Data-Structures
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Interval Trees Storing and Searching Intervals
Interval Trees Storing and Searching Intervals • Instead of points, suppose you want to keep track of axis-aligned segments: • Range queries: return all segments that have any part of them inside the rectangle. • Motivation: wiring diagrams, genes on genomes Simpler Problem: 1-d intervals • Segments with at least one endpoint in the rectangle can be found by building a 2d range tree on the 2n endpoints. - Keep pointer from each endpoint stored in tree to the segments - Mark segments as you output them, so that you don’t output contained segments twice. • Segments with no endpoints in range are the harder part. - Consider just horizontal segments - They must cross a vertical side of the region - Leads to subproblem: Given a vertical line, find segments that it crosses. - (y-coords become irrelevant for this subproblem) Interval Trees query line interval Recursively build tree on interval set S as follows: Sort the 2n endpoints Let xmid be the median point Store intervals that cross xmid in node N intervals that are intervals that are completely to the completely to the left of xmid in Nleft right of xmid in Nright Another view of interval trees x Interval Trees, continued • Will be approximately balanced because by choosing the median, we split the set of end points up in half each time - Depth is O(log n) • Have to store xmid with each node • Uses O(n) storage - each interval stored once, plus - fewer than n nodes (each node contains at least one interval) • Can be built in O(n log n) time. • Can be searched in O(log n + k) time [k = # -
Lecture 04 Linear Structures Sort
Algorithmics (6EAP) MTAT.03.238 Linear structures, sorting, searching, etc Jaak Vilo 2018 Fall Jaak Vilo 1 Big-Oh notation classes Class Informal Intuition Analogy f(n) ∈ ο ( g(n) ) f is dominated by g Strictly below < f(n) ∈ O( g(n) ) Bounded from above Upper bound ≤ f(n) ∈ Θ( g(n) ) Bounded from “equal to” = above and below f(n) ∈ Ω( g(n) ) Bounded from below Lower bound ≥ f(n) ∈ ω( g(n) ) f dominates g Strictly above > Conclusions • Algorithm complexity deals with the behavior in the long-term – worst case -- typical – average case -- quite hard – best case -- bogus, cheating • In practice, long-term sometimes not necessary – E.g. for sorting 20 elements, you dont need fancy algorithms… Linear, sequential, ordered, list … Memory, disk, tape etc – is an ordered sequentially addressed media. Physical ordered list ~ array • Memory /address/ – Garbage collection • Files (character/byte list/lines in text file,…) • Disk – Disk fragmentation Linear data structures: Arrays • Array • Hashed array tree • Bidirectional map • Heightmap • Bit array • Lookup table • Bit field • Matrix • Bitboard • Parallel array • Bitmap • Sorted array • Circular buffer • Sparse array • Control table • Sparse matrix • Image • Iliffe vector • Dynamic array • Variable-length array • Gap buffer Linear data structures: Lists • Doubly linked list • Array list • Xor linked list • Linked list • Zipper • Self-organizing list • Doubly connected edge • Skip list list • Unrolled linked list • Difference list • VList Lists: Array 0 1 size MAX_SIZE-1 3 6 7 5 2 L = int[MAX_SIZE] -
Optimizing Systems for Byte-Addressable NVM by Reducing Bit Flipping
Optimizing Systems for Byte-Addressable NVM by Reducing Bit Flipping Daniel Bittman Peter Alvaro Darrell D. E. Long Ethan L. Miller FAST ‘19 2019-02-26 1 Byte-addressable Non-volatile Memory BNVM is coming, and with it, new optimization targets CRSS Confidential 2 Byte-addressable Non-volatile Memory 0 1 0 1 0 0 0 1 It’s not just writes... ...it’s the bits flipped by those writes 0 1 1 0 0 1 0 1 CRSS Confidential 3 BNVM power usage 4 Can we take advantage of this? Software vs. hardware? 5 Can we take advantage of this? Software vs. hardware? How hard is it to reason about bit flips? 6 Can we take advantage of this? Software vs. hardware? How hard is it to reason about bit flips? How do we design data structures to reduce bit flips? 7 8 Reducing Bit ● Flips in Software ● ● 9 XOR linked lists Traditional doubly linked list value value value next next next prev prev prev XOR linked list value value value xptr xptr xptr xptr = next ⊕ prev 10 Pointers! Some actual pointers A = 0x000055b7bda8f260 B = 0x000055b7bda8f6a0 A ⊕ B = 0x4C0 = 0b10011000000 11 Using XOR in hash tables key value xnext ... key key value value xnext xnext ... key value xnext 12 Using XOR in hash tables key value xnext D key key value value 00000 0 xxxxx 1 Both indicate “entry is empty” 13 From XOR linked lists to Red Black Trees L P R Standard 3-pointer red-black tree design 14 From XOR linked lists to Red Black Trees ⊕ RX = R P L P R LX RX ⊕ LX = L P Now 2-pointer, and XOR pointers 15 Evaluation ● ● 16 Experimental framework , at the memory controller Test different data -
