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31,725
When is MenzerathAltmann law mathematically trivial? A new approach
 Statistical Applications in Genetics and Molecular Biology , 13
, 2014
"... Menzerath’s law, the tendency of Z, the mean size of the parts, to decrease as X, the number of parts, increases is found in language, music and genomes. Recently, it has been argued that the presence of the law in genomes is an inevitable consequence of the fact that Z = Y/X, which would imply that ..."
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Cited by 2 (2 self)
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that Z scales with X as Z ∼ 1/X. That scaling is a very particular case of MenzerathAltmann law that has been rejected by means of a correlation test between X and Y in genomes, being X the number of chromosomes of a species, Y its genome size in bases and Z the mean chromosome size. Here we review
Dynamic topic models
 In ICML
, 2006
"... Scientists need new tools to explore and browse large collections of scholarly literature. Thanks to organizations such as JSTOR, which scan and index the original bound archives of many journals, modern scientists can search digital libraries spanning hundreds of years. A scientist, suddenly ..."
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Cited by 656 (28 self)
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Scientists need new tools to explore and browse large collections of scholarly literature. Thanks to organizations such as JSTOR, which scan and index the original bound archives of many journals, modern scientists can search digital libraries spanning hundreds of years. A scientist, suddenly
Modeling and simulation of genetic regulatory systems: A literature review
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
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Cited by 729 (15 self)
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In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rulebased formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems.
Graphical models, exponential families, and variational inference
, 2008
"... The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fiel ..."
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Cited by 800 (26 self)
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The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fields, including bioinformatics, communication theory, statistical physics, combinatorial optimization, signal and image processing, information retrieval and statistical machine learning. Many problems that arise in specific instances — including the key problems of computing marginals and modes of probability distributions — are best studied in the general setting. Working with exponential family representations, and exploiting the conjugate duality between the cumulant function and the entropy for exponential families, we develop general variational representations of the problems of computing likelihoods, marginal probabilities and most probable configurations. We describe how a wide varietyof algorithms — among them sumproduct, cluster variational methods, expectationpropagation, mean field methods, maxproduct and linear programming relaxation, as well as conic programming relaxations — can all be understood in terms of exact or approximate forms of these variational representations. The variational approach provides a complementary alternative to Markov chain Monte Carlo as a general source of approximation methods for inference in largescale statistical models.
From data mining to knowledge discovery in databases
 AI Magazine
, 1996
"... ■ Data mining and knowledge discovery in databases have been attracting a significant amount of research, industry, and media attention of late. What is all the excitement about? This article provides an overview of this emerging field, clarifying how data mining and knowledge discovery in databases ..."
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Cited by 510 (0 self)
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■ Data mining and knowledge discovery in databases have been attracting a significant amount of research, industry, and media attention of late. What is all the excitement about? This article provides an overview of this emerging field, clarifying how data mining and knowledge discovery in databases are related both to each other and to related fields, such as machine learning, statistics, and databases. The article mentions particular realworld applications, specific datamining techniques, challenges involved in realworld applications of knowledge discovery, and current and future research directions in the field. Across a wide variety of fields, data are
Community detection in graphs
, 2009
"... The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of th ..."
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Cited by 801 (1 self)
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The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such
An introduction to variable and feature selection
 Journal of Machine Learning Research
, 2003
"... Variable and feature selection have become the focus of much research in areas of application for which datasets with tens or hundreds of thousands of variables are available. ..."
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Cited by 1283 (16 self)
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Variable and feature selection have become the focus of much research in areas of application for which datasets with tens or hundreds of thousands of variables are available.
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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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 for large n, and for all Φ’s except a negligible fraction, the following property holds: For every y having a representation y = Φα0 by a coefficient vector α0 ∈ R m with fewer than ρ · n nonzeros, the solution α1 of the ℓ 1 minimization problem min �x�1 subject to Φα = y is unique and equal to α0. 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 of random Wishart matrices.
A Guided Tour to Approximate String Matching
 ACM COMPUTING SURVEYS
, 1999
"... We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining t ..."
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Cited by 584 (38 self)
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We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining the problem and its relevance, its statistical behavior, its history and current developments, and the central ideas of the algorithms and their complexities. We present a number of experiments to compare the performance of the different algorithms and show which are the best choices according to each case. We conclude with some future work directions and open problems.
Evolution of indirect reciprocity by image scoring, Nature
, 1998
"... review. Views or opinions expressed herein do not necessarily represent those of the Institute, its National Member Organizations, or other organizations supporting the work. IIASA STUDIES IN ADAPTIVE DYNAMICS NO. 27 The Adaptive Dynamics Network at IIASA fosters the development of new mathematical ..."
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Cited by 486 (16 self)
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review. Views or opinions expressed herein do not necessarily represent those of the Institute, its National Member Organizations, or other organizations supporting the work. IIASA STUDIES IN ADAPTIVE DYNAMICS NO. 27 The Adaptive Dynamics Network at IIASA fosters the development of new mathematical and conceptual techniques for understanding the evolution of complex adaptive systems. Focusing on these longterm implications of adaptive processes in systems of limited growth, the Adaptive Dynamics Network brings together scientists and institutions from around the world with IIASA acting as the central node. Scientific progress within the network
Results 1  10
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31,725