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This article presents the MAGI software package for the inference of dynamic systems. The focus of MAGI is on dynamics modeled by nonlinear ordinary differential equations with unknown parameters. While such models are widely used in science and engineering, the available experimental data for parameter estimation may be noisy and sparse. Furthermore, some system components may be entirely unobserved. MAGI solves this inference problem with the help of manifold-constrained Gaussian processes within a Bayesian statistical framework, whereas unobserved components have posed a significant challenge for existing software. We use several realistic examples to illustrate the functionality of MAGI. The user may choose to use the package in any of the R, MATLAB, and Python environments.

This work studies an experimental design problem where {the values of a predictor variable, denoted by $x$}, are to be determined with the goal of estimating a function $m(x)$, which is observed with noise. A linear model is fitted to $m(x)$ but it is not assumed that the model is correctly specified. It follows that the quantity of interest is the best linear approximation of $m(x)$, which is denoted by $\ell(x)$. It is shown that in this framework the ordinary least squares estimator typically leads to an inconsistent estimation of $\ell(x)$, and rather weighted least squares should be considered. An asymptotic minimax criterion is formulated for this estimator, and a design that minimizes the criterion is constructed. An important feature of this problem is that the $x$'s should be random, rather than fixed. Otherwise, the minimax risk is infinite. It is shown that the optimal random minimax design is different from its deterministic counterpart, which was studied previously, and a simulation study indicates that it generally performs better when $m(x)$ is a quadratic or a cubic function. Another finding is that when the variance of the noise goes to infinity, the random and deterministic minimax designs coincide. The results are illustrated for polynomial regression models and the general case is also discussed.

We study the problem of list-decodable Gaussian covariance estimation. Given a multiset $T$ of $n$ points in $\mathbb R^d$ such that an unknown $\alpha<1/2$ fraction of points in $T$ are i.i.d. samples from an unknown Gaussian $\mathcal{N}(\mu, \Sigma)$, the goal is to output a list of $O(1/\alpha)$ hypotheses at least one of which is close to $\Sigma$ in relative Frobenius norm. Our main result is a $\mathrm{poly}(d,1/\alpha)$ sample and time algorithm for this task that guarantees relative Frobenius norm error of $\mathrm{poly}(1/\alpha)$. Importantly, our algorithm relies purely on spectral techniques. As a corollary, we obtain an efficient spectral algorithm for robust partial clustering of Gaussian mixture models (GMMs) -- a key ingredient in the recent work of [BDJ+22] on robustly learning arbitrary GMMs. Combined with the other components of [BDJ+22], our new method yields the first Sum-of-Squares-free algorithm for robustly learning GMMs. At the technical level, we develop a novel multi-filtering method for list-decodable covariance estimation that may be useful in other settings.

An inner-product Hilbert space formulation of the Kemeny distance is defined over the domain of all permutations with ties upon the extended real line, and results in an unbiased minimum variance (Gauss-Markov) correlation estimator upon a homogeneous i.i.d. sample. In this work, we construct and prove the necessary requirements to extend this linear topology for both Spearman's \(\rho\) and Kendall's \(\tau_{b}\), showing both spaces to be both biased and inefficient upon practical data domains. A probability distribution is defined for the Kemeny \(\tau_{\kappa}\) estimator, and a Studentisation adjustment for finite samples is provided as well. This work allows for a general purpose linear model duality to be identified as a unique consistent solution to many biased and unbiased estimation scenarios.

This paper studies the causal representation learning problem when the latent causal variables are observed indirectly through an unknown linear transformation. The objectives are: (i) recovering the unknown linear transformation (up to scaling) and (ii) determining the directed acyclic graph (DAG) underlying the latent variables. Sufficient conditions for DAG recovery are established, and it is shown that a large class of non-linear models in the latent space (e.g., causal mechanisms parameterized by two-layer neural networks) satisfy these conditions. These sufficient conditions ensure that the effect of an intervention can be detected correctly from changes in the score. Capitalizing on this property, recovering a valid transformation is facilitated by the following key property: any valid transformation renders latent variables' score function to necessarily have the minimal variations across different interventional environments. This property is leveraged for perfect recovery of the latent DAG structure using only \emph{soft} interventions. For the special case of stochastic \emph{hard} interventions, with an additional hypothesis testing step, one can also uniquely recover the linear transformation up to scaling and a valid causal ordering.