Advanced Data Structures
Advanced Data Structures PETER BRASS City College of New York CAMBRIDGE UNIVERSITY PRESS Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo Cambridge University Press The Edinburgh Building, Cambridge CB2 8RU, UK Published in the United States of America by Cambridge University Press, New York www.cambridge.org Information on this title: www.cambridge.org/9780521880374 © Peter Brass 2008 This publication is in copyright. Subject to statutory exception and to the provision of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. First published in print format 2008 ISBN-13 978-0-511-43685-7 eBook (EBL) ISBN-13 978-0-521-88037-4 hardback Cambridge University Press has no responsibility for the persistence or accuracy of urls for external or third-party internet websites referred to in this publication, and does not guarantee that any content on such websites is, or will remain, accurate or appropriate. Contents Preface page xi 1 Elementary Structures 1 1.1 Stack 1 1.2 Queue 8 1.3 Double-Ended Queue 16 1.4 Dynamical Allocation of Nodes 16 1.5 Shadow Copies of Array-Based Structures 18 2 Search Trees 23 2.1 Two Models of Search Trees 23 2.2 General Properties and Transformations 26 2.3 Height of a Search Tree 29 2.4 Basic Find, Insert, and Delete 31 2.5ReturningfromLeaftoRoot35 2.6 Dealing with Nonunique Keys 37 2.7 Queries for the Keys in an Interval 38 2.8 Building Optimal Search Trees 40 2.9 Converting Trees into Lists 47 2.10 -
Search Trees
Lecture III Page 1 “Trees are the earth’s endless effort to speak to the listening heaven.” – Rabindranath Tagore, Fireflies, 1928 Alice was walking beside the White Knight in Looking Glass Land. ”You are sad.” the Knight said in an anxious tone: ”let me sing you a song to comfort you.” ”Is it very long?” Alice asked, for she had heard a good deal of poetry that day. ”It’s long.” said the Knight, ”but it’s very, very beautiful. Everybody that hears me sing it - either it brings tears to their eyes, or else -” ”Or else what?” said Alice, for the Knight had made a sudden pause. ”Or else it doesn’t, you know. The name of the song is called ’Haddocks’ Eyes.’” ”Oh, that’s the name of the song, is it?” Alice said, trying to feel interested. ”No, you don’t understand,” the Knight said, looking a little vexed. ”That’s what the name is called. The name really is ’The Aged, Aged Man.’” ”Then I ought to have said ’That’s what the song is called’?” Alice corrected herself. ”No you oughtn’t: that’s another thing. The song is called ’Ways and Means’ but that’s only what it’s called, you know!” ”Well, what is the song then?” said Alice, who was by this time completely bewildered. ”I was coming to that,” the Knight said. ”The song really is ’A-sitting On a Gate’: and the tune’s my own invention.” So saying, he stopped his horse and let the reins fall on its neck: then slowly beating time with one hand, and with a faint smile lighting up his gentle, foolish face, he began.. -
2 Dynamization
6.851: Advanced Data Structures Spring 2010 Lecture 4 — February 11, 2010 Prof. Andr´eSchulz Scribe: Peter Caday 1 Overview In the previous lecture, we studied range trees and kd-trees, two structures which support efficient orthogonal range queries on a set of points. In this second of four lectures on geometric data structures, we will tie up a loose end from the last lecture — handling insertions and deletions. The main topic, however, will be two new structures addressing the vertical line stabbing problem: interval trees and segment trees. We will conclude with an application of vertical line stabbing to a windowing problem. 2 Dynamization In our previous discussion of range trees, we assumed that the point set was static. On the other hand, we may be interested in supporting insertions and deletions as time progresses. Unfortunately, it is not trivial to modify our data structures to handle this dynamic scenario. We can, however, dynamize them using general techniques; the techniques and their application here are due to Overmars [1]. Idea. Overmars’ dynamization is based on the idea of decomposable searches. A search (X,q) for the value q among the keys X is decomposable if the search result can be obtained in O(1) time from the results of searching (X1,q) and (X2,q), where X1 ∪ X2 = X. For instance, in the 2D kd-tree, the root node splits R2 into two halves. If we want to search for all points lying in a rectangle q, we may do this by combining the results of searching for q in each half. -
