Related papers: Efficiently decoding strings from their shingles
A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph. These correspond to regions of genetic variation and are…
In the Palindrome Problem one tries to find all palindromes (palindromic substrings) in a given string. A palindrome is defined as a string which reads forwards the same as backwards, e.g., the string "racecar". A related problem is the…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
We consider the problem of finding a minimum cut of a weighted graph presented as a single-pass stream. While graph sparsification in streams has been intensively studied, the specific application of finding minimum cuts in streams is less…
A string is said to be closed if its length is one, or if it has a non-empty factor that occurs both as a prefix and as a suffix of the string, but does not occur elsewhere. The notion of closed words was introduced by [Fici, WORDS 2011].…
In this short note we present a comprehensive bibliography for the online exact string matching problem. The problem consists in finding all occurrences of a given pattern in a text. It is an extensively studied problem in computer science,…
String similarity models are vital for record linkage, entity resolution, and search. In this work, we present STANCE --a learned model for computing the similarity of two strings. Our approach encodes the characters of each string, aligns…
Random access to highly compressed strings -- represented by straight-line programs or Lempel-Ziv parses, for example -- is a well-studied topic. Random access to such strings in strongly sublogarithmic time is impossible in the worst case,…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
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…
Motivated by a concrete problem and with the goal of understanding the sense in which the complexity of streaming algorithms is related to the complexity of formal languages, we investigate the problem Dyck(s) of checking matching…
Given a set of pattern strings $\mathcal{P}=\{P_1, P_2,\ldots P_k\}$ and a text string $S$, the classic dictionary matching problem is to report all occurrences of each pattern in $S$. We study the dictionary problem in the compressed…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…
Thread-like structures are pervasive across scales, from polymeric proteins to root systems to galaxy filaments, and their characteristics can be readily investigated in the network formalism. Yet, network links usually represent only parts…
We study the problem of estimating the number of triangles in a graph stream. No streaming algorithm can get sublinear space on all graphs, so methods in this area bound the space in terms of parameters of the input graph such as the…
We address the satisfiability problem for string constraints that combine relational constraints represented by transducers, word equations, and string length constraints. This problem is undecidable in general. Therefore, we propose a new…
String matching is one of the most fundamental problems in computer science. A natural problem is to determine the number of characters that need to be queried (i.e. the decision tree complexity) in a string in order to decide whether this…
In deep neural networks, better results can often be obtained by increasing the complexity of previously developed basic models. However, it is unclear whether there is a way to boost performance by decreasing the complexity of such models.…