Tissue characterisation with CMR parametric mapping has the potential to detect and quantify both focal and diffuse alterations in myocardial structure not assessable by late gadolinium enhancement. Native T1 mapping in particular has shown promise as a useful biomarker to support diagnostic, therapeutic and prognostic decision-making in ischaemic and non-ischaemic cardiomyopathies. Convolutional neural networks with Bayesian inference are a category of artificial neural networks which model the uncertainty of the network output. This study presents an automated framework for tissue characterisation from native ShMOLLI T1 mapping at 1.5T using a Probabilistic Hierarchical Segmentation (PHiSeg) network. In addition, we use the uncertainty information provided by the PHiSeg network in a novel automated quality control (QC) step to identify uncertain T1 values. The PHiSeg network and QC were validated against manual analysis on a cohort of the UK Biobank containing healthy subjects and chronic cardiomyopathy patients. We used the proposed method to obtain reference T1 ranges for the left ventricular myocardium in healthy subjects as well as common clinical cardiac conditions. T1 values computed from automatic and manual segmentations were highly correlated (r=0.97). Bland-Altman analysis showed good agreement between the automated and manual measurements. The average Dice metric was 0.84 for the left ventricular myocardium. The sensitivity of detection of erroneous outputs was 91%. Finally, T1 values were automatically derived from 14,683 CMR exams from the UK Biobank. The proposed pipeline allows for automatic analysis of myocardial native T1 mapping and includes a QC process to detect potentially erroneous results. T1 reference values were presented for healthy subjects and common clinical cardiac conditions from the largest cohort to date using T1-mapping images.
We showed how to use trained neural networks to perform Bayesian reasoning in order to solve tasks outside their initial scope. Deep generative models provide prior knowledge, and classification/regression networks impose constraints. The tasks at hand were formulated as Bayesian inference problems, which we approximately solved through variational or sampling techniques. The approach built on top of already trained networks, and the addressable questions grew super-exponentially with the number of available networks. In its simplest form, the approach yielded conditional generative models. However, multiple simultaneous constraints constitute elaborate questions. We compared the approach to specifically trained generators, showed how to solve riddles, and demonstrated its compatibility with state-of-the-art architectures.
Gaussian process (GP) priors are non-parametric generative models with appealing modelling properties for Bayesian inference: they can model non-linear relationships through noisy observations, have closed-form expressions for training and inference, and are governed by interpretable hyperparameters. However, GP models rely on Gaussianity, an assumption that does not hold in several real-world scenarios, e.g., when observations are bounded or have extreme-value dependencies, a natural phenomenon in physics, finance and social sciences. Although beyond-Gaussian stochastic processes have caught the attention of the GP community, a principled definition and rigorous treatment is still lacking. In this regard, we propose a methodology to construct stochastic processes, which include GPs, warped GPs, Student-t processes and several others under a single unified approach. We also provide formulas and algorithms for training and inference of the proposed models in the regression problem. Our approach is inspired by layers-based models, where each proposed layer changes a specific property over the generated stochastic process. That, in turn, allows us to push-forward a standard Gaussian white noise prior towards other more expressive stochastic processes, for which marginals and copulas need not be Gaussian, while retaining the appealing properties of GPs. We validate the proposed model through experiments with real-world data.
The key distinguishing property of a Bayesian approach is marginalization instead of optimization, not the prior, or Bayes rule. Bayesian inference is especially compelling for deep neural networks. (1) Neural networks are typically underspecified by the data, and can represent many different but high performing models corresponding to different settings of parameters, which is exactly when marginalization will make the biggest difference for both calibration and accuracy. (2) Deep ensembles have been mistaken as competing approaches to Bayesian methods, but can be seen as approximate Bayesian marginalization. (3) The structure of neural networks gives rise to a structured prior in function space, which reflects the inductive biases of neural networks that help them generalize. (4) The observed correlation between parameters in flat regions of the loss and a diversity of solutions that provide good generalization is further conducive to Bayesian marginalization, as flat regions occupy a large volume in a high dimensional space, and each different solution will make a good contribution to a Bayesian model average. (5) Recent practical advances for Bayesian deep learning provide improvements in accuracy and calibration compared to standard training, while retaining scalability.
