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We consider the longest common subsequence problem in the context of subsequences with gap constraints. In particular, following Day et al. 2022, we consider the setting when the distance (i. e., the gap) between two consecutive symbols of…
We show that a large fraction of the data-structure lower bounds known today in fact follow by reduction from the communication complexity of lopsided (asymmetric) set disjointness. This includes lower bounds for: * high-dimensional…
In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are at Hamming distance at most k from y.…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
The densest subgraph problem, introduced in the 80s by Picard and Queyranne as well as Goldberg, is a classic problem in combinatorial optimization with a wide range of applications. The lowest outdegree orientation problem is known to be…
By considering the task of finding the shortest walk through a network we find an algorithm for which the run time is not as O(2^n), with n being the number of nodes, but instead scales with the number of nodes in a coarsened network. This…
The problem of best subset selection in linear regression is considered with the aim to find a fixed size subset of features that best fits the response. This is particularly challenging when the total available number of features is very…
A curious property of randomized log-space search algorithms is that their outputs are often longer than their workspace. This leads to the question: how can we reproduce the results of a randomized log space computation without storing the…
The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a…
We study sketching and streaming algorithms for the Longest Common Subsequence problem (LCS) on strings of small alphabet size $|\Sigma|$. For the problem of deciding whether the LCS of strings $x,y$ has length at least $L$, we obtain a…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…
We introduce a novel criterion in clustering that seeks clusters with limited range of values associated with each cluster's elements. In clustering or classification the objective is to partition a set of objects into subsets, called…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
With the advent of large-scale heterogeneous search engines comes the problem of unified search control resulting in mismatches that could have otherwise avoided. A mechanism is needed to determine exact patterns in web mining and…
We consider the problem of sorting $n$ elements subject to persistent random comparison errors. In this problem, each comparison between two elements can be wrong with some fixed (small) probability $p$, and comparing the same pair of…
Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…
Longest common substring (LCS), longest palindrome substring (LPS), and Ulam distance (UL) are three fundamental string problems that can be classically solved in near linear time. In this work, we present sublinear time quantum algorithms…
We solve the problems of detecting and counting various forms of regularities in a string represented as a Straight Line Program (SLP). Given an SLP of size $n$ that represents a string $s$ of length $N$, our algorithm compute all runs and…