We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let @math be the text length and @math be the alphabet size. We first provide two algorithms that enumerate all LCP values and suffix tree intervals in @math time using just @math bits of working space on top of the input BWT. Using these algorithms as building blocks, for any parameter @math we show how to build the PLCP bitvector and the balanced parentheses representation of the suffix tree topology in @math time using at most @math bits of working space on top of the input BWT and the output. In particular, this implies that we can build a compressed suffix tree from the BWT using just succinct working space (i.e. @math bits) and any time in @math . This improves the previous most space-efficient algorithms, which worked in @math bits and @math time. We also consider the problem of merging BWTs of string collections, and provide a solution running in @math time and using just @math bits of working space. An efficient implementation of our LCP construction and BWT merge algorithms use (in RAM) as few as @math bits on top of a packed representation of the input output and process data as fast as @math megabases per second.
In this paper, we give new space-time trade-offs that allow building the CST's components in smaller working space (and in some cases even faster) with respect to the existing solutions. We start by combining 's algorithm @cite_38 with the suffix-tree enumeration procedure of Belazzougui @cite_21 to obtain an algorithm that enumerates (i) all pairs @math , and (ii) all suffix tree intervals in @math time using just @math bits of working space on top of the input BWT. We use this procedure to obtain algorithms that build (working space is on top of the input BWT and the output):
@cite_38 @cite_21
2042175004 1988110322
The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations and applications of string indexes based on the Burrows-Wheeler transform (BWT) have been developed, all taking an amount of space that is close to the input size in bits. In many large-scale applications, the construction of the index and its usage need to be considered as one unit of computation. Efficient string indexing and analysis in small space lies also at the core of a number of primitives in the data-intensive field of high-throughput DNA sequencing. We report the following advances in string indexing and analysis. We show that the BWT of a string @math can be built in deterministic @math time using just @math bits of space, where @math . Within the same time and space budget, we can build an index based on the BWT that allows one to enumerate all the internal nodes of the suffix tree of @math . Many fundamental string analysis problems can be mapped to such enumeration, and can thus be solved in deterministic @math time and in @math bits of space from the input string. We also show how to build many of the existing indexes based on the BWT, such as the CSA, the compressed suffix tree (CST), and the bidirectional BWT index, in randomized @math time and in @math bits of space. The previously fastest construction algorithms for BWT, CSA and CST, which used @math bits of space, took @math time for the first two structures, and @math time for the third, where @math is any positive constant. Contrary to the state of the art, our bidirectional BWT index supports every operation in constant time per element in its output. Suffix trees and suffix arrays are the most prominent full-text indices, and their construction algorithms are well studied. In the literature, the fastest algorithm runs in @math time, while it requires @math -bit working space, where @math denotes the length of the text. On the other hand, the most space-efficient algorithm requires @math -bit working space while it runs in @math time. It was open whether these indices can be constructed in both @math time and @math -bit working space. This paper breaks the above time-and-space barrier under the unit-cost word RAM. We give an algorithm for constructing the suffix array, which takes @math time and @math -bit working space, for texts with constant-size alphabets. Note that both the time and the space bounds are optimal. For constructing the suffix tree, our algorithm requires @math time and @math -bit working space for any @math . Apart from that, our algorithm can also be adopted to build other existing full-text indices, such as compressed suffix tree, compressed suffix arrays, and FM-index. We also study the general case where the size of the alphabet @math is not constant. Our algorithm can construct a suffix array and a suffix tree using optimal @math -bit working space while running in @math time and @math time, respectively. These are the first algorithms that achieve @math time with optimal working space. Moreover, for the special case where @math , we can speed up our suffix array construction algorithm to the optimal @math . Suffix trees and suffix arrays are the most prominent full-text indices, and their construction algorithms are well studied. It has been open for a long time whether these indices can be constructed in both O(n log n) time and O(n log n)-bit working space, where n denotes the length of the text. In the literature, the fastest algorithm runs in O(n) time, while it requires O(n log n)-bit working space. On the other hand, the most space-efficient algorithm requires O(n)-bit working space while it runs in O(n log n) time. This paper breaks the long-standing time-and-space barrier under the unit-cost word RAM. We give an algorithm for