Results 1  10
of
33
Fullyfunctional succinct trees
 In Proc. 21st SODA
, 2010
"... We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any nnode static tree can be represented in 2n + o(n) bits and a large number of operations on the tree can be supported in constant time under the wordRAM model. However existing data s ..."
Abstract

Cited by 64 (22 self)
 Add to MetaCart
(Show Context)
We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any nnode static tree can be represented in 2n + o(n) bits and a large number of operations on the tree can be supported in constant time under the wordRAM model. However existing data structures are not satisfactory in both theory and practice because (1) the lowerorder term is Ω(nlog log n / log n), which cannot be neglected in practice, (2) the hidden constant is also large, (3) the data structures are complicated and difficult to implement, and (4) the techniques do not extend to dynamic trees supporting insertions and deletions of nodes. We propose a simple and flexible data structure, called the range minmax tree, that reduces the large number of relevant tree operations considered in the literature to a few primitives, which are carried out in constant time on sufficiently small trees. The result is then extended to trees of arbitrary size, achieving 2n + O(n/polylog(n)) bits of space. The redundancy is significantly lower than in any previous proposal, and the data structure is easily implemented. Furthermore, using the same framework, we derive the first fullyfunctional dynamic succinct trees. 1
Space Efficient Hash Tables With Worst Case Constant Access Time
 In STACS
, 2003
"... We generalize Cuckoo Hashing [23] to dary Cuckoo Hashing and show how this yields a simple hash table data structure that stores n elements in (1 + ffl) n memory cells, for any constant ffl ? 0. Assuming uniform hashing, accessing or deleting table entries takes at most d = O(ln ffl ) probes ..."
Abstract

Cited by 60 (4 self)
 Add to MetaCart
(Show Context)
We generalize Cuckoo Hashing [23] to dary Cuckoo Hashing and show how this yields a simple hash table data structure that stores n elements in (1 + ffl) n memory cells, for any constant ffl ? 0. Assuming uniform hashing, accessing or deleting table entries takes at most d = O(ln ffl ) probes and the expected amortized insertion time is constant. This is the first dictionary that has worst case constant access time and expected constant update time, works with (1 + ffl) n space, and supports satellite information. Experiments indicate that d = 4 choices suffice for ffl 0:03. We also describe variants of the data structure that allow the use of hash functions that can be evaluted in constant time.
Fullycompressed suffix trees
 IN: PACS 2000. LNCS
, 2000
"... Suffix trees are by far the most important data structure in stringology, with myriads of applications in fields like bioinformatics and information retrieval. Classical representations of suffix trees require O(n log n) bits of space, for a string of size n. This is considerably more than the nlog ..."
Abstract

Cited by 31 (20 self)
 Add to MetaCart
Suffix trees are by far the most important data structure in stringology, with myriads of applications in fields like bioinformatics and information retrieval. Classical representations of suffix trees require O(n log n) bits of space, for a string of size n. This is considerably more than the nlog 2 σ bits needed for the string itself, where σ is the alphabet size. The size of suffix trees has been a barrier to their wider adoption in practice. Recent compressed suffix tree representations require just the space of the compressed string plus Θ(n) extra bits. This is already spectacular, but still unsatisfactory when σ is small as in DNA sequences. In this paper we introduce the first compressed suffix tree representation that breaks this linearspace barrier. Our representation requires sublinear extra space and supports a large set of navigational operations in logarithmic time. An essential ingredient of our representation is the lowest common ancestor (LCA) query. We reveal important connections between LCA queries and suffix tree navigation.
Fullyfunctional static and dynamic succinct trees
, 2010
"... We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any nnode static tree can be represented in 2n + o(n) bits and various operations on the tree can be supported in constant time under the wordRAM model. However the data structures are c ..."
Abstract

