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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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, 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.
Probabilistic Latent Semantic Analysis
 In Proc. of Uncertainty in Artificial Intelligence, UAI’99
, 1999
"... Probabilistic Latent Semantic Analysis is a novel statistical technique for the analysis of twomode and cooccurrence data, which has applications in information retrieval and filtering, natural language processing, machine learning from text, and in related areas. Compared to standard Latent Sema ..."
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Cited by 760 (9 self)
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Semantic Analysis which stems from linear algebra and performs a Singular Value Decomposition of cooccurrence tables, the proposed method is based on a mixture decomposition derived from a latent class model. This results in a more principled approach which has a solid foundation in statistics. In order
Quantum Gravity
, 2004
"... We describe the basic assumptions and key results of loop quantum gravity, which is a background independent approach to quantum gravity. The emphasis is on the basic physical principles and how one deduces predictions from them, at a level suitable for physicists in other areas such as string theor ..."
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Cited by 566 (11 self)
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integral quantizations, coupling to matter, extensions to supergravity and higher dimensional theories, as well as applications to black holes, cosmology and Plank scale phenomenology. We describe the near term prospects for observational tests of quantum theories of gravity and the expectations that loop
String theory and noncommutative geometry
 JHEP
, 1999
"... We extend earlier ideas about the appearance of noncommutative geometry in string theory with a nonzero Bfield. We identify a limit in which the entire string dynamics is described by a minimally coupled (supersymmetric) gauge theory on a noncommutative space, and discuss the corrections away from ..."
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Cited by 801 (8 self)
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We extend earlier ideas about the appearance of noncommutative geometry in string theory with a nonzero Bfield. We identify a limit in which the entire string dynamics is described by a minimally coupled (supersymmetric) gauge theory on a noncommutative space, and discuss the corrections away from
KodairaSpencer theory of gravity and exact results for quantum string amplitudes
 Commun. Math. Phys
, 1994
"... We develop techniques to compute higher loop string amplitudes for twisted N = 2 theories with ĉ = 3 (i.e. the critical case). An important ingredient is the discovery of an anomaly at every genus in decoupling of BRST trivial states, captured to all orders by a master anomaly equation. In a particu ..."
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Cited by 545 (60 self)
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We develop techniques to compute higher loop string amplitudes for twisted N = 2 theories with ĉ = 3 (i.e. the critical case). An important ingredient is the discovery of an anomaly at every genus in decoupling of BRST trivial states, captured to all orders by a master anomaly equation. In a
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, planning under uncertainty, sensorbased planning, visibility, decisiontheoretic planning, game theory, information spaces, reinforcement learning, nonlinear systems, trajectory planning, nonholonomic planning, and kinodynamic planning.
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.
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