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143,339
Virtual Time and Global States of Distributed Systems
 PARALLEL AND DISTRIBUTED ALGORITHMS
, 1988
"... A distributed system can be characterized by the fact that the global state is distributed and that a common time base does not exist. However, the notion of time is an important concept in every day life of our decentralized "real world" and helps to solve problems like getting a consiste ..."
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Cited by 741 (6 self)
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A distributed system can be characterized by the fact that the global state is distributed and that a common time base does not exist. However, the notion of time is an important concept in every day life of our decentralized "real world" and helps to solve problems like getting a consistent population census or determining the potential causality between events. We argue that a linearly ordered structure of time is not (always) adequate for distributed systems and propose a generalized nonstandardmodel of time which consists of vectors of clocks. These clockvectors arepartially orderedand form a lattice. By using timestamps and a simple clock update mechanism the structure of causality is represented in an isomorphic way. The new model of time has a close analogy to Minkowski's relativistic spacetime and leads among others to an interesting characterization of the global state problem. Finally, we present a new algorithm to compute a consistent global snapshot of a distributed system where messages may bereceived out of order.
Improved Approximation Algorithms for Maximum Cut and Satisfiability Problems Using Semidefinite Programming
 Journal of the ACM
, 1995
"... We present randomized approximation algorithms for the maximum cut (MAX CUT) and maximum 2satisfiability (MAX 2SAT) problems that always deliver solutions of expected value at least .87856 times the optimal value. These algorithms use a simple and elegant technique that randomly rounds the solution ..."
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Cited by 1231 (13 self)
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We present randomized approximation algorithms for the maximum cut (MAX CUT) and maximum 2satisfiability (MAX 2SAT) problems that always deliver solutions of expected value at least .87856 times the optimal value. These algorithms use a simple and elegant technique that randomly rounds the solution to a nonlinear programming relaxation. This relaxation can be interpreted both as a semidefinite program and as an eigenvalue minimization problem. The best previously known approximation algorithms for these problems had performance guarantees of ...
Convex Analysis
, 1970
"... In this book we aim to present, in a unified framework, a broad spectrum of mathematical theory that has grown in connection with the study of problems of optimization, equilibrium, control, and stability of linear and nonlinear systems. The title Variational Analysis reflects this breadth. For a lo ..."
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Cited by 5350 (67 self)
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In this book we aim to present, in a unified framework, a broad spectrum of mathematical theory that has grown in connection with the study of problems of optimization, equilibrium, control, and stability of linear and nonlinear systems. The title Variational Analysis reflects this breadth. For a long time, ‘variational ’ problems have been identified mostly with the ‘calculus of variations’. In that venerable subject, built around the minimization of integral functionals, constraints were relatively simple and much of the focus was on infinitedimensional function spaces. A major theme was the exploration of variations around a point, within the bounds imposed by the constraints, in order to help characterize solutions and portray them in terms of ‘variational principles’. Notions of perturbation, approximation and even generalized differentiability were extensively investigated. Variational theory progressed also to the study of socalled stationary points, critical points, and other indications of singularity that a point might have relative to its neighbors, especially in association with existence theorems for differential equations.
The swissprot protein knowledgebase and its supplement trembl in 2003
 Nucleic Acids Res
, 2003
"... The SWISSPROT protein knowledgebase ..."
Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. sect
 A
, 1991
"... Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the q ..."
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Cited by 1016 (9 self)
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Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the modelbuilding process, quantify the goodness of fit of the model on a perresidue basis and locate possible errors in peptide and sidechain conformations.
Parameterized Complexity
, 1998
"... the rapidly developing systematic connections between FPT and useful heuristic algorithms  a new and exciting bridge between the theory of computing and computing in practice. The organizers of the seminar strongly believe that knowledge of parameterized complexity techniques and results belongs ..."
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Cited by 1218 (75 self)
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the rapidly developing systematic connections between FPT and useful heuristic algorithms  a new and exciting bridge between the theory of computing and computing in practice. The organizers of the seminar strongly believe that knowledge of parameterized complexity techniques and results belongs into the toolkit of every algorithm designer. The purpose of the seminar was to bring together leading experts from all over the world, and from the diverse areas of computer science that have been attracted to this new framework. The seminar was intended as the rst larger international meeting with a specic focus on parameterized complexity, and it hopefully serves as a driving force in the development of the eld. 1 We had 49 participants from Australia, Canada, India, Israel, New Zealand, USA, and various European countries. During the workshop 25 lectures were given. Moreover, one night session was devoted to open problems and Thursday was basically used for problem discussion
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
, 2003
"... The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The ..."
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Cited by 2109 (30 self)
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The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The core of this method is a simple hillclimbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distancebased method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximumlikelihood programs and much higher than the performance of distancebased and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximumlikelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distancebased and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page:
Modeling and simulation of genetic regulatory systems: A literature review
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
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Cited by 729 (15 self)
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In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rulebased formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems.
Results 1  10
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