In identifying infected patients in a population, group testing is an effective method to reduce the number of tests and correct the test errors. In the group testing procedure, tests are performed on pools of specimens collected from patients, where the number of pools is lower than that of patients. The performance of group testing heavily depends on the design of pools and algorithms that are used in inferring the infected patients from the test outcomes. In this paper, an adaptive design method of pools based on the predictive distribution is proposed in the framework of Bayesian inference. The proposed method executed using the belief propagation algorithm results in more accurate identification of the infected patients, as compared to the group testing performed on random pools determined in advance.

Bayesian geoacoustic inversion problems are conventionally solved by Markov chain Monte Carlo methods or its variants, which are computationally expensive. This paper extends the classic Bayesian geoacoustic inversion framework using the mixture density network (MDN), which provides a much more efficient way to solve geoacoustic inversion problems in Bayesian inference framework. Some important geoacoustic statistics of Bayesian geoacoustic inversion are derived from the multidimensional posterior probability density (PPD) using the MDN theory. These statistics make it convenient to train the network directly on the whole parameter space and get the multidimensional PPD of model parameters. The network is trained on a simulated dataset of surface-wave dispersion curves with shear-wave velocities as labels. The results show that the network gives reliable predictions and has good generalization performance on unseen data. Once trained, the network can rapidly (within seconds) give a fully probabilistic solution which is comparable to Monte Carlo methods. It provides an promissing approach for real-time inversion.

Context: Demonstrating high reliability and safety for safety-critical systems (SCSs) remains a hard problem. Diverse evidence needs to be combined in a rigorous way: in particular, results of operational testing with other evidence from design and verification. Growing use of machine learning in SCSs, by precluding most established methods for gaining assurance, makes operational testing even more important for supporting safety and reliability claims. Objective: We use Autonomous Vehicles (AVs) as a current example to revisit the problem of demonstrating high reliability. AVs are making their debut on public roads: methods for assessing whether an AV is safe enough are urgently needed. We demonstrate how to answer 5 questions that would arise in assessing an AV type, starting with those proposed by a highly-cited study. Method: We apply new theorems extending Conservative Bayesian Inference (CBI), which exploit the rigour of Bayesian methods while reducing the risk of involuntary misuse associated with now-common applications of Bayesian inference; we define additional conditions needed for applying these methods to AVs. Results: Prior knowledge can bring substantial advantages if the AV design allows strong expectations of safety before road testing. We also show how naive attempts at conservative assessment may lead to over-optimism instead; why extrapolating the trend of disengagements is not suitable for safety claims; use of knowledge that an AV has moved to a less stressful environment. Conclusion: While some reliability targets will remain too high to be practically verifiable, CBI removes a major source of doubt: it allows use of prior knowledge without inducing dangerously optimistic biases. For certain ranges of required reliability and prior beliefs, CBI thus supports feasible, sound arguments. Useful conservative claims can be derived from limited prior knowledge.

Probabilistic sentential decision diagrams are logic circuits where the inputs of disjunctive gates are annotated by probability values. They allow for a compact representation of joint probability mass functions defined over sets of Boolean variables, that are also consistent with the logical constraints defined by the circuit. The probabilities in such a model are usually learned from a set of observations. This leads to overconfident and prior-dependent inferences when data are scarce, unreliable or conflicting. In this work, we develop the credal sentential decision diagrams, a generalisation of their probabilistic counterpart that allows for replacing the local probabilities with (so-called credal) sets of mass functions. These models induce a joint credal set over the set of Boolean variables, that sharply assigns probability zero to states inconsistent with the logical constraints. Three inference algorithms are derived for these models, these allow to compute: (i) the lower and upper probabilities of an observation for an arbitrary number of variables; (ii) the lower and upper conditional probabilities for the state of a single variable given an observation; (iii) whether or not all the probabilistic sentential decision diagrams compatible with the credal specification have the same most probable explanation of a given set of variables given an observation of the other variables. These inferences are tractable, as all the three algorithms, based on bottom-up traversal with local linear programming tasks on the disjunctive gates, can be solved in polynomial time with respect to the circuit size. For a first empirical validation, we consider a simple application based on noisy seven-segment display images. The credal models are observed to properly distinguish between easy and hard-to-detect instances and outperform other generative models not able to cope with logical constraints.

The sparse Cholesky parametrization of the inverse covariance matrix can be interpreted as a Gaussian Bayesian network; however its counterpart, the covariance Cholesky factor, has received, with few notable exceptions, little attention so far, despite having a natural interpretation as a hidden variable model for ordered signal data. To fill this gap, in this paper we focus on arbitrary zero patterns in the Cholesky factor of a covariance matrix. We discuss how these models can also be extended, in analogy with Gaussian Bayesian networks, to data where no apparent order is available. For the ordered scenario, we propose a novel estimation method that is based on matrix loss penalization, as opposed to the existing regression-based approaches. The performance of this sparse model for the Cholesky factor, together with our novel estimator, is assessed in a simulation setting, as well as over spatial and temporal real data where a natural ordering arises among the variables. We give guidelines, based on the empirical results, about which of the methods analysed is more appropriate for each setting.

