We present a model inversion algorithm, CKLEMAP, for data assimilation and parameter estimation in partial differential equation models of physical systems with spatially heterogeneous parameter fields. These fields are approximated using low-dimensional conditional Karhunen-Lo\'{e}ve expansions, which are constructed using Gaussian process regression models of these fields trained on the parameters' measurements. We then assimilate measurements of the state of the system and compute the maximum a posteriori estimate of the CKLE coefficients by solving a nonlinear least-squares problem. When solving this optimization problem, we efficiently compute the Jacobian of the vector objective by exploiting the sparsity structure of the linear system of equations associated with the forward solution of the physics problem. The CKLEMAP method provides better scalability compared to the standard MAP method. In the MAP method, the number of unknowns to be estimated is equal to the number of elements in the numerical forward model. On the other hand, in CKLEMAP, the number of unknowns (CKLE coefficients) is controlled by the smoothness of the parameter field and the number of measurements, and is in general much smaller than the number of discretization nodes, which leads to a significant reduction of computational cost with respect to the standard MAP method. To show its advantage in scalability, we apply CKLEMAP to estimate the transmissivity field in a two-dimensional steady-state subsurface flow model of the Hanford Site by assimilating synthetic measurements of transmissivity and hydraulic head. We find that the execution time of CKLEMAP scales nearly linearly as $N^{1.33}$, where $N$ is the number of discretization nodes, while the execution time of standard MAP scales as $N^{2.91}$. The CKLEMAP method improved execution time without sacrificing accuracy when compared to the standard MAP.

Personalised federated learning (FL) aims at collaboratively learning a machine learning model taylored for each client. Albeit promising advances have been made in this direction, most of existing approaches works do not allow for uncertainty quantification which is crucial in many applications. In addition, personalisation in the cross-device setting still involves important issues, especially for new clients or those having small number of observations. This paper aims at filling these gaps. To this end, we propose a novel methodology coined FedPop by recasting personalised FL into the population modeling paradigm where clients' models involve fixed common population parameters and random effects, aiming at explaining data heterogeneity. To derive convergence guarantees for our scheme, we introduce a new class of federated stochastic optimisation algorithms which relies on Markov chain Monte Carlo methods. Compared to existing personalised FL methods, the proposed methodology has important benefits: it is robust to client drift, practical for inference on new clients, and above all, enables uncertainty quantification under mild computational and memory overheads. We provide non-asymptotic convergence guarantees for the proposed algorithms and illustrate their performances on various personalised federated learning tasks.

We consider the problem of performing Bayesian inference in probabilistic models where observations are accompanied by uncertainty, referred to as "uncertain evidence." We explore how to interpret uncertain evidence, and by extension the importance of proper interpretation as it pertains to inference about latent variables. We consider a recently-proposed method "distributional evidence" as well as revisit two older methods: Jeffrey's rule and virtual evidence. We devise guidelines on how to account for uncertain evidence and we provide new insights, particularly regarding consistency. To showcase the impact of different interpretations of the same uncertain evidence, we carry out experiments in which one interpretation is defined as "correct." We then compare inference results from each different interpretation illustrating the importance of careful consideration of uncertain evidence.

The Expectation Maximization (EM) algorithm is widely used as an iterative modification to maximum likelihood estimation when the data is incomplete. We focus on a semi-supervised case to learn the model from labeled and unlabeled samples. Existing work in the semi-supervised case has focused mainly on performance rather than convergence guarantee, however we focus on the contribution of the labeled samples to the convergence rate. The analysis clearly demonstrates how the labeled samples improve the convergence rate for the exponential family mixture model. In this case, we assume that the population EM (EM with unlimited data) is initialized within the neighborhood of global convergence for the population EM that consists solely of samples that have not been labeled. The analysis for the labeled samples provides a comprehensive description of the convergence rate for the Gaussian mixture model. In addition, we extend the findings for labeled samples and offer an alternative proof for the population EM's convergence rate with unlabeled samples for the symmetric mixture of two Gaussians.

In text mining, topic models are a type of probabilistic generative models for inferring latent semantic topics from text corpus. One of the most popular inference approaches to topic models is perhaps collapsed Gibbs sampling (CGS), which typically samples one single topic label for each observed document-word pair. In this paper, we aim at improving the inference of CGS for topic models. We propose to leverage state augmentation technique by maximizing the number of topic samples to infinity, and then develop a new inference approach, called infinite latent state replication (ILR), to generate robust soft topic assignment for each given document-word pair. Experimental results on the publicly available datasets show that ILR outperforms CGS for inference of existing established topic models.

