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197
Boltzmann Samplers For The Random Generation Of Combinatorial Structures
 Combinatorics, Probability and Computing
, 2004
"... This article proposes a surprisingly simple framework for the random generation of combinatorial configurations based on what we call Boltzmann models. The idea is to perform random generation of possibly complex structured objects by placing an appropriate measure spread over the whole of a combina ..."
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Cited by 67 (2 self)
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This article proposes a surprisingly simple framework for the random generation of combinatorial configurations based on what we call Boltzmann models. The idea is to perform random generation of possibly complex structured objects by placing an appropriate measure spread over the whole of a combinatorial class  an object receives a probability essentially proportional to an exponential of its size. As demonstrated here, the resulting algorithms based on realarithmetic operations often operate in linear time. They can be implemented easily, be analysed mathematically with great precision, and, when suitably tuned, tend to be very efficient in practice.
On Pattern Frequency Occurrences In A Markovian Sequence?
 Algorithmica
, 1997
"... Consider a given pattern H and a random text T generated by a Markovian source. We study the frequency of pattern occurrences in a random text when overlapping copies of the pattern are counted separately. We present exact and asymptotic formulae for all moments (including the variance), and probabi ..."
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Cited by 63 (24 self)
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Consider a given pattern H and a random text T generated by a Markovian source. We study the frequency of pattern occurrences in a random text when overlapping copies of the pattern are counted separately. We present exact and asymptotic formulae for all moments (including the variance), and probability of r pattern occurrences for three different regions of r, namely: (i) r = O(1), (ii) central limit regime, and (iii) large deviations regime. In order to derive these results, we first construct some language expressions that characterize pattern occurrences which are later translated into generating functions. Finally, we use analytical methods to extract asymptotic behaviors of the pattern frequency. Applications of these results include molecular biology, source coding, synchronization, wireless communications, approximate pattern matching, game theory, and stock market analysis. These findings are of particular interest to information theory (e.g., secondorder properties of the re...
Approximation Algorithms for Finding Highly Connected Subgraphs
, 1996
"... Contents 1 Introduction 2 1.1 Outline of Chapter : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 3 2 EdgeConnectivity Problems 3 2.1 Weighted EdgeConnectivity : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 3 2.2 Unweighted EdgeConnectivity : : : : : ..."
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Cited by 60 (1 self)
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Contents 1 Introduction 2 1.1 Outline of Chapter : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 3 2 EdgeConnectivity Problems 3 2.1 Weighted EdgeConnectivity : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 3 2.2 Unweighted EdgeConnectivity : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 4 2.2.1 2 EdgeConnectivity : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 4 2.2.2 EdgeConnectivity : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 8 3 VertexConnectivity Problems 11 3.1 Weighted VertexConnectivity : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 11 3.2 Unweighted VertexConnectivity : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 12 3.2.1 2 VertexConnectivity : : : : : : : : : : : : : : : : :
Algebraic Properties of Cellular Automata
, 1984
"... This paper details and extends the discussion of global proper72 L a T E X filename: Algebraic.tex (Paper: 1.2 [2]) 12:08 p.m. October 20, 1993 Algebraic Properties of Cellular Automata (1984) Figure 2. Global state transition diagrams for finite cellular automata with size N and periodic boundary c ..."
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Cited by 58 (1 self)
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This paper details and extends the discussion of global proper72 L a T E X filename: Algebraic.tex (Paper: 1.2 [2]) 12:08 p.m. October 20, 1993 Algebraic Properties of Cellular Automata (1984) Figure 2. Global state transition diagrams for finite cellular automata with size N and periodic boundary conditions evolving according to the rule Ö(x) = x + x
Dynamical Recognizers: Realtime Language Recognition by Analog Computers
 Theoretical Computer Science
, 1996
"... We consider a model of analog computation which can recognize various languages in real time. We encode an input word as a point in R d by composing iterated maps, and then apply inequalities to the resulting point to test for membership in the language. Each class of maps and inequalities, suc ..."
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Cited by 57 (4 self)
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We consider a model of analog computation which can recognize various languages in real time. We encode an input word as a point in R d by composing iterated maps, and then apply inequalities to the resulting point to test for membership in the language. Each class of maps and inequalities, such as quadratic functions with rational coefficients, is capable of recognizing a particular class of languages; for instance, linear and quadratic maps can have both stacklike and queuelike memories. We use methods equivalent to the VapnikChervonenkis dimension to separate some of our classes from each other, e.g. linear maps are less powerful than quadratic or piecewiselinear ones, polynomials are less powerful than elementary (trigonometric and exponential) maps, and deterministic polynomials of each degree are less powerful than their nondeterministic counterparts. Comparing these dynamical classes with various discrete language classes helps illuminate how iterated maps can...
Consensus Folding of Aligned Sequences as a New Measure for the Detection of Functional RNAs by Comparative Genomics
, 2004
"... Facing the evergrowing list of newly discovered classes of functional RNAs, it can be expected that further types of functional RNAs are still hidden in recently completed genomes. The computational identification of such RNA genes is, therefore, of major importance. While most known functional RNA ..."
