Parallel Wavelet Tree Construction

We present parallel algorithms for wavelet tree construction with polylogarithmic depth, improving upon the linear depth of the recent parallel algorithms by Fuentes-Sepulveda et al. We experimentally show on a 40-core machine with two-way hyper-threading that we outperform the existing parallel algorithms by 1.3--5.6x and achieve up to 27x speedup over the sequential algorithm on a variety of real-world and artificial inputs. Our algorithms show good scalability with increasing thread count, input size and alphabet size. We also discuss extensions to variants of the standard wavelet tree.Comment: This is a longer version of the paper that appears in the Proceedings of the IEEE Data Compression Conference, 201

Detecting Activations over Graphs using Spanning Tree Wavelet Bases

We consider the detection of activations over graphs under Gaussian noise, where signals are piece-wise constant over the graph. Despite the wide applicability of such a detection algorithm, there has been little success in the development of computationally feasible methods with proveable theoretical guarantees for general graph topologies. We cast this as a hypothesis testing problem, and first provide a universal necessary condition for asymptotic distinguishability of the null and alternative hypotheses. We then introduce the spanning tree wavelet basis over graphs, a localized basis that reflects the topology of the graph, and prove that for any spanning tree, this approach can distinguish null from alternative in a low signal-to-noise regime. Lastly, we improve on this result and show that using the uniform spanning tree in the basis construction yields a randomized test with stronger theoretical guarantees that in many cases matches our necessary conditions. Specifically, we obtain near-optimal performance in edge transitive graphs, $k$-nearest neighbor graphs, and $\epsilon$-graphs

Wavelet Trees Meet Suffix Trees

We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings. Given a string of length n over an alphabet of size $\sigma\leq n$, our method builds the wavelet tree in $O(n \log \sigma/ \sqrt{\log{n}})$ time, improving upon the state-of-the-art algorithm by a factor of $\sqrt{\log n}$. As a consequence, given an array of n integers we can construct in $O(n \sqrt{\log n})$ time a data structure consisting of $O(n)$ machine words and capable of answering rank/select queries for the subranges of the array in $O(\log n / \log \log n)$ time. This is a $\log \log n$-factor improvement in query time compared to Chan and P\u{a}tra\c{s}cu and a $\sqrt{\log n}$-factor improvement in construction time compared to Brodal et al. Next, we switch to stringological context and propose a novel notion of wavelet suffix trees. For a string w of length n, this data structure occupies $O(n)$ words, takes $O(n \sqrt{\log n})$ time to construct, and simultaneously captures the combinatorial structure of substrings of w while enabling efficient top-down traversal and binary search. In particular, with a wavelet suffix tree we are able to answer in $O(\log |x|)$ time the following two natural analogues of rank/select queries for suffixes of substrings: for substrings x and y of w count the number of suffixes of x that are lexicographically smaller than y, and for a substring x of w and an integer k, find the k-th lexicographically smallest suffix of x. We further show that wavelet suffix trees allow to compute a run-length-encoded Burrows-Wheeler transform of a substring x of w in $O(s \log |x|)$ time, where s denotes the length of the resulting run-length encoding. This answers a question by Cormode and Muthukrishnan, who considered an analogous problem for Lempel-Ziv compression.Comment: 33 pages, 5 figures; preliminary version published at SODA 201

Parallel Construction of Wavelet Trees on Multicore Architectures

The wavelet tree has become a very useful data structure to efficiently represent and query large volumes of data in many different domains, from bioinformatics to geographic information systems. One problem with wavelet trees is their construction time. In this paper, we introduce two algorithms that reduce the time complexity of a wavelet tree's construction by taking advantage of nowadays ubiquitous multicore machines. Our first algorithm constructs all the levels of the wavelet in parallel in $O(n)$ time and $O(n\lg\sigma + \sigma\lg n)$ bits of working space, where $n$ is the size of the input sequence and $\sigma$ is the size of the alphabet. Our second algorithm constructs the wavelet tree in a domain-decomposition fashion, using our first algorithm in each segment, reaching $O(\lg n)$ time and $O(n\lg\sigma + p\sigma\lg n/\lg\sigma)$ bits of extra space, where $p$ is the number of available cores. Both algorithms are practical and report good speedup for large real datasets.Comment: This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094

The Wavelet Trie: Maintaining an Indexed Sequence of Strings in Compressed Space

An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of column-oriented databases, log processing, and other storage and query tasks. In these applications each string can appear several times and the order of the strings in the sequence is relevant. The prefix structure of the strings is relevant as well: common prefixes are sought in strings to extract interesting features from the sequence. Moreover, space-efficiency is highly desirable as it translates directly into higher performance, since more data can fit in fast memory. We introduce and study the problem of compressed indexed sequence of strings, representing indexed sequences of strings in nearly-optimal compressed space, both in the static and dynamic settings, while preserving provably good performance for the supported operations. We present a new data structure for this problem, the Wavelet Trie, which combines the classical Patricia Trie with the Wavelet Tree, a succinct data structure for storing a compressed sequence. The resulting Wavelet Trie smoothly adapts to a sequence of strings that changes over time. It improves on the state-of-the-art compressed data structures by supporting a dynamic alphabet (i.e. the set of distinct strings) and prefix queries, both crucial requirements in the aforementioned applications, and on traditional indexes by reducing space occupancy to close to the entropy of the sequence

Simulation of Gegenbauer Processes using Wavelet Packets

In this paper, we study the synthesis of Gegenbauer processes using the wavelet packets transform. In order to simulate a 1-factor Gegenbauer process, we introduce an original algorithm, inspired by the one proposed by Coifman and Wickerhauser [1], to adaptively search for the best-ortho-basis in the wavelet packet library where the covariance matrix of the transformed process is nearly diagonal. Our method clearly outperforms the one recently proposed by [2], is very fast, does not depend on the wavelet choice, and is not very sensitive to the length of the time series. From these first results we propose an algorithm to build bases to simulate k-factor Gegenbauer processes. Given its practical simplicity, we feel the general practitioner will be attracted to our simulator. Finally we evaluate the approximation due to the fact that we consider the wavelet packet coefficients as uncorrelated. An empirical study is carried out which supports our results

Tensor network and (pp-adic) AdS/CFT

We use the tensor network living on the Bruhat-Tits tree to give a concrete realization of the recently proposed $p$-adic AdS/CFT correspondence (a holographic duality based on the $p$-adic number field $\mathbb{Q}_p$). Instead of assuming the $p$-adic AdS/CFT correspondence, we show how important features of AdS/CFT such as the bulk operator reconstruction and the holographic computation of boundary correlators are automatically implemented in this tensor network.Comment: 59 pages, 18 figures; v3: improved presentation, added figures and reference