Cited by 28 (15 self)
 Add to MetaCart
(Show Context)
We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any nnode static tree can be represented in 2n + o(n) bits and various operations on the tree can be supported in constant time under the wordRAM model. However the data structures are complicated and difficult to dynamize. We propose a simple and flexible data structure, called the range minmax tree, that reduces the large number of relevant tree operations considered in the literature, to a few primitives that are carried out in constant time on sufficiently small trees. The result is extended to trees of arbitrary size, achieving 2n + O(n/polylog(n)) bits of space. The redundancy is significantly lower than any previous proposal. For the dynamic case, where insertion/deletion of nodes is allowed, the existing data structures support very limited operations. Our data structure builds on the range minmax tree to achieve 2n + O(n / log n) bits of space and O(log n) time for all the operations. We also propose an improved data structure using 2n+O(n loglog n / logn) bits and improving the time to O(log n / loglog n) for most operations.
Improved dynamic rankselect entropybound structures
 in Proc. of the Latin American Theoretical Informatics (LATIN
"... Abstract. Operations rank and select over a sequence of symbols have many applications to the design of succinct and compressed data structures to manage text collections, structured text, binary relations, trees, graphs, and so on. We are interested in the case where the collections can be updated ..."
Abstract

Cited by 18 (4 self)
 Add to MetaCart
(Show Context)
Abstract. Operations rank and select over a sequence of symbols have many applications to the design of succinct and compressed data structures to manage text collections, structured text, binary relations, trees, graphs, and so on. We are interested in the case where the collections can be updated via insertions and deletions of symbols. Two current solutions stand out as the best in the tradeoff of space versus time (considering all the operations). One by Mäkinen and Navarro achieves compressed space (i.e., nH0 + o(n log σ) bits) and O(log nlog σ) worstcase time for all the operations, where n is the sequence length, σ is the alphabet size, and H0 is the zeroorder entropy of the sequence. The other log σ log log n solution, by Lee and Park, achieves O(log n(1 +)) amortized time and uncompressed space, i.e. nlog σ +O(n)+o(nlog σ) bits. In this paper we show that the best of both worlds can be achieved. We log σ combine the solutions to obtain nH0+o(nlog σ) bits of space and O(log n(1+)) worstcase time log log n for all the operations. Apart from the best current solution, we obtain some byproducts that might be
Rank/Select on Dynamic Compressed Sequences and Applications
, 2008
"... Operations rank and select over a sequence of symbols have many applications to the design of succinct and compressed data structures managing text collections, structured text, binary relations, trees, graphs, and so on. We are interested in the case where the collections can be updated via inserti ..."
Abstract

Cited by 17 (5 self)
 Add to MetaCart
(Show Context)
Operations rank and select over a sequence of symbols have many applications to the design of succinct and compressed data structures managing text collections, structured text, binary relations, trees, graphs, and so on. We are interested in the case where the collections can be updated via insertions and deletions of symbols. Two current solutions stand out as the best in the tradeoff of space versus time (when considering all the operations). One solution, by Mäkinen and Navarro, achieves compressed space (i.e., nH0 +o(n log σ) bits) and O(log n log σ) worstcase time for all the operations, where n is the sequence length, σ is the alphabet size, and H0 is the zeroorder entropy of the sequence. The other solution, by Lee and log σ Park, achieves O(log n(1 + log log n)) amortized time and uncompressed space, i.e. n log2 σ +O(n)+o(n log σ) bits. In this paper we show that the best of both worlds can be achieved. We combine the solutions to obtain nH0 + o(n log σ) bits of space log σ log log n and O(log n(1 +)) worstcase time for all the operations. Apart from the best current solution to the problem, we obtain several byproducts of independent interest applicable to partial sums, text indexes, suffix arrays, the BurrowsWheeler transform, and others.
Optimal Dynamic Sequence Representations
"... We describe a data structure that supports access, rank and select queries, as well as symbol insertions and deletions, on a string S[1, n] over alphabet [1..σ] in time O(lg n / lg lg n), which is optimal. The time is worstcase for the queries and amortized for the updates. This complexity is bette ..."
Abstract

