The Complexity of the Co-Occurrence Problem

Abstract

Let $S$ be a string of length $n$ over an alphabet $Σ$ and let $Q$ be a subset of $Σ$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$ return the number of length-$w$ substrings of $S$ that contain each character of $Q$ at least once. This is a natural string problem with applications to, e.g., data mining, natural language processing, and DNA analysis. The state of the art is an $O(\sqrt{nq})$ space data structure that -- with some minor additions -- supports queries in $O(\log\log n)$ time [CPM 2021]. Our contributions are as follows. Firstly, we analyze the problem in terms of a new, natural parameter $d$, giving a simple data structure that uses $O(d)$ space and supports queries in $O(\log\log n)$ time. The preprocessing algorithm does a single pass over $S$, runs in expected $O(n)$ time, and uses $O(d)$ space in addition to the input. Furthermore, we show that $O(d)$ space is optimal and that $O(\log\log n)$-time queries are optimal given optimal space. Secondly, we bound $d = O(\sqrt{nq})$, giving clean bounds in terms of $n$ and $q$ that match the state of the art. Furthermore, we prove that $Ω(\sqrt{nq})$ bits of space is necessary in the worst case, meaning that the $O(\sqrt{nq})$ upper bound is tight to within polylogarithmic factors. All of our results are based on simple and intuitive combinatorial ideas that simplify the state of the art.