arXiv subjects

Riccardo Maso

Publications and source records attributed to Riccardo Maso.

2 recordsLinked to original sources

arXiv2026

Faster Cache-Efficient Pattern Matching for Deterministic Wheeler Pangenome Graphs

Pattern matching on strings is regarded as one of the core operations in computer science. Although researchers proposed several solutions to this problem, some of the most elegant and widely used approaches are based on the renowned Burrows-Wheeler transform (BWT). The success of the BWT lies in its pattern matching algorithm known as backward search, which is not only near-optimal in the RAM model, but also runs directly on a compressed representation of the input string. More recently, the backward search has been generalized to Wheeler deterministic finite automata (DFAs), a subclass of standard DFAs, without losing its near-optimal time efficiency. Similarly to the case of strings, this pattern matching algorithm for Wheeler DFAs has found applications in bioinformatics, where researchers have shown that specific pangenome graphs of human chromosomes can be transformed into Wheeler DFAs and consequently indexed using this strategy. However, this BWT-based index on Wheeler DFAs inherited a significant drawback from the original backward search, namely the high number of I/O operations triggered during the algorithm execution, which are in the worst-case lower-bounded by the length of the pattern. In this paper, we address this limitation by proposing the first cache-friendly algorithm specifically designed for Wheeler DFAs. Our new data structure reduces the number of I/O operations by employing a strategy analogous to the suffix array: it interleaves a binary search with fast sequential scans of the automaton. We empirically validate this new indexing strategy by running our algorithm on real-world Wheeler pangenome graphs. We show that while our data structure can use up to 15 times the space required by the backward search, it can also be 500 times faster and able to process a single character of the pattern in less than 3 ns.

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arXiv2024

Random Wheeler Automata

Wheeler automata were introduced in 2017 as a tool to generalize existing indexing and compression techniques based on the Burrows-Wheeler transform. Intuitively, an automaton is said to be Wheeler if there exists a total order on its states reflecting the co-lexicographic order of the strings labeling the automaton's paths; this property makes it possible to represent the automaton's topology in a constant number of bits per transition, as well as efficiently solving pattern matching queries on its accepted regular language. After their introduction, Wheeler automata have been the subject of a prolific line of research, both from the algorithmic and language-theoretic points of view. A recurring issue faced in these studies is the lack of large datasets of Wheeler automata on which the developed algorithms and theories could be tested. One possible way to overcome this issue is to generate random Wheeler automata. Motivated by this observation, in this paper we initiate the theoretical study of random Wheeler automata, focusing on the deterministic case (Wheeler DFAs -- WDFAs). We start by extending the Erdős-Rényi random graph model to WDFAs, and proceed by providing an algorithm generating uniform WDFAs according to this model. Our algorithm generates a uniform WDFA with $n$ states, $m$ transitions, and alphabet's cardinality $σ$ in $O(m)$ expected time ($O(m\log m)$ worst-case time w.h.p.) and constant working space for all alphabets of size $σ\le m/\ln m$. As a by-product, we also give formulas for the number of distinct WDFAs and obtain that $ nσ+ (n - σ) \log σ$ bits are necessary and sufficient to encode a WDFA with $n$ states and alphabet of size $σ$, up to an additive $Θ(n)$ term. We present an implementation of our algorithm and show that it is extremely fast in practice, with a throughput of over 8 million transitions per second.

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