Related papers: String Attractors: Verification and Optimization
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…
The normalized substring complexity $\delta$ of a string is defined as $\max_k \{c[k]/k\}$, where $c[k]$ is the number of \textit{distinct} substrings of length $k$. This simply defined measure has recently attracted attention due to its…
We consider the Low Rank Approximation problem, where the input consists of a matrix $A \in \mathbb{R}^{n_R \times n_C}$ and an integer $k$, and the goal is to find a matrix $B$ of rank at most $k$ that minimizes $\| A - B \|_0$, which is…
The problem of non-monotone $k$-submodular maximization under a knapsack constraint ($\kSMK$) over the ground set size $n$ has been raised in many applications in machine learning, such as data summarization, information propagation, etc.…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…
In the $k$-mismatch problem, given a pattern and a text of length $n$ and $m$ respectively, we have to find if the text has a sub-string with a Hamming distance of at most $k$ from the pattern. This has been studied in the classical setting…
The "Subset Sum problem" is a very well-known NP-complete problem. In this work, a top-k variation of the "Subset Sum problem" is considered. This problem has wide application in recommendation systems, where instead of k best objects the k…
Optimizing the acquisition matrix is useful for compressed sensing of signals that are sparse in overcomplete dictionaries, because the acquisition matrix can be adapted to the particular correlations of the dictionary atoms. In this paper…
Given $n$ length-$\ell$ strings $S =\{s_1, ..., s_n\}$ over a constant size alphabet $\Sigma$ together with parameters $d$ and $k$, the objective in the {\em Consensus String with Outliers} problem is to find a subset $S^*$ of $S$ of size…
Minimum $k$-Section denotes the NP-hard problem to partition the vertex set of a graph into $k$ sets of sizes as equal as possible while minimizing the cut width, which is the number of edges between these sets. When $k$ is an input…
In the $k$-cut problem, we are given an edge-weighted graph and want to find the least-weight set of edges whose deletion breaks the graph into $k$ connected components. Algorithms due to Karger-Stein and Thorup showed how to find such a…
This paper investigates the approximability of the Longest Common Subsequence (LCS) problem. The fastest algorithm for solving the LCS problem exactly runs in essentially quadratic time in the length of the input, and it is known that under…
In this paper, we investigate optimization problems with nonnegative and orthogonal constraints, where any feasible matrix of size $n \times p$ exhibits a sparsity pattern such that each row accommodates at most one nonzero entry. Our…
The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…
The phenomenon of self-organization has been of special interest to the neural network community for decades. In this paper, we study a variant of the Self-Organizing Map (SOM) that models the phenomenon of self-organization of the…
With the growing focus on semantic searches and interpretations, an increasing number of standardized vocabularies and ontologies are being designed and used to describe data. We investigate the querying of objects described by a…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
In the Shortest Superstring problem, we are given a set of strings and we are asking for a common superstring, which has the minimum number of characters. The Shortest Superstring problem is NP-hard and several constant-factor approximation…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…