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Peter Green

Publications and source records attributed to Peter Green.

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Investigating Batch Inference in a Sequential Monte Carlo Framework for Neural Networks

Bayesian inference allows us to define a posterior distribution over the weights of a generic neural network (NN). Exact posteriors are usually intractable, in which case approximations can be employed. One such approximation - variational inference - is computationally efficient when using mini-batch stochastic gradient descent as subsets of the data are used for likelihood and gradient evaluations, though the approach relies on the selection of a variational distribution which sufficiently matches the form of the posterior. Particle-based methods such as Markov chain Monte Carlo and Sequential Monte Carlo (SMC) do not assume a parametric family for the posterior by typically require higher computational cost. These sampling methods typically use the full-batch of data for likelihood and gradient evaluations, which contributes to this computational expense. We explore several methods of gradually introducing more mini-batches of data (data annealing) into likelihood and gradient evaluations of an SMC sampler. We find that we can achieve up to $6\times$ faster training with minimal loss in accuracy on benchmark image classification problems using NNs.

cs.LG

Bayesian Protein Sequence and Structure Alignment

The structure of a protein is crucial in determining its functionality, and is much more conserved than sequence during evolution. A key task in structural biology is to compare protein structures in order to determine evolutionary relationships, estimate the function of newly-discovered structures, and predict unknown structures. We propose a Bayesian method for protein structure alignment, with the prior on alignments based on functions which penalise ``gaps'' in the aligned sequences. We show how a broad class of penalty functions fits into this framework, and how the resulting posterior distribution can be efficiently sampled. A commonly-used gap penalty function is shown to be a special case, and we propose a new penalty function which alleviates an undesirable feature of the commonly-used penalty. We illustrate our method on benchmark data sets, and find it competes well with popular tools from computational biology. Our method has the benefit of being able to potentially explore multiple competing alignments and quantify their merits probabilistically. The framework naturally allows for further information such as amino acid sequence to be included, and could be adapted to other situations such as flexible proteins or domain swaps.

stat.ME