Weak Heaps and Friends Recent Developments Edelkamp, Stefan; Elmasry, Amr; Katajainen, Jyrki; Weiß, Armin
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Podcast Ch23a
Podcast Ch23a • Title: Bit Arrays • Description: Overview; bit operations in Java; BitArray class • Participants: Barry Kurtz (instructor); John Helfert and Tobie Williams (students) • Textbook: Data Structures for Java; William H. Ford and William R. Topp Bit Arrays • Applications such as compiler code generation and compression algorithms create data that includes specific sequences of bits. – Many applications, such as compilers, generate specific sequences of bits. Bit Arrays (continued) • Java binary bit handling operators |, &, and ^ act on pairs of bits and return the new value. The unary operator ~ inverts the bits of its operand. BitBit OperationsOperations x y ~x x | y x & y x ^ y 0 0 1 0 0 0 0 1 1 1 0 1 1 0 0 1 0 1 1 1 0 1 1 0 Bit Arrays (continued) Bit Arrays (continued) • Operator << shifts integer or char values to the left. Operators >> and >>> shift values to the right using signed or unsigned arithmetic, respectively. Assume x and y are 32-bit integers. x = 0...10110110 x << 2 = 0...1011011000 x = 101...11011100 x >> 3 = 111101...11011 x = 101...11011100 x >>> 3 = 000101...11011 Bit Arrays (continued) Before performing the bitwise operator |, &, or ^, Java performs binary numeric promotion on the operands. The type of the bitwise operator expression is the promoted type of the operands. The rules of promotion are as follows: • If either operand is of type long, the other is converted to long. • Otherwise, both operands are converted to type int. In the case of the unary operator ~, Java converts a byte, char, short to int before applying the operator, and the resulting value is an int. -
Binary Index Trees a Cumulative Frequency Array Allows Us To
Binary Index Trees A cumulative frequency array allows us to calculate the sum of the range of values in O(1), as long as there are no changes to the data once the queries start. But consider situations where we might change the value at an index in an array, then query for the sum of a range of values in the array, followed by some more changes and more queries. In this sort of situation, a cumulative frequency array would still give us O(1) query times, but it would take O(n) time to update after each change!!! (Basically, if we change one index in a cumulative frequency array, all other indexes above it would have to have this value added to it as well.) Here is a quick illustration: Current cumulative frequency array: Index 0 1 2 3 4 5 6 7 8 Value 2 4 4 4 6 8 11 13 17 Now, consider adding the value 2 to the data, recalling that index i stores the number of values less than or equal to i. The adjusted array is: Index 0 1 2 3 4 5 6 7 8 Value 2 4 5 5 7 9 12 14 18 We had to edit each index 2 or greater, which would take O(n) for a cumulative frequency array of size n. Thus, we want a new arrangement where both the query AND the update are relatively fast. The creative insight here is that perhaps if we store data in a different way, perhaps we can reduce the update time by quite a bit while incurring only a modest increase in query time. -
B-Bit Sketch Trie: Scalable Similarity Search on Integer Sketches
b-Bit Sketch Trie: Scalable Similarity Search on Integer Sketches Shunsuke Kanda Yasuo Tabei RIKEN Center for Advanced Intelligence Project RIKEN Center for Advanced Intelligence Project Tokyo, Japan Tokyo, Japan [email protected] [email protected] Abstract—Recently, randomly mapping vectorial data to algorithms intending to build sketches of non-negative inte- strings of discrete symbols (i.e., sketches) for fast and space- gers (i.e., b-bit sketches) have been proposed for efficiently efficient similarity searches has become popular. Such random approximating various similarity measures. Examples are b-bit mapping is called similarity-preserving hashing and approximates a similarity metric by using the Hamming distance. Although minwise hashing (minhash) [12]–[14] for Jaccard similarity, many efficient similarity searches have been proposed, most of 0-bit consistent weighted sampling (CWS) for min-max ker- them are designed for binary sketches. Similarity searches on nel [15], and 0-bit CWS for generalized min-max kernel [16]. integer sketches are in their infancy. In this paper, we present Thus, developing scalable similarity search methods for b-bit a novel space-efficient trie named b-bit sketch trie on integer sketches is a key issue in large-scale applications of similarity sketches for scalable similarity searches by leveraging the idea behind succinct data structures (i.e., space-efficient data structures search. while supporting various data operations in the compressed Similarity searches on binary sketches are classified -
Space-Efficient Data Structures, Streams, and Algorithms
Andrej Brodnik Alejandro López-Ortiz Venkatesh Raman Alfredo Viola (Eds.) Festschrift Space-Efficient Data Structures, Streams, LNCS 8066 and Algorithms Papers in Honor of J. Ian Munro on the Occasion of His 66th Birthday 123 Lecture Notes in Computer Science 8066 Commenced Publication in 1973 Founding and Former Series Editors: Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen Editorial Board David Hutchison Lancaster University, UK Takeo Kanade Carnegie Mellon University, Pittsburgh, PA, USA Josef Kittler University of Surrey, Guildford, UK Jon M. Kleinberg Cornell University, Ithaca, NY, USA Alfred Kobsa University of California, Irvine, CA, USA Friedemann Mattern ETH Zurich, Switzerland John C. Mitchell Stanford University, CA, USA Moni Naor Weizmann Institute of Science, Rehovot, Israel Oscar Nierstrasz University of Bern, Switzerland C. Pandu Rangan Indian Institute of Technology, Madras, India Bernhard Steffen TU Dortmund University, Germany Madhu Sudan Microsoft Research, Cambridge, MA, USA Demetri Terzopoulos University of California, Los Angeles, CA, USA Doug Tygar University of California, Berkeley, CA, USA Gerhard Weikum Max Planck Institute for Informatics, Saarbruecken, Germany Andrej Brodnik Alejandro López-Ortiz Venkatesh Raman Alfredo Viola (Eds.) Space-Efficient Data Structures, Streams, and Algorithms Papers in Honor of J. Ian Munro on the Occasion of His 66th Birthday 13 Volume Editors Andrej Brodnik University of Ljubljana, Faculty of Computer and Information Science Ljubljana, Slovenia and University of Primorska, -
Compact Fenwick Trees for Dynamic Ranking and Selection
Compact Fenwick trees for dynamic ranking and selection Stefano Marchini Sebastiano Vigna Dipartimento di Informatica, Universit`adegli Studi di Milano, Italy October 15, 2019 Abstract The Fenwick tree [3] is a classical implicit data structure that stores an array in such a way that modifying an element, accessing an element, computing a prefix sum and performing a predecessor search on prefix sums all take logarithmic time. We introduce a number of variants which improve the classical implementation of the tree: in particular, we can reduce its size when an upper bound on the array element is known, and we can perform much faster predecessor searches. Our aim is to use our variants to implement an efficient dynamic bit vector: our structure is able to perform updates, ranking and selection in logarithmic time, with a space overhead in the order of a few percents, outperforming existing data structures with the same purpose. Along the way, we highlight the pernicious interplay between the arithmetic behind the Fenwick tree and the structure of current CPU caches, suggesting simple solutions that improve performance significantly. 1 Introduction The problem of building static data structures which perform rank and select operations on vectors of n bits in constant time using additional o(n) bits has received a great deal of attention in the last two decades starting form Jacobson's seminal work on succinct data structures. [7] The rank operator takes a position in the bit vector and returns the number of preceding ones. The select operation returns the position of the k-th one in the vector, given k. -
