The k-mismatch problem revisited

We revisit the complexity of one of the most basic problems in pattern matching. In the k-mismatch problem we must compute the Hamming distance between a pattern of length m and every m-length substring of a text of length n, as long as that Hamming distance is at most k. Where the Hamming distance is greater than k at some alignment of the pattern and text, we simply output "No". We study this problem in both the standard offline setting and also as a streaming problem. In the streaming k-mismatch problem the text arrives one symbol at a time and we must give an output before processing any future symbols. Our main results are as follows: 1) Our first result is a deterministic $O(n k^2\log{k} / m+n \text{polylog} m)$ time offline algorithm for k-mismatch on a text of length n. This is a factor of k improvement over the fastest previous result of this form from SODA 2000 by Amihood Amir et al. 2) We then give a randomised and online algorithm which runs in the same time complexity but requires only $O(k^2\text{polylog} {m})$ space in total. 3) Next we give a randomised $(1+\epsilon)$-approximation algorithm for the streaming k-mismatch problem which uses $O(k^2\text{polylog} m / \epsilon^2)$ space and runs in $O(\text{polylog} m / \epsilon^2)$ worst-case time per arriving symbol. 4) Finally we combine our new results to derive a randomised $O(k^2\text{polylog} {m})$ space algorithm for the streaming k-mismatch problem which runs in $O(\sqrt{k}\log{k} + \text{polylog} {m})$ worst-case time per arriving symbol. This improves the best previous space complexity for streaming k-mismatch from FOCS 2009 by Benny Porat and Ely Porat by a factor of k. We also improve the time complexity of this previous result by an even greater factor to match the fastest known offline algorithm (up to logarithmic factors)

Parameterized Streaming Algorithms for Min-Ones d-SAT

In this work, we initiate the study of the Min-Ones d-SAT problem in the parameterized streaming model. An instance of the problem consists of a d-CNF formula F and an integer k, and the objective is to determine if F has a satisfying assignment which sets at most k variables to 1. In the parameterized streaming model, input is provided as a stream, just as in the usual streaming model. A key difference is that the bound on the read-write memory available to the algorithm is O(f(k) log n) (f: N -> N, a computable function) as opposed to the O(log n) bound of the usual streaming model. The other important difference is that the number of passes the algorithm makes over its input must be a (preferably small) function of k. We design a (k + 1)-pass parameterized streaming algorithm that solves Min-Ones d-SAT (d >= 2) using space O((kd^(ck) + k^d)log n) (c > 0, a constant) and a (d + 1)^k-pass algorithm that uses space O(k log n). We also design a streaming kernelization for Min-Ones 2-SAT that makes (k + 2) passes and uses space O(k^6 log n) to produce a kernel with O(k^6) clauses. To complement these positive results, we show that any k-pass algorithm for or Min-Ones d-SAT (d >= 2) requires space Omega(max{n^(1/k) / 2^k, log(n / k)}) on instances (F, k). This is achieved via a reduction from the streaming problem POT Pointer Chasing (Guha and McGregor [ICALP 2008]), which might be of independent interest. Given this, our (k + 1)-pass parameterized streaming algorithm is the best possible, inasmuch as the number of passes is concerned. In contrast to the results of Fafianie and Kratsch [MFCS 2014] and Chitnis et al. [SODA 2015], who independently showed that there are 1-pass parameterized streaming algorithms for Vertex Cover (a restriction of Min-Ones 2-SAT), we show using lower bounds from Communication Complexity that for any d >= 1, a 1-pass streaming algorithm for Min-Ones d-SAT requires space Omega(n). This excludes the possibility of a 1-pass parameterized streaming algorithm for the problem. Additionally, we show that any p-pass algorithm for the problem requires space Omega(n/p)

Streaming Algorithms for Submodular Function Maximization

We consider the problem of maximizing a nonnegative submodular set function $f:2^{\mathcal{N}} \rightarrow \mathbb{R}^+$ subject to a $p$-matchoid constraint in the single-pass streaming setting. Previous work in this context has considered streaming algorithms for modular functions and monotone submodular functions. The main result is for submodular functions that are {\em non-monotone}. We describe deterministic and randomized algorithms that obtain a $\Omega(\frac{1}{p})$-approximation using $O(k \log k)$-space, where $k$ is an upper bound on the cardinality of the desired set. The model assumes value oracle access to $f$ and membership oracles for the matroids defining the $p$-matchoid constraint.Comment: 29 pages, 7 figures, extended abstract to appear in ICALP 201