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In this note, we examine the forward-Euler discretization for simulating Wasserstein gradient flows. We provide two counter-examples showcasing the failure of this discretization even for a simple case where the energy functional is defined as the KL divergence against some nicely structured probability densities. A simple explanation of this failure is also discussed.

It is well known since 1960s that by exploring the tensor product structure of the discrete Laplacian on Cartesian meshes, one can develop a simple direct Poisson solver with an $\mathcal O(N^{\frac{d+1}d})$ complexity in d-dimension, where N is the number of the total unknowns. The GPU acceleration of numerically solving PDEs has been explored successfully around fifteen years ago and become more and more popular in the past decade, driven by significant advancement in both hardware and software technologies, especially in the recent few years. We present in this paper a simple but extremely fast MATLAB implementation on a modern GPU, which can be easily reproduced, for solving 3D Poisson type equations using a spectral-element method. In particular, it costs less than one second on a Nvidia A100 for solving a Poisson equation with one billion degree of freedoms. We also present applications of this fast solver to solve a linear (time-independent) Schr\"odinger equation and a nonlinear (time-dependent) Cahn-Hilliard equation.

Bayesian optimization (BO) is a principled approach to molecular design tasks. In this paper we explain three pitfalls of BO which can cause poor empirical performance: an incorrect prior width, over-smoothing, and inadequate acquisition function maximization. We show that with these issues addressed, even a basic BO setup is able to achieve the highest overall performance on the PMO benchmark for molecule design (Gao et al, 2022). These results suggest that BO may benefit from more attention in the machine learning for molecules community.

In Parts I and II of this series of papers, three new methods for the computation of eigenvalues of singular pencils were developed: rank-completing perturbations, rank-projections, and augmentation. It was observed that a straightforward structure-preserving adaption for symmetric pencils was not possible and it was left as an open question how to address this challenge. In this Part III, it is shown how the observed issue can be circumvented by using Hermitian perturbations. This leads to structure-preserving analogues of the three techniques from Parts I and II for Hermitian pencils (including real symmetric pencils) as well as for related structures. It is an important feature of these methods that the sign characteristic of the given pencil is preserved. As an application, it is shown that the resulting methods can be used to solve systems of bivariate polynomials.

Nonparametric estimators for the mean and the covariance functions of functional data are proposed. The setup covers a wide range of practical situations. The random trajectories are, not necessarily differentiable, have unknown regularity, and are measured with error at discrete design points. The measurement error could be heteroscedastic. The design points could be either randomly drawn or common for all curves. The estimators depend on the local regularity of the stochastic process generating the functional data. We consider a simple estimator of this local regularity which exploits the replication and regularization features of functional data. Next, we use the ``smoothing first, then estimate'' approach for the mean and the covariance functions. They can be applied with both sparsely or densely sampled curves, are easy to calculate and to update, and perform well in simulations. Simulations built upon an example of real data set, illustrate the effectiveness of the new approach.

In this paper we propose a Monte Carlo maximum likelihood estimation strategy for discretely observed Wright-Fisher diffusions. Our approach provides an unbiased estimator of the likelihood function and is based on exact simulation techniques that are of special interest for diffusion processes defined on a bounded domain, where numerical methods typically fail to remain within the required boundaries. We start by building unbiased likelihood estimators for scalar diffusions and later present an extension to the multidimensional case. Consistency results of our proposed estimator are also presented and the performance of our method is illustrated through numerical examples.

In this paper, under certain conditions we consider two-dimensional cellular automata with the Moore neighborhood. Namely, the characterization of 2D linear cellular automata defined by the Moore neighborhood with some mixed boundary conditions over the field $\mathbb{Z}_{p}$ is studied. Furthermore, we investigate the rule matrices of 2D Moore CA under some mixed boundary conditions by applying rotation. Finally, we give the conditions under which the obtained rule matrices for 2D finite CAs are reversible.

This position paper takes a broad look at Physics-Enhanced Machine Learning (PEML) -- also known as Scientific Machine Learning -- with particular focus to those PEML strategies developed to tackle dynamical systems' challenges. The need to go beyond Machine Learning (ML) strategies is driven by: (i) limited volume of informative data, (ii) avoiding accurate-but-wrong predictions; (iii) dealing with uncertainties; (iv) providing Explainable and Interpretable inferences. A general definition of PEML is provided by considering four physics and domain knowledge biases, and three broad groups of PEML approaches are discussed: physics-guided, physics-encoded and physics-informed. The advantages and challenges in developing PEML strategies for guiding high-consequence decision making in engineering applications involving complex dynamical systems, are presented.

Problems from metric graph theory like Metric Dimension, Geodetic Set, and Strong Metric Dimension have recently had a strong impact in parameterized complexity by being the first known problems in NP to admit double-exponential lower bounds in the treewidth, and even in the vertex cover number for the latter, assuming the Exponential Time Hypothesis. We initiate the study of enumerating minimal solution sets for these problems and show that they are also of great interest in enumeration. Specifically, we show that enumerating minimal resolving sets in graphs and minimal geodetic sets in split graphs are equivalent to enumerating minimal transversals in hypergraphs (denoted Trans-Enum), whose solvability in total-polynomial time is one of the most important open problems in algorithmic enumeration. This provides two new natural examples to a question that emerged in recent works: for which vertex (or edge) set graph property $\Pi$ is the enumeration of minimal (or maximal) subsets satisfying $\Pi$ equivalent to Trans-Enum? As very few properties are known to fit within this context -- namely, those related to minimal domination -- our results make significant progress in characterizing such properties, and provide new angles to approach Trans-Enum. In contrast, we observe that minimal strong resolving sets can be enumerated with polynomial delay. Additionally, we consider cases where our reductions do not apply, namely graphs with no long induced paths, and show both positive and negative results related to the enumeration and extension of partial solutions.

This paper proposes a second-order accurate numerical scheme for the Patlak-Keller-Segel system with various mobilities for the description of chemotaxis. Formulated in a variational structure, the entropy part is novelly discretized by a modified Crank-Nicolson approach so that the solution to the proposed nonlinear scheme corresponds to a minimizer of a convex functional. A careful theoretical analysis reveals that the unique solvability and positivity-preserving property could be theoretically justified. More importantly, such a second order numerical scheme is able to preserve the dissipative property of the original energy functional, instead of a modified one. To the best of our knowledge, the proposed scheme is the first second-order accurate one in literature that could achieve both the numerical positivity and original energy dissipation. In addition, an optimal rate convergence estimate is provided for the proposed scheme, in which rough and refined error estimate techniques have to be included to accomplish such an analysis. Ample numerical results are presented to demonstrate robust performance of the proposed scheme in preserving positivity and original energy dissipation in blowup simulations.