A Complete Bibliography of Publications in Nordisk Tidskrift for Informationsbehandling, BIT, and BIT Numerical Mathematics
A Complete Bibliography of Publications in Nordisk Tidskrift for Informationsbehandling, BIT,andBIT Numerical Mathematics Nelson H. F. Beebe University of Utah Department of Mathematics, 110 LCB 155 S 1400 E RM 233 Salt Lake City, UT 84112-0090 USA Tel: +1 801 581 5254 FAX: +1 801 581 4148 E-mail: [email protected], [email protected], [email protected] (Internet) WWW URL: http://www.math.utah.edu/~beebe/ 09 June 2021 Version 3.54 Title word cross-reference [3105, 328, 469, 655, 896, 524, 873, 455, 779, 946, 2944, 297, 1752, 670, 2582, 1409, 1987, 915, 808, 761, 916, 2071, 2198, 1449, 780, 959, 1105, 1021, 497, 2589]. A(α) #24873 [1089]. [896, 2594, 333]. A∗ [2013]. A∗Ax = b [2369]. n A [1640, 566, 947, 1580, 1460]. A = a2 +1 − 0 n (3) [2450]. (A λB) [1414]. 0=1 [1242]. 1 [334]. α [824, 1580]. AN [1622]. A(#) [3439]. − 12 [3037, 2711]. 1 2 [1097]. 1:0 [3043]. 10 AX − XB = C [2195, 2006]. [838]. 11 [1311]. 2 AXD − BXC = E [1101]. B [2144, 1953, 2291, 2162, 3047, 886, 2551, 957, [2187, 1575, 1267, 1409, 1489, 1991, 1191, 2007, 2552, 1832, 949, 3024, 3219, 2194]. 2; 3 979, 1819, 1597, 1823, 1773]. β [824]. BN n − p − − [1490]. 2 1 [320]. 2 1 [100]. 2m 4 [1181]. BS [1773]. BSI [1446]. C0 [2906]. C1 [1105]. 3 [2119, 1953, 2531, 1351, 2551, 1292, [3202]. C2 [3108, 2422, 3000, 2036]. χ2 1793, 949, 1356, 2711, 2227, 570]. [30, 31]. Cln(θ); (n ≥ 2) [2929]. cos [228]. D 3; 000; 000; 000 [575, 637]. -
Efficient Data Structures for High Speed Packet Processing
Efficient data structures for high speed packet processing Paolo Giaccone Notes for the class on \Computer aided simulations and performance evaluation " Politecnico di Torino November 2020 Outline 1 Applications 2 Theoretical background 3 Tables Direct access arrays Hash tables Multiple-choice hash tables Cuckoo hash 4 Set Membership Problem definition Application Fingerprinting Bit String Hashing Bloom filters Cuckoo filters 5 Longest prefix matching Patricia trie Giaccone (Politecnico di Torino) Hash, Cuckoo, Bloom and Patricia Nov. 2020 2 / 93 Applications Section 1 Applications Giaccone (Politecnico di Torino) Hash, Cuckoo, Bloom and Patricia Nov. 2020 3 / 93 Applications Big Data and probabilistic data structures 3 V's of Big Data Volume (amount of data) Velocity (speed at which data is arriving and is processed) Variety (types of data) Main efficiency metrics for data structures space time to write, to update, to read, to delete Probabilistic data structures based on different hashing techniques approximated answers, but reliable estimation of the error typically, low memory, constant query time, high scaling Giaccone (Politecnico di Torino) Hash, Cuckoo, Bloom and Patricia Nov. 2020 4 / 93 Applications Probabilistic data structures Membership answer approximate membership queries e.g., Bloom filter, counting Bloom filter, quotient filter, Cuckoo filter Cardinality estimate the number of unique elements in a dataset. e.g., linear counting, probabilistic counting, LogLog and HyperLogLog Frequency in streaming applications, find the frequency of some element, filter the most frequent elements in the stream, detect the trending elements, etc. e.g., majority algorithm, frequent algorithm, count sketch, count{min sketch Giaccone (Politecnico di Torino) Hash, Cuckoo, Bloom and Patricia Nov. -
K-Mer Data Structures Rayan Chikhi CNRS, Univ
