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Mike Hobson

Publications and source records attributed to Mike Hobson.

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Split personalities in Bayesian Neural Networks: the case for full marginalisation

The true posterior distribution of a Bayesian neural network is massively multimodal. Whilst most of these modes are functionally equivalent, we demonstrate that there remains a level of real multimodality that manifests in even the simplest neural network setups. It is only by fully marginalising over all posterior modes, using appropriate Bayesian sampling tools, that we can capture the split personalities of the network. The ability of a network trained in this manner to reason between multiple candidate solutions dramatically improves the generalisability of the model, a feature we contend is not consistently captured by alternative approaches to the training of Bayesian neural networks. We provide a concise minimal example of this, which can provide lessons and a future path forward for correctly utilising the explainability and interpretability of Bayesian neural networks.

stat.ML

Compromise-free Bayesian neural networks

We conduct a thorough analysis of the relationship between the out-of-sample performance and the Bayesian evidence (marginal likelihood) of Bayesian neural networks (BNNs), as well as looking at the performance of ensembles of BNNs, both using the Boston housing dataset. Using the state-of-the-art in nested sampling, we numerically sample the full (non-Gaussian and multimodal) network posterior and obtain numerical estimates of the Bayesian evidence, considering network models with up to 156 trainable parameters. The networks have between zero and four hidden layers, either $\tanh$ or $ReLU$ activation functions, and with and without hierarchical priors. The ensembles of BNNs are obtained by determining the posterior distribution over networks, from the posterior samples of individual BNNs re-weighted by the associated Bayesian evidence values. There is good correlation between out-of-sample performance and evidence, as well as a remarkable symmetry between the evidence versus model size and out-of-sample performance versus model size planes. Networks with $ReLU$ activation functions have consistently higher evidences than those with $\tanh$ functions, and this is reflected in their out-of-sample performance. Ensembling over architectures acts to further improve performance relative to the individual BNNs.

stat.ML

Logolinear series expansions with applications to primordial cosmology

We develop a method for computing series expansions for solutions to ordinary differential equations when the asymptotic form contains both linear and logarithmic terms. Such situations are common in primordial cosmology when considering series expansions out of a singularity in the equations arising from a pre-inflationary phase of the universe. We develop mathematical techniques for generating these series expansions, and apply them to polynomial and Starobinsky inflationary potentials with kinetic initial conditions. Code for analytic and numerical computation of logolinear series is provided on GitHub.

gr-qc

Bayesian surrogate learning in dynamic simulator-based regression problems

The estimation of unknown values of parameters (or hidden variables, control variables) that characterise a physical system often relies on the comparison of measured data with synthetic data produced by some numerical simulator of the system as the parameter values are varied. This process often encounters two major difficulties: the generation of synthetic data for each considered set of parameter values can be computationally expensive if the system model is complicated; and the exploration of the parameter space can be inefficient and/or incomplete, a typical example being when the exploration becomes trapped in a local optimum of the objection function that characterises the mismatch between the measured and synthetic data. A method to address both these issues is presented, whereby: a surrogate model (or proxy), which emulates the computationally expensive system simulator, is constructed using deep recurrent networks (DRN); and a nested sampling (NS) algorithm is employed to perform efficient and robust exploration of the parameter space. The analysis is performed in a Bayesian context, in which the samples characterise the full joint posterior distribution of the parameters, from which parameter estimates and uncertainties are easily derived. The proposed approach is compared with conventional methods in some numerical examples, for which the results demonstrate that one can accelerate the parameter estimation process by at least an order of magnitude.

cs.LG

Improving the efficiency and robustness of nested sampling using posterior repartitioning

