Accelerating Monte Carlo Methods For Bayesian Inference In Dynamical Models
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Accelerating Monte Carlo methods for Bayesian inference in dynamical models
Author: Johan Dahlin
language: en
Publisher: Linköping University Electronic Press
Release Date: 2016-03-22
Making decisions and predictions from noisy observations are two important and challenging problems in many areas of society. Some examples of applications are recommendation systems for online shopping and streaming services, connecting genes with certain diseases and modelling climate change. In this thesis, we make use of Bayesian statistics to construct probabilistic models given prior information and historical data, which can be used for decision support and predictions. The main obstacle with this approach is that it often results in mathematical problems lacking analytical solutions. To cope with this, we make use of statistical simulation algorithms known as Monte Carlo methods to approximate the intractable solution. These methods enjoy well-understood statistical properties but are often computational prohibitive to employ. The main contribution of this thesis is the exploration of different strategies for accelerating inference methods based on sequential Monte Carlo (SMC) and Markov chain Monte Carlo (MCMC). That is, strategies for reducing the computational effort while keeping or improving the accuracy. A major part of the thesis is devoted to proposing such strategies for the MCMC method known as the particle Metropolis-Hastings (PMH) algorithm. We investigate two strategies: (i) introducing estimates of the gradient and Hessian of the target to better tailor the algorithm to the problem and (ii) introducing a positive correlation between the point-wise estimates of the target. Furthermore, we propose an algorithm based on the combination of SMC and Gaussian process optimisation, which can provide reasonable estimates of the posterior but with a significant decrease in computational effort compared with PMH. Moreover, we explore the use of sparseness priors for approximate inference in over-parametrised mixed effects models and autoregressive processes. This can potentially be a practical strategy for inference in the big data era. Finally, we propose a general method for increasing the accuracy of the parameter estimates in non-linear state space models by applying a designed input signal. Borde Riksbanken höja eller sänka reporäntan vid sitt nästa möte för att nå inflationsmålet? Vilka gener är förknippade med en viss sjukdom? Hur kan Netflix och Spotify veta vilka filmer och vilken musik som jag vill lyssna på härnäst? Dessa tre problem är exempel på frågor där statistiska modeller kan vara användbara för att ge hjälp och underlag för beslut. Statistiska modeller kombinerar teoretisk kunskap om exempelvis det svenska ekonomiska systemet med historisk data för att ge prognoser av framtida skeenden. Dessa prognoser kan sedan användas för att utvärdera exempelvis vad som skulle hända med inflationen i Sverige om arbetslösheten sjunker eller hur värdet på mitt pensionssparande förändras när Stockholmsbörsen rasar. Tillämpningar som dessa och många andra gör statistiska modeller viktiga för många delar av samhället. Ett sätt att ta fram statistiska modeller bygger på att kontinuerligt uppdatera en modell allteftersom mer information samlas in. Detta angreppssätt kallas för Bayesiansk statistik och är särskilt användbart när man sedan tidigare har bra insikter i modellen eller tillgång till endast lite historisk data för att bygga modellen. En nackdel med Bayesiansk statistik är att de beräkningar som krävs för att uppdatera modellen med den nya informationen ofta är mycket komplicerade. I sådana situationer kan man istället simulera utfallet från miljontals varianter av modellen och sedan jämföra dessa mot de historiska observationerna som finns till hands. Man kan sedan medelvärdesbilda över de varianter som gav bäst resultat för att på så sätt ta fram en slutlig modell. Det kan därför ibland ta dagar eller veckor för att ta fram en modell. Problemet blir särskilt stort när man använder mer avancerade modeller som skulle kunna ge bättre prognoser men som tar för lång tid för att bygga. I denna avhandling använder vi ett antal olika strategier för att underlätta eller förbättra dessa simuleringar. Vi föreslår exempelvis att ta hänsyn till fler insikter om systemet och därmed minska antalet varianter av modellen som behöver undersökas. Vi kan således redan utesluta vissa modeller eftersom vi har en bra uppfattning om ungefär hur en bra modell ska se ut. Vi kan också förändra simuleringen så att den enklare rör sig mellan olika typer av modeller. På detta sätt utforskas rymden av alla möjliga modeller på ett mer effektivt sätt. Vi föreslår ett antal olika kombinationer och förändringar av befintliga metoder för att snabba upp anpassningen av modellen till observationerna. Vi visar att beräkningstiden i vissa fall kan minska ifrån några dagar till någon timme. Förhoppningsvis kommer detta i framtiden leda till att man i praktiken kan använda mer avancerade modeller som i sin tur resulterar i bättre prognoser och beslut.
