Related papers: Efficient algorithms for the longest common subseq…
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…
Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact definition of a chain, there are several $O(n \log n)$ time…
Finding the length of the longest increasing subsequence (LIS) is a classic algorithmic problem. Let $n$ denote the size of the array. Simple $O(n\log n)$ algorithms are known for this problem. We develop a polylogarithmic time randomized…
The densest $k$-subgraph problem is the problem of finding a $k$-vertex subgraph of a graph with the maximum number of edges. In order to solve large instances of the densest $k$-subgraph problem, we introduce two algorithms that are based…
We consider two optimization problems related to finding dense subgraphs. The densest at-least-k-subgraph problem (DalkS) is to find an induced subgraph of highest average degree among all subgraphs with at least k vertices, and the densest…
The problem of best subset selection in linear regression is considered with the aim to find a fixed size subset of features that best fits the response. This is particularly challenging when the total available number of features is very…
Given \(k\) strings each of length at most $n$, computing the shortest common supersequence of them is a well-known NP-hard problem (when \(k\) is unbounded). On the other hand, when \(k=2\), such a shortest common supersequence can be…
The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…
Given a sequence of integers, we want to find a longest increasing subsequence of the sequence. It is known that this problem can be solved in $O(n \log n)$ time and space. Our goal in this paper is to reduce the space consumption while…
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…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
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 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…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…
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)…
We present a new efficient method for approximate search in electronic lexica. Given an input string (the pattern) and a similarity threshold, the algorithm retrieves all entries of the lexicon that are sufficiently similar to the pattern.…
The longest run subsequence (LRS) problem is an NP-hard combinatorial optimization problem belonging to the class of subsequence problems from bioinformatics. In particular, the problem plays a role in genome reassembly. In this paper, we…
We present an algorithm computing the longest periodic subsequence of a string of length $n$ in $O(n^7)$ time with $O(n^4)$ words of space. We obtain improvements when restricting the exponents or extending the search allowing the reported…
We study a variation of the classical Shortest Common Superstring (SCS) problem in which a shortest superstring of a finite set of strings $S$ is sought containing as a factor every string of $S$ or its reversal. We call this problem…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…