In real-world Bayesian inference applications, prior assumptions regarding the parameters of interest may be unrepresentative of their actual values for a given dataset. In particular, if the likelihood is concentrated far out in the wings of the assumed prior distribution, this can lead to extremely inefficient exploration of the resulting posterior by nested sampling algorithms, with unnecessarily high associated computational costs. Simple solutions such as broadening the prior range in such cases might not be appropriate or possible in real-world applications, for example when one wishes to assume a single standardised prior across the analysis of a large number of datasets for which the true values of the parameters of interest may vary. This work therefore introduces a posterior repartitioning (PR) method for nested sampling algorithms, which addresses the problem by redefining the likelihood and prior while keeping their product fixed, so that the posterior inferences and evidence estimates remain unchanged but the efficiency of the nested sampling process is significantly increased. Numerical results show that the PR method provides a simple yet powerful refinement for nested sampling algorithms to address the issue of unrepresentative priors.

stat.CO

Dynamic nested sampling: an improved algorithm for parameter estimation and evidence calculation

We introduce dynamic nested sampling: a generalisation of the nested sampling algorithm in which the number of "live points" varies to allocate samples more efficiently. In empirical tests the new method significantly improves calculation accuracy compared to standard nested sampling with the same number of samples; this increase in accuracy is equivalent to speeding up the computation by factors of up to ~72 for parameter estimation and ~7 for evidence calculations. We also show that the accuracy of both parameter estimation and evidence calculations can be improved simultaneously. In addition, unlike in standard nested sampling, more accurate results can be obtained by continuing the calculation for longer. Popular standard nested sampling implementations can be easily adapted to perform dynamic nested sampling, and several dynamic nested sampling software packages are now publicly available.

stat.CO

nestcheck: diagnostic tests for nested sampling calculations

Nested sampling is an increasingly popular technique for Bayesian computation, in particular for multimodal, degenerate problems of moderate to high dimensionality. Without appropriate settings, however, nested sampling software may fail to explore such posteriors correctly; for example producing correlated samples or missing important modes. This paper introduces new diagnostic tests to assess the reliability both of parameter estimation and evidence calculations using nested sampling software, and demonstrates them empirically. We present two new diagnostic plots for nested sampling, and give practical advice for nested sampling software users in astronomy and beyond. Our diagnostic tests and diagrams are implemented in nestcheck: a publicly available Python package for analysing nested sampling calculations, which is compatible with output from MultiNest, PolyChord and dyPolyChord.

stat.CO

Sampling Errors in Nested Sampling Parameter Estimation

Sampling errors in nested sampling parameter estimation differ from those in Bayesian evidence calculation, but have been little studied in the literature. This paper provides the first explanation of the two main sources of sampling errors in nested sampling parameter estimation, and presents a new diagrammatic representation for the process. We find no current method can accurately measure the parameter estimation errors of a single nested sampling run, and propose a method for doing so using a new algorithm for dividing nested sampling runs. We empirically verify our conclusions and the accuracy of our new method.

stat.ME

Bayesian analysis of radial velocity data of GJ667C with correlated noise: evidence for only 2 planets

GJ667C is the least massive component of a triple star system which lies at a distance of about 6.8 pc (22.1 light-years) from Earth. GJ667C has received much attention recently due to the claims that it hosts up to seven planets including three super-Earths inside the habitable zone. We present a Bayesian technique for the analysis of radial velocity (RV) data-sets in the presence of correlated noise component ("red noise"), with unknown parameters. We also introduce hyper-parameters in our model in order to deal statistically with under or over-estimated error bars on measured RVs as well as inconsistencies between different data-sets. By applying this method to the RV data-set of GJ667C, we show that this data-set contains a significant correlated (red) noise component with correlation timescale for HARPS data of order 9 days. Our analysis shows that the data only provides strong evidence for the presence of two planets: GJ667Cb and c with periods 7.19d and 28.13d respectively, with some hints towards the presence of a third signal with period 91d. The planetary nature of this third signal is not clear and additional RV observations are required for its confirmation. Previous claims of the detection of additional planets in this system are due the erroneous assumption of white noise. Using the standard white noise assumption, our method leads to the detection of up to five signals in this system. We also find that with the red noise model, the measurement uncertainties from HARPS for this system are under-estimated at the level of ~50 per cent.

