Related papers: On The Closest String and Substring Problems
The $k$-center problem is a classical combinatorial optimization problem which asks to find $k$ centers such that the maximum distance of any input point in a set $P$ to its assigned center is minimized. The problem allows for elegant…
Given a satisfiable 3-SAT formula, how hard is it to find an assignment to the variables that has Hamming distance at most n/2 to a satisfying assignment? More generally, consider any polynomial-time verifier for any NP-complete language. A…
The recently introduced longest common substring with $k$-mismatches ($k$-LCF) problem is to find, given two sequences $S_1$ and $S_2$ of length $n$ each, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance…
When implementing regular enough functions (e.g., elementary or special functions) on a computing system, we frequently use polynomial approximations. In most cases, the polynomial that best approximates (for a given distance and in a given…
Given a graph G, the {\em maximum internal spanning tree problem} (MIST for short) asks for computing a spanning tree T of G such that the number of internal vertices in T is maximized. MIST has possible applications in the design of…
We study two fundamental problems dealing with curves in the plane, namely, the nearest-neighbor problem and the center problem. Let $\mathcal{C}$ be a set of $n$ polygonal curves, each of size $m$. In the nearest-neighbor problem, the goal…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
We study the Parallel Task Scheduling problem $Pm|size_j|C_{\max}$ with a constant number of machines. This problem is known to be strongly NP-complete for each $m \geq 5$, while it is solvable in pseudo-polynomial time for each $m \leq 3$.…
In nearly every discipline, scientific computations are limited by the cost and speed of computation. For example, the best-known exact algorithms for the canonical Traveling Salesman Problem would take centuries to run on an instance of…
In the Shortest Common Superstring problem, one needs to find the shortest superstring for a set of strings. This problem is APX-hard, and many approximation algorithms were proposed, with the current best approximation factor of 2.466.…
We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized…
In this short note we present a comprehensive bibliography for the online exact string matching problem. The problem consists in finding all occurrences of a given pattern in a text. It is an extensively studied problem in computer science,…
We consider the following model for sampling pairs of strings: $s_1$ is a uniformly random bitstring of length $n$, and $s_2$ is the bitstring arrived at by applying substitutions, insertions, and deletions to each bit of $s_1$ with some…
We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
We give sublinear-time approximation algorithms for some optimization problems arising in machine learning, such as training linear classifiers and finding minimum enclosing balls. Our algorithms can be extended to some kernelized versions…
We study the fundamental problem of approximate nearest neighbor search in $d$-dimensional Hamming space $\{0,1\}^d$. We study the complexity of the problem in the famous cell-probe model, a classic model for data structures. We consider…
A well-known fact in the field of lossless text compression is that high-order entropy is a weak model when the input contains long repetitions. Motivated by this, decades of research have generated myriads of so-called dictionary…
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…