We revisit the complexity of online computation in the cell probe model. We consider a class of problems where we are first given a fixed pattern F of n symbols and then one symbol arrives at a time in a stream. After each symbol has arrived we must output some function of F and the n-length suffix of the arriving stream. Cell probe bounds of Omega(delta lg n/w) have previously been shown for both convolution and Hamming distance in this setting, where delta is the size of a symbol in bits and w in Omega(lg n) is the cell size in bits. However, when delta is a constant, as it is in many natural situations, the existing approaches no longer give us non-trivial bounds. We introduce a lop-sided information transfer proof technique which enables us to prove meaningful lower bounds even for constant size input alphabets. Our new framework is capable of proving amortised cell probe lower bounds of Omega(lg^2 n/(w lg lg n)) time per arriving bit. We demonstrate this technique by showing a new lower bound for a problem known as pattern matching with address errors or the L_2-rearrangement distance problem. This gives the first non-trivial cell probe lower bound for any online problem on bit streams that still holds when the cell size is large.

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: Our first result is a deterministic O(nk2 log k/m + n 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 [9, 10]. We then give a randomised and online algorithm which runs in the same time complexity but requires only O(k2 polylog m) space in total. Next we give a randomised (1 + ∊)-approximation algorithm for the streaming k-mismatch problem which uses O(k2 polylog m/∊2) space and runs in O(polylog m/∊2) worst-case time per arriving symbol. Finally we combine our new results to derive a randomised O(k2 polylog m) space algorithm for the streaming k-mismatch problem which runs in worst-case time per arriving symbol. This improves the best previous space complexity for streaming k-mismatch from FOCS 2009 [26] 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).

Defining and computing distances between tree structures is a classical area of study in theoretical computer science, with practical applications in the areas of computational biology, information retrieval, text analysis, and many others. In this paper, we focus on rooted, unordered, uniquely-labelled trees such as taxonomies and other hierarchies. For trees as these, we introduce the intuitive concept of a ‘local move’ operation as an atomic edit of a tree. We then introduce SuMoTED, a new edit distance measure between such trees, defined as the minimal number of local moves required to convert one tree into another. We show how SuMoTED can be computed using a scalable algorithm with quadratic time complexity. Finally, we demonstrate its use on a collection of music genre taxonomies.

In this work, we present efficient algorithms for constructing sparse suffix trees, sparse suffix arrays, and sparse position heaps for b arbitrary positions of a text T of length n while using only O ( b ) words of space during the construction. Attempts at breaking the naïve bound of Ω( nb ) time for constructing sparse suffix trees in O ( b ) space can be traced back to the origins of string indexing in 1968. First results were not obtained until 1996, but only for the case in which the b suffixes were evenly spaced in T . In this article, there is no constraint on the locations of the suffixes. Our main contribution is to show that the sparse suffix tree (and array) can be constructed in O ( n log 2 b ) time. To achieve this, we develop a technique that allows one to efficiently answer b longest common prefix queries on suffixes of T , using only O ( b ) space. We expect that this technique will prove useful in many other applications in which space usage is a concern. Our first solution is Monte Carlo, and outputs the correct tree with high probability. We then give a Las Vegas algorithm, which also uses O ( b ) space and runs in the same time bounds with high probability when b = O (√ n). Additional trade-offs between space usage and construction time for the Monte Carlo algorithm are given. Finally, we show that, at the expense of slower pattern queries, it is possible to construct sparse position heaps in O ( n + b log b ) time and O ( b ) space.

We give cell-probe bounds for the computation of edit distance, Hamming distance, convolution and longest common subsequence in a stream. In this model, a fixed string of n symbols is given and one δ-bit symbol arrives at a time in a stream. After each symbol arrives, the distance between the fixed string and a suffix of most recent symbols of the stream is reported. The cell-probe model is perhaps the strongest model of computation for showing data structure lower bounds, subsuming in particular the popular word-RAM model.

We show tight bounds for online Hamming distance computation in the cell-probe model with word size w. The task is to output the Hamming distance between a fixed string of length n and the last n symbols of a stream. We give a lower bound of time on average per output, where δ is the number of bits needed to represent an input symbol. We argue that this bound is tight within the model. The lower bound holds under randomisation and amortisation.

We study the problem of parameterized matching in a stream where we want to output matches between a pattern of length m and the last m symbols of the stream before the next symbol arrives. Parameterized matching is a natural generalisation of exact matching where an arbitrary one-to-one relabelling of pattern symbols is allowed. We show how this problem can be solved in constant time per arriving stream symbol and sublinear, near optimal space with high probability. Our results are surprising and important: it has been shown that almost no streaming pattern matching problems can be solved (not even randomised) in less than Theta(m) space, with exact matching as the only known problem to have a sublinear, near optimal space solution. Here we demonstrate that a similar sublinear, near optimal space solution is achievable for an even more challenging problem.

We consider a class of pattern matching problems where a normalizing polynomial transformation can be applied at every alignment of the pattern and text. Normalized pattern matching plays a key role in fields as diverse as image processing and musical information processing, where application specific transformations are often applied to the input. By considering a wide range of such transformations, we provide fast algorithms and the first lower bounds for both new and old problems. Given a pattern of length $m$ and a longer text of length $n$, where both are assumed to contain integer values only, we first show $O(n\log m)$ time algorithms for pattern matching under linear transformations even when wildcard symbols can occur in the input. We then show how to extend the technique to polynomial transformations of arbitrary degree. Next we consider the problem of finding the minimum Hamming distance under polynomial transformation. We show that, for any $\varepsilon>0$, there cannot exist an $O(nm^{1-\varepsilon})$ time algorithm for additive and linear transformations conditional on the hardness of the classic 3Sum problem. Finally, we consider a version of the Hamming distance problem under additive transformations with a bound $k$ on the maximum distance that needs to be reported. We give a deterministic $O(nk\log k)$ time solution, which we then improve by careful use of randomization to $O(n\sqrt{k\log k}\log n)$ time for sufficiently small $k$. Our randomized solution outputs the correct answer at every position with high probability.