arXiv subjects

Adam D. Cobb

Publications and source records attributed to Adam D. Cobb.

28 records · Page 2Linked to original sources

arXiv2020

Scaling Hamiltonian Monte Carlo Inference for Bayesian Neural Networks with Symmetric Splitting

Hamiltonian Monte Carlo (HMC) is a Markov chain Monte Carlo (MCMC) approach that exhibits favourable exploration properties in high-dimensional models such as neural networks. Unfortunately, HMC has limited use in large-data regimes and little work has explored suitable approaches that aim to preserve the entire Hamiltonian. In our work, we introduce a new symmetric integration scheme for split HMC that does not rely on stochastic gradients. We show that our new formulation is more efficient than previous approaches and is easy to implement with a single GPU. As a result, we are able to perform full HMC over common deep learning architectures using entire data sets. In addition, when we compare with stochastic gradient MCMC, we show that our method achieves better performance in both accuracy and uncertainty quantification. Our approach demonstrates HMC as a feasible option when considering inference schemes for large-scale machine learning problems.

stat.ML↗

arXiv2020

URSABench: Comprehensive Benchmarking of Approximate Bayesian Inference Methods for Deep Neural Networks

While deep learning methods continue to improve in predictive accuracy on a wide range of application domains, significant issues remain with other aspects of their performance including their ability to quantify uncertainty and their robustness. Recent advances in approximate Bayesian inference hold significant promise for addressing these concerns, but the computational scalability of these methods can be problematic when applied to large-scale models. In this paper, we describe initial work on the development ofURSABench(the Uncertainty, Robustness, Scalability, and Accu-racy Benchmark), an open-source suite of bench-marking tools for comprehensive assessment of approximate Bayesian inference methods with a focus on deep learning-based classification tasks

cs.LG↗

arXiv2020

HumBug Zooniverse: a crowd-sourced acoustic mosquito dataset

Mosquitoes are the only known vector of malaria, which leads to hundreds of thousands of deaths each year. Understanding the number and location of potential mosquito vectors is of paramount importance to aid the reduction of malaria transmission cases. In recent years, deep learning has become widely used for bioacoustic classification tasks. In order to enable further research applications in this field, we release a new dataset of mosquito audio recordings. With over a thousand contributors, we obtained 195,434 labels of two second duration, of which approximately 10 percent signify mosquito events. We present an example use of the dataset, in which we train a convolutional neural network on log-Mel features, showcasing the information content of the labels. We hope this will become a vital resource for those researching all aspects of malaria, and add to the existing audio datasets for bioacoustic detection and signal processing.

cs.LG↗

arXiv2019

Introducing an Explicit Symplectic Integration Scheme for Riemannian Manifold Hamiltonian Monte Carlo

We introduce a recent symplectic integration scheme derived for solving physically motivated systems with non-separable Hamiltonians. We show its relevance to Riemannian manifold Hamiltonian Monte Carlo (RMHMC) and provide an alternative to the currently used generalised leapfrog symplectic integrator, which relies on solving multiple fixed point iterations to convergence. Via this approach, we are able to reduce the number of higher-order derivative calculations per leapfrog step. We explore the implications of this integrator and demonstrate its efficacy in reducing the computational burden of RMHMC. Our code is provided in a new open-source Python package, hamiltorch.

stat.ML↗

arXiv2019

An Ensemble of Bayesian Neural Networks for Exoplanetary Atmospheric Retrieval

Machine learning is now used in many areas of astrophysics, from detecting exoplanets in Kepler transit signals to removing telescope systematics. Recent work demonstrated the potential of using machine learning algorithms for atmospheric retrieval by implementing a random forest to perform retrievals in seconds that are consistent with the traditional, computationally-expensive nested-sampling retrieval method. We expand upon their approach by presenting a new machine learning model, \texttt{plan-net}, based on an ensemble of Bayesian neural networks that yields more accurate inferences than the random forest for the same data set of synthetic transmission spectra. We demonstrate that an ensemble provides greater accuracy and more robust uncertainties than a single model. In addition to being the first to use Bayesian neural networks for atmospheric retrieval, we also introduce a new loss function for Bayesian neural networks that learns correlations between the model outputs. Importantly, we show that designing machine learning models to explicitly incorporate domain-specific knowledge both improves performance and provides additional insight by inferring the covariance of the retrieved atmospheric parameters. We apply \texttt{plan-net} to the Hubble Space Telescope Wide Field Camera 3 transmission spectrum for WASP-12b and retrieve an isothermal temperature and water abundance consistent with the literature. We highlight that our method is flexible and can be expanded to higher-resolution spectra and a larger number of atmospheric parameters.

astro-ph.EP↗

arXiv2018

Bayesian deep neural networks for low-cost neurophysiological markers of Alzheimer's disease severity

