The streaming $k$-mismatch problem

TL;DR

This paper introduces a streaming algorithm for the $k$-mismatch problem that efficiently computes approximate pattern matches with low space and near-optimal time, extending previous open problems.

Contribution

It presents a novel streaming algorithm for the $k$-mismatch problem with near-optimal space and time complexity, resolving an open problem from FOCS'09.

Findings

Uses $O(k ext{log}n ext{log}rac{n}{k})$ bits of space

Processes each input symbol in nearly optimal time

Provides a deterministic encoding for alignments with Hamming distance at most $k$

Abstract

We consider the streaming complexity of a fundamental task in approximate pattern matching: the $k$-mismatch problem. It asks to compute Hamming distances between a pattern of length $n$ and all length-$n$ substrings of a text for which the Hamming distance does not exceed a given threshold $k$. In our problem formulation, we report not only the Hamming distance but also, on demand, the full \emph{mismatch information}, that is the list of mismatched pairs of symbols and their indices. The twin challenges of streaming pattern matching derive from the need both to achieve small working space and also to guarantee that every arriving input symbol is processed quickly. We present a streaming algorithm for the $k$-mismatch problem which uses $O(k\log{n}\log\frac{n}{k})$ bits of space and spends \ourcomplexity time on each symbol of the input stream, which consists of the pattern followed by the text. The running time almost matches the classic offline solution and the space usage is within a logarithmic factor of optimal. Our new algorithm therefore effectively resolves and also extends an open problem first posed in FOCS'09. En route to this solution, we also give a deterministic $O( k (\log \frac{n}{k} + \log |\Sigma|) )$-bit encoding of all the alignments with Hamming distance at most $k$ of a length-$n$ pattern within a text of length $O(n)$. This secondary result provides an optimal solution to a natural communication complexity problem which may be of independent interest.