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32
Compressed representations of sequences and fulltext indexes
 ACM Transactions on Algorithms
, 2007
"... Abstract. Given a sequence S = s1s2... sn of integers smaller than r = O(polylog(n)), we show how S can be represented using nH0(S) + o(n) bits, so that we can know any sq, as well as answer rank and select queries on S, in constant time. H0(S) is the zeroorder empirical entropy of S and nH0(S) pro ..."
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Cited by 110 (62 self)
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Abstract. Given a sequence S = s1s2... sn of integers smaller than r = O(polylog(n)), we show how S can be represented using nH0(S) + o(n) bits, so that we can know any sq, as well as answer rank and select queries on S, in constant time. H0(S) is the zeroorder empirical entropy of S and nH0(S) provides an Information Theoretic lower bound to the bit storage of any sequence S via a fixed encoding of its symbols. This extends previous results on binary sequences, and improves previous results on general sequences where those queries are answered in O(log r) time. For larger r, we can still represent S in nH0(S) + o(n log r) bits and answer queries in O(log r / log log n) time. Another contribution of this paper is to show how to combine our compressed representation of integer sequences with an existing compression boosting technique to design compressed fulltext indexes that scale well with the size of the input alphabet Σ. Namely, we design a variant of the FMindex that indexes a string T [1, n] within nHk(T) + o(n) bits of storage, where Hk(T) is the kth order empirical entropy of T. This space bound holds simultaneously for all k ≤ α log Σ  n, constant 0 < α < 1, and Σ  = O(polylog(n)). This index counts the occurrences of an arbitrary pattern P [1, p] as a substring of T in O(p) time; it locates each pattern occurrence in O(log 1+ε n) time, for any constant 0 < ε < 1; and it reports a text substring of length ℓ in O(ℓ + log 1+ε n) time.
S.S.: Succinct indexes for strings, binary relations, and multilabeled trees
 In: Proc. SODA
, 2007
"... We define and design succinct indexes for several abstract data types (ADTs). The concept is to design auxiliary data structures that ideally occupy asymptotically less space than the informationtheoretic lower bound on the space required to encode the given data, and support an extended set of ope ..."
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Cited by 42 (11 self)
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We define and design succinct indexes for several abstract data types (ADTs). The concept is to design auxiliary data structures that ideally occupy asymptotically less space than the informationtheoretic lower bound on the space required to encode the given data, and support an extended set of operations using the basic operators defined in the ADT. The main advantage of succinct indexes as opposed to succinct (integrated data/index) encodings is that we make assumptions only on the ADT through which the main data is accessed, rather than the way in which the data is encoded. This allows more freedom in the encoding of the main data. In this paper, we present succinct indexes for various data types, namely strings, binary relations and multilabeled trees. Given the support for the interface of the ADTs of these data types, we can support various useful operations efficiently by constructing succinct indexes for them. When the operators in the ADTs are supported in constant time, our results are comparable to previous results, while allowing more flexibility in the encoding of the given data. Usingourtechniques,wedesignasuccinctencodingthatrepresentsastringoflengthnoveranalphabetof size σ using nHk(S)+lgσ·o(n)+O ( nlgσ lglglgσ) bits to support access/rank/select operations in o((lglgσ)1+ɛ) time, for any fixed constant ɛ> 0. We also design a succinct text index using nH0(S)+O ( nlgσ) bits that lglgσ
A simple optimal representation for balanced parentheses
 In Proc. 15th Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS v. 3109 (2004
, 2004
"... b Institute of Mathematical Sciences, Chennai 600 113, India. We consider succinct, or highly spaceefficient, representations of a (static) string consisting of n pairs of balanced parentheses, that support natural operations such as finding the matching parenthesis for a given parenthesis, or find ..."
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Cited by 41 (3 self)
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b Institute of Mathematical Sciences, Chennai 600 113, India. We consider succinct, or highly spaceefficient, representations of a (static) string consisting of n pairs of balanced parentheses, that support natural operations such as finding the matching parenthesis for a given parenthesis, or finding the pair of parentheses that most tightly enclose a given pair. This problem was considered by Jacobson, [Proc. 30th FOCS, 549–554, 1989] and Munro and Raman, [SIAM J. Comput. 31 (2001), 762–776], who gave O(n)bit and 2n + o(n)bit representations, respectively, that supported the above operations in O(1) time on the RAM model of computation. This data structure is a fundamental tool in succinct representations, and has applications in representing suffix trees, ordinal trees, planar graphs and permutations. We consider the practical performance of parenthesis representations. First, we give a new 2n + o(n)bit representation that supports all the above operations in O(1) time. This representation is conceptually simpler, its space bound has a smaller o(n) term and it also has a simple and uniform o(n) time and space construction algorithm. We implement our data structure and a variant of Jacobson’s, and evaluate their practical performance (speed and memory usage), when used in a succinct representation of trees derived from XML documents. As a baseline, we compare our representations against a widelyused implementation of the standard DOM (Document Object Model) representation of XML documents. Both succinct representations use orders of magnitude less space than DOM and tree traversal operations are usually only slightly slower than in DOM. Key words: Succinct data structures, parentheses representation of trees, compressed dictionaries, XML DOM. Preprint submitted to Theoretical Computer Science 29 November 2006 1
Practical rank/select queries over arbitrary sequences
 In Proc. 15th SPIRE, LNCS 5280
, 2008
"... Abstract. We present a practical study on the compact representation of sequences supporting rank, select, and access queries. While there are several theoretical solutions to the problem, only a few have been tried out, and there is little idea on how the others would perform, especially in the cas ..."
