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.
Also contribution ) improves the state-of-the-art, due to @cite_21 @cite_31 . In those papers, the authors show how to merge the BWTs of two texts @math and obtain the BWT of the collection @math in @math time and @math bits of working space for any @math [Thm. 7] belazzougui2016linear . When @math , this running time is the same as our result ), but the working space is much higher on small alphabets.
@cite_31 @cite_21
2522621913 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. 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...) 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 . 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. Let @math @math be a given set of @math string documents of total length @math , our task is to index @math , such that the @math most relevant documents for an online query pattern @math of length @math can be retrieved efficiently. We propose an index of size @math bits and @math query time for the basic relevance metric , where @math is the size (in bits) of a compressed full text index of @math , with @math time for searching a pattern of length @math . We further reduce the space to @math bits, however the query time will be @math , where @math is the alphabet size and @math is any constant. For any real number @math , we nearly completely characterize the space complexity of estimating @math for @math matrices @math in which each row and each column has @math non-zero entries and whose entries are presented one at a time in a data stream model. Here the @math are the singular values of @math , and when @math , @math is the @math -th power of the Schatten @math -norm. We show that when @math is not an even integer, to obtain a @math -approximation to @math with constant probability, any @math -pass algorithm requires @math bits of space, where @math as @math and @math is a constant independent of @math . However, when @math is an even integer, we give an upper bound of @math bits of space, which holds even in the turnstile data stream model. The latter is optimal up to @math factors. Our results considerably strengthen lower bounds in previous work for arbitrary (not necessarily sparse) matrices @math : the previous best lower bound was @math for @math , @math for @math and @math for @math . We note for @math , while our lower bound for even integers is the same, for other @math in this range our lower bound is @math , which is considerably stronger than the previous @math for small enough constant @math . We obtain similar near-linear lower bounds for Ky-Fan norms, SVD entropy, eigenvalue shrinkers, and M-estimators, many of which could have been solvable in logarithmic space prior to our work. We consider document listing on string collections, that is, finding in which strings a given pattern appears. In particular, we focus on repetitive collections: a collection of size @math over alphabet @math is composed of @math copies of a string of size @math , and @math edits are applied on ranges of copies. We introduce the first document listing index with size @math , precisely @math bits, and with useful worst-case time guarantees: Given a pattern of length @math , the index reports the @math strings where it appears in time @math , for any constant @math (and tells in time @math if @math ). Our technique is to augment a range data structure that is commonly used on grammar-based indexes, so that instead of retrieving all the pattern occurrences, it computes useful summaries on them. We show that the idea has independent interest: we introduce the first grammar-based index that, on a text @math with a grammar of size @math , uses @math bits and counts the number of occurrences of a pattern @math in time @math , for any constant @math . We also give the first index using @math bits, where @math is parsed by Lempel-Ziv into @math phrases, counting occurrences in time @math . Karpinski and Nekrich (2008) introduced the problem of parameterized range majority, which asks to preprocess a string of length @math such that, given the endpoints of a range, one can quickly find all the distinct elements whose relative frequencies in that range are more than a threshold @math . Subsequent authors have reduced their time and space bounds such that, when @math is given at preprocessing time, we need either @math space and optimal @math query time or linear space and @math query time, where @math is the alphabet size. In this paper we give the first linear-space solution with optimal @math query time. For the case when @math is given at query time, we significantly improve previous bounds, achieving either @math space and optimal @math query time or compressed space and @math query time. Along the way, we consider the complementary problem of parameterized range minority that was recently introduced by (2012), who achieved linear space and @math query time even for variable @math . We improve their solution to use either nearly optimally compressed space with no slowdown, or optimally compressed space with nearly no slowdown. Some of our intermediate results, such as density-sensitive query time for one-dimensional range counting, may be of independent interest. We present new approximation algorithms for the @math -median and @math -means clustering problems. To this end, we obtain small coresets for @math -median and @math -means clustering in general metric spaces and in Euclidean spaces. In @math , these coresets are of size with polynomial dependency on the dimension @math . This leads to @math -approximation algorithms to the optimal @math -median and @math -means clustering in @math , with running time @math , where @math is the number of points. This improves over previous results. We use those coresets to maintain a @math -approximate @math -median and @math -means clustering of a stream of points in @math , using @math space. These are the first streaming algorithms, for those problems, that have space complexity with polynomial dependency on the dimension. 