scholarly journals On the Uniqueness of Loopy Belief Propagation Fixed Points

2004 ◽  
Vol 16 (11) ◽  
pp. 2379-2413 ◽  
Author(s):  
Tom Heskes
Keyword(s):  
Free Energy ◽  
Fixed Points ◽  
Belief Propagation ◽  
Sufficient Conditions ◽  
Free Energies ◽  
Strengthened Version ◽  
Bethe Free Energy ◽  
Loopy Belief Propagation

We derive sufficient conditions for the uniqueness of loopy belief propagation fixed points. These conditions depend on both the structure of the graph and the strength of the potentials and naturally extend those for convexity of the Bethe free energy. We compare them with (a strengthened version of) conditions derived elsewhere for pairwise potentials. We discuss possible implications for convergent algorithms, as well as for other approximate free energies.

scholarly journals Convexity Arguments for Efficient Minimization of the Bethe and Kikuchi Free Energies

2006 ◽  
Vol 26 ◽  
pp. 153-190 ◽  
Author(s):  
T. Heskes
Keyword(s):  
Free Energy ◽  
Random Fields ◽  
Markov Random Fields ◽  
Belief Propagation ◽  
Helmholtz Free Energy ◽  
Upper Bounds ◽  
Free Energies ◽  
Markov Random ◽  
Bethe Free Energy ◽  
Constrained Minimization Problem

Loopy and generalized belief propagation are popular algorithms for approximate inference in Markov random fields and Bayesian networks. Fixed points of these algorithms have been shown to correspond to extrema of the Bethe and Kikuchi free energy, both of which are approximations of the exact Helmholtz free energy. However, belief propagation does not always converge, which motivates approaches that explicitly minimize the Kikuchi/Bethe free energy, such as CCCP and UPS. Here we describe a class of algorithms that solves this typically non-convex constrained minimization problem through a sequence of convex constrained minimizations of upper bounds on the Kikuchi free energy. Intuitively one would expect tighter bounds to lead to faster algorithms, which is indeed convincingly demonstrated in our simulations. Several ideas are applied to obtain tight convex bounds that yield dramatic speed-ups over CCCP.

scholarly journals Marginal Inference in Continuous Markov Random Fields Using Mixtures

2019 ◽  
Vol 33 ◽  
pp. 7834-7841
Author(s):  
Yuanzhen Guo ◽  
Hao Xiong ◽  
Nicholas Ruozzi
Keyword(s):  
Graphical Models ◽  
Markov Random Fields ◽  
Belief Propagation ◽  
Current State ◽  
Special Cases ◽  
Bethe Free Energy ◽  
Practical Performance ◽  
Belief Propagation Algorithm ◽  
Loopy Belief Propagation ◽  
Marginal Inference

Exact marginal inference in continuous graphical models is computationally challenging outside of a few special cases. Existing work on approximate inference has focused on approximately computing the messages as part of the loopy belief propagation algorithm either via sampling methods or moment matching relaxations. In this work, we present an alternative family of approximations that, instead of approximating the messages, approximates the beliefs in the continuous Bethe free energy using mixture distributions. We show that these types of approximations can be combined with numerical quadrature to yield algorithms with both theoretical guarantees on the quality of the approximation and significantly better practical performance in a variety of applications that are challenging for current state-of-the-art methods.

scholarly journals Properties of Bethe Free Energies and Message Passing in Gaussian Models

2011 ◽  
Vol 41 ◽  
pp. 1-24 ◽  
Author(s):  
B. Cseke ◽  
T. Heskes
Keyword(s):  
Free Energy ◽  
Message Passing ◽  
Probabilistic Models ◽  
Mean Field ◽  
Necessary Condition ◽  
Free Energies ◽  
Gaussian Models ◽  
Message Passing Algorithm ◽  
Bethe Free Energy ◽  
The Moment