Cited by 15 (6 self)
 Add to MetaCart
(Show Context)
We describe a data structure that supports access, rank and select queries, as well as symbol insertions and deletions, on a string S[1, n] over alphabet [1..σ] in time O(lg n / lg lg n), which is optimal. The time is worstcase for the queries and amortized for the updates. This complexity is better than the best previous ones by a Θ(1 + lg σ / lg lg n) factor. Our structure uses nH0(S) + O(n + σ(lg σ + lg 1+ε n)) bits, where H0(S) is the zeroorder entropy of S and 0 < ε < 1 is any constant. This space redundancy over nH0(S) is also better, almost always, than that of the best previous dynamic structures, o(n lg σ)+O(σ(lg σ+lg n)). We can also handle general alphabets in optimal time, which has been an open problem in dynamic sequence representations.
Spaces, trees and colors: The algorithmic landscape of document retrieval on sequences
 CoRR
"... Document retrieval is one of the best established information retrieval activities since the sixties, pervading all search engines. Its aim is to obtain, from a collection of text documents, those most relevant to a pattern query. Current technology is mostly oriented to “natural language” text coll ..."
Abstract

Cited by 14 (9 self)
 Add to MetaCart
Document retrieval is one of the best established information retrieval activities since the sixties, pervading all search engines. Its aim is to obtain, from a collection of text documents, those most relevant to a pattern query. Current technology is mostly oriented to “natural language” text collections, where inverted indexes are the preferred solution. As successful as this paradigm has been, it fails to properly handle various East Asian languages and other scenarios where the “natural language ” assumptions do not hold. In this survey we cover the recent research in extending the document retrieval techniques to a broader class of sequence collections, which has applications in bioinformatics, data and Web mining, chemoinformatics, software engineering, multimedia information retrieval, and many other fields. We focus on the algorithmic aspects of the techniques, uncovering a rich world of relations between document retrieval challenges and fundamental problems on trees, strings, range queries, discrete geometry, and other areas.
Invertible Bloom Lookup Tables
 In Proceedings of the 49th Allerton Conference
, 2011
"... We present a version of the Bloom filter data structure that supports not only the insertion, deletion, and lookup of keyvalue pairs, but also allows a complete listing of the pairs it contains with high probability, as long the number of keyvalue pairs is below a designed threshold. Our structure ..."
Abstract

Cited by 14 (6 self)
 Add to MetaCart
(Show Context)
We present a version of the Bloom filter data structure that supports not only the insertion, deletion, and lookup of keyvalue pairs, but also allows a complete listing of the pairs it contains with high probability, as long the number of keyvalue pairs is below a designed threshold. Our structure allows the number of keyvalue pairs to greatly exceed this threshold during normal operation. Exceeding the threshold simply temporarily prevents content listing and reduces the probability of a successful lookup. If entries are later deleted to return the structure below the threshold, everything again functions appropriately. We also show that simple variations of our structure are robust to certain standard errors, such as the deletion of a key without a corresponding insertion or the insertion of two distinct values for a key. The properties of our structure make it suitable for several applications, including database and networking applications that we highlight. 1
Backyard Cuckoo Hashing: Constant WorstCase Operations with a Succinct Representation
, 2010
"... The performance of a dynamic dictionary is measured mainly by its update time, lookup time, and space consumption. In terms of update time and lookup time there are known constructions that guarantee constanttime operations in the worst case with high probability, and in terms of space consumption ..."
Abstract

Cited by 13 (5 self)
 Add to MetaCart
The performance of a dynamic dictionary is measured mainly by its update time, lookup time, and space consumption. In terms of update time and lookup time there are known constructions that guarantee constanttime operations in the worst case with high probability, and in terms of space consumption there are known constructions that use essentially optimal space. In this paper we settle two fundamental open problems: • We construct the first dynamic dictionary that enjoys the best of both worlds: we present a twolevel variant of cuckoo hashing that stores n elements using (1+ϵ)n memory words, and guarantees constanttime operations in the worst case with high probability. Specifically, for any ϵ = Ω((log log n / log n) 1/2) and for any sequence of polynomially many operations, with high probability over the randomness of the initialization phase, all operations are performed in constant time which is independent of ϵ. The construction is based on augmenting cuckoo hashing with a “backyard ” that handles a large fraction of the elements, together with a deamortized perfect hashing scheme for eliminating the dependency on ϵ.