Bayesian Inference

Modelling Latent Travel Behaviour Characteristics with Generative Machine Learning Machine Learning

In this paper, we implement an information-theoretic approach to travel behaviour analysis by introducing a generative modelling framework to identify informative latent characteristics in travel decision making. It involves developing a joint tri-partite Bayesian graphical network model using a Restricted Boltzmann Machine (RBM) generative modelling framework. We apply this framework on a mode choice survey data to identify abstract latent variables and compare the performance with a traditional latent variable model with specific latent preferences -- safety, comfort, and environmental. Data collected from a joint stated and revealed preference mode choice survey in Quebec, Canada were used to calibrate the RBM model. Results show that a signficant impact on model likelihood statistics and suggests that machine learning tools are highly suitable for modelling complex networks of conditional independent behaviour interactions.

Alternate Estimation of a Classifier and the Class-Prior from Positive and Unlabeled Data Machine Learning

We consider a problem of learning a binary classifier only from positive data and unlabeled data (PU learning) and estimating the class-prior in unlabeled data under the case-control scenario. Most of the recent methods of PU learning require an estimate of the class-prior probability in unlabeled data, and it is estimated in advance with another method. However, such a two-step approach which first estimates the class prior and then trains a classifier may not be the optimal approach since the estimation error of the class-prior is not taken into account when a classifier is trained. In this paper, we propose a novel unified approach to estimating the class-prior and training a classifier alternately. Our proposed method is simple to implement and computationally efficient. Through experiments, we demonstrate the practical usefulness of the proposed method.

Cluster Variational Approximations for Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data Machine Learning

Continuous-time Bayesian networks (CTBNs) constitute a general and powerful framework for modeling continuous-time stochastic processes on networks. This makes them particularly attractive for learning the directed structures among interacting entities. However, if the available data is incomplete, one needs to simulate the prohibitively complex CTBN dynamics. Existing approximation techniques, such as sampling and low-order variational methods, either scale unfavorably in system size, or are unsatisfactory in terms of accuracy. Inspired by recent advances in statistical physics, we present a new approximation scheme based on cluster-variational methods significantly improving upon existing variational approximations. We can analytically marginalize the parameters of the approximate CTBN, as these are of secondary importance for structure learning. This recovers a scalable scheme for direct structure learning from incomplete and noisy time-series data. Our approach outperforms existing methods in terms of scalability.

Bayesian sparse reconstruction: a brute-force approach to astronomical imaging and machine learning Machine Learning

We present a principled Bayesian framework for signal reconstruction, in which the signal is modelled by basis functions whose number (and form, if required) is determined by the data themselves. This approach is based on a Bayesian interpretation of conventional sparse reconstruction and regularisation techniques, in which sparsity is imposed through priors via Bayesian model selection. We demonstrate our method for noisy 1- and 2-dimensional signals, including astronomical images. Furthermore, by using a product-space approach, the number and type of basis functions can be treated as integer parameters and their posterior distributions sampled directly. We show that order-of-magnitude increases in computational efficiency are possible from this technique compared to calculating the Bayesian evidences separately, and that further computational gains are possible using it in combination with dynamic nested sampling. Our approach can be readily applied to neural networks, where it allows the network architecture to be determined by the data in a principled Bayesian manner by treating the number of nodes and hidden layers as parameters.

Probabilistic approach to limited-data computed tomography reconstruction Machine Learning

We consider the problem of reconstructing the internal structure of an object from limited x-ray projections. In this work, we use a Gaussian process to model the target function. In contrast to other established methods, this comes with the advantage of not requiring any manual parameter tuning, which usually arises in classical regularization strategies. The Gaussian process is well-known in a heavy computation for the inversion of a covariance matrix, and in this work, by employing an approximative spectral-based technique, we reduce the computational complexity and avoid the need of numerical integration. Results from simulated and real data indicate that this approach is less sensitive to streak artifacts as compared to the commonly used method of filteredback projection, an analytic reconstruction algorithm using Radon inversion formula.

Change-Point Detection on Hierarchical Circadian Models Machine Learning

This paper addresses the problem of change-point detection on sequences of high-dimensional and heterogeneous observations, which also possess a periodic temporal structure. Due to the dimensionality problem, when the time between change-points is on the order of the dimension of the model parameters, drifts in the underlying distribution can be misidentified as changes. To overcome this limitation we assume that the observations lie in a lower dimensional manifold that admits a latent variable representation. In particular, we propose a hierarchical model that is computationally feasible, widely applicable to heterogeneous data and robust to missing instances. Additionally, to deal with the observations' periodic dependencies, we employ a circadian model where the data periodicity is captured by non-stationary covariance functions. We validate the proposed technique on synthetic examples and we demonstrate its utility in the detection of changes for human behavior characterization.

Differentially Private Bayesian Inference for Exponential Families Machine Learning

The study of private inference has been sparked by growing concern regarding the analysis of data when it stems from sensitive sources. We present the first method for private Bayesian inference in exponential families that properly accounts for noise introduced by the privacy mechanism. It is efficient because it works only with sufficient statistics and not individual data. Unlike other methods, it gives properly calibrated posterior beliefs in the non-asymptotic data regime.

Collapsed Variational Inference for Nonparametric Bayesian Group Factor Analysis Machine Learning

Group factor analysis (GFA) methods have been widely used to infer the common structure and the group-specific signals from multiple related datasets in various fields including systems biology and neuroimaging. To date, most available GFA models require Gibbs sampling or slice sampling to perform inference, which prevents the practical application of GFA to large-scale data. In this paper we present an efficient collapsed variational inference (CVI) algorithm for the nonparametric Bayesian group factor analysis (NGFA) model built upon an hierarchical beta Bernoulli process. Our CVI algorithm proceeds by marginalizing out the group-specific beta process parameters, and then approximating the true posterior in the collapsed space using mean field methods. Experimental results on both synthetic and real-world data demonstrate the effectiveness of our CVI algorithm for the NGFA compared with state-of-the-art GFA methods.

Variational Approximation Accuracy in Bayesian Non-negative Matrix Factorization Machine Learning

Non-negative matrix factorization (NMF) is a knowledge discovery method that is used for many fields, besides, its variational inference and Gibbs sampling method are also well-known. However, the variational approximation accuracy is not yet clarified, since NMF is not statistically regular and the prior used in the variational Bayesian NMF (VBNMF) has zero or divergence points. In this paper, using algebraic geometrical methods, we theoretically analyze the difference of the negative log evidence/marginal likelihood (free energy) between VBNMF and Bayesian NMF, and give a lower bound of the approximation accuracy, asymptotically. The results quantitatively show how well the VBNMF algorithm can approximate Bayesian NMF.

Hands-on Experience with Gaussian Processes (GPs): Implementing GPs in Python - I Machine Learning

This document serves to complement our website which was developed with the aim of exposing the students to Gaussian Processes (GPs). GPs are non-parametric Bayesian regression models that are largely used by statisticians and geospatial data scientists for modeling spatial data. Several open source libraries spanning from Matlab [1], Python [2], R [3] etc., are already available for simple plug-and-use. The objective of this handout and in turn the website was to allow the users to develop stand-alone GPs in Python by relying on minimal external dependencies. To this end, we only use the default python modules and assist the users in developing their own GPs from scratch giving them an in-depth knowledge of what goes on under the hood. The module covers GP inference using maximum likelihood estimation (MLE) and gives examples of 1D (dummy) spatial data.