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. We introduce the first grammar-compressed representation of a sequence that supports searches in time that depends only logarithmically on the size of the grammar. Given a text @math that is represented by a (context-free) grammar of @math (terminal and nonterminal) symbols and size @math (measured as the sum of the lengths of the right hands of the rules), a basic grammar-based representation of @math takes @math bits of space. Our representation requires @math bits of space, for any @math . It can find the positions of the @math occurrences of a pattern of length @math in @math in @math time, and extract any substring of length @math of @math in time @math , where @math is the height of the grammar tree. The distributed @math -coloring problem is one of the most fundamental and well-studied problems in distributed algorithms. Starting with the work of Cole and Vishkin in 1986, a long line of gradually improving algorithms has been published. The state-of-the-art running time, prior to our work, is @math , due to Kuhn and Wattenhofer [Proceedings of the @math th Annual ACM Symposium on Principles of Distributed Computing, Denver, CO, 2006, pp. 7--15]. Linial [Proceedings of the @math th Annual IEEE Symposium on Foundation of Computer Science, Los Angeles, CA, 1987, pp. 331--335] proved a lower bound of @math for the problem, and Szegedy and Vishwanathan [Proceedings of the 25th Annual ACM Symposium on Theory of Computing, San Diego, CA, 1993, pp. 201--207] provided a heuristic argument that shows that algorithms from a wide family of locally iterative algorithms are unlikely to achieve a running time smaller than @math . We present a de... We study approximate distributed solutions to the weighted all-pairs-shortest-paths (APSP) problem in the CONGEST model. We obtain the following results. @math A deterministic @math -approximation to APSP in @math rounds. This improves over the best previously known algorithm, by both derandomizing it and by reducing the running time by a @math factor. In many cases, routing schemes involve relabeling, i.e., assigning new names to nodes and require that these names are used in distance and routing queries. It is known that relabeling is necessary to achieve running times of @math . In the relabeling model, we obtain the following results. @math A randomized @math -approximation to APSP, for any integer @math , running in @math rounds, where @math is the hop diameter of the network. This algorithm simplifies the best previously known result and reduces its approximation ratio from @math to @math . Also, the new algorithm uses uses labels of asymptotically optimal size, namely @math bits. @math A randomized @math -approximation to APSP, for any integer @math , running in time @math and producing compact routing tables of size @math . The node lables consist of @math bits. This improves on the approximation ratio of @math for tables of that size achieved by the best previously known algorithm, which terminates faster, in @math rounds. 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 . Understanding the local behaviour of structured multi-dimensional data is a fundamental problem in various areas of computer science. As the amount of data is often huge, it is desirable to obtain sublinear time algorithms, and specifically property testers, to understand local properties of the data. We focus on the natural local problem of testing pattern freeness: given a large @math -dimensional array @math and a fixed @math -dimensional pattern @math over a finite alphabet, we say that @math is @math -free if it does not contain a copy of the forbidden pattern @math as a consecutive subarray. The distance of @math to @math -freeness is the fraction of entries of @math that need to be modified to make it @math -free. For any @math and any large enough pattern @math over any alphabet, other than a very small set of exceptional patterns, we design a tolerant tester that distinguishes between the case that the distance is at least @math and the case that it is at most @math , with query complexity and running time @math , where @math and @math depend only on @math . To analyze the testers we establish several combinatorial results, including the following @math -dimensional modification lemma, which might be of independent interest: for any large enough pattern @math over any alphabet (excluding a small set of exceptional patterns for the binary case), and any array @math containing a copy of @math , one can delete this copy by modifying one of its locations without creating new @math -copies in @math . Our results address an open question of Fischer and Newman, who asked whether there exist efficient testers for properties related to tight substructures in multi-dimensional structured data. They serve as a first step towards a general understanding of local properties of multi-dimensional arrays, as any such property can be characterized by a fixed family of forbidden patterns. We present a succinct representation of a set of n points on an n ×n grid using @math bits to support orthogonal range counting in @math time, and range reporting in @math time, where