We propose a posterior for Bayesian Likelihood-Free Inference (LFI) based on generalized Bayesian inference. To define the posterior, we use Scoring Rules (SRs), which evaluate probabilistic models given an observation. In LFI, we can sample from the model but not evaluate the likelihood; hence, we employ SRs which admit unbiased empirical estimates. We use the Energy and Kernel SRs, for which our posterior enjoys consistency in a well-specified setting and outlier robustness. We perform inference with pseudo-marginal (PM) Markov Chain Monte Carlo (MCMC) or stochastic-gradient (SG) MCMC. While PM-MCMC works satisfactorily for simple setups, it mixes poorly for concentrated targets. Conversely, SG-MCMC requires differentiating the simulator model but improves performance over PM-MCMC when both work and scales to higher-dimensional setups as it is rejection-free. Although both techniques target the SR posterior approximately, the error diminishes as the number of model simulations at each MCMC step increases. In our simulations, we employ automatic differentiation to effortlessly differentiate the simulator model. We compare our posterior with related approaches on standard benchmarks and a chaotic dynamical system from meteorology, for which SG-MCMC allows inferring the parameters of a neural network used to parametrize a part of the update equations of the dynamical system.

Score-based diffusion models (SBDM) have recently emerged as state-of-the-art approaches for image generation. Existing SBDMs are typically formulated in a finite-dimensional setting, where images are considered as tensors of a finite size. This papers develops SBDMs in the infinite-dimensional setting, that is, we model the training data as functions supported on a rectangular domain. Besides the quest for generating images at ever higher resolution our primary motivation is to create a well-posed infinite-dimensional learning problem so that we can discretize it consistently on multiple resolution levels. We thereby hope to obtain diffusion models that generalize across different resolution levels and improve the efficiency of the training process. We demonstrate how to overcome two shortcomings of current SBDM approaches in the infinite-dimensional setting. First, we modify the forward process to ensure that the latent distribution is well-defined in the infinite-dimensional setting using the notion of trace class operators. Second, we illustrate that approximating the score function with an operator network, in our case Fourier neural operators (FNOs), is beneficial for multilevel training. After deriving the forward process in the infinite-dimensional setting and reverse processes for finite approximations, we show their well-posedness, derive adequate discretizations, and investigate the role of the latent distributions. We provide first promising numerical results on two datasets, MNIST and material structures. In particular, we show that multilevel training is feasible within this framework.

We present an alternative to reweighting techniques for modifying distributions to account for a desired change in an underlying conditional distribution, as is often needed to correct for mis-modelling in a simulated sample. We employ conditional normalizing flows to learn the full conditional probability distribution from which we sample new events for conditional values drawn from the target distribution to produce the desired, altered distribution. In contrast to common reweighting techniques, this procedure is independent of binning choice and does not rely on an estimate of the density ratio between two distributions. In several toy examples we show that normalizing flows outperform reweighting approaches to match the distribution of the target.We demonstrate that the corrected distribution closes well with the ground truth, and a statistical uncertainty on the training dataset can be ascertained with bootstrapping. In our examples, this leads to a statistical precision up to three times greater than using reweighting techniques with identical sample sizes for the source and target distributions. We also explore an application in the context of high energy particle physics.

We present algorithms based on satisfiability problem (SAT) solving, as well as answer set programming (ASP), for solving the problem of determining inconsistency degrees in propositional knowledge bases. We consider six different inconsistency measures whose respective decision problems lie on the first level of the polynomial hierarchy. Namely, these are the contension inconsistency measure, the forgetting-based inconsistency measure, the hitting set inconsistency measure, the max-distance inconsistency measure, the sum-distance inconsistency measure, and the hit-distance inconsistency measure. In an extensive experimental analysis, we compare the SAT-based and ASP-based approaches with each other, as well as with a set of naive baseline algorithms. Our results demonstrate that overall, both the SAT-based and the ASP-based approaches clearly outperform the naive baseline methods in terms of runtime. The results further show that the proposed ASP-based approaches perform superior to the SAT-based ones with regard to all six inconsistency measures considered in this work. Moreover, we conduct additional experiments to explain the aforementioned results in greater detail.

The electron density is a key parameter to characterize any plasma. Most of the plasma applications and research in the area of low-temperature plasmas (LTPs) is based on plasma density and plasma temperature. The conventional methods for electron density measurements offer axial and radial profiles for any given linear LTP device. These methods have major disadvantages of operational range (not very wide), cumbersome instrumentation, and complicated data analysis procedures. To address such practical concerns, the article proposes a novel machine learning (ML) assisted microwave-plasma interaction based strategy which is capable enough to determine the electron density profile within the plasma. The electric field pattern due to microwave scattering is measured to estimate the density profile. The proof of concept is tested for a simulated training data set comprising a low-temperature, unmagnetized, collisional plasma. Different types of Gaussian-shaped density profiles, in the range $10^{16}-10^{19}m^{-3}$, addressing a range of experimental configurations have been considered in our study. The results obtained show promising performance in estimating the 2D radial profile of the density for the given linear plasma device. The performance of the proposed deep learning based approach has been evaluated using three metrics- SSIM, RMSLE and MAPE. The favourable performance affirms the potential of the proposed ML based approach in plasma diagnostics.