Related papers: Indexing Finite-State Automata Using Forward-Stabl…
An index for a finite automaton is a powerful data structure that supports locating paths labeled with a query pattern, thus solving pattern matching on the underlying regular language. In this paper, we solve the long-standing problem of…
Sorting is a fundamental algorithmic pre-processing technique which often allows to represent data more compactly and, at the same time, speeds up search queries on it. In this paper, we focus on the well-studied problem of sorting and…
The states of a deterministic finite automaton A can be identified with collections of words in Pf(L(A)) -- the set of prefixes of words belonging to the regular language accepted by A. But words can be ordered and among the many possible…
The Burrows-Wheeler transform (BWT) is a string transformation that enhances string indexing and compressibility. Cotumaccio and Prezza [SODA '21] extended this transformation to nondeterministic finite automata (NFAs) through…
Co-lex partial orders were recently introduced in (Cotumaccio et al., SODA 2021 and JACM 2023) as a powerful tool to index finite state automata, with applications to regular expression matching. They generalize Wheeler orders (Gagie et…
Wheeler nondeterministic finite automata (WNFAs) were introduced as a generalization of prefix sorting from strings to labeled graphs. WNFAs admit optimal solutions to classic hard problems on labeled graphs and languages. The problem of…
The FM-index is a celebrated compressed data structure for full-text pattern searching. After the first wave of interest in its theoretical developments, we can observe a surge of interest in practical FM-index variants in the last few…
In the present work, we tackle the regular language indexing problem by first studying the hierarchy of $p$-sortable languages: regular languages accepted by automata of width $p$. We show that the hierarchy is strict and does not collapse,…
In this work, we present a literature review for full-text and keyword indexes as well as our contributions (which are mostly practice-oriented). The first contribution is the FM-bloated index, which is a modification of the well-known…
In the present work, we lay out a new theory showing that all automata can always be co-lexicographically partially ordered, and an intrinsic measure of their complexity can be defined and effectively determined, namely, the minimum width…
The problem of Text Indexing is a fundamental algorithmic problem in which one wishes to preprocess a text in order to quickly locate pattern queries within the text. In the ever evolving world of dynamic and on-line data, there is also a…
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same…
Partially ordered automata are automata where the transition relation induces a partial order on states. The expressive power of partially ordered automata is closely related to the expressivity of fragments of first-order logic on finite…
FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…
FIAT (the FInite element Automatic Tabulator) provides a powerful Python library for the generation and evaluation of finite element basis functions on a reference element. This release paper describes recent improvements to FIAT aimed at…
Previous authors have shown how to build FM-indexes efficiently in external memory, but querying them efficiently remains an open problem. Searching na\"{i}vely for a pattern $P$ requires (\Theta (|P|)) random access. In this paper we show…
We define a new subclass of nondeterministic finite automata for prefix-closed languages called Flanked Finite Automata (FFA). We show that this class enjoys good complexity properties while preserving the succinctness of nondeterministic…
Indexed pattern search in text has been studied for many decades. For small alphabets, the FM-Index provides unmatched performance, in terms of both space required and search speed. For large alphabets -- for example, when the tokens are…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…