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Cited by 57 (14 self)
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Facing the evergrowing list of newly discovered classes of functional RNAs, it can be expected that further types of functional RNAs are still hidden in recently completed genomes. The computational identification of such RNA genes is, therefore, of major importance. While most known functional RNAs have characteristic secondary structures, their free energies are generally not statistically significant enough to distinguish RNA genes from the genomic background. Additional information is required. Considering the wide availability of new genomic data of closely related species, comparative studies seem to be the most promising approach. Here we show that prediction of consensus structures of aligned sequences can be a significant measure to detect functional RNAs. We report a new method how to test multiple sequence alignments for the existence of an unusually structured and conserved fold. We show for alignments of six types of well known functional RNA that an energy score consisting of free energy and a covariation term significantly improves sensitivity compared to single sequence predictions. We further test our method on a number of non coding RNAs from C. elegans/C. briggsae and seven Saccharomyces species. Most RNAs can be detected with high significance. We provide a Perl implementation which can be readily used to score single alignments and discuss how the methods described here can be extended to allow for e#cient genomewide screens.
A timespace tradeoff for sorting on a general sequential model of computation
 SIAM Journal on Computing
, 1982
"... Abstract. In a general sequential model of computation, no restrictions are placed on theway in which the computation may proceed, except that parallel operations are not allowed. We show that in such an unrestricted environment TIME.SPACE fl(N2/logN) in order to sort N integers, each in the range [ ..."
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Cited by 55 (6 self)
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Abstract. In a general sequential model of computation, no restrictions are placed on theway in which the computation may proceed, except that parallel operations are not allowed. We show that in such an unrestricted environment TIME.SPACE fl(N2/logN) in order to sort N integers, each in the range [,N]. Key words, timespace tradeoffs, conputational complexity, sorting, time lower bounds, space lower bounds
Aspects of Networking in Multiplayer Computer Games
, 2001
"... Distributed, realtime multiplayer computer games (MCGs) are in the vanguard of utilizing the networking possibilities. Although related research have been done in military simulations, virtual reality systems, and computer supported cooperative working, the suggested solutions diverge from the prob ..."
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Cited by 51 (1 self)
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Distributed, realtime multiplayer computer games (MCGs) are in the vanguard of utilizing the networking possibilities. Although related research have been done in military simulations, virtual reality systems, and computer supported cooperative working, the suggested solutions diverge from the problems posed by MCGs. With this in mind, this paper provides a concise overview of four aspects affecting networking in MCGs. Firstly, networking resources (bandwidth, latency, and computational power) set the technical boundaries within which the MCG must operate. Secondly, distribution concepts encompass communication architectures (peertopeer, client/server, servernetwork), and both data and control architectures (centralized, distributed, replicated). Thirdly, scalability allows the MCG to adapt to the resource changes by parametrization. Finally, security aims at fighting back against cheating and vandalism, which are common in online gaming. KeywordsComputer games, networking, online entertainment, distributed interactive simulation, virtual environments.
On the efficient implementation of fair queueing
 Journal of Internetworking: Research and Experience
, 1991
"... The performance of packet switched data networks is greatly influenced by the queue service discipline in routers and switches. In particular, the Fair Queueing discipline [1] has several advantages over the traditional firstcomefirstserved discipline. This paper studies data structures and algo ..."
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Cited by 49 (0 self)
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The performance of packet switched data networks is greatly influenced by the queue service discipline in routers and switches. In particular, the Fair Queueing discipline [1] has several advantages over the traditional firstcomefirstserved discipline. This paper studies data structures and algorithms for the efficient implementation of Fair Queueing. We present a novel performance evaluation methodology and use it to evaluate the relative merits of several alternate implementations.
A subexponential algorithm for abstract optimization problems
 SIAM J. Comput
, 1995
"... An Abstract Optimization Problem (AOP) is a triple (H, <, Φ) where H is a finite set, < a total order on 2 H and Φ an oracle that, for given F ⊆ G ⊆ H, either reports that F = min<{F ′  F ′ ⊆ G} or returns a set F ′ ⊆ G with F ′ < F. To solve the problem means to find the minimum set in H. We pr ..."
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Cited by 49 (5 self)
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An Abstract Optimization Problem (AOP) is a triple (H, <, Φ) where H is a finite set, < a total order on 2 H and Φ an oracle that, for given F ⊆ G ⊆ H, either reports that F = min<{F ′  F ′ ⊆ G} or returns a set F ′ ⊆ G with F ′ < F. To solve the problem means to find the minimum set in H. We present a randomized algorithm that solves any AOP with an expected number of at most e 2 √ n+O ( 4 √ n ln n) oracle calls, n = H. In contrast, any deterministic algorithm needs to make 2 n − 1 oracle calls in the worst case. The algorithm is applied to the problem of finding the distance between two nvertex (or nfacet) convex polyhedra in dspace, and to the computation of the smallest ball containing n points in dspace; for both problems we give the first subexponential bounds in the arithmetic model of computation.