k is the size of the output. This achieves an improvement on query time by a factor of @math upon the previous result of Makinen and Navarro [1], while using essentially the information-theoretic minimum space. Our data structure not only can be used as a key component in solutions to the general orthogonal range search problem to save storage cost, but also has applications in text indexing. In particular, we apply it to improve two previous space-efficient text indexes that support substring search [2] and position-restricted substring search [1]. We also use it to extend previous results on succinct representations of sequences of small integers, and to design succinct data structures supporting certain types of orthogonal range query in the plane. We give two new quantum algorithms for solving semidefinite programs (SDPs) providing quantum speed-ups. We consider SDP instances with @math constraint matrices, each of dimension @math , rank @math , and sparsity @math . The first algorithm assumes an input model where one is given access to entries of the matrices at unit cost. We show that it has run time @math , where @math is the error. This gives an optimal dependence in terms of @math and quadratic improvement over previous quantum algorithms when @math . The second algorithm assumes a fully quantum input model in which the matrices are given as quantum states. We show that its run time is @math , with @math an upper bound on the trace-norm of all input matrices. In particular the complexity depends only poly-logarithmically in @math and polynomially in @math . We apply the second SDP solver to the problem of learning a good description of a quantum state with respect to a set of measurements: Given @math measurements and copies of an unknown state @math , we show we can find in time @math a description of the state as a quantum circuit preparing a density matrix which has the same expectation values as @math on the @math measurements, up to error @math . The density matrix obtained is an approximation to the maximum entropy state consistent with the measurement data considered in Jaynes' principle from statistical mechanics. As in previous work, we obtain our algorithm by "quantizing" classical SDP solvers based on the matrix multiplicative weight method. One of our main technical contributions is a quantum Gibbs state sampler for low-rank Hamiltonians with a poly-logarithmic dependence on its dimension, which could be of independent interest. We investigate the minimization of Newton's functional for the problem of the body of minimal resistance with maximal height @math cite butt in the class of convex developable functions defined in a disc. This class is a natural candidate to find a (non-radial) minimizer in accordance with the results of cite lrp2. We prove that the minimizer in this class has a minimal set in the form of a regular polygon with @math sides centered in the disc, and numerical experiments indicate that the natural number @math is a non-decreasing function of @math . The corresponding functions all achieve a lower value of the functional than the optimal radially symmetric function with the same height @math . This paper addresses the cornerstone family of in distributed computing, and investigates the curious gap between randomized and deterministic solutions under bandwidth restrictions. Our main contribution is in providing tools for derandomizing solutions to local problems, when the @math nodes can only send @math -bit messages in each round of communication. We combine bounded independence, which we show to be sufficient for some algorithms, with the method of conditional expectations and with additional machinery, to obtain the following results. Our techniques give a deterministic maximal independent set (MIS) algorithm in the CONGEST model, where the communication graph is identical to the input graph, in @math rounds, where @math is the diameter of the graph. The best known running time in terms of @math alone is @math , which is super-polylogarithmic, and requires large messages. For the CONGEST model, the only known previous solution is a coloring-based @math -round algorithm, where @math is the maximal degree in the graph. On the way to obtaining the above, we show that in the model, which allows all-to-all communication, there is a deterministic MIS algorithm that runs in @math rounds. , where @math is the maximum degree. When @math , the bound improves to @math and holds also for @math -coloring. In addition, we deterministically construct a @math -spanner with @math edges in @math rounds. For comparison, in the more stringent CONGEST model, the best deterministic algorithm for constructing a @math -spanner with @math edges runs in @math rounds. High energy efficiency and low memory footprint are the key requirements for the deployment of deep learning based analytics on low-power microcontrollers. Here we present work-in-progress results with @math -bit Quantized Neural Networks (QNNs) deployed on a commercial Cortex-M7 class microcontroller by means of an extension to the ARM CMSIS-NN library. We show that i) for @math and @math low memory footprint QNNs can be deployed with an energy overhead of 30 and 36 respectively against the 8-bit CMSIS-NN due to the lack of quantization support in the ISA; ii) for @math native instructions can be used, yielding an energy and latency reduction of ∼3.8× with respect to CMSIS-NN. Our initial results suggest that a small set of QNN-related specialized instructions could improve performance by as much as 7.5× for @math , 13.6× for @math and 6.5× for binary NNs.