Related papers: On Solving the Multiple Variable Gapped Longest Co…
Longest Common Subsequence ($LCS$) deals with the problem of measuring similarity of two strings. While this problem has been analyzed for decades, the recent interest stems from a practical observation that considering single characters is…
Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…
A challenge in advancing Visual-Language Models (VLMs) is determining whether their failures on abstract reasoning tasks, such as Bongard problems, stem from flawed perception or faulty top-down reasoning. To disentangle these factors, we…
The problem of finding a longest common subsequence of two main sequences with some constraint that must be a substring of the result (STR-IC-LCS) was formulated recently. It is a variant of the constrained longest common subsequence…
A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…
Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…
Maximal Common Subsequences (MCSs) between two strings X and Y are subsequences of both X and Y that are maximal under inclusion. MCSs relax and generalize the well known and widely used concept of Longest Common Subsequences (LCSs), which…
We consider large-scale, implicit-search-based solutions to Shortest Path Problems on Graphs of Convex Sets (GCS). We propose GCS*, a forward heuristic search algorithm that generalizes A* search to the GCS setting, where a…
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…
This paper addresses the Longest Filled Common Subsequence (LFCS) problem, a challenging NP-hard problem with applications in bioinformatics, including gene mutation prediction and genomic data reconstruction. Existing approaches, including…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
The independent set on a graph $G=(V,E)$ is a subset of $V$ such that no two vertices in the subset have an edge between them. The MIS problem on $G$ seeks to identify an independent set with maximum cardinality, i.e. maximum independent…
We consider the problem of breaking a multivariate (vector) time series into segments over which the data is well explained as independent samples from a Gaussian distribution. We formulate this as a covariance-regularized maximum…
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…
For graph learning tasks, many existing methods utilize a message-passing mechanism where vertex features are updated iteratively by aggregation of neighbor information. This strategy provides an efficient means for graph features…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
In this paper, we consider a generalized longest common subsequence problem, the string-excluding constrained LCS problem. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a constraint string $P$ of length $r$, the…
This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…
Previously proposed quantum algorithms for solving linear systems of equations cannot be implemented in the near term due to the required circuit depth. Here, we propose a hybrid quantum-classical algorithm, called Variational Quantum…
We study a graph search problem in which a team of searchers attempts to find a mobile target located in a graph. Assuming that (a) the visibility field of the searchers is limited, (b) the searchers have unit speed and (c) the target has…