The development of human-robot systems able to leverage the strengths of both humans and their robotic counterparts has been greatly sought after because of the foreseen, broad-ranging impact across industry and research. We believe the true potential of these systems cannot be reached unless the robot is able to act with a high level of autonomy, reducing the burden of manual tasking or teleoperation. To achieve this level of autonomy, robots must be able to work fluidly with its human partners, inferring their needs without explicit commands. This inference requires the robot to be able to detect and classify the heterogeneity of its partners. We propose a framework for learning from heterogeneous demonstration based upon Bayesian inference and evaluate a suite of approaches on a real-world dataset of gameplay from StarCraft II. This evaluation provides evidence that our Bayesian approach can outperform conventional methods by up to 12.8$%$.
A reciprocal LASSO (rLASSO) regularization employs a decreasing penalty function as opposed to conventional penalization approaches that use increasing penalties on the coefficients, leading to stronger parsimony and superior model selection relative to traditional shrinkage methods. Here we consider a fully Bayesian formulation of the rLASSO problem, which is based on the observation that the rLASSO estimate for linear regression parameters can be interpreted as a Bayesian posterior mode estimate when the regression parameters are assigned independent inverse Laplace priors. Bayesian inference from this posterior is possible using an expanded hierarchy motivated by a scale mixture of double Pareto or truncated normal distributions. On simulated and real datasets, we show that the Bayesian formulation outperforms its classical cousin in estimation, prediction, and variable selection across a wide range of scenarios while offering the advantage of posterior inference. Finally, we discuss other variants of this new approach and provide a unified framework for variable selection using flexible reciprocal penalties. All methods described in this paper are publicly available as an R package at: https://github.com/himelmallick/BayesRecipe.
Value-at-Risk (VaR) and Expected Shortfall (ES) are widely used in the financial sector to measure the market risk and manage the extreme market movement. The recent link between the quantile score function and the Asymmetric Laplace density has led to a flexible likelihood-based framework for joint modelling of VaR and ES. It is of high interest in financial applications to be able to capture the underlying joint dynamics of these two quantities. We address this problem by developing a hybrid model that is based on the Asymmetric Laplace quasi-likelihood and employs the Long Short-Term Memory (LSTM) time series modelling technique from Machine Learning to capture efficiently the underlying dynamics of VaR and ES. We refer to this model as LSTM-AL. We adopt the adaptive Markov chain Monte Carlo (MCMC) algorithm for Bayesian inference in the LSTM-AL model. Empirical results show that the proposed LSTM-AL model can improve the VaR and ES forecasting accuracy over a range of well-established competing models.
The reconstruction from observations of high-dimensional chaotic dynamics such as geophysical flows is hampered by (i) the partial and noisy observations that can realistically be obtained, (ii) the need to learn from long time series of data, and (iii) the unstable nature of the dynamics. To achieve such inference from the observations over long time series, it has been suggested to combine data assimilation and machine learning in several ways. We show how to unify these approaches from a Bayesian perspective using expectation-maximization and coordinate descents. In doing so, the model, the state trajectory and model error statistics are estimated all together. Implementations and approximations of these methods are discussed. Finally, we numerically and successfully test the approach on two relevant low-order chaotic models with distinct identifiability.
We analyze the dynamics of an algorithm for approximate inference with large Gaussian latent variable models in a student-teacher scenario. To model nontrivial dependencies between the latent variables, we assume random covariance matrices drawn from rotation invariant ensembles. For the case of perfect data-model matching, the knowledge of static order parameters derived from the replica method allows us to obtain efficient algorithmic updates in terms of matrix-vector multiplications with a fixed matrix. Using the dynamical functional approach, we obtain an exact effective stochastic process in the thermodynamic limit for a single node. From this, we obtain closed-form expressions for the rate of the convergence. Analytical results are excellent agreement with simulations of single instances of large models.
In this paper, we propose a new stochastic optimization algorithm for Bayesian inference based on multilevel Monte Carlo (MLMC) methods. In Bayesian statistics, biased estimators of the model evidence have been often used as stochastic objectives because the existing debiasing techniques are computationally costly to apply. To overcome this issue, we apply an MLMC sampling technique to construct low-variance unbiased estimators both for the model evidence and its gradient. In the theoretical analysis, we show that the computational cost required for our proposed MLMC estimator to estimate the model evidence or its gradient with a given accuracy is an order of magnitude smaller than those of the previously known estimators. Our numerical experiments confirm considerable computational savings compared to the conventional estimators. Combining our MLMC estimator with gradient-based stochastic optimization results in a new scalable, efficient, debiased inference algorithm for Bayesian statistical models.
