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PARALLELMOLECULARDYNAMICS DepartmentofComputerScience DepartmentofChemistry J.AndrewMcCammon UniversityofHouston TerryW.Clark
"... tocommunicationandcomputationcosts.Heretheobjectivewastohavetimingdata wewantedtobeabletoquantifyvariouscomponentsofanMDsimulationwithrespect code,gromos[15],toadistributed{memoryparallelcomputer.Theobjectivesofthisstudy thatwouldaidinthedesignofascalablecodethatcouldexecuteecientlyonalarge portinge ..."
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tocommunicationandcomputationcosts.Heretheobjectivewastohavetimingdata wewantedtobeabletoquantifyvariouscomponentsofanMDsimulationwithrespect code,gromos[15],toadistributed{memoryparallelcomputer.Theobjectivesofthisstudy thatwouldaidinthedesignofascalablecodethatcouldexecuteecientlyonalarge portingexistingFortrancodes(dustydecks).ThisinvolveddevelopingFortranversions werethreefold.First,wewantedtoassessthesuitabilityofoursoftwaretools[14]for numberofprocessors.Finally,wewantedtoseeifexecutionspeedscomparabletoa aminimalamountofcodinganddebugging,dueprimarilytotheuseofoursoftwaretools. andcommunicationspeed.Oneofourprincipalconclusionsisthatwewereabletoachieve Cray{2usingbetween8and16processorsonaniPSC/860.Moreover,thiswasdonewith Craycouldbeachievedeasilywithamodestnumberofcurrent{generationnodes.Such performanceonastandardbenchmarkproblemcomparabletoreportedperformanceofa performanceseemedfeasiblebasedonaroughassessmentofcurrentprocessorperformance thegravitationalorelectrostaticforcesencounteredinbasicmechanics.Themodelreduces onlyclassicalmechanics,althoughtheforces,F,betweenatomsaremorecomplicatedthan 1.DescriptionofMDalgorithms.Thebasicmodelofmoleculardynamics[1,5,12]involves 1
A Spatial Logic based on Regions and Connection
 PROCEEDINGS 3RD INTERNATIONAL CONFERENCE ON KNOWLEDGE REPRESENTATION AND REASONING
, 1992
"... We describe an interval logic for reasoning about space. The logic simplifies an earlier theory developed by Randell and Cohn, and that of Clarke upon which the former was based. The theory supports a simpler ontology, has fewer defined functions and relations, yet does not suffer in terms of its us ..."
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Cited by 736 (32 self)
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We describe an interval logic for reasoning about space. The logic simplifies an earlier theory developed by Randell and Cohn, and that of Clarke upon which the former was based. The theory supports a simpler ontology, has fewer defined functions and relations, yet does not suffer in terms of its
Very simple classification rules perform well on most commonly used datasets
 Machine Learning
, 1993
"... The classification rules induced by machine learning systems are judged by two criteria: their classification accuracy on an independent test set (henceforth "accuracy"), and their complexity. The relationship between these two criteria is, of course, of keen interest to the machin ..."
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Cited by 542 (5 self)
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of pruning methods (e.g. Buntine & Niblett, 1992; Clark & Niblett, 1989; Mingers, 1989), where accuracy is rarely seen to decrease as pruning becomes more severe (for example, see Table 1) 1. This is so even when rules are pruned to the extreme, as happened with the "Errcomp &
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.
Freenet: A Distributed Anonymous Information Storage and Retrieval System
 INTERNATIONAL WORKSHOP ON DESIGNING PRIVACY ENHANCING TECHNOLOGIES: DESIGN ISSUES IN ANONYMITY AND UNOBSERVABILITY
, 2001
"... We describe Freenet, an adaptive peertopeer network application that permits the publication, replication, and retrieval of data while protecting the anonymity of both authors and readers. Freenet operates as a network of identical nodes that collectively pool their storage space to store data ..."
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Cited by 1062 (12 self)
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We describe Freenet, an adaptive peertopeer network application that permits the publication, replication, and retrieval of data while protecting the anonymity of both authors and readers. Freenet operates as a network of identical nodes that collectively pool their storage space to store data files and cooperate to route requests to the most likely physical location of data. No broadcast search or centralized location index is employed. Files are referred to in a locationindependent manner, and are dynamically replicated in locations near requestors and deleted from locations where there is no interest. It is infeasible to discover the true origin or destination of a file passing through the network, and difficult for a node operator to determine or be held responsible for the actual physical contents of her own node.