Lecture Notes of CSCI5610 Advanced Data Structures
Lecture Notes of CSCI5610 Advanced Data Structures Yufei Tao Department of Computer Science and Engineering Chinese University of Hong Kong July 17, 2020 Contents 1 Course Overview and Computation Models 4 2 The Binary Search Tree and the 2-3 Tree 7 2.1 The binary search tree . .7 2.2 The 2-3 tree . .9 2.3 Remarks . 13 3 Structures for Intervals 15 3.1 The interval tree . 15 3.2 The segment tree . 17 3.3 Remarks . 18 4 Structures for Points 20 4.1 The kd-tree . 20 4.2 A bootstrapping lemma . 22 4.3 The priority search tree . 24 4.4 The range tree . 27 4.5 Another range tree with better query time . 29 4.6 Pointer-machine structures . 30 4.7 Remarks . 31 5 Logarithmic Method and Global Rebuilding 33 5.1 Amortized update cost . 33 5.2 Decomposable problems . 34 5.3 The logarithmic method . 34 5.4 Fully dynamic kd-trees with global rebuilding . 37 5.5 Remarks . 39 6 Weight Balancing 41 6.1 BB[α]-trees . 41 6.2 Insertion . 42 6.3 Deletion . 42 6.4 Amortized analysis . 42 6.5 Dynamization with weight balancing . 43 6.6 Remarks . 44 1 CONTENTS 2 7 Partial Persistence 47 7.1 The potential method . 47 7.2 Partially persistent BST . 48 7.3 General pointer-machine structures . 52 7.4 Remarks . 52 8 Dynamic Perfect Hashing 54 8.1 Two random graph results . 54 8.2 Cuckoo hashing . 55 8.3 Analysis . 58 8.4 Remarks . 59 9 Binomial and Fibonacci Heaps 61 9.1 The binomial heap . -
Buffer Trees
Buffer Trees Lars Arge. The Buffer Tree: A New Technique for Optimal I/O Algorithms. In Proceedings of Fourth Workshop on Algorithms and Data Structures (WADS), Lecture Notes in Computer Science Vol. 955, Springer-Verlag, 1995, 334-345. 1 Computational Geometry 2 Pairwise Rectangle Intersection A Input N rectangles B D Output all R pairwise intersections F E Example (A; B) (B; C) (B; F ) (D; E) (D; F ) C Intersection Types Intersection Identified by: : : A B Orthogonal Line Segment Intersection on 4N rectangle sides D E Batched Range Searching on N rectangles and N upper-left corners Algorithm Orthogonal Line Segment Intersection + Batched Range Searching + Duplicate removal 3 Orthogonal Line Segment Intersection Input N segments, vertical and horizontal Output all R intersections Sweepline Algorithm Sort all endpoints w.r.t. x-coordinate • Sweep left-to-right with a range tree T y4 • storing the y-coordinates of horizontal segments intersecting the sweepline y3 Left endpoint insertion into T y • ) 2 Right endpoint deletion from T y • ) 1 Vertical segment [y ; y ] • 1 2 ) sweepline report T [y ; y ] \ 1 2 Total (internal) time O(N log N + R) · 2 4 Range Trees Create Create empty structure Insert(x) Insert element x Delete(x) Delete the inserted element x Report(x1; x2) Report all x [x1; x2] 2 x1 x2 Binary search trees B-trees (internal) (# I/Os) Updates O(log2 N) O(logB N) R Report O(log2 N + R) O(logB N + B ) Orthogonal Line Segment Intersection using B-trees O(Sort(N) + N log N + R ) I/Os : : : · B B 5 Batched Range Searching Input N rectangles and points Output all R (r; p) where point p is within rectangle r Sweepline Algorithm Sort all points and left/right rectangle • sides w.r.t. -
Efficient Data Structures for Range Searching on a Grid MARK H
JOURNAL OF ALGORITHMS 9,254-275 (1988) Efficient Data Structures for Range Searching on a Grid MARK H. OVERMARS Department of Computer Science, University of Utrecht, The Netherlands Received February 17,1987; accepted May 15.1987 We consider the 2-dimensional range searching problem in the case where all points lie on an integer grid. A new data structure is presented that solves range queries on a U * U grid in O( k + log log U) time using O( n log n) storage, where n is the number of points and k the number of reported answers. Although the query time is very good the preprocessing time of this method is very high. A second data structure is presented that can be built in time O( n log n) at the cost of an increase in query time to O(k + m). Similar techniques are used for solving the line segment intersection searching problem in a set of axis-parallel line segments on a grid. The methods presented also yield efficient structures for dominance searching and searching with half-infinite ranges that use only O(n) storage. A generalization to multi-dimensional space, using a normalization approach, yields a static solution to the general range searching problem that is better than any known solution when the dimension is at least 3. Q 1988 Academic Press, Inc. 1. INTRODUCTION One of the problems in computational geometry that has received a large amount of attention is the range searching problem. Given a set of n points in a d-dimensional space, the range searching problem asks to store these points such that for a given range ([A, * . -
Algorithms for Packet Classification Pankaj Gupta and Nick Mckeown, Stanford University
Algorithms for Packet Classification Pankaj Gupta and Nick McKeown, Stanford University Abstract The process of categorizing packets into “flows” in an Internet router is called packet classification. All packets belonging to the same flow obey a predefined rule and are processed in a similar manner by the router. For example, all packets with the same source and destination IP addresses may be defined to form a flow. Packet classification is needed for non-best-effort services, such as firewalls and quality of service; services that require the capability to distinguish and isolate traffic in differ- ent flows for suitable processing. In general, packet classification on multiple fields is a difficult problem. Hence, researchers have proposed a variety of algorithms which, broadly speaking, can be categorized as basic search algorithms, geometric algorithms, heuristic algorithms, or hardware-specific search algorithms. In this tutorial we describe algorithms that are representative of each category, and discuss which type of algorithm might be suitable for different applications. ntil recently, Internet routers provided only best- Table 2 shows the flows into which an incoming packet effort service, servicing packets in a first-come- must be classified by the router at interface X. Note that the first-served manner. Routers are now called on to flows specified may or may not be mutually exclusive. For provide different qualities of service to different example, the first and second flow in Table 2 overlap. This is Uapplications, which means routers need new mechanisms common in practice, and when no explicit priorities are speci- such as admission control, resource reservation, per-flow fied, we follow the convention that rules closer to the top of queuing, and fair scheduling. -
Optimizing Systems for Byte-Addressable NVM by Reducing Bit Flipping Daniel Bittman, Darrell D
Optimizing Systems for Byte-Addressable NVM by Reducing Bit Flipping Daniel Bittman, Darrell D. E. Long, Peter Alvaro, and Ethan L. Miller, UC Santa Cruz https://www.usenix.org/conference/fast19/presentation/bittman This paper is included in the Proceedings of the 17th USENIX Conference on File and Storage Technologies (FAST ’19). February 25–28, 2019 • Boston, MA, USA 978-1-931971-48-5 Open access to the Proceedings of the 17th USENIX Conference on File and Storage Technologies (FAST ’19) is sponsored by Optimizing Systems for Byte-Addressable NVM by Reducing Bit Flipping Daniel Bittman Peter Alvaro Darrell D. E. Long Ethan L. Miller UC Santa Cruz UC Santa Cruz UC Santa Cruz UC Santa Cruz Pure Storage Abstract stressing their weaknesses. Historically, such optimizations have included reducing the number of writes performed, ei- New byte-addressable non-volatile memory (BNVM) tech- ther by designing data structures that require fewer writes nologies such as phase change memory (PCM) enable the or by using hardware techniques such as caching to reduce construction of systems with large persistent memories, im- writes. However, it is the number of bits flipped that matter proving reliability and potentially reducing power consump- most for BNVMs such as phase-change memory (PCM), not tion. However, BNVM technologies only support a limited the number of words written. number of lifetime writes per cell and consume most of their BNVMs such as PCM suffer from two problems caused by power when flipping a bit’s state during a write; thus, PCM flipping bits: energy usage and cell wear-out. -
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