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Probabilistic graphical models are widely used to model complex systems under uncertainty. Traditionally, Gaussian directed graphical models are applied for analysis of large networks with continuous variables as they can provide conditional and marginal distributions in closed form simplifying the inferential task. The Gaussianity and linearity assumptions are often adequate, yet can lead to poor performance when dealing with some practical applications. In this paper, we model each variable in graph G as a polynomial regression of its parents to capture complex relationships between individual variables and with a utility function of polynomial form. We develop a message-passing algorithm to propagate information throughout the network solely using moments which enables the expected utility scores to be calculated exactly. Our propagation method scales up well and enables to perform inference in terms of a finite number of expectations. We illustrate how the proposed methodology works with examples and in an application to decision problems in energy planning and for real-time clinical decision support.

Untargeted metabolomic profiling through liquid chromatography-mass spectrometry (LC-MS) measures a vast array of metabolites within biospecimens, advancing drug development, disease diagnosis, and risk prediction. However, the low throughput of LC-MS poses a major challenge for biomarker discovery, annotation, and experimental comparison, necessitating the merging of multiple datasets. Current data pooling methods encounter practical limitations due to their vulnerability to data variations and hyperparameter dependence. Here we introduce GromovMatcher, a flexible and user-friendly algorithm that automatically combines LC-MS datasets using optimal transport. By capitalizing on feature intensity correlation structures, GromovMatcher delivers superior alignment accuracy and robustness compared to existing approaches. This algorithm scales to thousands of features requiring minimal hyperparameter tuning. Manually curated datasets for validating alignment algorithms are limited in the field of untargeted metabolomics, and hence we develop a dataset split procedure to generate pairs of validation datasets to test the alignments produced by GromovMatcher and other methods. Applying our method to experimental patient studies of liver and pancreatic cancer, we discover shared metabolic features related to patient alcohol intake, demonstrating how GromovMatcher facilitates the search for biomarkers associated with lifestyle risk factors linked to several cancer types.

Robust Bayesian analysis has been mainly devoted to detecting and measuring robustness to the prior distribution. Indeed, many contributions in the literature aim to define suitable classes of priors which allow the computation of variations of quantities of interest while the prior changes within those classes. The literature has devoted much less attention to the robustness of Bayesian methods to the likelihood function due to mathematical and computational complexity, and because it is often arguably considered a more objective choice compared to the prior. In this contribution, a new approach to Bayesian local robustness to the likelihood function is proposed and extended to robustness to the prior and to both. This approach is based on the notion of distortion function introduced in the literature on risk theory, and then successfully adopted to build suitable classes of priors for Bayesian global robustness to the prior. The novel robustness measure is a local sensitivity measure that turns out to be very tractable and easy to compute for certain classes of distortion functions. Asymptotic properties are derived and numerical experiments illustrate the theory and its applicability for modelling purposes.

Moderate calibration, the expected event probability among observations with predicted probability z being equal to z, is a desired property of risk prediction models. Current graphical and numerical techniques for evaluating moderate calibration of risk prediction models are mostly based on smoothing or grouping the data. As well, there is no widely accepted inferential method for the null hypothesis that a model is moderately calibrated. In this work, we discuss recently-developed, and propose novel, methods for the assessment of moderate calibration for binary responses. The methods are based on the limiting distributions of functions of standardized partial sums of prediction errors converging to the corresponding laws of Brownian motion. The novel method relies on well-known properties of the Brownian bridge which enables joint inference on mean and moderate calibration, leading to a unified "bridge" test for detecting miscalibration. Simulation studies indicate that the bridge test is more powerful, often substantially, than the alternative test. As a case study we consider a prediction model for short-term mortality after a heart attack, where we provide suggestions on graphical presentation and the interpretation of results. Moderate calibration can be assessed without requiring arbitrary grouping of data or using methods that require tuning of parameters. An accompanying R package implements this method (see //github.com/resplab/cumulcalib/).

Machine learning (ML) has recently shown significant promise in modelling atmospheric systems, such as the weather. Many of these ML models are autoregressive, and error accumulation in their forecasts is a key problem. However, there is no clear definition of what `error accumulation' actually entails. In this paper, we propose a definition and an associated metric to measure it. Our definition distinguishes between errors which are due to model deficiencies, which we may hope to fix, and those due to the intrinsic properties of atmospheric systems (chaos, unobserved variables), which are not fixable. We illustrate the usefulness of this definition by proposing a simple regularization loss penalty inspired by it. This approach shows performance improvements (according to RMSE and spread/skill) in a selection of atmospheric systems, including the real-world weather prediction task.

