Related papers: Efficient algorithms for the longest common subseq…
We present novel randomized approximation schemes for the Edit Distance (ED) problem and the Longest Common Subsequence (LCS) problem that, for any constant $\epsilon>0$, compute a $(1+\epsilon)$-approximation for ED and a…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
The Longest Common Subsequence (LCS) Problem asks for the longest sequence of (non-contiguous) matches between two given strings of characters. Using extensive Monte Carlo simulations, we find a finite size scaling law of the form E(L)/N =C…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
Sequence-to-Sequence models were introduced to tackle many real-life problems like machine translation, summarization, image captioning, etc. The standard optimization algorithms are mainly based on example-to-example matching like maximum…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE…
We revisit the exact shortest unique substring (SUS) finding problem, and propose its approximate version where mismatches are allowed, due to its applications in subfields such as computational biology. We design a generic in-place…
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…
Given a set of $t$ words of length $n$ over a $k$-letter alphabet, it is proved that there exists a common subsequence among two of them of length at least $\frac{n}{k}+cn^{1-1/(t-k-2)}$, for some $c>0$ depending on $k$ and $t$. This is…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…
We study the densest subgraph problem and its NP-hard densest at-most-$k$ subgraph variant through the lens of learning-augmented algorithms. We show that, given a reasonably accurate predictor that estimates whether a node belongs to the…
Given a string $T$ with length $n$ whose characters are drawn from an ordered alphabet of size $\sigma$, its longest Lyndon subsequence is a longest subsequence of $T$ that is a Lyndon word. We propose algorithms for finding such a…
Longest Increasing Subsequence (LIS) is a fundamental statistic of a sequence, and has been studied for decades. While the LIS of a sequence of length $n$ can be computed exactly in time $O(n\log n)$, the complexity of estimating the…
Given two random finite sequences from $[k]^n$ such that a prefix of the first sequence is a suffix of the second, we examine the length of their longest common subsequence. If $\ell$ is the length of the overlap, we prove that the expected…
This paper addresses the Variable Gapped Longest Common Subsequence (VGLCS) problem, a generalization of the classical LCS problem involving flexible gap constraints between consecutive solutions' characters. The problem arises in molecular…
The classical pattern matching asks for locating all occurrences of one string, called the pattern, in another, called the text, where a string is simply a sequence of characters. Due to the potential practical applications, it is desirable…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…