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Algorithms for Optimizing Production DNA Sequencing
"... We discuss the problem of optimally \nishing" a partially sequenced, reconstructed DNA segment. At rst sight, this appears to be computationally hard. We construct a series of increasingly realistic models for the problem and show that all of these can in fact be solved to optimality in polynom ..."
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in polynomial time, with nearoptimal solutions available in linear time. Implementation of our algorithms could result in a substantial eciency gain for automated DNA sequencing. 1 Introduction and summary of results The Human genome comprises 24 chromosomes. Each chromosome contains a double helix of DNA
Algorithms for Optimizing Production DNA Sequencing
"... We discuss the problem of optimally \nishing" a partially sequenced, reconstructed DNA segment. At rst sight, this appears to be computationally hard. We construct a series of increasingly realistic models for the problem and show that all of these can in fact be solved to optimality in polynom ..."
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in polynomial time, with nearoptimal solutions available in linear time. Implementation of our algorithms could result in a substantial eciency gain for automated DNA sequencing. 1 Introduction and summary of results The Human genome comprises 24 chromosomes. Each chromosome contains a double helix of DNA
A greedy algorithm for aligning DNA sequences
 J. COMPUT. BIOL
, 2000
"... For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy a ..."
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Cited by 576 (16 self)
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For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy
Factor Graphs and the SumProduct Algorithm
 IEEE TRANSACTIONS ON INFORMATION THEORY
, 1998
"... A factor graph is a bipartite graph that expresses how a "global" function of many variables factors into a product of "local" functions. Factor graphs subsume many other graphical models including Bayesian networks, Markov random fields, and Tanner graphs. Following one simple c ..."
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Cited by 1787 (72 self)
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computational rule, the sumproduct algorithm operates in factor graphs to computeeither exactly or approximatelyvarious marginal functions by distributed messagepassing in the graph. A wide variety of algorithms developed in artificial intelligence, signal processing, and digital communications can
A Limited Memory Algorithm for Bound Constrained Optimization
 SIAM Journal on Scientific Computing
, 1994
"... An algorithm for solving large nonlinear optimization problems with simple bounds is described. ..."
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Cited by 557 (9 self)
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An algorithm for solving large nonlinear optimization problems with simple bounds is described.
Optimization Flow Control, I: Basic Algorithm and Convergence
 IEEE/ACM TRANSACTIONS ON NETWORKING
, 1999
"... We propose an optimization approach to flow control where the objective is to maximize the aggregate source utility over their transmission rates. We view network links and sources as processors of a distributed computation system to solve the dual problem using gradient projection algorithm. In thi ..."
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Cited by 690 (64 self)
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We propose an optimization approach to flow control where the objective is to maximize the aggregate source utility over their transmission rates. We view network links and sources as processors of a distributed computation system to solve the dual problem using gradient projection algorithm
SNOPT: An SQP Algorithm For LargeScale Constrained Optimization
, 2002
"... Sequential quadratic programming (SQP) methods have proved highly effective for solving constrained optimization problems with smooth nonlinear functions in the objective and constraints. Here we consider problems with general inequality constraints (linear and nonlinear). We assume that first deriv ..."
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Cited by 582 (23 self)
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Sequential quadratic programming (SQP) methods have proved highly effective for solving constrained optimization problems with smooth nonlinear functions in the objective and constraints. Here we consider problems with general inequality constraints (linear and nonlinear). We assume that first
Planning Algorithms
, 2004
"... This book presents a unified treatment of many different kinds of planning algorithms. The subject lies at the crossroads between robotics, control theory, artificial intelligence, algorithms, and computer graphics. The particular subjects covered include motion planning, discrete planning, planning ..."
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Cited by 1108 (51 self)
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This book presents a unified treatment of many different kinds of planning algorithms. The subject lies at the crossroads between robotics, control theory, artificial intelligence, algorithms, and computer graphics. The particular subjects covered include motion planning, discrete planning
Efficient similarity search in sequence databases
, 1994
"... We propose an indexing method for time sequences for processing similarity queries. We use the Discrete Fourier Transform (DFT) to map time sequences to the frequency domain, the crucial observation being that, for most sequences of practical interest, only the first few frequencies are strong. Anot ..."
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Cited by 505 (21 self)
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We propose an indexing method for time sequences for processing similarity queries. We use the Discrete Fourier Transform (DFT) to map time sequences to the frequency domain, the crucial observation being that, for most sequences of practical interest, only the first few frequencies are strong
A training algorithm for optimal margin classifiers
 PROCEEDINGS OF THE 5TH ANNUAL ACM WORKSHOP ON COMPUTATIONAL LEARNING THEORY
, 1992
"... A training algorithm that maximizes the margin between the training patterns and the decision boundary is presented. The technique is applicable to a wide variety of classifiaction functions, including Perceptrons, polynomials, and Radial Basis Functions. The effective number of parameters is adjust ..."
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Cited by 1848 (44 self)
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A training algorithm that maximizes the margin between the training patterns and the decision boundary is presented. The technique is applicable to a wide variety of classifiaction functions, including Perceptrons, polynomials, and Radial Basis Functions. The effective number of parameters
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