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Finding motifs using random projections
, 2001
"... Pevzner and Sze [23] considered a precise version of the motif discovery problem and simultaneously issued an algorithmic challenge: find a motif Å of length 15, where each planted instance differs from Å in 4 positions. Whereas previous algorithms all failed to solve this (15,4)motif problem, Pevz ..."
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Cited by 287 (6 self)
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, Pevzner and Sze introduced algorithms that succeeded. However, their algorithms failed to solve the considerably more difficult (14,4), (16,5), and (18,6)motif problems. We introduce a novel motif discovery algorithm based on the use of random projections of the input’s substrings. Experiments
Finding Motifs Using Random Projections
"... Pevzner and Sze [23] considered a precise version of the motif discovery problem and simultaneously issued an algorithmic challenge: find a motif ¢ of length 15, where each planted instance differs from ¢ in 4 positions. Whereas previous algorithms all failed to solve this (15,4)motif problem, Pevz ..."
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, Pevzner and Sze introduced algorithms that succeeded. However, their algorithms failed to solve the considerably more difficult (14,4), (16,5), and (18,6)motif problems. We introduce a novel motif discovery algorithm based on the use of random projections of the input’s substrings. Experiments
Finding community structure in networks using the eigenvectors of matrices
, 2006
"... We consider the problem of detecting communities or modules in networks, groups of vertices with a higherthanaverage density of edges connecting them. Previous work indicates that a robust approach to this problem is the maximization of the benefit function known as “modularity ” over possible div ..."
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Cited by 500 (0 self)
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We consider the problem of detecting communities or modules in networks, groups of vertices with a higherthanaverage density of edges connecting them. Previous work indicates that a robust approach to this problem is the maximization of the benefit function known as “modularity ” over possible divisions of a network. Here we show that this maximization process can be written in terms of the eigenspectrum of a matrix we call the modularity matrix, which plays a role in community detection similar to that played by the graph Laplacian in graph partitioning calculations. This result leads us to a number of possible algorithms for detecting community structure, as well as several other results, including a spectral measure of bipartite structure in networks and a new centrality measure that identifies those vertices that occupy central positions within the communities to which they belong. The algorithms and measures proposed are illustrated with applications to a variety of realworld complex networks.
Near Optimal Signal Recovery From Random Projections: Universal Encoding Strategies?
, 2004
"... Suppose we are given a vector f in RN. How many linear measurements do we need to make about f to be able to recover f to within precision ɛ in the Euclidean (ℓ2) metric? Or more exactly, suppose we are interested in a class F of such objects— discrete digital signals, images, etc; how many linear m ..."
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Cited by 1513 (20 self)
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law), then it is possible to reconstruct f to within very high accuracy from a small number of random measurements. typical result is as follows: we rearrange the entries of f (or its coefficients in a fixed basis) in decreasing order of magnitude f  (1) ≥ f  (2) ≥... ≥ f  (N), and define the weakℓp ball
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
 Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology
, 1994
"... ABSTRACT: The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a twocomponent finite mixture model to the set of sequences. Multiple motifs are found by fitting a twocomponent finite ..."
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Cited by 941 (5 self)
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ABSTRACT: The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a twocomponent finite mixture model to the set of sequences. Multiple motifs are found by fitting a two
Randomized Algorithms
, 1995
"... Randomized algorithms, once viewed as a tool in computational number theory, have by now found widespread application. Growth has been fueled by the two major benefits of randomization: simplicity and speed. For many applications a randomized algorithm is the fastest algorithm available, or the simp ..."
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Cited by 2210 (37 self)
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, or the simplest, or both. A randomized algorithm is an algorithm that uses random numbers to influence the choices it makes in the course of its computation. Thus its behavior (typically quantified as running time or quality of output) varies from
DART: Directed automated random testing
 In Programming Language Design and Implementation (PLDI
, 2005
"... We present a new tool, named DART, for automatically testing software that combines three main techniques: (1) automated extraction of the interface of a program with its external environment using static sourcecode parsing; (2) automatic generation of a test driver for this interface that performs ..."
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Cited by 823 (41 self)
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We present a new tool, named DART, for automatically testing software that combines three main techniques: (1) automated extraction of the interface of a program with its external environment using static sourcecode parsing; (2) automatic generation of a test driver for this interface
Projection Pursuit Regression
 Journal of the American Statistical Association
, 1981
"... A new method for nonparametric multiple regression is presented. The procedure models the regression surface as a sum of general smooth functions of linear combinations of the predictor variables in an iterative manner. It is more general than standard stepwise and stagewise regression procedures, ..."
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Cited by 555 (6 self)
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A new method for nonparametric multiple regression is presented. The procedure models the regression surface as a sum of general smooth functions of linear combinations of the predictor variables in an iterative manner. It is more general than standard stepwise and stagewise regression procedures, does not require the definition of a metric in the predictor space, and lends itself to graphical interpretation.
Randomized Gossip Algorithms
 IEEE TRANSACTIONS ON INFORMATION THEORY
, 2006
"... Motivated by applications to sensor, peertopeer, and ad hoc networks, we study distributed algorithms, also known as gossip algorithms, for exchanging information and for computing in an arbitrarily connected network of nodes. The topology of such networks changes continuously as new nodes join a ..."
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Cited by 522 (5 self)
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distribute the computational burden and in which a node communicates with a randomly chosen neighbor. We analyze the averaging problem under the gossip constraint for an arbitrary network graph, and find that the averaging time of a gossip algorithm depends on the second largest eigenvalue of a doubly
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