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Cited by 32 (23 self)
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Abstract. We present a practical study on the compact representation of sequences supporting rank, select, and access queries. While there are several theoretical solutions to the problem, only a few have been tried out, and there is little idea on how the others would perform, especially in the case of sequences with very large alphabets. We first present a new practical implementation of the compressed representation for bit sequences proposed by Raman, Raman, and Rao [SODA 2002], that is competitive with the existing ones when the sequences are not too compressible. It also has nice local compression properties, and we show that this makes it an excellent tool for compressed text indexing in combination with the BurrowsWheeler transform. This shows the practicality of a recent theoretical proposal [Mäkinen and Navarro, SPIRE 2007], achieving spaces never seen before. Second, for general sequences, we tune wavelet trees for the case of very large alphabets, by removing their pointer information. We show that this gives an excellent solution for representing a sequence within zeroorder entropy space, in cases where the large alphabet poses a serious challenge to typical encoding methods. We also present the first implementation of Golynski et al.’s representation [SODA 2006], which offers another interesting time/space tradeoff. 1
Statistical encoding of succinct data structures
 In Proc. 17th CPM, LNCS 4009
, 2006
"... Abstract. In recent work, Sadakane and Grossi [SODA 2006] introduced a scheme to represent any (k log σ + log log n)) bits sequence S = s1s2... sn, over an alphabet of size σ, using nHk(S) + O ( n log σ n of space, where Hk(S) is the kth order empirical entropy of S. The representation permits extr ..."
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Cited by 26 (11 self)
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Abstract. In recent work, Sadakane and Grossi [SODA 2006] introduced a scheme to represent any (k log σ + log log n)) bits sequence S = s1s2... sn, over an alphabet of size σ, using nHk(S) + O ( n log σ n of space, where Hk(S) is the kth order empirical entropy of S. The representation permits extracting any substring of size Θ(log σ n) in constant time, and thus it completely replaces S under the RAM model. This is extremely important because it permits converting any succinct data structure requiring o(S) = o(n log σ) bits in addition to S, into another requiring nHk(S) + o(n log σ) (overall) for any k = o(log σ n). They achieve this result by using ZivLempel compression, and conjecture that the result can in particular be useful to implement compressed fulltext indexes. In this paper we extend their result, by obtaining the same space and time complexities using a simpler scheme based on statistical encoding. We show that the scheme supports appending symbols in constant amortized time. In addition, we prove some results on the applicability of the scheme for fulltext selfindexing. 1
Reducing the space requirement of LZindex
 in CPM, 2006
"... Abstract. The LZindex is a compressed fulltext selfindex able to represent a text T1...u, over an alphabet of size σ and with kth order empirical entropy Hk(T), using 4uHk(T)+o(ulog σ) bits for any k = o(log σ u). It can report all the occ occurrences of a pattern P1...m in T in O(m 3 logσ +(m+o ..."
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Cited by 24 (17 self)
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Abstract. The LZindex is a compressed fulltext selfindex able to represent a text T1...u, over an alphabet of size σ and with kth order empirical entropy Hk(T), using 4uHk(T)+o(ulog σ) bits for any k = o(log σ u). It can report all the occ occurrences of a pattern P1...m in T in O(m 3 logσ +(m+occ)log u) worst case time. This is the only existing data structure of size O(uHk(T)) able of spending O(logu) time per occurrence reported. Its main drawback is the factor 4 in its space complexity, which makes it larger than other stateoftheart alternatives. In this paper we present two different approaches to reduce the space requirement of LZindex. In both cases we achieve (2 + ε)uHk(T) + o(ulog σ) bits of space, for any constant ε> 0, and we simultaneously improve the search time to O(m 2 logm+(m+occ)logu). Both indexes support displaying any subtext of length ℓ in optimal O(ℓ/log σ u) time. In addition, we show how the space can be squeezed to (1+ε)uHk(T)+o(ulog σ) to obtain a structure with O(m 2) average search time for m � 2log σ u. 1 Introduction and Previous Work Text searching is a classical problem in Computer Science. Given a sequence of symbols T1...u (the text) over an alphabet Σ of size σ, and given another (short) sequence P1...m (the search pattern) over Σ, the fulltext search problem consists in finding all the occ occurrences of P in T. Applications of fulltext searching include text databases in general, which typically contain natural
Compressed representations of permutations, and applications
 SYMPOSIUM ON THEORETICAL ASPECTS OF COMPUTER SCIENCE
"... We explore various techniques to compress a permutation π over n integers, taking advantage of ordered subsequences in π, while supporting its application π(i) and the application of its inverse π −1 (i) in small time. Our compression schemes yield several interesting byproducts, in many cases mat ..."