Network-oriented research has been increasingly popular in many scientific areas. In neuroscience research, imaging-based network connectivity measures have become the key for understanding brain organizations, potentially serving as individual neural fingerprints. There are major challenges in analyzing connectivity matrices including the high dimensionality of brain networks, unknown latent sources underlying the observed connectivity, and the large number of brain connections leading to spurious findings. In this paper, we propose a novel blind source separation method with low-rank structure and uniform sparsity (LOCUS) as a fully data-driven decomposition method for network measures. Compared with the existing method that vectorizes connectivity matrices ignoring brain network topology, LOCUS achieves more efficient and accurate source separation for connectivity matrices using low-rank structure. We propose a novel angle-based uniform sparsity regularization that demonstrates better performance than the existing sparsity controls for low-rank tensor methods. We propose a highly efficient iterative Node-Rotation algorithm that exploits the block multi-convexity of the objective function to solve the non-convex optimization problem for learning LOCUS. We illustrate the advantage of LOCUS through extensive simulation studies. Application of LOCUS to Philadelphia Neurodevelopmental Cohort neuroimaging study reveals biologically insightful connectivity traits which are not found using the existing method.

In this paper, we propose a flexible model for survival analysis using neural networks along with scalable optimization algorithms. One key technical challenge for directly applying maximum likelihood estimation (MLE) to censored data is that evaluating the objective function and its gradients with respect to model parameters requires the calculation of integrals. To address this challenge, we recognize that the MLE for censored data can be viewed as a differential-equation constrained optimization problem, a novel perspective. Following this connection, we model the distribution of event time through an ordinary differential equation and utilize efficient ODE solvers and adjoint sensitivity analysis to numerically evaluate the likelihood and the gradients. Using this approach, we are able to 1) provide a broad family of continuous-time survival distributions without strong structural assumptions, 2) obtain powerful feature representations using neural networks, and 3) allow efficient estimation of the model in large-scale applications using stochastic gradient descent. Through both simulation studies and real-world data examples, we demonstrate the effectiveness of the proposed method in comparison to existing state-of-the-art deep learning survival analysis models.

In conducting non-linear dimensionality reduction and feature learning, it is common to suppose that the data lie near a lower-dimensional manifold. A class of model-based approaches for such problems includes latent variables in an unknown non-linear regression function; this includes Gaussian process latent variable models and variational auto-encoders (VAEs) as special cases. VAEs are artificial neural networks (ANNs) that employ approximations to make computation tractable; however, current implementations lack adequate uncertainty quantification in estimating the parameters, predictive densities, and lower-dimensional subspace, and can be unstable and lack interpretability in practice. We attempt to solve these problems by deploying Markov chain Monte Carlo sampling algorithms (MCMC) for Bayesian inference in ANN models with latent variables. We address issues of identifiability by imposing constraints on the ANN parameters as well as by using anchor points. This is demonstrated on simulated and real data examples. We find that current MCMC sampling schemes face fundamental challenges in neural networks involving latent variables, motivating new research directions.

Deep kernel learning (DKL) leverages the connection between Gaussian process (GP) and neural networks (NN) to build an end-to-end, hybrid model. It combines the capability of NN to learn rich representations under massive data and the non-parametric property of GP to achieve automatic regularization that incorporates a trade-off between model fit and model complexity. However, the deterministic encoder may weaken the model regularization of the following GP part, especially on small datasets, due to the free latent representation. We therefore present a complete deep latent-variable kernel learning (DLVKL) model wherein the latent variables perform stochastic encoding for regularized representation. We further enhance the DLVKL from two aspects: (i) the expressive variational posterior through neural stochastic differential equation (NSDE) to improve the approximation quality, and (ii) the hybrid prior taking knowledge from both the SDE prior and the posterior to arrive at a flexible trade-off. Intensive experiments imply that the DLVKL-NSDE performs similarly to the well calibrated GP on small datasets, and outperforms existing deep GPs on large datasets.

Latent variables may lead to spurious relationships that can be misinterpreted as causal relationships. In Bayesian Networks (BNs), this challenge is known as learning under causal insufficiency. Structure learning algorithms that assume causal insufficiency tend to reconstruct the ancestral graph of a BN, where bi-directed edges represent confounding and directed edges represent direct or ancestral relationships. This paper describes a hybrid structure learning algorithm, called CCHM, which combines the constraint-based part of cFCI with hill-climbing score-based learning. The score-based process incorporates Pearl s do-calculus to measure causal effects and orientate edges that would otherwise remain undirected, under the assumption the BN is a linear Structure Equation Model where data follow a multivariate Gaussian distribution. Experiments based on both randomised and well-known networks show that CCHM improves the state-of-the-art in terms of reconstructing the true ancestral graph.