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Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package)
"... Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and bas ..."
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Cited by 812 (119 self)
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and base pairing probabilities. An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment. All computer codes are written in ANSI C. They include
ModelBased Clustering, Discriminant Analysis, and Density Estimation
 JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
, 2000
"... Cluster analysis is the automated search for groups of related observations in a data set. Most clustering done in practice is based largely on heuristic but intuitively reasonable procedures and most clustering methods available in commercial software are also of this type. However, there is little ..."
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Cited by 557 (28 self)
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Cluster analysis is the automated search for groups of related observations in a data set. Most clustering done in practice is based largely on heuristic but intuitively reasonable procedures and most clustering methods available in commercial software are also of this type. However
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
A Language Modeling Approach to Information Retrieval
, 1998
"... Models of document indexing and document retrieval have been extensively studied. The integration of these two classes of models has been the goal of several researchers but it is a very difficult problem. We argue that much of the reason for this is the lack of an adequate indexing model. This sugg ..."
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Cited by 1142 (40 self)
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are used heuristically in many other retrieval models are an integral part of our model. We have...
Approximate Signal Processing
, 1997
"... It is increasingly important to structure signal processing algorithms and systems to allow for trading off between the accuracy of results and the utilization of resources in their implementation. In any particular context, there are typically a variety of heuristic approaches to managing these tra ..."
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Cited by 516 (2 self)
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It is increasingly important to structure signal processing algorithms and systems to allow for trading off between the accuracy of results and the utilization of resources in their implementation. In any particular context, there are typically a variety of heuristic approaches to managing
Gapped Blast and PsiBlast: a new generation of protein database search programs
 NUCLEIC ACIDS RESEARCH
, 1997
"... The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while ..."
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Cited by 8393 (85 self)
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enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced
The geometry of graphs and some of its algorithmic applications
 Combinatorica
, 1995
"... In this paper we explore some implications of viewing graphs as geometric objects. This approach offers a new perspective on a number of graphtheoretic and algorithmic problems. There are several ways to model graphs geometrically and our main concern here is with geometric representations that r ..."
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Cited by 543 (20 self)
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that respect the metric of the (possibly weighted) graph. Given a graph G we map its vertices to a normed space in an attempt to (i) Keep down the dimension of the host space and (ii) Guarantee a small distortion, i.e., make sure that distances between vertices in G closely match the distances between
Predicting Internet Network Distance with CoordinatesBased Approaches
 In INFOCOM
, 2001
"... In this paper, we propose to use coordinatesbased mechanisms in a peertopeer architecture to predict Internet network distance (i.e. roundtrip propagation and transmission delay) . We study two mechanisms. The first is a previously proposed scheme, called the triangulated heuristic, which is bas ..."
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Cited by 633 (5 self)
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In this paper, we propose to use coordinatesbased mechanisms in a peertopeer architecture to predict Internet network distance (i.e. roundtrip propagation and transmission delay) . We study two mechanisms. The first is a previously proposed scheme, called the triangulated heuristic, which
A theory of timed automata
, 1999
"... Model checking is emerging as a practical tool for automated debugging of complex reactive systems such as embedded controllers and network protocols (see [23] for a survey). Traditional techniques for model checking do not admit an explicit modeling of time, and are thus, unsuitable for analysis of ..."
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Cited by 2651 (32 self)
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and logic, and much progress has been made in developing verification algorithms, heuristics, and tools. This paper provides a survey of the theory of timed automata, and their role in specification and verification of realtime systems.
For Most Large Underdetermined Systems of Linear Equations the Minimal ℓ1norm Solution is also the Sparsest Solution
 Comm. Pure Appl. Math
, 2004
"... We consider linear equations y = Φα where y is a given vector in R n, Φ is a given n by m matrix with n < m ≤ An, and we wish to solve for α ∈ R m. We suppose that the columns of Φ are normalized to unit ℓ 2 norm 1 and we place uniform measure on such Φ. We prove the existence of ρ = ρ(A) so that ..."
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Cited by 560 (10 self)
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. In contrast, heuristic attempts to sparsely solve such systems – greedy algorithms and thresholding – perform poorly in this challenging setting. The techniques include the use of random proportional embeddings and almostspherical sections in Banach space theory, and deviation bounds for the eigenvalues
Results 11  20
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436,190