We address the problem of computing approximate marginals in Gaussian probabilistic models by using mean field and fractional Bethe approximations. We define the Gaussian fractional Bethe free energy in terms of the moment parameters of the approximate marginals, derive a lower and an upper bound on the fractional Bethe free energy and establish a necessary condition for the lower bound to be bounded from below. It turns out that the condition is identical to the pairwise normalizability condition, which is known to be a sufficient condition for the convergence of the message passing algorithm. We show that stable fixed points of the Gaussian message passing algorithm are local minima of the Gaussian Bethe free energy. By a counterexample, we disprove the conjecture stating that the unboundedness of the free energy implies the divergence of the message passing algorithm.

scholarly journals Correctness of Belief Propagation in Gaussian Graphical Models of Arbitrary Topology

2001 ◽  
Vol 13 (10) ◽  
pp. 2173-2200 ◽  
Author(s):  
Yair Weiss ◽  
William T. Freeman
Keyword(s):  
Graphical Models ◽  
Turbo Codes ◽  
Markov Random Fields ◽  
Belief Propagation ◽  
Analytical Formula ◽  
Sufficient Conditions ◽  
Posterior Probabilities ◽  
Theoretical Understanding ◽  
Single Loop ◽  
Loopy Belief Propagation

Graphical models, such as Bayesian networks and Markov random fields, represent statistical dependencies of variables by a graph. Local “belief propagation” rules of the sort proposed by Pearl (1988) are guaranteed to converge to the correct posterior probabilities in singly connected graphs. Recently, good performance has been obtained by using these same rules on graphs with loops, a method we refer to as loopy belief propagation. Perhaps the most dramatic instance is the near Shannon-limit performance of “Turbo codes,” whose decoding algorithm is equivalent to loopy propagation. Except for the case of graphs with a single loop, there has been little theoretical understanding of loopy propagation. Here we analyze belief propagation in networks with arbitrary topologies when the nodes in the graph describe jointly gaussian random variables. We give an analytical formula relating the true posterior probabilities with those calculated using loopy propagation. We give sufficient conditions for convergence and show that when belief propagation converges, it gives the correct posterior means for all graph topologies, not just networks with a single loop. These results motivate using the powerful belief propagation algorithm in a broader class of networks and help clarify the empirical performance results.

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

Molecular orientation of liquid aliphatic hydrocarbons on the surface and at the interface with water

1989 ◽  
Vol 54 (12) ◽  
pp. 3171-3186 ◽  
Author(s):  
Jan Kloubek
Keyword(s):  
Free Energy ◽  
Surface Free Energy ◽  
Molecular Orientation ◽  
Phase Changes ◽  
Aliphatic Hydrocarbons ◽  
Water Molecules ◽  
Free Energies ◽  
Dispersion Component ◽  
System Water ◽  
Orientation Of Molecules

The validity of the Fowkes theory for the interaction of dispersion forces at interfaces was inspected for the system water-aliphatic hydrocarbons with 5 to 16 C atoms. The obtained results lead to the conclusion that the hydrocarbon molecules cannot lie in a parallel position or be randomly arranged on the surface but that orientation of molecules increases there the ration of CH3 to CH2 groups with respect to that in the bulk. This ratio is changed at the interface with water so that the surface free energy of the hydrocarbon, γH, rises to a higher value, γ’H, which is effective in the interaction with water molecules. Not only the orientation of molecules depends on the adjoining phase and on the temperature but also the density of hydrocarbons on the surface of the liquid phase changes. It is lower than in the bulk and at the interface with water. Moreover, the volume occupied by the CH3 group increases on the surface more than that of the CH2 group. The dispersion component of the surface free energy of water, γdW = 19.09 mJ/m2, the non-dispersion component, γnW = 53.66 mJ/m2, and the surface free energies of the CH2 and CH3 groups, γ(CH2) = 32.94 mJ/m2 and γ(CH3) = 15.87 mJ/m2, were determined at 20 °C. The dependence of these values on the temperature in the range 15-40 °C was also evaluated.