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Cited by 19 (11 self)
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We explore various techniques to compress a permutation π over n integers, taking advantage of ordered subsequences in π, while supporting its application π(i) and the application of its inverse π −1 (i) in small time. Our compression schemes yield several interesting byproducts, in many cases matching, improving or extending the best existing results on applications such as the encoding of a permutation in order to support iterated applications π k (i) of it, of integer functions, and of inverted lists and suffix arrays.
A compressed selfindex using a ZivLempel dictionary
 In: SPIRE. Volume 4209 of LNCS. (2006) 163–180
"... Abstract. A compressed fulltext selfindex for a text T, of size u, is a data structure used to search patterns P, of size m, in T that requires reduced space, i.e. that depends on the empirical entropy (Hk, H0) of T, and is, furthermore, able to reproduce any substring of T. In this paper we prese ..."
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Cited by 18 (5 self)
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Abstract. A compressed fulltext selfindex for a text T, of size u, is a data structure used to search patterns P, of size m, in T that requires reduced space, i.e. that depends on the empirical entropy (Hk, H0) of T, and is, furthermore, able to reproduce any substring of T. In this paper we present a new compressed selfindex able to locate the occurrences of P in O((m + occ) log n) time, where occ is the number of occurrences and σ the size of the alphabet of T. The fundamental improvement over previous LZ78 based indexes is the reduction of the search time dependency on m from O(m 2) to O(m). To achieve this result we point out the main obstacle to linear time algorithms based on LZ78 data compression and expose and explore the nature of a recurrent structure in LZindexes, the T78 suffix tree. We show that our method is very competitive in practice by comparing it against the LZIndex, the FMindex and a compressed suffix array. 1
Alphabet Partitioning for Compressed Rank/Select and Applications
"... Abstract. We present a data structure that stores a string s[1..n] over the alphabet [1..σ] in nH0(s) + o(n)(H0(s)+1) bits, where H0(s) is the zeroorder entropy of s. This data structure supports the queries access and rank in time O (lg lg σ), and the select query in constant time. This result imp ..."
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Cited by 18 (13 self)
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Abstract. We present a data structure that stores a string s[1..n] over the alphabet [1..σ] in nH0(s) + o(n)(H0(s)+1) bits, where H0(s) is the zeroorder entropy of s. This data structure supports the queries access and rank in time O (lg lg σ), and the select query in constant time. This result improves on previously known data structures using nH0(s) + o(n lg σ) bits, where on highly compressible instances the redundancy o(n lg σ) cease to be negligible compared to the nH0(s) bits that encode the data. The technique is based on combining previous results through an ingenious partitioning of the alphabet, and practical enough to be implementable. It applies not only to strings, but also to several other compact data structures. For example, we achieve (i) faster search times and lower redundancy for the smallest existing fulltext selfindex; (ii) compressed permutations π with times for π() and π −1 () improved to loglogarithmic; and (iii) the first compressed representation of dynamic collections of disjoint sets. 1
Succinct Representation of Sequences
, 2004
"... Abstract. Given a sequence S = s1s2... sn such that 1 ≤ sq ≤ r for all q, where r = O(polylog(n)), we show how S can be represented using nH0(S)+o(n) bits (where H0(S) is the zeroorder entropy of S), so that we can know any sq, as well as answer rank and select queries on S, in constant time. This ..."
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Cited by 12 (5 self)
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Abstract. Given a sequence S = s1s2... sn such that 1 ≤ sq ≤ r for all q, where r = O(polylog(n)), we show how S can be represented using nH0(S)+o(n) bits (where H0(S) is the zeroorder entropy of S), so that we can know any sq, as well as answer rank and select queries on S, in constant time. This extends previous results on binary sequences, and improves previous results on general sequences where those queries are answered in O(log r) time. Furthermore, we show how our technique can be applied to improve a succinct fulltext index. 1