Johnson: Computers and Intractability-A Guide to the Theory of NP-Completeness

From the Publisher:
A valuable reference for the novice as well as for the expert who needs a wider scope of coverage within the area of cryptography, this book provides easy and rapid access of information and includes more than 200 algorithms and protocols; more than 200 tables and figures; more than 1,000 numbered definitions, facts, examples, notes, and remarks; and over 1,250 significant references, including brief comments on each paper.

Handbook of Applied Cryptography

ROUGE stands for Recall-Oriented Understudy for Gisting Evaluation. It includes measures to automatically determine the quality of a summary by comparing it to other (ideal) summaries created by humans. The measures count the number of overlapping units such as n-gram, word sequences, and word pairs between the computer-generated summary to be evaluated and the ideal summaries created by humans. This paper introduces four different ROUGE measures: ROUGE-N, ROUGE-L, ROUGE-W, and ROUGE-S included in the ROUGE summarization evaluation package and their evaluations. Three of them have been used in the Document Understanding Conference (DUC) 2004, a large-scale summarization evaluation sponsored by NIST.

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ROUGE: A Package for Automatic Evaluation of Summaries

The proliferation of mobile computing devices and local-area wireless networks has fostered a growing interest in location-aware systems and services. In this paper we present RADAR, a radio-frequency (RF)-based system for locating and tracking users inside buildings. RADAR operates by recording and processing signal strength information at multiple base stations positioned to provide overlapping coverage in the area of interest. It combines empirical measurements with signal propagation modeling to determine user location and thereby enable location-aware services and applications. We present experimental results that demonstrate the ability of RADAR to estimate user location with a high degree of accuracy.

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RADAR: an in-building RF-based user location and tracking system

We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w1118; iso-2; iso-3 strain and the reference y1; cn1 bw1 sp1 strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in...

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

From the Publisher:
The updated new edition of the classic Introduction to Algorithms is intended primarily for use in undergraduate or graduate courses in algorithms or data structures. Like the first edition,this text can also be used for self-study by technical professionals since it discusses engineering issues in algorithm design as well as the mathematical aspects. 
In its new edition,Introduction to Algorithms continues to provide a comprehensive introduction to the modern study of algorithms. The revision has been updated to reflect changes in the years since the book's original publication. New chapters on the role of algorithms in computing and on probabilistic analysis and randomized algorithms have been included. Sections throughout the book have been rewritten for increased clarity,and material has been added wherever a fuller explanation has seemed useful or new information warrants expanded coverage. 
As in the classic first edition,this new edition of Introduction to Algorithms presents a rich variety of algorithms and covers them in considerable depth while making their design and analysis accessible to all levels of readers. Further,the algorithms are presented in pseudocode to make the book easily accessible to students from all programming language backgrounds. 
Each chapter presents an algorithm,a design technique,an application area,or a related topic. The chapters are not dependent on one another,so the instructor can organize his or her use of the book in the way that best suits the course's needs. Additionally,the new edition offers a 25% increase over the first edition in the number of problems,giving the book 155 problems and over 900 exercises thatreinforcethe concepts the students are learning.

Introduction to Algorithms

If you had to buy just one text on algorithms, Introduction to Algorithms is a magnificent choice. The book begins by considering the mathematical foundations of the analysis of algorithms and maintains this mathematical rigor throughout the work. The tools developed in these opening sections are then applied to sorting, data structures, graphs, and a variety of selected algorithms including computational geometry, string algorithms, parallel models of computation, fast Fourier transforms (FFTs), and more. This book's strength lies in its encyclopedic range, clear exposition, and powerful analysis. Pseudo-code explanation of the algorithms coupled with proof of their accuracy makes this book is a great resource on the basic tools used to analyze the performance of algorithms.