astro-ph.EP

An investigation into the Multiple Optimised Parameter Estimation and Data compression algorithm

We investigate the use of the Multiple Optimised Parameter Estimation and Data compression algorithm (MOPED) for data compression and faster evaluation of likelihood functions. Since MOPED only guarantees maintaining the Fisher matrix of the likelihood at a chosen point, multimodal and some degenerate distributions will present a problem. We present examples of scenarios in which MOPED does faithfully represent the true likelihood but also cases in which it does not. Through these examples, we aim to define a set of criteria for which MOPED will accurately represent the likelihood and hence may be used to obtain a significant reduction in the time needed to calculate it. These criteria may involve the evaluation of the full likelihood function for comparison.

astro-ph.IM

The Mock LISA Data Challenges: from Challenge 3 to Challenge 4

The Mock LISA Data Challenges are a program to demonstrate LISA data-analysis capabilities and to encourage their development. Each round of challenges consists of one or more datasets containing simulated instrument noise and gravitational waves from sources of undisclosed parameters. Participants analyze the datasets and report best-fit solutions for the source parameters. Here we present the results of the third challenge, issued in Apr 2008, which demonstrated the positive recovery of signals from chirping Galactic binaries, from spinning supermassive--black-hole binaries (with optimal SNRs between ~ 10 and 2000), from simultaneous extreme-mass-ratio inspirals (SNRs of 10-50), from cosmic-string-cusp bursts (SNRs of 10-100), and from a relatively loud isotropic background with Omega_gw(f) ~ 10^-11, slightly below the LISA instrument noise.

gr-qc

Cosmological parameter estimation with large scale structure and supernovae data

Most cosmological parameter estimations are based on the same set of observations and are therefore not independent. Here, we test the consistency of parameter estimations using a combination of large-scale structure and supernovae data, without cosmic microwave background (CMB) data. We combine observations from the IRAS 1.2 Jy and Las Campanas redshift surveys, galaxy peculiar velocities and measurements of type Ia supernovae to obtain h=0.57_{-0.14}^{+0.15}, Omega_m=0.28+/-0.05 and sigma_8=0.87_{-0.05}^{+0.04} in agreement with the constraints from observations of the CMB anisotropies by the WMAP satellite. We also compare results from different subsets of data in order to investigate the effect of priors and residual errors in the data. We find that some parameters are consistently well constrained whereas others are consistently ill-determined, or even yield poorly consistent results, thereby illustrating the importance of priors and data contributions.

astro-ph

Bayesian joint estimation of non-Gaussianity and the power spectrum

We propose a rigorous, non-perturbative, Bayesian framework which enables one jointly to test Gaussianity and estimate the power spectrum of CMB anisotropies. It makes use of the Hilbert space of an harmonic oscillator to set up an exact likelihood function, dependent on the power spectrum and on a set of parameters $α_i$, which are zero for Gaussian processes. The latter can be expressed as series of cumulants; indeed they perturbatively reduce to cumulants. However they have the advantage that their variation is essentially unconstrained. Any truncation(i.e.: finite set of $α_i$) therefore still produces a proper distribution - something which cannot be said of the only other such tool on offer, the Edgeworth expansion. We apply our method to Very Small Array (VSA) simulations based on signal Gaussianity, showing that our algorithm is indeed not biased.

astro-ph

Cosmic Microwave Background experiments targeting the cosmic strings Doppler peak signal

We investigate which experiments are better suited to test the robust prediction that cosmic strings do not produce secondary Doppler peaks. We propose a statistic for detecting oscillations in the $C^l$ spectrum, and study its statistical relevance given the truth of an inflationary competitor to cosmic strings. The analysis is performed for single-dish experiments and interferometers, subject to a variety of noise levels and scanning features. A high resolution of 0.2 degrees is found to be required for single-dish experiments with realistic levels of noise. Interferometers appear to be more suitable for detecting this signal.

astro-ph