Phylogenetics is a classical methodology in computational biology that today has become highly relevant for medical investigation of single-cell data, e.g., in the context of cancer development. The exponential size of the tree space is, unfortunately, a substantial obstacle for Bayesian phylogenetic inference using Markov chain Monte Carlo based methods since these rely on local operations. And although more recent variational inference (VI) based methods offer speed improvements, they rely on expensive auto-differentiation operations for learning the variational parameters. We propose VaiPhy, a remarkably fast VI based algorithm for approximate posterior inference in an augmented tree space. VaiPhy produces marginal log-likelihood estimates on par with the state-of-the-art methods on real data and is considerably faster since it does not require auto-differentiation. Instead, VaiPhy combines coordinate ascent update equations with two novel sampling schemes: (i) SLANTIS, a proposal distribution for tree topologies in the augmented tree space, and (ii) the JC sampler, to the best of our knowledge, the first-ever scheme for sampling branch lengths directly from the popular Jukes-Cantor model. We compare VaiPhy in terms of density estimation and runtime. Additionally, we evaluate the reproducibility of the baselines.

Marginal-based methods achieve promising performance in the synthetic data competition hosted by the National Institute of Standards and Technology (NIST). To deal with high-dimensional data, the distribution of synthetic data is represented by a probabilistic graphical model (e.g., a Bayesian network), while the raw data distribution is approximated by a collection of low-dimensional marginals. Differential privacy (DP) is guaranteed by introducing random noise to each lowdimensional marginal distribution. Despite its promising performance in practice, the statistical properties of marginal-based methods are rarely studied in the literature. In this paper, we study DP data synthesis algorithms based on Bayesian networks (BN) from a statistical perspective. Related to downstream machine learning tasks, an upper bound for the utility error of the DP synthetic data is also derived. To complete the picture, we establish a lower bound for TV accuracy that holds for everyǫ-DP synthetic data generator. In recent years, the problem of privacy-preserving data analysis has become increasingly important and differential privacy (Dwork et al., 2006) appears as the foundation of data privacy. Differential privacy (DP) techniques are widely adopted by industrial companies and the U.S. Census Bureau (Johnson et al., 2017; Erlingsson et al., 2014; Nguyên et al., 2016; The U.S. Census Bureau, 2020; Abowd, 2018).

Bayesian neural networks (BNNs) can account for both aleatoric and epistemic uncertainty. However, in BNNs the priors are often specified over the weights which rarely reflects true prior knowledge in large and complex neural network architectures. We present a simple approach to incorporate prior knowledge in BNNs based on external summary information about the predicted classification probabilities for a given dataset. The available summary information is incorporated as augmented data and modeled with a Dirichlet process, and we derive the corresponding \emph{Summary Evidence Lower BOund}. The approach is founded on Bayesian principles, and all hyperparameters have a proper probabilistic interpretation. We show how the method can inform the model about task difficulty and class imbalance. Extensive experiments show that, with negligible computational overhead, our method parallels and in many cases outperforms popular alternatives in accuracy, uncertainty calibration, and robustness against corruptions with both balanced and imbalanced data.

Several years ago, before learning much about methods for reasoning with uncertainty, I and my colleagues began work on a large expert system, called Pathfinder, that assists community pathologists with the diagnosis of lymph node pathology. Because the Dempster-Shafer theory of belief was quite popular in our research group at the time, we developed a inference method for our expert system inspired by this theory. The program performed fairly well in the opinion of the expert pathologist who provided the knowledge for the system. In the months following the initial development of Pathfinder, several of us in the research group began exploring other methods for reasoning under uncertainty. We identified the Bayesian approach as a candidate for a new inference procedure. We realized that the measures of uncertainty we assessed from the expert could be interpreted as probabilities and we implemented a new inference method-- a special case of Bayes' theorem. During this time, the expert was running cases through the program to test the system's diagnostic performance. One day, without telling him, we changed the inference procedure to the Bayesian approach. After running several cases with the new approach, the expert exclaimed, "What did you do to the program?

We discuss the prediction accuracy of assumed statistical models in terms of prediction errors for the generalized linear model and penalized maximum likelihood methods. We derive the forms of estimators for the prediction errors, such as $C_p$ criterion, information criteria, and leave-one-out cross validation (LOOCV) error, using the generalized approximate message passing (GAMP) algorithm and replica method. These estimators coincide with each other when the number of model parameters is sufficiently small; however, there is a discrepancy between them in particular in the parameter region where the number of model parameters is larger than the data dimension. In this paper, we review the prediction errors and corresponding estimators, and discuss their differences. In the framework of GAMP, we show that the information criteria can be expressed by using the variance of the estimates. Further, we demonstrate how to approach LOOCV error from the information criteria by utilizing the expression provided by GAMP.