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

SUMMARY TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers. AVAILABILITY http://www.tree-puzzle.de. The program is written in ANSI C. TREE-PUZZLE can be run on UNIX, Windows and Mac systems, including Mac OS X. To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/).

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

https://users.dcc.uchile.cl/~clgutier/srikant95.pdf

Mining generalized association rules

In this paper, we give for constant $k$ a linear-time algorithm that, given a graph $G=(V,E)$, determines whether the treewidth of $G$ is at most $k$ and, if so, finds a tree-decomposition of $G$ with treewidth at most $k$. A consequence is that every minor-closed class of graphs that does not contain all planar graphs has a linear-time recognition algorithm. Another consequence is that a similar result holds when we look instead for path-decompositions with pathwidth at most some constant $k$.

/pdf/a-linear-time-algorithm-for-finding-tree-decompositions-of-4u8h6zpm0r.pdf

A Linear-Time Algorithm for Finding Tree-Decompositions of Small Treewidth

Written by an authority in the field, this book provides an introduction to the design and analysis of parallel algorithms. The emphasis is on the application of the PRAM (parallel random access machine) model of parallel computation, with all its variants, to algorithm analysis. Special attention is given to the selection of relevant data structures and to algorithm design principles that have proved to be useful. Features *Uses PRAM (parallel random access machine) as the model for parallel computation. *Covers all essential classes of parallel algorithms. *Rich exercise sets. *Written by a highly respected author within the field. 0201548569B04062001

/pdf/an-introduction-to-parallel-algorithms-c3tag3zjaf.pdf

An introduction to parallel algorithms

A guided tour of Chernoff bounds

http://www.mathcs.emory.edu/~whalen/Hash/Hash_Articles/A%20Reliable%20Randomized%20Algorithm%20for%20the%20Closest-Pair%20Problem%20(DUPLICATE%20GROUPING).pdf

A Reliable Randomized Algorithm for the Closest-Pair Problem

We show that a unit-cost RAM with a word length of bits can sort integers in the range in time, for arbitrary ! , a significant improvement over the bound of " # $ achieved by the fusion trees of Fredman and Willard. Provided that % & ' ( *),+., for some fixed /102 , the sorting can even be accomplished in linear expected time with a randomized algorithm. Both of our algorithms parallelize without loss on a unitcost PRAM with a word length of bits. The first one yields an algorithm that uses 3 4 5 $ time and 6 ( operations on a deterministic CRCW PRAM. The second one yields an algorithm that uses ' 5 7 expected time and " expected operations on a randomized EREW PRAM, provided that 8 ' 5 7 *),+.for some fixed /90: . Our deterministic and randomized sequential and parallel algorithms generalize to the lexicographic sorting problem of sorting multiple-precision integers represented in several words.

/pdf/sorting-in-linear-time-1x8lpo6xwh.pdf

Sorting in linear time

It is shown that a static dictionary that offers constant-time access to n elements with w-bit keys and occupies O(n) words of memory can be constructed deterministically in O(nlogn) time on a unit-cost RAM with word length w and a standard instruction set including multiplication. Whereas a randomized construction working in linear expected time was known, the running time of the best previous deterministic algorithm was ?(n2). Using a standard dynamization technique, the first deterministic dynamic dictionary with constant lookup time and sublinear update time is derived. The new algorithms are weakly nonuniform; i.e., they require access to a fixed number of precomputed constants dependent on w. The main technical tools employed are unit-cost error-correcting codes, word parallelism, and derandomization using conditional expectations.

Deterministic Dictionaries

A word RAM is a unit-cost random-access machine with a word length of w bits, for some w, and with an instruction repertoire similar to that found in present-day computers. The simple lower bounds for the problems of sorting and searching valid in the comparison-based model do not hold for the word RAM, so that the well-known algorithms for these tasks are not optimal for the word RAM. This paper gives an overview of faster algorithms known for sorting and searching on the word RAM, many of which were developed within the last few years.

Torben Hagerup

Papers

A guided tour of Chernoff bounds

A Reliable Randomized Algorithm for the Closest-Pair Problem

Sorting in linear time

Deterministic Dictionaries

Sorting and Searching on the Word RAM