Latent variable models serve as powerful tools to infer underlying dynamics from observed neural activity. However, due to the absence of ground truth data, prediction benchmarks are often employed as proxies. In this study, we reveal the limitations of the widely-used 'co-smoothing' prediction framework and propose an improved few-shot prediction approach that encourages more accurate latent dynamics. Utilizing a student-teacher setup with Hidden Markov Models, we demonstrate that the high co-smoothing model space can encompass models with arbitrary extraneous dynamics within their latent representations. To address this, we introduce a secondary metric -- a few-shot version of co-smoothing. This involves performing regression from the latent variables to held-out channels in the data using fewer trials. Our results indicate that among models with near-optimal co-smoothing, those with extraneous dynamics underperform in the few-shot co-smoothing compared to 'minimal' models devoid of such dynamics. We also provide analytical insights into the origin of this phenomenon. We further validate our findings on real neural data using two state-of-the-art methods: LFADS and STNDT. In the absence of ground truth, we suggest a proxy measure to quantify extraneous dynamics. By cross-decoding the latent variables of all model pairs with high co-smoothing, we identify models with minimal extraneous dynamics. We find a correlation between few-shot co-smoothing performance and this new measure. In summary, we present a novel prediction metric designed to yield latent variables that more accurately reflect the ground truth, offering a significant improvement for latent dynamics inference.

Characteristic formulae give a complete logical description of the behaviour of processes modulo some chosen notion of behavioural semantics. They allow one to reduce equivalence or preorder checking to model checking, and are exactly the formulae in the modal logics characterizing classic behavioural equivalences and preorders for which model checking can be reduced to equivalence or preorder checking. This paper studies the complexity of determining whether a formula is characteristic for some finite, loop-free process in each of the logics providing modal characterizations of the simulation-based semantics in van Glabbeek's branching-time spectrum. Since characteristic formulae in each of those logics are exactly the consistent and prime ones, it presents complexity results for the satisfiability and primality problems, and investigates the boundary between modal logics for which those problems can be solved in polynomial time and those for which they become computationally hard. Amongst other contributions, this article also studies the complexity of constructing characteristic formulae in the modal logics characterizing simulation-based semantics, both when such formulae are presented in explicit form and via systems of equations.

We study the expressivity and the complexity of various logics in probabilistic team semantics with the Boolean negation. In particular, we study the extension of probabilistic independence logic with the Boolean negation, and a recently introduced logic FOPT. We give a comprehensive picture of the relative expressivity of these logics together with the most studied logics in probabilistic team semantics setting, as well as relating their expressivity to a numerical variant of second-order logic. In addition, we introduce novel entropy atoms and show that the extension of first-order logic by entropy atoms subsumes probabilistic independence logic. Finally, we obtain some results on the complexity of model checking, validity, and satisfiability of our logics.

The Fisher-Rao distance between two probability distributions of a statistical model is defined as the Riemannian geodesic distance induced by the Fisher information metric. In order to calculate the Fisher-Rao distance in closed-form, we need (1) to elicit a formula for the Fisher-Rao geodesics, and (2) to integrate the Fisher length element along those geodesics. We consider several numerically robust approximation and bounding techniques for the Fisher-Rao distances: First, we report generic upper bounds on Fisher-Rao distances based on closed-form 1D Fisher-Rao distances of submodels. Second, we describe several generic approximation schemes depending on whether the Fisher-Rao geodesics or pregeodesics are available in closed-form or not. In particular, we obtain a generic method to guarantee an arbitrarily small additive error on the approximation provided that Fisher-Rao pregeodesics and tight lower and upper bounds are available. Third, we consider the case of Fisher metrics being Hessian metrics, and report generic tight upper bounds on the Fisher-Rao distances using techniques of information geometry. Uniparametric and biparametric statistical models always have Fisher Hessian metrics, and in general a simple test allows to check whether the Fisher information matrix yields a Hessian metric or not. Fourth, we consider elliptical distribution families and show how to apply the above techniques to these models. We also propose two new distances based either on the Fisher-Rao lengths of curves serving as proxies of Fisher-Rao geodesics, or based on the Birkhoff/Hilbert projective cone distance. Last, we consider an alternative group-theoretic approach for statistical transformation models based on the notion of maximal invariant which yields insights on the structures of the Fisher-Rao distance formula which may be used fruitfully in applications.

Similar to the notion of h-adaptivity, where the discretization resolution is adaptively changed, I propose the notion of model adaptivity, where the underlying model (the governing equations) is adaptively changed in space and time. Specifically, this work introduces a hybrid and adaptive coupling of a 3D bulk fluid flow model with a 2D thin film flow model. As a result, this work extends the applicability of existing thin film flow models to complex scenarios where, for example, bulk flow develops into thin films after striking a surface. At each location in space and time, the proposed framework automatically decides whether a 3D model or a 2D model must be applied. Using a meshless approach for both 3D and 2D models, at each particle, the decision to apply a 2D or 3D model is based on the user-prescribed resolution and a local principal component analysis. When a particle needs to be changed from a 3D model to 2D, or vice versa, the discretization is changed, and all relevant data mapping is done on-the-fly. Appropriate two-way coupling conditions and mass conservation considerations between the 3D and 2D models are also developed. Numerical results show that this model adaptive framework shows higher flexibility and compares well against finely resolved 3D simulations. In an actual application scenario, a 3 factor speed up is obtained, while maintaining the accuracy of the solution.