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102,283
Knowledgebased Analysis of Microarray Gene Expression Data By Using Support Vector Machines
, 2000
"... We introduce a method of functionally classifying genes by using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines (SVMs). SVMs are considered a supervised computer learning method because they exploit prior knowledge of ..."
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Cited by 514 (8 self)
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of gene function to identify unknown genes of similar function from expression data. SVMs avoid several problems associated with unsupervised clustering methods, such as hierarchical clustering and selforganizing maps. SVMs have many mathematical features that make them attractive for gene expression
Symbolic Model Checking for Realtime Systems
 INFORMATION AND COMPUTATION
, 1992
"... We describe finitestate programs over realnumbered time in a guardedcommand language with realvalued clocks or, equivalently, as finite automata with realvalued clocks. Model checking answers the question which states of a realtime program satisfy a branchingtime specification (given in an ..."
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Cited by 574 (50 self)
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We describe finitestate programs over realnumbered time in a guardedcommand language with realvalued clocks or, equivalently, as finite automata with realvalued clocks. Model checking answers the question which states of a realtime program satisfy a branchingtime specification (given
UPPAAL in a Nutshell
, 1997
"... . This paper presents the overall structure, the design criteria, and the main features of the tool box Uppaal. It gives a detailed user guide which describes how to use the various tools of Uppaal version 2.02 to construct abstract models of a realtime system, to simulate its dynamical behavior, ..."
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Cited by 663 (49 self)
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. This paper presents the overall structure, the design criteria, and the main features of the tool box Uppaal. It gives a detailed user guide which describes how to use the various tools of Uppaal version 2.02 to construct abstract models of a realtime system, to simulate its dynamical behavior, to specify and verify its safety and bounded liveness properties in terms of its model. In addition, the paper also provides a short review on casestudies where Uppaal is applied, as well as references to its theoretical foundation. 1 Introduction Uppaal is a tool box for modeling, simulation and verification of realtime systems, based on constraintsolving and onthefly techniques, developed jointly by Uppsala University and Aalborg University. It is appropriate for systems that can be modeled as a collection of nondeterministic processes with finite control structure and realvalued clocks, communicating through channels and (or) shared variables [34, 26]. Typical application areas in...
A New Kind of Science
, 2002
"... “Somebody says, ‘You know, you people always say that space is continuous. How do you know when you get to a small enough dimension that there really are enough points in between, that it isn’t just a lot of dots separated by little distances? ’ Or they say, ‘You know those quantum mechanical amplit ..."
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Cited by 850 (0 self)
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“Somebody says, ‘You know, you people always say that space is continuous. How do you know when you get to a small enough dimension that there really are enough points in between, that it isn’t just a lot of dots separated by little distances? ’ Or they say, ‘You know those quantum mechanical amplitudes you told me about, they’re so complicated and absurd, what makes you think those are right? Maybe they aren’t right. ’ Such remarks are obvious and are perfectly clear to anybody who is working on this problem. It does not do any good to point this out.” —Richard Feynman [1, p.161]
Temporal and modal logic
 HANDBOOK OF THEORETICAL COMPUTER SCIENCE
, 1995
"... We give a comprehensive and unifying survey of the theoretical aspects of Temporal and modal logic. ..."
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Cited by 1300 (17 self)
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We give a comprehensive and unifying survey of the theoretical aspects of Temporal and modal logic.
Genetic Programming
, 1997
"... Introduction Genetic programming is a domainindependent problemsolving approach in which computer programs are evolved to solve, or approximately solve, problems. Genetic programming is based on the Darwinian principle of reproduction and survival of the fittest and analogs of naturally occurring ..."