Automatic verification of finitestate concurrent systems using temporal logic specifications
 ACM Transactions on Programming Languages and Systems
, 1986
"... We give an efficient procedure for verifying that a finitestate concurrent system meets a specification expressed in a (propositional, branchingtime) temporal logic. Our algorithm has complexity linear in both the size of the specification and the size of the global state graph for the concurrent ..."
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Cited by 1384 (62 self)
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We give an efficient procedure for verifying that a finitestate concurrent system meets a specification expressed in a (propositional, branchingtime) temporal logic. Our algorithm has complexity linear in both the size of the specification and the size of the global state graph for the concurrent system. We also show how this approach can be adapted to handle fairness. We argue that our technique can provide a practical alternative to manual proof construction or use of a mechanical theorem prover for verifying many finitestate concurrent systems. Experimental results show that state machines with several hundred states can be checked in a matter of seconds.
Constrained model predictive control: Stability and optimality
 AUTOMATICA
, 2000
"... Model predictive control is a form of control in which the current control action is obtained by solving, at each sampling instant, a finite horizon openloop optimal control problem, using the current state of the plant as the initial state; the optimization yields an optimal control sequence and t ..."
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Cited by 696 (15 self)
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Model predictive control is a form of control in which the current control action is obtained by solving, at each sampling instant, a finite horizon openloop optimal control problem, using the current state of the plant as the initial state; the optimization yields an optimal control sequence and the first control in this sequence is applied to the plant. An important advantage of this type of control is its ability to cope with hard constraints on controls and states. It has, therefore, been widely applied in petrochemical and related industries where satisfaction of constraints is particularly important because efficiency demands operating points on or close to the boundary of the set of admissible states and controls. In this review, we focus on model predictive control of constrained systems, both linear and nonlinear and discuss only briefly model predictive control of unconstrained nonlinear and/or timevarying systems. We concentrate our attention on research dealing with stability and optimality; in these areas the subject has developed, in our opinion, to a stage where it has achieved sufficient maturity to warrant the active interest of researchers in nonlinear control. We distill from an extensive literature essential principles that ensure stability and use these to present a concise characterization of most of the model predictive controllers that have been proposed in the literature. In some cases the finite horizon optimal control problem solved online is exactly equivalent to the same problem with an infinite horizon; in other cases it is equivalent to a modified infinite horizon optimal control problem. In both situations, known advantages of infinite horizon optimal control accrue.
Integrating classification and association rule mining
 In Proc of KDD
, 1998
"... Classification rule mining aims to discover a small set of rules in the database that forms an accurate classifier. Association rule mining finds all the rules existing in the database that satisfy some minimum support and minimum confidence constraints. For association rule mining, the target of di ..."
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Cited by 561 (21 self)
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Classification rule mining aims to discover a small set of rules in the database that forms an accurate classifier. Association rule mining finds all the rules existing in the database that satisfy some minimum support and minimum confidence constraints. For association rule mining, the target of discovery is not predetermined, while for classification rule mining there is one and only one predetermined target. In this paper, we propose to integrate these two mining techniques. The integration is done by focusing on mining a special subset of association rules, called class association rules (CARs). An efficient algorithm is also given for building a classifier based on the set of discovered CARs. Experimental results show that the classifier built this way is, in general, more accurate than that produced by the stateoftheart classification system C4.5. In addition, this integration helps to solve a number of problems that exist in the current classification systems.
Constraint Logic Programming: A Survey
"... Constraint Logic Programming (CLP) is a merger of two declarative paradigms: constraint solving and logic programming. Although a relatively new field, CLP has progressed in several quite different directions. In particular, the early fundamental concepts have been adapted to better serve in differe ..."
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Cited by 864 (25 self)
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Constraint Logic Programming (CLP) is a merger of two declarative paradigms: constraint solving and logic programming. Although a relatively new field, CLP has progressed in several quite different directions. In particular, the early fundamental concepts have been adapted to better serve in different areas of applications. In this survey of CLP, a primary goal is to give a systematic description of the major trends in terms of common fundamental concepts. The three main parts cover the theory, implementation issues, and programming for applications.
Learning to rank using gradient descent
 In ICML
, 2005
"... We investigate using gradient descent methods for learning ranking functions; we propose a simple probabilistic cost function, and we introduce RankNet, an implementation of these ideas using a neural network to model the underlying ranking function. We present test results on toy data and on data f ..."
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Cited by 510 (17 self)
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We investigate using gradient descent methods for learning ranking functions; we propose a simple probabilistic cost function, and we introduce RankNet, an implementation of these ideas using a neural network to model the underlying ranking function. We present test results on toy data and on data from a commercial internet search engine. 1.
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