric space, by inserting one additional edge in order to minimize the diameter of the resulting graph. We present exact algorithms for the cases when (i) the input…

One of the landmarks in approximation algorithms is the $O(\sqrt{\log n})$-approximation algorithm for the Uniform Sparsest Cut problem by Arora, Rao and Vazirani from 2004. The algorithm is based on a semidefinite program that finds an…

While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of {\em both} time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a…

In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are at Hamming distance at most k from y.…

There is a high demand of space-efficient algorithms in built-in or embedded softwares. In this paper, we consider the problem of designing space-efficient algorithms for computing the maximum area empty rectangle (MER) among a set of…

In this paper, we develop new algorithms for the basic RNA folding problem. Given an RNA sequence that contains $n$ nucleotides, the goal of the problem is to compute a pseudoknot-free secondary structure that maximizes the number of base…

We develop catalytic algorithms for fundamental problems in algorithm design that run in polynomial time, use only $\mathcal{O}(\log(n))$ workspace, and use sublinear catalytic space matching the best-known space bounds of non-catalytic…

We study the problem of multiway number partition optimization, which has a myriad of applications in the decision, learning and optimization literature. Even though the original multiway partitioning problem is NP-hard and requires…

We consider the problem of encoding a string of length $n$ from an integer alphabet of size $\sigma$ so that access and substring equality queries (that is, determining the equality of any two substrings) can be answered efficiently. Any…