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Cited by 1051 (12 self)
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Introduction Genetic programming is a domainindependent problemsolving approach in which computer programs are evolved to solve, or approximately solve, problems. Genetic programming is based on the Darwinian principle of reproduction and survival of the fittest and analogs of naturally occurring genetic operations such as crossover (sexual recombination) and mutation. John Holland's pioneering Adaptation in Natural and Artificial Systems (1975) described how an analog of the evolutionary process can be applied to solving mathematical problems and engineering optimization problems using what is now called the genetic algorithm (GA). The genetic algorithm attempts to find a good (or best) solution to the problem by genetically breeding a population of individuals over a series of generations. In the genetic algorithm, each individual in the population represents a candidate solut
Statecharts: A Visual Formalism For Complex Systems
, 1987
"... We present a broad extension of the conventional formalism of state machines and state diagrams, that is relevant to the specification and design of complex discreteevent systems, such as multicomputer realtime systems, communication protocols and digital control units. Our diagrams, which we cal ..."
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Cited by 2683 (56 self)
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We present a broad extension of the conventional formalism of state machines and state diagrams, that is relevant to the specification and design of complex discreteevent systems, such as multicomputer realtime systems, communication protocols and digital control units. Our diagrams, which we call statecharts, extend conventional statetransition diagrams with essentially three olements, dealing, respectively, with the notions of hierarchy, concurrency and communication. These transform the language of state diagrams into a highly structured' and economical description language. Statecharts are thus compact and expressivesmall diagrams can express complex behavioras well as compositional and modular. When coupled with the capabilities of computerized graphics, statecharts enable viewing the description at different levels of detail, and make even very large specifications manageable and comprehensible. In fact, we intend to demonstrate here that statecharts counter many of the objections raised against conventional state diagrams, and thus appear to render specification by diagrams an attractive and plausible approach. Statecharts can be used either as a standalone behavioral description or as part of a more general design methodology that deals also with the system's other aspects, such as functional decomposition and dataflow specification. We also discuss some practical experience that was gained over the last three years in applying the statechart formalism to the specification of a particularly complex system.
WaitFree Synchronization
 ACM Transactions on Programming Languages and Systems
, 1993
"... A waitfree implementation of a concurrent data object is one that guarantees that any process can complete any operation in a finite number of steps, regardless of the execution speeds of the other processes. The problem of constructing a waitfree implementation of one data object from another lie ..."
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Cited by 873 (28 self)
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A waitfree implementation of a concurrent data object is one that guarantees that any process can complete any operation in a finite number of steps, regardless of the execution speeds of the other processes. The problem of constructing a waitfree implementation of one data object from another lies at the heart of much recent work in concurrent algorithms, concurrent data structures, and multiprocessor architectures. In the first part of this paper, we introduce a simple and general technique, based on reduction to a consensus protocol, for proving statements of the form "there is no waitfree implementation of X by Y ." We derive a hierarchy of objects such that no object at one level has a waitfree implementation in terms of objects at lower levels. In particular, we show that atomic read/write registers, which have been the focus of much recent attention, are at the bottom of the hierarchy: they cannot be used to construct waitfree implementations of many simple and familiar da...
A Structural Approach to Operational Semantics
, 1981
"... Syntax of a very simple programming language called L. What is abstract about it will be discussed a little here and later at greater length. For us syntax is a collection of syntactic sets of phrases; each set corresponds to a different type of phrase. Some of these sets are very simple and can be ..."
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Cited by 1541 (3 self)
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Syntax of a very simple programming language called L. What is abstract about it will be discussed a little here and later at greater length. For us syntax is a collection of syntactic sets of phrases; each set corresponds to a different type of phrase. Some of these sets are very simple and can be taken as given: Truthvalues This is the set T = ftt; ffg and is ranged over by (the metavariable) t (and we also happily employ for this (and any other) metavariable sub and superscripts to generate other metavariables: t ; t 0 ; t 1k ).
A Guided Tour to Approximate String Matching
 ACM COMPUTING SURVEYS
, 1999
"... We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining t ..."
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Cited by 584 (38 self)
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We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices according to each case. We conclude with some future work directions and open problems.
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