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

Recognizing Partial Cubes in Quadratic Time

We show how to test whether a graph with n vertices and m edges is a partial cube, and if so how to find a distance-preserving embedding of the graph into a hypercube, in the near-optimal time bound O(n^2), improving previous O(nm)-time solutions.Comment: 25 pages, five figures. This version significantly expands previous versions, including a new report on an implementation of the algorithm and experiments with i

New Algorithms for Position Heaps

We present several results about position heaps, a relatively new alternative to suffix trees and suffix arrays. First, we show that, if we limit the maximum length of patterns to be sought, then we can also limit the height of the heap and reduce the worst-case cost of insertions and deletions. Second, we show how to build a position heap in linear time independent of the size of the alphabet. Third, we show how to augment a position heap such that it supports access to the corresponding suffix array, and vice versa. Fourth, we introduce a variant of a position heap that can be simulated efficiently by a compressed suffix array with a linear number of extra bits

Online Sorting via Searching and Selection

In this paper, we present a framework based on a simple data structure and parameterized algorithms for the problems of finding items in an unsorted list of linearly ordered items based on their rank (selection) or value (search). As a side-effect of answering these online selection and search queries, we progressively sort the list. Our algorithms are based on Hoare's Quickselect, and are parameterized based on the pivot selection method. For example, if we choose the pivot as the last item in a subinterval, our framework yields algorithms that will answer q<=n unique selection and/or search queries in a total of O(n log q) average time. After q=\Omega(n) queries the list is sorted. Each repeated selection query takes constant time, and each repeated search query takes O(log n) time. The two query types can be interleaved freely. By plugging different pivot selection methods into our framework, these results can, for example, become randomized expected time or deterministic worst-case time. Our methods are easy to implement, and we show they perform well in practice

Towards Verifying Nonlinear Integer Arithmetic

We eliminate a key roadblock to efficient verification of nonlinear integer arithmetic using CDCL SAT solvers, by showing how to construct short resolution proofs for many properties of the most widely used multiplier circuits. Such short proofs were conjectured not to exist. More precisely, we give n^{O(1)} size regular resolution proofs for arbitrary degree 2 identities on array, diagonal, and Booth multipliers and quasipolynomial- n^{O(\log n)} size proofs for these identities on Wallace tree multipliers.Comment: Expanded and simplified with improved result

Document Retrieval on Repetitive Collections

Document retrieval aims at finding the most important documents where a pattern appears in a collection of strings. Traditional pattern-matching techniques yield brute-force document retrieval solutions, which has motivated the research on tailored indexes that offer near-optimal performance. However, an experimental study establishing which alternatives are actually better than brute force, and which perform best depending on the collection characteristics, has not been carried out. In this paper we address this shortcoming by exploring the relationship between the nature of the underlying collection and the performance of current methods. Via extensive experiments we show that established solutions are often beaten in practice by brute-force alternatives. We also design new methods that offer superior time/space trade-offs, particularly on repetitive collections.Comment: Accepted to ESA 2014. Implementation and experiments at http://www.cs.helsinki.fi/group/suds/rlcsa