Related papers: Longest Increasing Subsequence under Persistent Co…
We consider the problem of computing the Maximal Exact Matches (MEMs) of a given pattern $P[1 .. m]$ on a large repetitive text collection $T[1 .. n]$, which is represented as a (hopefully much smaller) run-length context-free grammar of…
In the Longest Common Factor with $k$ Mismatches (LCF$_k$) problem, we are given two strings $X$ and $Y$ of total length $n$, and we are asked to find a pair of maximal-length factors, one of $X$ and the other of $Y$, such that their…
Let $B$ be a set of natural numbers of size $n$. We prove that the length of the longest arithmetic progression contained in the product set $B.B = \{bb'| \, b, b' \in B\}$ cannot be greater than $O(\frac{n\log^2 n}{\log \log n})$ and…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
We present a near-linear time approximation algorithm for the subtrajectory cluster problem of $c$-packed trajectories. The problem involves finding $m$ subtrajectories within a given trajectory $T$ such that their Fr\'echet distances are…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
The bin packing problem is to find the minimum number of bins of size one to pack a list of items with sizes $a_1,..., a_n$ in $(0,1]$. Using uniform sampling, which selects a random element from the input list each time, we develop a…
Approximate nearest-neighbor search is a fundamental algorithmic problem that continues to inspire study due its essential role in numerous contexts. In contrast to most prior work, which has focused on point sets, we consider…
We present two deterministic dynamic algorithms for the maximum matching problem. (1) An algorithm that maintains a $(2+\epsilon)$-approximate maximum matching in general graphs with $O(\text{poly}(\log n, 1/\epsilon))$ update time. (2) An…
This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…
We consider the problem of counting the copies of a length-$k$ pattern $\sigma$ in a sequence $f \colon [n] \to \mathbb{R}$, where a copy is a subset of indices $i_1 < \ldots < i_k \in [n]$ such that $f(i_j) < f(i_\ell)$ if and only if…
Mergesort is one of the few efficient sorting algorithms and, despite being the oldest one, often still the method of choice today. In contrast to some alternative algorithms, it always runs efficiently using O(n log n) element comparisons…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
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…
Consider a finite set of sources, each producing i.i.d. observations that follow a unique probability distribution on a finite alphabet. We study the problem of matching a finite set of observed sequences to the set of sources under the…
We present combinatorial and parallelizable algorithms for maximization of a submodular function, not necessarily monotone, with respect to a size constraint. We improve the best approximation factor achieved by an algorithm that has…
We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…
We consider the classic Set Cover problem in the data stream model. For $n$ elements and $m$ sets ($m\geq n$) we give a $O(1/\delta)$-pass algorithm with a strongly sub-linear $\tilde{O}(mn^{\delta})$ space and logarithmic approximation…
The longest common substring problem consists in finding a longest string that appears as a (contiguous) substring of two input strings. We consider the dynamic variant of this problem, in which we are to maintain two dynamic strings $S$…
The Longest Common Subsequence (LCS) is a fundamental string similarity measure, and computing the LCS of two strings is a classic algorithms question. A textbook dynamic programming algorithm gives an exact algorithm in quadratic time, and…