Related papers: The colored longest common prefix array computed v…
Correlation clustering is a central topic in unsupervised learning, with many applications in ML and data mining. In correlation clustering, one receives as input a signed graph and the goal is to partition it to minimize the number of…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
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,…
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…
Molecular sequence analysis is crucial for comprehending several biological processes, including protein-protein interactions, functional annotation, and disease classification. The large number of sequences and the inherently complicated…
Medical image segmentation is a crucial task in medical image analysis, but it can be very challenging especially when there are less labeled data but with large unlabeled data. Contrastive learning has proven to be effective for medical…
In the minimum common string partition (MCSP) problem two related input strings are given. "Related" refers to the property that both strings consist of the same set of letters appearing the same number of times in each of the two strings.…
Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…
Indexing of very large collections of strings such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheeler Transform (BWT), and for this problem various in-memory…
Selecting the top-$m$ variables with the $m$ largest population parameters from a larger set of candidates is a fundamental problem in statistics. In this paper, we propose a novel methodology called Sequential Correct Screening (SCS),…
Linear nested codes, where two or more sub-codes are nested in a global code, have been proposed as candidates for reliable multi-terminal communication. In this paper, we consider nested array-based spatially coupled low-density…
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…
The range closest-pair (RCP) problem is the range-search version of the classical closest-pair problem, which aims to store a given dataset of points in some data structure such that when a query range $X$ is specified, the closest pair of…
We show how to modify the linear-time construction algorithm for suffix arrays based on induced sorting (Nong et al., DCC'09) such that it computes the array of longest common prefixes (LCP-array) as well. Practical tests show that this…
Connected Component Labeling (CCL) is an important step in pattern recognition and image processing. It assigns labels to the pixels such that adjacent pixels sharing the same features are assigned the same label. Typically, CCL requires…
In this paper, we study for the first time the Diverse Longest Common Subsequences (LCSs) problem under Hamming distance. Given a set of a constant number of input strings, the problem asks to decide if there exists some subset $\mathcal X$…
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…
Getting a robust time-series clustering with best choice of distance measure and appropriate representation is always a challenge. We propose a novel mechanism to identify the clusters combining learned compact representation of…
The problem of finding network codes for general connections is inherently difficult in capacity constrained networks. Resource minimization for general connections with network coding is further complicated. Existing methods for…
For a set of mulitple sequences, their patterns,Longest Common Subsequences (LCS) and Shortest Common Supersequences (SCS) represent different aspects of these sequences profile, and they can all be used for biological sequence comparisons…