Introduction to Algorithms, third edition

problems To understand the class of polynomial-time solvable problems, we must first have a formal notion of what a "problem" is. We define an abstract problem Q to be a binary relation on a set I of problem instances and a set S of problem solutions. For example, an instance for SHORTEST-PATH is a triple consisting of a graph and two vertices. A solution is a sequence of vertices in the graph, with perhaps the empty sequence denoting that no path exists. The problem SHORTEST-PATH itself is the relation that associates each instance of a graph and two vertices with a shortest path in the graph that connects the two vertices. Since shortest paths are not necessarily unique, a given problem instance may have more than one solution. This formulation of an abstract problem is more general than is required for our purposes. As we saw above, the theory of NP-completeness restricts attention to decision problems: those having a yes/no solution. In this case, we can view an abstract decision problem as a function that maps the instance set I to the solution set {0, 1}. For example, a decision problem related to SHORTEST-PATH is the problem PATH that we saw earlier. If i = G, u, v, k is an instance of the decision problem PATH, then PATH(i) = 1 (yes) if a shortest path from u to v has at most k edges, and PATH(i) = 0 (no) otherwise. Many abstract problems are not decision problems, but rather optimization problems, in which some value must be minimized or maximized. As we saw above, however, it is usually a simple matter to recast an optimization problem as a decision problem that is no harder. Encodings If a computer program is to solve an abstract problem, problem instances must be represented in a way that the program understands. An encoding of a set S of abstract objects is a mapping e from S to the set of binary strings. For example, we are all familiar with encoding the natural numbers N = {0, 1, 2, 3, 4,...} as the strings {0, 1, 10, 11, 100,...}. Using this encoding, e(17) = 10001. Anyone who has looked at computer representations of keyboard characters is familiar with either the ASCII or EBCDIC codes. In the ASCII code, the encoding of A is 1000001. Even a compound object can be encoded as a binary string by combining the representations of its constituent parts. Polygons, graphs, functions, ordered pairs, programs-all can be encoded as binary strings. Thus, a computer algorithm that "solves" some abstract decision problem actually takes an encoding of a problem instance as input. We call a problem whose instance set is the set of binary strings a concrete problem. We say that an algorithm solves a concrete problem in time O(T (n)) if, when it is provided a problem instance i of length n = |i|, the algorithm can produce the solution in O(T (n)) time. A concrete problem is polynomial-time solvable, therefore, if there exists an algorithm to solve it in time O(n) for some constant k. We can now formally define the complexity class P as the set of concrete decision problems that are polynomial-time solvable. We can use encodings to map abstract problems to concrete problems. Given an abstract decision problem Q mapping an instance set I to {0, 1}, an encoding e : I → {0, 1}* can be used to induce a related concrete decision problem, which we denote by e(Q). If the solution to an abstract-problem instance i I is Q(i) {0, 1}, then the solution to the concreteproblem instance e(i) {0, 1}* is also Q(i). As a technicality, there may be some binary strings that represent no meaningful abstract-problem instance. For convenience, we shall assume that any such string is mapped arbitrarily to 0. Thus, the concrete problem produces the same solutions as the abstract problem on binary-string instances that represent the encodings of abstract-problem instances. We would like to extend the definition of polynomial-time solvability from concrete problems to abstract problems by using encodings as the bridge, but we would like the definition to be independent of any particular encoding. That is, the efficiency of solving a problem should not depend on how the problem is encoded. Unfortunately, it depends quite heavily on the encoding. For example, suppose that an integer k is to be provided as the sole input to an algorithm, and suppose that the running time of the algorithm is Θ(k). If the integer k is provided in unary-a string of k 1's-then the running time of the algorithm is O(n) on length-n inputs, which is polynomial time. If we use the more natural binary representation of the integer k, however, then the input length is n = ⌊lg k⌋ + 1. In this case, the running time of the algorithm is Θ (k) = Θ(2), which is exponential in the size of the input. Thus, depending on the encoding, the algorithm runs in either polynomial or superpolynomial time. The encoding of an abstract problem is therefore quite important to our under-standing of polynomial time. We cannot really talk about solving an abstract problem without first specifying an encoding. Nevertheless, in practice, if we rule out "expensive" encodings such as unary ones, the actual encoding of a problem makes little difference to whether the problem can be solved in polynomial time. For example, representing integers in base 3 instead of binary has no effect on whether a problem is solvable in polynomial time, since an integer represented in base 3 can be converted to an integer represented in base 2 in polynomial time. We say that a function f : {0, 1}* → {0,1}* is polynomial-time computable if there exists a polynomial-time algorithm A that, given any input x {0, 1}*, produces as output f (x). For some set I of problem instances, we say that two encodings e1 and e2 are polynomially related if there exist two polynomial-time computable functions f12 and f21 such that for any i I , we have f12(e1(i)) = e2(i) and f21(e2(i)) = e1(i). That is, the encoding e2(i) can be computed from the encoding e1(i) by a polynomial-time algorithm, and vice versa. If two encodings e1 and e2 of an abstract problem are polynomially related, whether the problem is polynomial-time solvable or not is independent of which encoding we use, as the following lemma shows. Lemma 34.1 Let Q be an abstract decision problem on an instance set I , and let e1 and e2 be polynomially related encodings on I . Then, e1(Q) P if and only if e2(Q) P. Proof We need only prove the forward direction, since the backward direction is symmetric. Suppose, therefore, that e1(Q) can be solved in time O(nk) for some constant k. Further, suppose that for any problem instance i, the encoding e1(i) can be computed from the encoding e2(i) in time O(n) for some constant c, where n = |e2(i)|. To solve problem e2(Q), on input e2(i), we first compute e1(i) and then run the algorithm for e1(Q) on e1(i). How long does this take? The conversion of encodings takes time O(n), and therefore |e1(i)| = O(n), since the output of a serial computer cannot be longer than its running time. Solving the problem on e1(i) takes time O(|e1(i)|) = O(n), which is polynomial since both c and k are constants. Thus, whether an abstract problem has its instances encoded in binary or base 3 does not affect its "complexity," that is, whether it is polynomial-time solvable or not, but if instances are encoded in unary, its complexity may change. In order to be able to converse in an encoding-independent fashion, we shall generally assume that problem instances are encoded in any reasonable, concise fashion, unless we specifically say otherwise. To be precise, we shall assume that the encoding of an integer is polynomially related to its binary representation, and that the encoding of a finite set is polynomially related to its encoding as a list of its elements, enclosed in braces and separated by commas. (ASCII is one such encoding scheme.) With such a "standard" encoding in hand, we can derive reasonable encodings of other mathematical objects, such as tuples, graphs, and formulas. To denote the standard encoding of an object, we shall enclose the object in angle braces. Thus, G denotes the standard encoding of a graph G. As long as we implicitly use an encoding that is polynomially related to this standard encoding, we can talk directly about abstract problems without reference to any particular encoding, knowing that the choice of encoding has no effect on whether the abstract problem is polynomial-time solvable. Henceforth, we shall generally assume that all problem instances are binary strings encoded using the standard encoding, unless we explicitly specify the contrary. We shall also typically neglect the distinction between abstract and concrete problems. The reader should watch out for problems that arise in practice, however, in which a standard encoding is not obvious and the encoding does make a difference. A formal-language framework One of the convenient aspects of focusing on decision problems is that they make it easy to use the machinery of formal-language theory. It is worthwhile at this point to review some definitions from that theory. An alphabet Σ is a finite set of symbols. A language L over Σ is any set of strings made up of symbols from Σ. For example, if Σ = {0, 1}, the set L = {10, 11, 101, 111, 1011, 1101, 10001,...} is the language of binary representations of prime numbers. We denote the empty string by ε, and the empty language by Ø. The language of all strings over Σ is denoted Σ*. For example, if Σ = {0, 1}, then Σ* = {ε, 0, 1, 00, 01, 10, 11, 000,...} is the set of all binary strings. Every language L over Σ is a subset of Σ*. There are a variety of operations on languages. Set-theoretic operations, such as union and intersection, follow directly from the set-theoretic definitions. We define the complement of L by . The concatenation of two languages L1 and L2 is the language L = {x1x2 : x1 L1 and x2 L2}. The closure or Kleene star of a language L is the language L*= {ε} L L L ···, where Lk is the language obtained by