We propose a formalization of the three-tier causal hierarchy of association, intervention, and counterfactuals as a series of probabilistic logical languages. Our languages are of strictly increasing expressivity, the first capable of expressing quantitative probabilistic reasoning -- including conditional independence and Bayesian inference -- the second encoding do-calculus reasoning for causal effects, and the third capturing a fully expressive do-calculus for arbitrary counterfactual queries. We give a corresponding series of finitary axiomatizations complete over both structural causal models and probabilistic programs, and show that satisfiability and validity for each language are decidable in polynomial space.
The free energy principle has been proposed as a unifying account of brain function. It is closely related, and in some cases subsumes, earlier unifying ideas such as Bayesian inference, predictive coding, and active learning. This article clarifies these connections, teasing apart distinctive and shared predictions.
We describe a method for Bayesian optimization by which one may incorporate data from multiple systems whose quantitative interrelationships are unknown a priori. All general (nonreal-valued) features of the systems are associated with continuous latent variables that enter as inputs into a single metamodel that simultaneously learns the response surfaces of all of the systems. Bayesian inference is used to determine appropriate beliefs regarding the latent variables. We explain how the resulting probabilistic metamodel may be used for Bayesian optimization tasks and demonstrate its implementation on a variety of synthetic and real-world examples, comparing its performance under zero-, one-, and few-shot settings against traditional Bayesian optimization, which usually requires substantially more data from the system of interest.
Robustness to out-of-distribution (OOD) data is an important goal in building reliable machine learning systems. Especially in autonomous systems, wrong predictions for OOD inputs can cause safety critical situations. As a first step towards a solution, we consider the problem of detecting such data in a value-based deep reinforcement learning (RL) setting. Modelling this problem as a one-class classification problem, we propose a framework for uncertainty-based OOD classification: UBOOD. It is based on the effect that an agent's epistemic uncertainty is reduced for situations encountered during training (in-distribution), and thus lower than for unencountered (OOD) situations. Being agnostic towards the approach used for estimating epistemic uncertainty, combinations with different uncertainty estimation methods, e.g. approximate Bayesian inference methods or ensembling techniques are possible. We further present a first viable solution for calculating a dynamic classification threshold, based on the uncertainty distribution of the training data. Evaluation shows that the framework produces reliable classification results when combined with ensemble-based estimators, while the combination with concrete dropout-based estimators fails to reliably detect OOD situations. In summary, UBOOD presents a viable approach for OOD classification in deep RL settings by leveraging the epistemic uncertainty of the agent's value function.
Due to their inherent variabilities,nanomaterial-based sensors are challenging to translate into real-world applications,where reliability/reproducibility is key.Recently we showed Bayesian inference can be employed on engineered variability in layered nanomaterial-based optical transmission filters to determine optical wavelengths with high accuracy/precision.In many practical applications the sensing cost/speed and long-term reliability can be equal or more important considerations.Though various machine learning tools are frequently used on sensor/detector networks to address these,nonetheless their effectiveness on nanomaterial-based sensors has not been explored.Here we show the best choice of ML algorithm in a cyber-nanomaterial detector is mainly determined by specific use considerations,e.g.,accuracy, computational cost,speed, and resilience against drifts/ageing effects.When sufficient data/computing resources are provided,highest sensing accuracy can be achieved by the kNN and Bayesian inference algorithms,but but can be computationally expensive for real-time applications.In contrast,artificial neural networks are computationally expensive to train,but provide the fastest result under testing conditions and remain reasonably accurate.When data is limited,SVMs perform well even with small training sets,while other algorithms show considerable reduction in accuracy if data is scarce,hence,setting a lower limit on the size of required training data.We show by tracking/modeling the long-term drifts of the detector performance over large (1year) period,it is possible to improve the predictive accuracy with no need for recalibration.Our research shows for the first time if the ML algorithm is chosen specific to use-case,low-cost solution-processed cyber-nanomaterial detectors can be practically implemented under diverse operational requirements,despite their inherent variabilities.
