Related papers: Dynamic data structures for parameterized string p…
A key principle in string processing is local consistency: using short contexts to handle matching fragments of a string consistently. String synchronizing sets [Kempa, Kociumaka; STOC 2019] are an influential instantiation of this…
Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
Geometric data structures have been extensively studied in the regime where the dimension is much smaller than the number of input points. But in many scenarios in Machine Learning, the dimension can be much higher than the number of points…
The domains of data mining and knowledge discovery make use of large amounts of textual data, which need to be handled efficiently. Specific problems, like finding the maximum weight ordered common subset of a set of ordered sets or…
Fixed-parameter algorithms and kernelization are two powerful methods to solve $\mathsf{NP}$-hard problems. Yet, so far those algorithms have been largely restricted to static inputs. In this paper we provide fixed-parameter algorithms and…
We revisit the vertex-failure connectivity oracle problem. This is one of the most basic graph data structure problems under vertex updates, yet its complexity is still not well-understood. We essentially settle the complexity of this…
Recently [Bhattacharya et al., STOC 2015] provide the first non-trivial algorithm for the densest subgraph problem in the streaming model with additions and deletions to its edges, i.e., for dynamic graph streams. They present a…
We consider the problem of tracking with small relative error an integer function $f(n)$ defined by a distributed update stream $f'(n)$. Existing streaming algorithms with worst-case guarantees for this problem assume $f(n)$ to be monotone;…
This paper presents an evolutionary algorithm for modeling the arrival dates of document streams, which is any time-stamped collection of documents, such as newscasts, e-mails, IRC conversations, scientific journals archives and weblog…
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
We propose a theoretically-efficient and practical parallel batch-dynamic data structure for the closest pair problem. Our solution is based on a serial dynamic closest pair data structure by Golin et al., and supports batches of insertions…
In the restricted shortest paths problem, we are given a graph $G$ whose edges are assigned two non-negative weights: lengths and delays, a source $s$, and a delay threshold $D$. The goal is to find, for each target $t$, the length of the…
We study the density estimation problem defined as follows: given $k$ distributions $p_1, \ldots, p_k$ over a discrete domain $[n]$, as well as a collection of samples chosen from a ``query'' distribution $q$ over $[n]$, output $p_i$ that…
Writing concurrent programs is notoriously hard due to scheduling non-determinism. The most common concurrency bugs are data races, which are accesses to a shared resource that can be executed concurrently. Dynamic data-race prediction is…
The field of dynamic graph algorithms aims at achieving a thorough understanding of real-world networks whose topology evolves with time. Traditionally, the focus has been on the classic sequential, centralized setting where the main…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…