Related papers: Faster Algorithms for Shortest Unique or Absent Su…
A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…
We describe a RAM algorithm computing all runs (maximal repetitions) of a given string of length $n$ over a general ordered alphabet in $O(n\log^{\frac{2}3} n)$ time and linear space. Our algorithm outperforms all known solutions working in…
Consider an undirected weighted graph $G = (V,E,w)$. We study the problem of computing $(1+\epsilon)$-approximate shortest paths for $S \times V$, for a subset $S \subseteq V$ of $|S| = n^r$ sources, for some $0 < r \le 1$. We devise a…
A substring $u$ of a string $T$ is called a minimal unique substring (MUS) of $T$ if $u$ occurs exactly once in $T$ and any proper substring of $u$ occurs at least twice in $T$. A string $w$ is called a minimal absent word (MAW) of $T$ if…
For a text given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence in the text. We develop a data structure answering…
The scheduling problem consists of finding a common 1 in two remotely located N bit strings. Denote the number of 1s in the string with the fewer 1s by epsilon*N. Classically, it needs at least O(epsilon*N) bits of communication to find the…
While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of {\em both} time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a…
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…
A border of a string is a non-empty proper prefix of the string that is also a suffix. A string is unbordered if it has no border. The longest unbordered factor is a fundamental notion in stringology, closely related to string periodicity.…
We study the problem of indexing text with wildcard positions, motivated by the challenge of aligning sequencing data to large genomes that contain millions of single nucleotide polymorphisms (SNPs)---positions known to differ between…
Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…
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…
We revisit the classic problem of simplex range searching and related problems in computational geometry. We present a collection of new results which improve previous bounds by multiple logarithmic factors that were caused by the use of…
This paper studies parallel algorithms for the longest increasing subsequence (LIS) problem. Let $n$ be the input size and $k$ be the LIS length of the input. Sequentially, LIS is a simple problem that can be solved using dynamic…
Given a graph and an integer $k$, Densest $k$-Subgraph is the algorithmic task of finding the subgraph on $k$ vertices with the maximum number of edges. This is a fundamental problem that has been subject to intense study for decades, with…
In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…
We are given a read-only memory for input and a write-only stream for output. For a positive integer parameter s, an s-workspace algorithm is an algorithm using only $O(s)$ words of workspace in addition to the memory for input. In this…
In this paper we investigate the problem of partitioning an input string T in such a way that compressing individually its parts via a base-compressor C gets a compressed output that is shorter than applying C over the entire T at once.…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…
Let $\mathcal{P}$ be the surface of a convex polyhedron with $n$ vertices. We consider the two-point shortest path query problem for $\mathcal{P}$: Constructing a data structure so that given any two query points $s$ and $t$ on…