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Constructing Free Energy Approximations and Generalized Belief Propagation Algorithms
 IEEE Transactions on Information Theory
, 2005
"... Important inference problems in statistical physics, computer vision, errorcorrecting coding theory, and artificial intelligence can all be reformulated as the computation of marginal probabilities on factor graphs. The belief propagation (BP) algorithm is an efficient way to solve these problems t ..."
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Cited by 585 (13 self)
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that is exact when the factor graph is a tree, but only approximate when the factor graph has cycles. We show that BP fixed points correspond to the stationary points of the Bethe approximation of the free energy for a factor graph. We explain how to obtain regionbased free energy approximations that improve
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
 J. Comput. Chem
, 1998
"... ABSTRACT: A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a ..."
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Cited by 380 (4 self)
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ABSTRACT: A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies
Free energy
, 2006
"... What is thermodynamics? Science of heat I how heat is transformed, stored, converted I how heat flows I science of heat engines (and fridges) I based on thermodynamics laws The actors: ..."
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What is thermodynamics? Science of heat I how heat is transformed, stored, converted I how heat flows I science of heat engines (and fridges) I based on thermodynamics laws The actors:
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 809 (117 self)
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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
Convexifying the bethe free energy
 in Conference on Uncertainty in Artifical Intelligence (UAI
, 2009
"... The introduction of loopy belief propagation (LBP) revitalized the application of graphical models in many domains. Many recent works present improvements on the basic LBP algorithm in an attempt to overcome convergence and local optima problems. Notable among these are convexified free energy appro ..."
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Cited by 17 (2 self)
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The introduction of loopy belief propagation (LBP) revitalized the application of graphical models in many domains. Many recent works present improvements on the basic LBP algorithm in an attempt to overcome convergence and local optima problems. Notable among these are convexified free energy
A View Of The Em Algorithm That Justifies Incremental, Sparse, And Other Variants
 Learning in Graphical Models
, 1998
"... . The EM algorithm performs maximum likelihood estimation for data in which some variables are unobserved. We present a function that resembles negative free energy and show that the M step maximizes this function with respect to the model parameters and the E step maximizes it with respect to the d ..."
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Cited by 993 (18 self)
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. The EM algorithm performs maximum likelihood estimation for data in which some variables are unobserved. We present a function that resembles negative free energy and show that the M step maximizes this function with respect to the model parameters and the E step maximizes it with respect
The Free Energy Formula
, 1999
"... Abstract. The Onsager formula for the free energy of the two dimensional Ising model with periodic boundary conditions is proved. 1 ..."
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Abstract. The Onsager formula for the free energy of the two dimensional Ising model with periodic boundary conditions is proved. 1
Interface Free Energy *
"... "Interface free energy is the contribution to the free energy of a system due to the presence of an interface separating two coexisting phases at equilibrium". It is also called interfacial free energy or surface tension. The content of the article is 1) the definition of the interface fr ..."
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"Interface free energy is the contribution to the free energy of a system due to the presence of an interface separating two coexisting phases at equilibrium". It is also called interfacial free energy or surface tension. The content of the article is 1) the definition of the interface
Results 1  10
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20,285