Simple and Efficient Fully-Functional Succinct Trees

The fully-functional succinct tree representation of Navarro and Sadakane (ACM Transactions on Algorithms, 2014) supports a large number of operations in constant time using $2n+o(n)$ bits. However, the full idea is hard to implement. Only a simplified version with $O(\log n)$ operation time has been implemented and shown to be practical and competitive. We describe a new variant of the original idea that is much simpler to implement and has worst-case time $O(\log\log n)$ for the operations. An implementation based on this version is experimentally shown to be superior to existing implementations

Combined Data Structure for Previous- and Next-Smaller-Values

Let $A$ be a static array storing $n$ elements from a totally ordered set. We present a data structure of optimal size at most $n\log_2(3+2\sqrt{2})+o(n)$ bits that allows us to answer the following queries on $A$ in constant time, without accessing $A$: (1) previous smaller value queries, where given an index $i$, we wish to find the first index to the left of $i$ where $A$ is strictly smaller than at $i$, and (2) next smaller value queries, which search to the right of $i$. As an additional bonus, our data structure also allows to answer a third kind of query: given indices $i<j$, find the position of the minimum in $A[i..j]$. Our data structure has direct consequences for the space-efficient storage of suffix trees.Comment: to appear in Theoretical Computer Scienc

Online Self-Indexed Grammar Compression

Although several grammar-based self-indexes have been proposed thus far, their applicability is limited to offline settings where whole input texts are prepared, thus requiring to rebuild index structures for given additional inputs, which is often the case in the big data era. In this paper, we present the first online self-indexed grammar compression named OESP-index that can gradually build the index structure by reading input characters one-by-one. Such a property is another advantage which enables saving a working space for construction, because we do not need to store input texts in memory. We experimentally test OESP-index on the ability to build index structures and search query texts, and we show OESP-index's efficiency, especially space-efficiency for building index structures.Comment: To appear in the Proceedings of the 22nd edition of the International Symposium on String Processing and Information Retrieval (SPIRE2015

LRM-Trees: Compressed Indices, Adaptive Sorting, and Compressed Permutations

LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to index integer arrays in order to support range minimum queries on them. We describe how they yield many other convenient results in a variety of areas, from data structures to algorithms: some compressed succinct indices for range minimum queries; a new adaptive sorting algorithm; and a compressed succinct data structure for permutations supporting direct and indirect application in time all the shortest as the permutation is compressible.Comment: 13 pages, 1 figur

Online Pattern Matching for String Edit Distance with Moves

Edit distance with moves (EDM) is a string-to-string distance measure that includes substring moves in addition to ordinal editing operations to turn one string to the other. Although optimizing EDM is intractable, it has many applications especially in error detections. Edit sensitive parsing (ESP) is an efficient parsing algorithm that guarantees an upper bound of parsing discrepancies between different appearances of the same substrings in a string. ESP can be used for computing an approximate EDM as the L1 distance between characteristic vectors built by node labels in parsing trees. However, ESP is not applicable to a streaming text data where a whole text is unknown in advance. We present an online ESP (OESP) that enables an online pattern matching for EDM. OESP builds a parse tree for a streaming text and computes the L1 distance between characteristic vectors in an online manner. For the space-efficient computation of EDM, OESP directly encodes the parse tree into a succinct representation by leveraging the idea behind recent results of a dynamic succinct tree. We experimentally test OESP on the ability to compute EDM in an online manner on benchmark datasets, and we show OESP's efficiency.Comment: This paper has been accepted to the 21st edition of the International Symposium on String Processing and Information Retrieval (SPIRE2014