Related papers: Pattern Matching with Mismatches and Wildcards
We study polynomial-time approximation algorithms for (edge/vertex) Sparsest Cut and Small Set Expansion in terms of $k$, the number of edges or vertices cut in the optimal solution. Our main results are $\mathcal{O}(\text{polylog}\,…
In this paper, a fully compressed pattern matching problem is studied. The compression is represented by straight-line programs (SLPs), i.e. a context-free grammars generating exactly one string; the term fully means that both the pattern…
In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, the goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that the length-$m$ substrings of $T$ starting at positions $i$ and $j$…
We present a new approach for solving (minimum disagreement) correlation clustering that results in sublinear algorithms with highly efficient time and space complexity for this problem. In particular, we obtain the following algorithms for…
We consider the problem of preprocessing a text $T$ of length $n$ and a dictionary $\mathcal{D}$ in order to be able to efficiently answer queries $CountDistinct(i,j)$, that is, given $i$ and $j$ return the number of patterns from…
Consider an $m$-bit query $q$ to a bitwise trie $T$. A wildcard $*$ is an unspecified bit in $q$ for which the query asks the membership for both cases $*=0$ and $*=1$. It is common that such partial-match queries with wildcards are issued…
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…
Permutation patterns and pattern avoidance have been intensively studied in combinatorics and computer science, going back at least to the seminal work of Knuth on stack-sorting (1968). Perhaps the most natural algorithmic question in this…
In this paper we consider graph algorithms in models of computation where the space usage (random accessible storage, in addition to the read only input) is sublinear in the number of edges $m$ and the access to input data is constrained.…
In the Maximum Independent Set of Objects problem, we are given an $n$-vertex planar graph $G$ and a family $\mathcal{D}$ of $N$ objects, where each object is a connected subgraph of $G$. The task is to find a subfamily $\mathcal{F}…
We develop new approximation algorithms for classical graph and set problems in the RAM model under space constraints. As one of our main results, we devise an algorithm for d-Hitting Set that runs in time n^{O(d^2 + d/\epsilon})}, uses…
A family of comparison-based exact pattern matching algorithms is described. They utilize multi-dimensional arrays in order to process more than one adjacent text window in each iteration of the search cycle. This approach leads to a lower…
We consider the problem of finding \textit{semi-matching} in bipartite graphs which is also extensively studied under various names in the scheduling literature. We give faster algorithms for both weighted and unweighted case. For the…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
We revisit the fundamental problem of dictionary look-up with mismatches. Given a set (dictionary) of $d$ strings of length $m$ and an integer $k$, we must preprocess it into a data structure to answer the following queries: Given a query…
Maximum bipartite matching (MBM) is a fundamental problem in combinatorial optimization with a long and rich history. A classic result of Hopcroft and Karp (1973) provides an $O(m \sqrt{n})$-time algorithm for the problem, where $n$ and $m$…
In a seminal paper on finding large matchings in sparse random graphs, Karp and Sipser proposed two algorithms for this task. The second algorithm has been intensely studied, but due to technical difficulties, the first algorithm has…
Given a positive integer $d$, the d-CUT is the problem of deciding if an undirected graph $G=(V,E)$ has a cut $(A,B)$ such that every vertex in $A$ (resp. $B$) has at most $d$ neighbors in $B$ (resp. $A$). For $d=1$, the problem is referred…
We initiate the study of approximation algorithms and computational barriers for constructing sparse $\alpha$-navigable graphs [IX23, DGM+24], a core primitive underlying recent advances in graph-based nearest neighbor search. Given an…
Discrepancy theory provides powerful tools for producing higher-quality objects which "beat the union bound" in fundamental settings throughout combinatorics and computer science. However, this quality has often come at the price of more…