Crowdsourcing is a relatively economic and efficient solution to collect annotations from the crowd through online platforms. Answers collected from workers with different expertise may be noisy and unreliable, and the quality of annotated data needs to be further maintained. Various solutions have been attempted to obtain high-quality annotations. However, they all assume that workers' label quality is stable over time (always at the same level whenever they conduct the tasks). In practice, workers' attention level changes over time, and the ignorance of which can affect the reliability of the annotations. In this paper, we focus on a novel and realistic crowdsourcing scenario involving attention-aware annotations. We propose a new probabilistic model that takes into account workers' attention to estimate the label quality. Expectation propagation is adopted for efficient Bayesian inference of our model, and a generalized Expectation Maximization algorithm is derived to estimate both the ground truth of all tasks and the label-quality of each individual crowd worker with attention. In addition, the number of tasks best suited for a worker is estimated according to changes in attention. Experiments against related methods on three real-world and one semi-simulated datasets demonstrate that our method quantifies the relationship between workers' attention and label-quality on the given tasks, and improves the aggregated labels.
Consider a Bayesian inference problem where a variable of interest does not take values in a Euclidean space. These "non-standard" data structures are in reality fairly common. They are frequently used in problems involving latent discrete factor models, networks, and domain specific problems such as sequence alignments and reconstructions, pedigrees, and phylogenies. In principle, Bayesian inference should be particularly well-suited in such scenarios, as the Bayesian paradigm provides a principled way to obtain confidence assessment for random variables of any type. However, much of the recent work on making Bayesian analysis more accessible and computationally efficient has focused on inference in Euclidean spaces. In this paper, we introduce Blang, a domain specific language and library aimed at bridging this gap. Blang allows users to perform Bayesian analysis on arbitrary data types while using a declarative syntax similar to BUGS. Blang is augmented with intuitive language additions to create data types of the user's choosing. To perform inference at scale on such arbitrary state spaces, Blang leverages recent advances in sequential Monte Carlo and non-reversible Markov chain Monte Carlo methods.
Approximate inference techniques are the cornerstone of probabilistic methods based on Gaussian process priors. Despite this, most work approximately optimizes standard divergence measures such as the Kullback-Leibler (KL) divergence, which lack the basic desiderata for the task at hand, while chiefly offering merely technical convenience. We develop a new approximate inference method for Gaussian process models which overcomes the technical challenges arising from abandoning these convenient divergences. Our method---dubbed Quantile Propagation (QP)---is similar to expectation propagation (EP) but minimizes the $L_2$ Wasserstein distance (WD) instead of the KL divergence. The WD exhibits all the required properties of a distance metric, while respecting the geometry of the underlying sample space. We show that QP matches quantile functions rather than moments as in EP and has the same mean update but a smaller variance update than EP, thereby alleviating EP's tendency to over-estimate posterior variances. Crucially, despite the significant complexity of dealing with the WD, QP has the same favorable locality property as EP, and thereby admits an efficient algorithm. Experiments on classification and Poisson regression show that QP outperforms both EP and variational Bayes.
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with a new algorithm for numerically computing likelihoods of quantitative traits. The diffusion approach allows for analysis of datasets containing hundreds or thousands of individuals. The method, which we call \snapper, has been implemented as part of the Beast2 package. We introduce the models, the efficient algorithms, and report performance of \snapper on simulated data sets and on SNP data from rattlesnakes and freshwater turtles.
Anomaly detection is a challenging task that frequently arises in practically all areas of industry and science, from fraud detection and data quality monitoring to finding rare cases of diseases and searching for new physics. Most of the conventional approaches to anomaly detection, such as one-class SVM and Robust Auto-Encoder, are one-class classification methods, i.e. focus on separating normal data from the rest of the space. Such methods are based on the assumption of separability of normal and anomalous classes, and subsequently do not take into account any available samples of anomalies. Nonetheless, in practical settings, some anomalous samples are often available; however, usually in amounts far lower than required for a balanced classification task, and the separability assumption might not always hold. This leads to an important task -- incorporating known anomalous samples into training procedures of anomaly detection models. In this work, we propose a novel model-agnostic training procedure to address this task. We reformulate one-class classification as a binary classification problem with normal data being distinguished from pseudo-anomalous samples. The pseudo-anomalous samples are drawn from low-density regions of a normalizing flow model by feeding tails of the latent distribution into the model. Such an approach allows to easily include known anomalies into the training process of an arbitrary classifier. We demonstrate that our approach shows comparable performance on one-class problems, and, most importantly, achieves comparable or superior results on tasks with variable amounts of known anomalies.