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Dynamics-based sampling methods, such as Hybrid Monte Carlo (HMC) and Langevin dynamics (LD), are commonly used to sample target distributions. Recently , such approaches have been combined with stochastic gradient techniques to increase sampling efficiency when dealing with large datasets. An outstanding problem with this approach is that the stochastic(More)
Many members of the animal kingdom display coat or skin color differences along their dorsoventral axis. To determine the mechanisms that control regional differences in pigmentation, we have studied how a classical mouse mutation, droopy ear (de(H)), affects dorsoventral skin characteristics, especially those under control of the Agouti gene. Mice carrying(More)
Hierarchical modeling and reasoning are fundamental in machine intelligence, and for this the two-parameter Poisson-Dirichlet Process (PDP) plays an important role. The most popular MCMC sampling algorithm for the hierarchical PDP and hierarchical Dirichlet Process is to conduct an incremental sampling based on the Chinese restaurant metaphor, which(More)
Effective training of deep neural networks suffers from two main issues. The first is that the parameter spaces of these models exhibit pathological curvature. Recent methods address this problem by using adaptive pre-conditioning for Stochastic Gradient Descent (SGD). These methods improve convergence by adapting to the local geometry of parameter space. A(More)
We develop dependent hierarchical normalized random measures and apply them to dynamic topic modeling. The dependency arises via superposition, subsampling and point transition on the underlying Poisson processes of these measures. The measures used include normalised generalised Gamma processes that demonstrate power law properties , unlike Dirichlet(More)
A new framework for topic modeling is developed , based on deep graphical models, where interactions between topics are inferred through deep latent binary hierarchies. The proposed multi-layer model employs a deep sigmoid belief network or restricted Boltzmann machine, the bottom binary layer of which selects topics for use in a Poisson factor analysis(More)
In this paper we propose two constructions of dependent normalized random measures, a class of nonparametric priors over dependent probability measures. Our constructions , which we call mixed normalized random measures (MNRM) and thinned normalized random measures (TNRM), involve (respectively) weighting and thinning parts of a shared underlying Poisson(More)
Recent advances in Bayesian learning with large-scale data have witnessed emergence of stochastic gradient MCMC algorithms (SG-MCMC), such as stochas-tic gradient Langevin dynamics (SGLD), stochastic gradient Hamiltonian MCMC (SGHMC), and the stochastic gradient thermostat. While finite-time convergence properties of the SGLD with a 1st-order Euler(More)
Stochastic gradient Markov chain Monte Carlo (SG-MCMC) methods are Bayesian analogs to popular stochastic optimization methods; however, this connection is not well studied. We explore this relationship by applying simulated annealing to an SG-MCMC algorithm. Furthermore, we extend recent SG-MCMC methods with two key components: i) adaptive preconditioners(More)
A chemical genetics approach identified a cellular target of several proapoptotic farnesyl transferase inhibitors (FTIs). Treatment with these FTIs caused p53-independent apoptosis in Caenorhabditis elegans, which was mimicked by knockdown of endosomal trafficking proteins, including Rab5, Rab7, the HOPS complex, and notably the enzyme Rab geranylgeranyl(More)