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A fast learning algorithm for deep belief nets
 Neural Computation
, 2006
"... We show how to use “complementary priors ” to eliminate the explaining away effects that make inference difficult in denselyconnected belief nets that have many hidden layers. Using complementary priors, we derive a fast, greedy algorithm that can learn deep, directed belief networks one layer at a ..."
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Cited by 970 (49 self)
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very good generative model of the joint distribution of handwritten digit images and their labels. This generative model gives better digit classification than the best discriminative learning algorithms. The lowdimensional manifolds on which the digits lie are modelled by long ravines in the freeenergy
Scalable molecular dynamics with NAMD.
 J Comput Chem
, 2005
"... Abstract: NAMD is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems. NAMD scales to hundreds of processors on highend parallel platforms, as well as tens of processors on lowcost commodity clusters, and also runs on individual desktop and la ..."
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Cited by 849 (63 self)
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, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a
Targeted free energy perturbation
 Physical Review E
"... A generalization of the free energy perturbation identity is derived, and a computational strategy based on this result is presented. A simple example illustrates the efficiency gains that can be achieved with this method. The development of efficient methods for the numerical estimation of free ene ..."
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Cited by 9 (0 self)
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A generalization of the free energy perturbation identity is derived, and a computational strategy based on this result is presented. A simple example illustrates the efficiency gains that can be achieved with this method. The development of efficient methods for the numerical estimation of free
Free Energy, Value, and Attractors
, 2012
"... It has been suggested recently that action and perception can be understood as minimising the free energy of sensory samples. This ensures that agents sample the environment to maximise the evidence for their model of the world, such that exchanges with the environment are predictable and adaptive ..."
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Cited by 6 (2 self)
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It has been suggested recently that action and perception can be understood as minimising the free energy of sensory samples. This ensures that agents sample the environment to maximise the evidence for their model of the world, such that exchanges with the environment are predictable
Freeenergy and the brain
, 2007
"... If one formulates Helmholtz’s ideas about perception in terms of modernday theories one arrives at a model of perceptual inference and learning that can explain a remarkable range of neurobiological facts. Using constructs from statistical physics it can be shown that the problems of inferring wh ..."
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Cited by 18 (0 self)
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processes are just one emergent property of systems that conform to a freeenergy principle. The freeenergy considered here represents a bound on the surprise inherent in any exchange with the environment, under expectations encoded by its state or configuration. A system can minimise freeenergy
Reconstructing the freeenergy Reconstructing the freeenergy landscape
, 2014
"... We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and considers the presence of a competitive inhibition reaction by ..."
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by ADP. We first first reconstruct a continuous freeenergy landscape of the cycle catalyst process that allows us to calculate the number of steps given by a single molecular motor. Then, we calculate an analytical expression associated to the translational velocity and the stopping time
TWIST FREE ENERGY
, 2002
"... One may impose to a system with spontaneous broken symmetry, boundary conditions which correspond to different pure states at two ends of a sample. For a discrete Isinglike broken symmetry, boundary conditions with opposite spins in two parallel limiting planes, generate an interface and a cost in ..."
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in free energy per unit area of the interface. For continuum symmetries the order parameter interpolates smoothly between the end planes carrying two different directions of the order parameter. The cost in free energy is then proportional to L d−2 for a system of characteristic size L. The power of L
Activity recognition from userannotated acceleration data
, 2004
"... In this work, algorithms are developed and evaluated to detect physical activities from data acquired using five small biaxial accelerometers worn simultaneously on different parts of the body. Acceleration data was collected from 20 subjects without researcher supervision or observation. Subjects ..."
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Cited by 515 (7 self)
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. Subjects were asked to perform a sequence of everyday tasks but not told specifically where or how to do them. Mean, energy, frequencydomain entropy, and correlation of acceleration data was calculated and several classifiers using these features were tested. Decision tree classifiers showed the best
Free energy simulations”.
 Ann. Acad. Sci. N.Y.,
, 1986
"... INTRODUCTION. Monte Carlo or molecular dynamics simulations involve the numerical determinations of the statistical thermodynamics and related structural, energetics and (in the case of MD) dynamical properties of an atomic or molecular assembly on a high speed digital computer. Applications to mol ..."
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Cited by 10 (2 self)
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activated complex theory also require a particular knowledge of the configurational free energy, which in principle follows directly from the statistical thermodynamic partition function for the system. Considerations on free energy in molecular simulations take a distinctly different form
Results 11  20
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20,285