As societies around the world are ageing, the number of Alzheimer's disease (AD) patients is rapidly increasing. To date, no low-cost, non-invasive biomarkers have been established to advance the objectivization of AD diagnosis and progression assessment. Here, we utilize Bayesian neural networks to develop a multivariate predictor for AD severity using a wide range of quantitative EEG (QEEG) markers. The Bayesian treatment of neural networks both automatically controls model complexity and provides a predictive distribution over the target function, giving uncertainty bounds for our regression task. It is therefore well suited to clinical neuroscience, where data sets are typically sparse and practitioners require a precise assessment of the predictive uncertainty. We use data of one of the largest prospective AD EEG trials ever conducted to demonstrate the potential of Bayesian deep learning in this domain, while comparing two distinct Bayesian neural network approaches, i.e., Monte Carlo dropout and Hamiltonian Monte Carlo.

stat.ML↗

arXiv2018

Bayesian Deep Learning for Exoplanet Atmospheric Retrieval

Over the past decade, the study of extrasolar planets has evolved rapidly from plain detection and identification to comprehensive categorization and characterization of exoplanet systems and their atmospheres. Atmospheric retrieval, the inverse modeling technique used to determine an exoplanetary atmosphere's temperature structure and composition from an observed spectrum, is both time-consuming and compute-intensive, requiring complex algorithms that compare thousands to millions of atmospheric models to the observational data to find the most probable values and associated uncertainties for each model parameter. For rocky, terrestrial planets, the retrieved atmospheric composition can give insight into the surface fluxes of gaseous species necessary to maintain the stability of that atmosphere, which may in turn provide insight into the geological and/or biological processes active on the planet. These atmospheres contain many molecules, some of them biosignatures, spectral fingerprints indicative of biological activity, which will become observable with the next generation of telescopes. Runtimes of traditional retrieval models scale with the number of model parameters, so as more molecular species are considered, runtimes can become prohibitively long. Recent advances in machine learning (ML) and computer vision offer new ways to reduce the time to perform a retrieval by orders of magnitude, given a sufficient data set to train with. Here we present an ML-based retrieval framework called Intelligent exoplaNet Atmospheric RetrievAl (INARA) that consists of a Bayesian deep learning model for retrieval and a data set of 3,000,000 synthetic rocky exoplanetary spectra generated using the NASA Planetary Spectrum Generator. Our work represents the first ML retrieval model for rocky, terrestrial exoplanets and the first synthetic data set of terrestrial spectra generated at this scale.

astro-ph.EP↗

arXiv2018

Identifying Sources and Sinks in the Presence of Multiple Agents with Gaussian Process Vector Calculus

In systems of multiple agents, identifying the cause of observed agent dynamics is challenging. Often, these agents operate in diverse, non-stationary environments, where models rely on hand-crafted environment-specific features to infer influential regions in the system's surroundings. To overcome the limitations of these inflexible models, we present GP-LAPLACE, a technique for locating sources and sinks from trajectories in time-varying fields. Using Gaussian processes, we jointly infer a spatio-temporal vector field, as well as canonical vector calculus operations on that field. Notably, we do this from only agent trajectories without requiring knowledge of the environment, and also obtain a metric for denoting the significance of inferred causal features in the environment by exploiting our probabilistic method. To evaluate our approach, we apply it to both synthetic and real-world GPS data, demonstrating the applicability of our technique in the presence of multiple agents, as well as its superiority over existing methods.

cs.MA↗

arXiv2018

Loss-Calibrated Approximate Inference in Bayesian Neural Networks

Current approaches in approximate inference for Bayesian neural networks minimise the Kullback-Leibler divergence to approximate the true posterior over the weights. However, this approximation is without knowledge of the final application, and therefore cannot guarantee optimal predictions for a given task. To make more suitable task-specific approximations, we introduce a new loss-calibrated evidence lower bound for Bayesian neural networks in the context of supervised learning, informed by Bayesian decision theory. By introducing a lower bound that depends on a utility function, we ensure that our approximation achieves higher utility than traditional methods for applications that have asymmetric utility functions. Furthermore, in using dropout inference, we highlight that our new objective is identical to that of standard dropout neural networks, with an additional utility-dependent penalty term. We demonstrate our new loss-calibrated model with an illustrative medical example and a restricted model capacity experiment, and highlight failure modes of the comparable weighted cross entropy approach. Lastly, we demonstrate the scalability of our method to real world applications with per-pixel semantic segmentation on an autonomous driving data set.

stat.ML↗

arXiv2017

Learning from lions: inferring the utility of agents from their trajectories

We build a model using Gaussian processes to infer a spatio-temporal vector field from observed agent trajectories. Significant landmarks or influence points in agent surroundings are jointly derived through vector calculus operations that indicate presence of sources and sinks. We evaluate these influence points by using the Kullback-Leibler divergence between the posterior and prior Laplacian of the inferred spatio-temporal vector field. Through locating significant features that influence trajectories, our model aims to give greater insight into underlying causal utility functions that determine agent decision-making. A key feature of our model is that it infers a joint Gaussian process over the observed trajectories, the time-varying vector field of utility and canonical vector calculus operators. We apply our model to both synthetic data and lion GPS data collected at the Bubye Valley Conservancy in southern Zimbabwe.

cs.AI↗