constructing the suffix array which takes O(n) time and O(n)-bit working space, for texts with constant-size alphabets. Note that both the time and the space bounds are optimal. For constructing the suffix tree, our algorithm requires O(n log sup spl epsi n) time and O(n)-bit working space for any 0 < spl epsi < 1. Apart from that, our algorithm can also be adopted to build other existing full-text indices, such as Compressed Suffix Tree, Compressed Suffix Arrays and FM-index. We also study the general case where the size of the alphabet A is not constant. Our algorithm can construct a suffix array and a suffix tree using optimal O(n log |A|)-bit working space while running in O(n log log |A|) time and O(n log sup spl epsi n) time, respectively. These are the first algorithms that achieve 0(n log n) time with optimal working space, under a reasonable assumption that log |A| = o(log n). A new and conceptually simple data structure, called a suffix array, for on-line string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees is that, in practice, they use three to five times less space. From a complexity standpoint, suffix arrays permit on-line string searches of the type, “Is W a substring of A?” to be answered in time @math , where P is the length of W and N is the length of A, which is competitive with (and in some cases slightly better than) suffix trees. The only drawback is that in those instances where the underlying alphabet is finite and small, suffix trees can be constructed in @math time in the worst case, versus @math time for suffix arrays. However, an augmented algorithm is given that, regardless of the alphabet size, constructs suffix arrays in @math expected time, albeit with lesser space efficiency. It is ... Re-Pair is an efficient grammar compressor that operates by recursively replacing high-frequency character pairs with new grammar symbols. The most space-efficient linear-time algorithm computing Re-Pair uses @math words on top of the re-writable text (of length @math and stored in @math words), for any constant @math ; in practice however, this solution uses complex sub-procedures preventing it from being practical. In this paper, we present an implementation of the above-mentioned result making use of more practical solutions; our tool further improves the working space to @math words (text included), for some small constant @math . As a second contribution, we focus on compact representations of the output grammar. The lower bound for storing a grammar with @math rules is @math bits, and the most efficient encoding algorithm in the literature uses at most @math bits and runs in @math time. We describe a linear-time heuristic maximizing the compressibility of the output Re-Pair grammar. On real datasets, our grammar encoding uses---on average---only @math more bits than the information-theoretic minimum. In half of the tested cases, our compressor improves the output size of 7-Zip with maximum compression rate turned on. We show that the compressed suffix array and the compressed suffix tree for a string of length n over an integer alphabet of size σ ≤ n can both be built in O(n) (randomized) time using only O(n log σ) bits of working space. The previously fastest construction algorithms that used O(n log σ) bits of space took times O(n log log σ) and O(n loge n) respectively (where e is any positive constant smaller than 1). Given a set @math of @math strings of total length @math , our task is to report the "most relevant"strings for a given query pattern @math . This involves somewhat more advanced query functionality than the usual pattern matching, as some notion of "most relevant" is involved. In information retrieval literature, this task is best achieved by using inverted indexes. However, inverted indexes work only for some predefined set of patterns. In the pattern matching community, the most popular pattern-matching data structures are suffix trees and suffix arrays. However, a typical suffix tree search involves going through all the occurrences of the pattern over the entire string collection, which might be a lot more than the required relevant documents. The first formal framework to study such kind of retrieval problems was given by [Muthukrishnan, 2002]. He considered two metrics for relevance: frequency and proximity. He took a threshold-based approach on these metrics and gave data structures taking @math words of space. We study this problem in a slightly different framework of reporting the top @math most relevant documents (in sorted order) under similar and more general relevance metrics. Our framework gives linear space data structure with optimal query times for arbitrary score functions. As a corollary, it improves the space utilization for the problems in [Muthukrishnan, 2002] while maintaining optimal query performance. We also develop compressed variants of these data structures for several specific relevance metrics. Suffix tree is one of the most important data structures in string algorithms and biological sequence analysis. Unfortunately, when it comes to implementing those algorithms and applying them to real genomic sequences, often the main memory size becomes the bottleneck. This is easily explained by the fact that while a DNA sequence of length n from alphabet Σ e A,C,G,T can be stored in n log vΣv e 2n bits, its suffix tree occupiesO(n log n) bits. In practice, the size difference easily reaches factor 50. We report on an implementation of the compressed suffix tree very recently proposed by Sadakane (2007). The