k-mer data structures Rayan Chikhi CNRS, Univ. Lille, France CGSI - July 24, 2018 Baseline problem In-memory representation of a large set of short k-mers: e.g. ACTGAT GTATGC ATTAAA GAATTG ... (Indirect) applications ● Assembly ● Error-correction of reads ● Detection of similarity between sequences ● Detection of distances between datasets ● Alignment ● Pseudoalignment / quasi-mapping ● Detection of taxonomy ● Indexing large collections of sequencing datasets ● Quality control ● Detection of events (e.g. SNPs, indels, CNVs, alt. transcription) ● ... Goals of this lecture ● Broad sweep of state of the art, with applications ● Refresher of basic CS elements Au programme: ● Basic structures (Bloom Filters, CQF, Hashing, Perfect Hashing) ● k-mer data structures (SBT, BFT, dBG ds) ● Some reference-free applications k-mers Sequences of k consecutive letters, e.g. ACAG or TAGG for k=4 Problem statement: Framing the problem Representation of a set of k-mers: ACTGAT 6 11 Large set of k-mers : 10 - 10 elements GTATGC k in [11; 103] .. Problem statement: Operations to support Representation of a set of k-mers: - Construction (from a disk stream) ACTGAT - Membership (“is X in the set?”) GTATGC - Iteration (enumerate all elements in the set) - ... .. 106 - 1011 elements Extensions: k: 11 - 500 - Associate value(s) to k-mers (e.g. abundance) - - Navigate the de Bruijn graph Problem statement: Data structures Representation of a set of k-mers: ACTGAT “In computer science, a data structure is a GTATGC particular way of organizing and storing data in a -
CMU SCS 15-721 (Spring 2020) :: OLTP Indexes (Trie Data Structures)
ADVANCED DATABASE SYSTEMS OLTP Indexes (Trie Data Structures) @Andy_Pavlo // 15-721 // Spring 2020 Lecture #07 2 Latches B+Trees Judy Array ART Masstree 15-721 (Spring 2020) 3 LATCH IMPLEMENTATION GOALS Small memory footprint. Fast execution path when no contention. Deschedule thread when it has been waiting for too long to avoid burning cycles. Each latch should not have to implement their own queue to track waiting threads. Source: Filip Pizlo 15-721 (Spring 2020) 3 LATCH IMPLEMENTATION GOALS Small memory footprint. Fast execution path when no contention. Deschedule thread when it has been waiting for too long to avoid burning cycles. Each latch should not have to implement their own queue to track waiting threads. Source: Filip Pizlo 15-721 (Spring 2020) 4 LATCH IMPLEMENTATIONS Test-and-Set Spinlock Blocking OS Mutex Adaptive Spinlock Queue-based Spinlock Reader-Writer Locks 15-721 (Spring 2020) 5 LATCH IMPLEMENTATIONS Choice #1: Test-and-Set Spinlock (TaS) → Very efficient (single instruction to lock/unlock) → Non-scalable, not cache friendly, not OS friendly. → Example: std::atomic<T> std::atomic_flag latch; ⋮ while (latch.test_and_set(…)) { // Yield? Abort? Retry? } 15-721 (Spring 2020) 5 LATCH IMPLEMENTATIONS Choice #1: Test-and-Set Spinlock (TaS) → Very efficient (single instruction to lock/unlock) → Non-scalable, not cache friendly, not OS friendly. → Example: std::atomic<T> std::atomic_flag latch; ⋮ while (latch.test_and_set(…)) { // Yield? Abort? Retry? } 15-721 (Spring 2020) 6 LATCH IMPLEMENTATIONS Choice #2: Blocking OS Mutex → Simple to use → Non-scalable (about 25ns per lock/unlock invocation) → Example: std::mutex std::mutex m; ⋮ m.lock(); // Do something special... m.unlock(); 15-721 (Spring 2020) 6 LATCH IMPLEMENTATIONS Choice #2: Blocking OS Mutex → Simple to use → Non-scalable (about 25ns per lock/unlock invocation) → Example: std::mutex std::mutex m; pthread_mutex_t ⋮ m.lock(); futex // Do something special.. -
Space- and Time-Efficient String Dictionaries
Tokushima University Ph.D. Thesis Space- and Time-Efficient String Dictionaries z間¹率hB間¹率noD文W列辞ø Author: Supervisor: Shunsuke Kanda Prof. Masao Fuketa A thesis submitted in fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Advanced Technology and Science Department of Information Science and Intelligent Systems March 2018 iii Abstract In modern computer science, the management of massive data is a fundamental problem because the amount of data is growing faster than we can easily handle them. Such data are often represented as strings such as documents, Web contents and genomics data; therefore, data structures and algorithms for space-efficient string processing have been developed by many researchers. In this thesis, we focus on a string dictionary that is an in-memory data structure for storing a set of strings. It has been traditionally used to manage vocabulary in natural language processing and information retrieval. The size of the