Introduction to Algorithms, Second Edition

Cilk: An Efficient Multithreaded Runtime System

The fifth release of the multithreaded language Cilk uses a provably good "work-stealing" scheduling algorithm similar to the first system, but the language has been completely redesigned and the runtime system completely reengineered. The efficiency of the new implementation was aided by a clear strategy that arose from a theoretical analysis of the scheduling algorithm: concentrate on minimizing overheads that contribute to the work, even at the expense of overheads that contribute to the critical path. Although it may seem counterintuitive to move overheads onto the critical path, this "work-first" principle has led to a portable Cilk-5 implementation in which the typical cost of spawning a parallel thread is only between 2 and 6 times the cost of a C function call on a variety of contemporary machines. Many Cilk programs run on one processor with virtually no degradation compared to equivalent C programs. This paper describes how the work-first principle was exploited in the design of Cilk-5's compiler and its runtime system. In particular, we present Cilk-5's novel "two-clone" compilation strategy and its Dijkstra-like mutual-exclusion protocol for implementing the ready deque in the work-stealing scheduler.

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Charles E. Leiserson

Papers

Introduction to Algorithms

Introduction to Algorithms, third edition

Introduction to Algorithms, Second Edition

Cilk: An Efficient Multithreaded Runtime System

The implementation of the Cilk-5 multithreaded language