compressed suffix tree occupies space proportional to the text size, that is, O(n log vΣv) bits, and supports all typical suffix tree operations with at most log n factor slowdown. Our experiments show that, for example, on a 10 MB DNA sequence, the compressed suffix tree takes 10p of the space of the normal suffix tree. At the same time, a representative algorithm is slowed down by factor 30. Our implementation follows the original proposal in spirit, but some internal parts are tailored toward practical implementation. Our construction algorithm has time requirement O(n log n log vΣv) and uses closely the same space as the final structure while constructing it: on the 10MB DNA sequence, the maximum space usage during construction is only 1.5 times the final product size. As by-products, we develop a method to create Succinct Suffix Array directly from Burrows-Wheeler transform and a space-efficient version of the suffixes-insertion algorithm to build balanced parentheses representation of suffix tree from LCP information. We show that the compressed suffix array and the compressed suffix tree of a string T can be built in O(n) deterministic time using O(n log σ) bits of space, where n is the string length and σ is the alphabet size. Previously described deterministic algorithms either run in time that depends on the alphabet size or need ω(n log σ) bits of working space. Our result has immediate applications to other problems, such as yielding the first deterministic linear-time LZ77 and LZ78 parsing algorithms that use O(n log σ) bits. We develop an extension of recently developed methods for obtaining time-space tradeoff lower bounds for problems of learning from random test samples to handle the situation where the space of tests is signficantly smaller than the space of inputs, a class of learning problems that is not handled by prior work. This extension is based on a measure of how matrices amplify the 2-norms of probability distributions that is more refined than the 2-norms of these matrices. As applications that follow from our new technique, we show that any algorithm that learns @math -variate homogeneous polynomial functions of degree at most @math over @math from evaluations on randomly chosen inputs either requires space @math or @math time where @math is the dimension of the space of such functions. These bounds are asymptotically optimal since they match the tradeoffs achieved by natural learning algorithms for the problems. Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts is @math , the number of runs in their Burrows-Wheeler Transform (BWT). One of the earliest indexes for repetitive collections, the Run-Length FM-index, used @math space and was able to efficiently count the number of occurrences of a pattern of length @math in the text (in loglogarithmic time per pattern symbol, with current techniques). However, it was unable to locate the positions of those occurrences efficiently within a space bounded in terms of @math . Since then, a number of other indexes with space bounded by other measures of repetitiveness --- the number of phrases in the Lempel-Ziv parse, the size of the smallest grammar generating the text, the size of the smallest automaton recognizing the text factors --- have been proposed for efficiently locating, but not directly counting, the occurrences of a pattern. In this paper we close this long-standing problem, showing how to extend the Run-Length FM-index so that it can locate the @math occurrences efficiently within @math space (in loglogarithmic time each), and reaching optimal time @math within @math space, on a RAM machine of @math bits. Within @math space, our index can also count in optimal time @math . Raising the space to @math , we support count and locate in @math and @math time, which is optimal in the packed setting and had not been obtained before in compressed space. We also describe a structure using @math space that replaces the text and extracts any text substring of length @math in almost-optimal time @math . (...continues...) Let @math be a tree space (or tree network) represented by a weighted tree with @math vertices, and @math be a set of @math stochastic points in @math , each of which has a fixed location with an independent existence probability. We investigate two fundamental problems under such a stochastic setting, the closest-pair problem and the nearest-neighbor search. For the former, we study the computation of the @math -threshold probability and the expectation of the closest-pair distance of a realization of @math . We propose the first algorithm to compute the @math -threshold probability in @math time for any given threshold @math , which immediately results in an @math -time algorithm for computing the expected closest-pair distance. Based on this, we further show that one can compute a @math -approximation for the expected closest-pair distance in @math time, by arguing that the expected closest-pair distance can be approximated via @math threshold probability queries. For the latter, we study the @math most-likely nearest-neighbor search ( @math -LNN) via a notion called @math most-likely Voronoi Diagram ( @math -LVD). We show that the size of the @math -LVD @math of @math on @math is bounded by @math if the existence probabilities of the points in @math are constant-far from 0. Furthermore, we establish an @math average-case upper bound for the size of @math , by regarding the existence probabilities as i.i.d. random variables drawn from some fixed distribution. Our results imply the existence of an LVD data structure which answers @math -LNN queries in @math time using average-case @math space, and worst-case @math space if the existence probabilities are constant-far from 0. Finally, we also give an @math -time algorithm to construct the LVD data structure. A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N . Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically huge collection is plausible using suffix trees. However, suffix tree occupies O (N logN ) bits, which very soon inhibits in-memory analyses. Recent advances in full-text self-indexing reduce the space of suffix tree to O (N log*** ) bits, where *** is the alphabet size. In practice, the space reduction is more than 10-fold, for example on suffix tree of Human Genome. However, this reduction factor remains constant when more sequences are added to the collection. We develop a new family of self-indexes suited for the repetitive sequence collection setting. Their expected space requirement depends only on the length n of the base sequence and the number s of variations in its repeated copies. That is, the space reduction factor is no longer constant, but depends on N n . We believe the structures developed in this work will provide a fundamental basis for storage and retrieval of individual genomes as they become available due to rapid progress in the sequencing technologies. We consider @math -median clustering in finite metric spaces and @math -means clustering in Euclidean spaces, in the setting where @math is part of the input (not a constant). For the @math -means problem, show that if the optimal @math -means clustering of the input is more expensive than the optimal @math -means clustering by a factor of @math , then one can achieve a @math -approximation to the @math -means optimal in time polynomial in @math and @math by using a variant of Lloyd's algorithm. In this work we substantially improve this approximation guarantee. We show that given only the condition that the @math -means optimal is more expensive than the @math -means optimal by a factor @math for some constant @math , we can obtain a PTAS. In particular, under this assumption, for any @math we achieve a @math -approximation to the @math -means optimal in time polynomial in @math and @math , and exponential in @math and @math . We thus decouple the strength of the assumption from the quality of the approximation ratio. We also give a PTAS for the @math -median problem in finite metrics under the analogous assumption as well. For @math -means, we in addition give a randomized algorithm with improved running time of @math . Our technique also obtains a PTAS under the assumption of that all @math approximations are @math -close to a desired target clustering, in the case that all target clusters have size greater than @math and @math is constant. Note that the motivation of is that for many clustering problems, the objective function is only a proxy for the true goal of getting close to the target. From this perspective, our improvement is that for @math -means in Euclidean spaces we reduce the distance of the clustering found to the target from @math to @math when all target clusters are large, and for @math -median we improve the largeness'' condition needed in the work of to get exactly @math -close from @math to @math . Our results are based on a new notion of clustering stability. This paper provides the first general technique for proving information lower bounds on two-party unbounded-rounds communication problems. We show that the discrepancy lower bound, which applies to randomized communication complexity, also applies to information complexity. More precisely, if the discrepancy of a two-party function @math with respect to a distribution @math is @math , then any two party randomized protocol computing @math must reveal at least @math bits of information to the participants. As a corollary, we obtain that any two-party protocol for computing a random function on @math must reveal @math bits of information to the participants. In addition, we prove that the discrepancy of the Greater-Than function is @math , which provides an alternative proof to the recent proof of Viola Viola11 of the @math lower bound on the communication complexity of this well-studied function and, combined with our main result, proves the tight @math lower bound on its information complexity. The proof of our main result develops a new simulation procedure that may be of an independent interest. In a very recent breakthrough work of kerenidis2012lower , this simulation procedure was the main building block for proving that almost all known lower bound techniques for communication complexity (and not just discrepancy) apply to information complexity. The problem of finding a minimum spanning tree connecting n points in a k-dimensional space is discussed under three common distance metrics -- Euclidean, rectilinear, and @math . By employing a subroutine that solves the post office problem, we show that, for fixed k @math 3, such a minimum spanning tree can be found in time O( @math ), where a(k) = @math . The bound can be improved to O( @math ) for points in the 3-dimensional Euclidean space. We also obtain o( @math ) algorithms for finding a farthest pair in a set of n points and for other related problems. We study the aggregate group nearest neighbor searching for the MAX operator in the plane. For a set @math of @math points and a query set @math of @math points, the query asks for a point of @math whose maximum distance to the points in @math is