Chemical equilibrium and chemical kinetics

2018 ◽  
Author(s):  
Dennis Sherwood ◽  
Paul Dalby
Keyword(s):  
Free Energy ◽  
Equilibrium Constant ◽  
Gibbs Free Energy ◽  
Chemical Kinetics ◽  
Chemical Equilibrium ◽  
First Principles ◽  
Effect Of Temperature ◽  
Total System ◽  
Free Energies

Building on the previous chapter, this chapter examines gas phase chemical equilibrium, and the equilibrium constant. This chapter takes a rigorous, yet very clear, ‘first principles’ approach, expressing the total Gibbs free energy of a reaction mixture at any time as the sum of the instantaneous Gibbs free energies of each component, as expressed in terms of the extent-of-reaction. The equilibrium reaction mixture is then defined as the point at which the total system Gibbs free energy is a minimum, from which concepts such as the equilibrium constant emerge. The chapter also explores the temperature dependence of equilibrium, this being one example of Le Chatelier’s principle. Finally, the chapter links thermodynamics to chemical kinetics by showing how the equilibrium constant is the ratio of the forward and backward rate constants. We also introduce the Arrhenius equation, closing with a discussion of the overall effect of temperature on chemical equilibrium.

scholarly journals Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Germano Heinzelmann ◽  
Michael K. Gilson
Keyword(s):  
Free Energy ◽  
Early Stage ◽  
Binding Free Energy ◽  
Low Cost ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Energy Calculations ◽  
Drug Candidates ◽  
Binding Free Energy Calculations ◽  
Binding Free Energies

AbstractAbsolute binding free energy calculations with explicit solvent molecular simulations can provide estimates of protein-ligand affinities, and thus reduce the time and costs needed to find new drug candidates. However, these calculations can be complex to implement and perform. Here, we introduce the software BAT.py, a Python tool that invokes the AMBER simulation package to automate the calculation of binding free energies for a protein with a series of ligands. The software supports the attach-pull-release (APR) and double decoupling (DD) binding free energy methods, as well as the simultaneous decoupling-recoupling (SDR) method, a variant of double decoupling that avoids numerical artifacts associated with charged ligands. We report encouraging initial test applications of this software both to re-rank docked poses and to estimate overall binding free energies. We also show that it is practical to carry out these calculations cheaply by using graphical processing units in common machines that can be built for this purpose. The combination of automation and low cost positions this procedure to be applied in a relatively high-throughput mode and thus stands to enable new applications in early-stage drug discovery.

scholarly journals Solution of Some Impulsive Differential Equations via Coupled Fixed Point

Symmetry ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 501
Author(s):  
Ahmed Boudaoui ◽  
Khadidja Mebarki ◽  
Wasfi Shatanawi ◽  
Kamaleldin Abodayeh
Keyword(s):  
Fixed Point ◽  
Differential Equations ◽  
Fixed Points ◽  
Metric Space ◽  
Fixed Point Theorems ◽  
Coupled Fixed Point ◽  
Sufficient Conditions ◽  
Impulsive Differential Equations ◽  
System Of Differential Equations ◽  
Coupled Fixed Points

In this article, we employ the notion of coupled fixed points on a complete b-metric space endowed with a graph to give sufficient conditions to guarantee a solution of system of differential equations with impulse effects. We derive recisely some new coupled fixed point theorems under some conditions and then apply our results to achieve our goal.

scholarly journals The bulk, surface and corner free energies of the anisotropic triangular Ising model

2020 ◽  
Vol 476 (2234) ◽  
pp. 20190713
Author(s):  
Rodney J. Baxter
Keyword(s):  
Free Energy ◽  
Ising Model ◽  
Partition Function ◽  
Temperature Series ◽  
Isotropic Case ◽  
Series Expansions ◽  
Exact Results ◽  
Free Energies ◽  
Bulk Surface ◽  
Bulk Free Energy

We consider the anisotropic Ising model on the triangular lattice with finite boundaries, and use Kaufman’s spinor method to calculate low-temperature series expansions for the partition function to high order. From these, we can obtain 108-term series expansions for the bulk, surface and corner free energies. We extrapolate these to all terms and thereby conjecture the exact results for each. Our results agree with the exactly known bulk-free energy and with Cardy and Peschel’s conformal invariance predictions for the dominant behaviour at criticality. For the isotropic case, they also agree with Vernier and Jacobsen’s conjecture for the 60 ° corners.

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