Machine learning using approximate inference
Author: Christian Andersson Naesseth
language: en
Publisher: Linköping University Electronic Press
Release Date: 2018-11-27
Automatic decision making and pattern recognition under uncertainty are difficult tasks that are ubiquitous in our everyday life. The systems we design, and technology we develop, requires us to coherently represent and work with uncertainty in data. Probabilistic models and probabilistic inference gives us a powerful framework for solving this problem. Using this framework, while enticing, results in difficult-to-compute integrals and probabilities when conditioning on the observed data. This means we have a need for approximate inference, methods that solves the problem approximately using a systematic approach. In this thesis we develop new methods for efficient approximate inference in probabilistic models. There are generally two approaches to approximate inference, variational methods and Monte Carlo methods. In Monte Carlo methods we use a large number of random samples to approximate the integral of interest. With variational methods, on the other hand, we turn the integration problem into that of an optimization problem. We develop algorithms of both types and bridge the gap between them. First, we present a self-contained tutorial to the popular sequential Monte Carlo (SMC) class of methods. Next, we propose new algorithms and applications based on SMC for approximate inference in probabilistic graphical models. We derive nested sequential Monte Carlo, a new algorithm particularly well suited for inference in a large class of high-dimensional probabilistic models. Then, inspired by similar ideas we derive interacting particle Markov chain Monte Carlo to make use of parallelization to speed up approximate inference for universal probabilistic programming languages. After that, we show how we can make use of the rejection sampling process when generating gamma distributed random variables to speed up variational inference. Finally, we bridge the gap between SMC and variational methods by developing variational sequential Monte Carlo, a new flexible family of variational approximations.
Probabilistic modeling for sensor fusion with inertial measurements
Author: Manon Kok
language: en
Publisher: Linköping University Electronic Press
Release Date: 2016-12-15
In recent years, inertial sensors have undergone major developments. The quality of their measurements has improved while their cost has decreased, leading to an increase in availability. They can be found in stand-alone sensor units, so-called inertial measurement units, but are nowadays also present in for instance any modern smartphone, in Wii controllers and in virtual reality headsets. The term inertial sensor refers to the combination of accelerometers and gyroscopes. These measure the external specific force and the angular velocity, respectively. Integration of their measurements provides information about the sensor's position and orientation. However, the position and orientation estimates obtained by simple integration suffer from drift and are therefore only accurate on a short time scale. In order to improve these estimates, we combine the inertial sensors with additional sensors and models. To combine these different sources of information, also called sensor fusion, we make use of probabilistic models to take the uncertainty of the different sources of information into account. The first contribution of this thesis is a tutorial paper that describes the signal processing foundations underlying position and orientation estimation using inertial sensors. In a second contribution, we use data from multiple inertial sensors placed on the human body to estimate the body's pose. A biomechanical model encodes the knowledge about how the different body segments are connected to each other. We also show how the structure inherent to this problem can be exploited. This opens up for processing long data sets and for solving the problem in a distributed manner. Inertial sensors can also be combined with time of arrival measurements from an ultrawideband (UWB) system. We focus both on calibration of the UWB setup and on sensor fusion of the inertial and UWB measurements. The UWB measurements are modeled by a tailored heavy-tailed asymmetric distribution. This distribution naturally handles the possibility of measurement delays due to multipath and non-line-of-sight conditions while not allowing for the possibility of measurements arriving early, i.e. traveling faster than the speed of light. Finally, inertial sensors can be combined with magnetometers. We derive an algorithm that can calibrate a magnetometer for the presence of metallic objects attached to the sensor. Furthermore, the presence of metallic objects in the environment can be exploited by using them as a source of position information. We present a method to build maps of the indoor magnetic field and experimentally show that if a map of the magnetic field is available, accurate position estimates can be obtained by combining inertial and magnetometer measurements.