minimized. We present data structures for answering such queries for both @math and @math distance measures. Previously, only heuristic and approximation algorithms were given for both versions. For the @math version, we build a data structure of O(n) size in @math time, such that each query can be answered in @math time. For the @math version, we build a data structure in @math time and @math space, such that each query can be answered in @math time, and alternatively, we build a data structure in @math time and space for any @math , such that each query can be answered in @math time. Further, we extend our result for the @math version to the top- @math queries where each query asks for the @math points of @math whose maximum distances to @math are the smallest for any @math with @math : We build a data structure of O(n) size in @math time, such that each top- @math query can be answered in @math time. The min-sum k-clustering problem in a metric space is to find a partition of the space into k clusters as to minimize the total sum of distances between pairs of points assigned to the same cluster. We give the first polynomial time non-trivial approximation algorithm for this problem. The algorithm provides an @math approximation to the min-sum k -clustering problem in general metric spaces, with running time @math . The result is based on embedding of metric spaces into hierarchically separated trees. We also provide a bicriteria approximation result that provides a constant approximation factor solution with only a constant factor increase in the number of clusters. This result is obtained by modifying and drawing ideas from recently developed primal dual approximation algorithms for facility location. Data compression is when you take a big chunk of data and crunch it down to fit into a smaller space. That data is put on ice; you have to un-crunch the compressed data to get at it. Data optimization, on the other hand, is when you take a chunk of data plus a collection of operations you can perform on that data, and crunch it into a smaller space while retaining the ability to perform the operations efficiently. This thesis investigates the problem of data optimization for some fundamental static data types, concentrating on linked data structures such as trees. I chose to restrict my attention to static data structures because they are easier to optimize since the optimization can be performed off-line. Data optimization comes in two different flavors: concrete and abstract. Concrete optimization finds minimal representations within a given implementation of a data structure; abstract optimization seeks implementations with guaranteed economy of space and time. I consider the problem of concrete optimization of various pointer-based implementations of trees and graphs. The only legitimate use of a pointer is as a reference, so we are free to map the pieces of a linked structure into memory as we choose. The problem is to find a mapping that maximizes overlap of the pieces, and hence minimizes the space they occupy. I solve the problem of finding a minimal representation for general unordered trees where pointers to children are stored in a block of consecutive locations. The algorithm presented is based on weighted matching. I also present an analysis showing that the average number of cons-cells required to store a binary tree of n nodes as a minimal binary DAG is asymptotic to @math lg @math . Methods for representing trees of n nodes in @math ( @math ) bits that allow efficient tree-traversal are presented. I develop tools for abstract optimization based on a succinct representation for ordered sets that supports ranking and selection. These tools are put to use in a building an @math ( @math )-bit data structure that represents n-node planar graphs, allowing efficient traversal and adjacency-testing. We present new and improved data structures that answer exact node-to-node distance queries in planar graphs. Such data structures are also known as distance oracles. For any directed planar graph on n nodes with non-negative lengths we obtain the following: * Given a desired space allocation @math , we show how to construct in @math time a data structure of size @math that answers distance queries in @math time per query. As a consequence, we obtain an improvement over the fastest algorithm for k-many distances in planar graphs whenever @math . * We provide a linear-space exact distance oracle for planar graphs with query time @math for any constant eps>0. This is the first such data structure with provable sublinear query time. * For edge lengths at least one, we provide an exact distance oracle of space @math such that for any pair of nodes at distance D the query time is @math . Comparable query performance had been observed experimentally but has never been explained theoretically. Our data structures are based on the following new tool: given a non-self-crossing cycle C with @math nodes, we can preprocess G in @math time to produce a data structure of size @math that can answer the following queries in @math time: for a query node u, output the distance from u to all the nodes of C. This data structure builds on and extends a related data structure of Klein (SODA'05), which reports distances to the boundary of a face, rather than a cycle. The best distance oracles for planar graphs until the current work are due to Cabello (SODA'06), Djidjev (WG'96), and Fakcharoenphol and Rao (FOCS'01). For @math and space @math , we essentially improve the query time from @math to @math .