dictionaries is not problematic because of Heaps’ Law. However, string dictionaries in recent applications, such as Web search engines, RDF stores, geographic information systems and bioinformatics, need to handle very large datasets. As the space usage of string dictionaries is a significant issue in those applications, it is necessary to develop space-efficient data structures. If limited to static applications, existing data structures have already achieved very high space efficiency by exploiting succinct data structures and text compression techniques. For example, state-of-the-art string dictionaries can be implemented in space up to 5% of the original dataset size. However, there remain trade-off problems among space efficiency, lookup-time performance and construction costs. -
Fundamental Data Structures Contents
Fundamental Data Structures Contents 1 Introduction 1 1.1 Abstract data type ........................................... 1 1.1.1 Examples ........................................... 1 1.1.2 Introduction .......................................... 2 1.1.3 Defining an abstract data type ................................. 2 1.1.4 Advantages of abstract data typing .............................. 4 1.1.5 Typical operations ...................................... 4 1.1.6 Examples ........................................... 5 1.1.7 Implementation ........................................ 5 1.1.8 See also ............................................ 6 1.1.9 Notes ............................................. 6 1.1.10 References .......................................... 6 1.1.11 Further ............................................ 7 1.1.12 External links ......................................... 7 1.2 Data structure ............................................. 7 1.2.1 Overview ........................................... 7 1.2.2 Examples ........................................... 7 1.2.3 Language support ....................................... 8 1.2.4 See also ............................................ 8 1.2.5 References .......................................... 8 1.2.6 Further reading ........................................ 8 1.2.7 External links ......................................... 9 1.3 Analysis of algorithms ......................................... 9 1.3.1 Cost models ......................................... 9 1.3.2 Run-time analysis -
*Dictionary Data Structures 3
CHAPTER *Dictionary Data Structures 3 The exploration efficiency of algorithms like A* is often measured with respect to the number of expanded/generated problem graph nodes, but the actual runtimes depend crucially on how the Open and Closed lists are implemented. In this chapter we look closer at efficient data structures to represent these sets. For the Open list, different options for implementing a priority queue data structure are consid- ered. We distinguish between integer and general edge costs, and introduce bucket and advanced heap implementations. For efficient duplicate detection and removal we also look at hash dictionaries. We devise a variety of hash functions that can be computed efficiently and that minimize the number of collisions by approximating uniformly distributed addresses, even if the set of chosen keys is not (which is almost always the case). Next we explore memory-saving dictionaries, the space requirements of which come close to the information-theoretic lower bound and provide a treatment of approximate dictionaries. Subset dictionaries address the problem of finding partial state vectors in a set. Searching the set is referred to as the Subset Query or the Containment Query problem. The two problems are equivalent to the Partial Match retrieval problem for retrieving a partially specified input query word from a file of k-letter words with k being fixed. A simple example is the search for a word in a crossword puzzle. In a state space search, subset dictionaries are important to store partial state vectors like dead-end patterns in Sokoban that generalize pruning rules (see Ch.