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Computational Biology Lecture 5: Time speedup, General gap penalty function
"... We saw earlier that it is possible to compute optimal global alignments in linear space (it can also be done for local alignments). Now we will look at how to speedup time in some cases. Similar sequences: Bounded dynamic programming If we believe that the two sequences x and y are similar then we m ..."
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We saw earlier that it is possible to compute optimal global alignments in linear space (it can also be done for local alignments). Now we will look at how to speedup time in some cases. Similar sequences: Bounded dynamic programming If we believe that the two sequences x and y are similar then we
Pegasos: Primal Estimated subgradient solver for SVM
"... We describe and analyze a simple and effective stochastic subgradient descent algorithm for solving the optimization problem cast by Support Vector Machines (SVM). We prove that the number of iterations required to obtain a solution of accuracy ɛ is Õ(1/ɛ), where each iteration operates on a singl ..."
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Cited by 542 (20 self)
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runtime of our method is Õ(d/(λɛ)), where d is a bound on the number of nonzero features in each example. Since the runtime does not depend directly on the size of the training set, the resulting algorithm is especially suited for learning from large datasets. Our approach also extends to non
Transfer of Cognitive Skill
, 1989
"... A framework for skill acquisition is proposed that includes two major stages in the development of a cognitive skill: a declarative stage in which facts about the skill domain are interpreted and a procedural stage in which the domain knowledge is directly embodied in procedures for performing the s ..."
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Cited by 894 (22 self)
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. These processes include generalization, discrimination, and strengthening of productions. Comparisons are made to similar concepts from past learning theories. How these learning mechanisms apply to produce the power law speedup in processing time with practice is discussed. It requires at least 100 hours
Evaluation of Release Consistent Software Distributed Shared Memory on Emerging Network Technology
"... We evaluate the effect of processor speed, network characteristics, and software overhead on the performance of releaseconsistent software distributed shared memory. We examine five different protocols for implementing release consistency: eager update, eager invalidate, lazy update, lazy invalidat ..."
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Cited by 467 (43 self)
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independent of the protocol used. Mediumgrained applications, such as Water, can achieve good performance, but the choice of protocol is critical. For sixteen processors, the best protocol, lazy hybrid, performed more than three times better than the worst, the eager update. Finegrained applications
A scaled conjugate gradient algorithm for fast supervised learning
 NEURAL NETWORKS
, 1993
"... A supervised learning algorithm (Scaled Conjugate Gradient, SCG) with superlinear convergence rate is introduced. The algorithm is based upon a class of optimization techniques well known in numerical analysis as the Conjugate Gradient Methods. SCG uses second order information from the neural netwo ..."
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Cited by 451 (0 self)
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FletcherGoldfarbShanno memoryless quasiNewton algorithm (BFGS) [1]. SCG yields a speedup of at least an order of magnitude relative to BP. The speedup depends on the convergence criterion, i.e., the bigger demand for reduction in error the bigger the speedup. SCG is fully automated including no user dependent parameters
Fast approximate nearest neighbors with automatic algorithm configuration
 In VISAPP International Conference on Computer Vision Theory and Applications
, 2009
"... nearestneighbors search, randomized kdtrees, hierarchical kmeans tree, clustering. For many computer vision problems, the most time consuming component consists of nearest neighbor matching in highdimensional spaces. There are no known exact algorithms for solving these highdimensional problems ..."
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Cited by 455 (2 self)
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nearestneighbors search, randomized kdtrees, hierarchical kmeans tree, clustering. For many computer vision problems, the most time consuming component consists of nearest neighbor matching in highdimensional spaces. There are no known exact algorithms for solving these high
Efficient ray tracing of volume data
 ACM Transactions on Graphics
, 1990
"... Volume rendering is a technique for visualizing sampled scalar or vector fields of three spatial dimensions without fitting geometric primitives to the data. A subset of these techniques generates images by computing 2D projections of a colored semitransparent volume, where the color and opacity at ..."
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Cited by 392 (5 self)
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performance. The first technique employs a pyramid of binary volumes to encode spatial coherence present in the data, and the second technique uses an opacity threshold to adaptively terminate ray tracing. Although the actual time saved depends on the data, speedups of an order of magnitude have been observed
Optimal Speedup of Las Vegas Algorithms
 Information Processing Letters
, 1993
"... Let A be a Las Vegas algorithm, i.e., A is a randomized algorithm that always produces the correct answer when it stops but whose running time is a random variable. We consider the problem of minimizing the expected time required to obtain an answer from A using strategies which simulate A as follow ..."
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Cited by 153 (0 self)
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Let A be a Las Vegas algorithm, i.e., A is a randomized algorithm that always produces the correct answer when it stops but whose running time is a random variable. We consider the problem of minimizing the expected time required to obtain an answer from A using strategies which simulate A
Routing In Clustered Multihop, Mobile Wireless Networks With Fading Channel
, 2005
"... A clusterheadtoken infrastructure for multihop, mobile wireless networks has been designed. Traditional routing algorithms in wireline networks are not feasible for mobile wireless environment due to the dynamic change in link connectivity. To gain better performance for clustered multihop, mobile ..."
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Cited by 368 (9 self)
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compared with shortestpathscheme, making multimedia tra c viable. A radio channel model has been included to investigate the impact of channel fading on our protocols. To reduce the run time, a parallel simulator has been designed. Speedups of up to tenfold have been observed on a 16 processor SP/2.
Boosting combinatorial search through randomization
, 1998
"... Unpredictability in the running time of complete search procedures can often be explained by the phenomenon of “heavytailed cost distributions”, meaning that at any time during the experiment there is a nonnegligible probability of hitting a problem that requires exponentially more time to solve t ..."
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Cited by 361 (35 self)
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tails to the left of the median (that is, a nonnegligible chance of very short runs) to dramatically shorten the solution time. We demonstrate speedups of several orders of magnitude for stateoftheart complete search procedures running on hard, realworld problems.
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