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Using dominating sets to separate vertices of graphs is a well-studied problem in the larger domain of identification problems. In such problems, the objective is to choose a suitable dominating set $C$ of a graph $G$ such that the neighbourhoods of all vertices of $G$ have distinct intersections with $C$. Such a dominating and separating set $C$ is often referred to as a \emph{code} in the literature. Depending on the types of dominating and separating sets used, various problems arise under various names in the literature. In this paper, we introduce a new problem in the same realm of identification problems whereby the code, called \emph{open-separating dominating code}, or \emph{OSD-code} for short, is a dominating set and uses open neighbourhoods for separating vertices. The paper studies the fundamental properties concerning the existence, hardness and minimality of OSD-codes. Due to the emergence of a close and yet difficult to establish relation of the OSD-codes with another well-studied code in the literature called open locating dominating codes, or OLD-codes for short, we compare the two on various graph families. Finally, we also provide an equivalent reformulation of the problem of finding OSD-codes of a graph as a covering problem in a suitable hypergraph and discuss the polyhedra associated with OSD-codes, again in relation to OLD-codes of some graph families already studied in this context.

Designing protein nanomaterials of predefined shape and characteristics has the potential to dramatically impact the medical industry. Machine learning (ML) has proven successful in protein design, reducing the need for expensive wet lab experiment rounds. However, challenges persist in efficiently exploring the protein fitness landscapes to identify optimal protein designs. In response, we propose the use of AlphaZero to generate protein backbones, meeting shape and structural scoring requirements. We extend an existing Monte Carlo tree search (MCTS) framework by incorporating a novel threshold-based reward and secondary objectives to improve design precision. This innovation considerably outperforms existing approaches, leading to protein backbones that better respect structural scores. The application of AlphaZero is novel in the context of protein backbone design and demonstrates promising performance. AlphaZero consistently surpasses baseline MCTS by more than 100% in top-down protein design tasks. Additionally, our application of AlphaZero with secondary objectives uncovers further promising outcomes, indicating the potential of model-based reinforcement learning (RL) in navigating the intricate and nuanced aspects of protein design

Semi-Lagrangian (SL) schemes are highly efficient for simulating transport equations and are widely used across various applications. Despite their success, designing genuinely multi-dimensional and conservative SL schemes remains a significant challenge. Building on our previous work [Chen et al., J. Comput. Phys., V490 112329, (2023)], we introduce a conservative machine-learning-based SL finite difference (FD) method that allows for extra-large time step evolution. At the core of our approach is a novel dynamical graph neural network designed to handle the complexities associated with tracking accurately upstream points along characteristics. This proposed neural transport solver learns the conservative SL FD discretization directly from data, improving accuracy and efficiency compared to traditional numerical schemes, while significantly simplifying algorithm implementation. We validate the method' s effectiveness and efficiency through numerical tests on benchmark transport equations in both one and two dimensions, as well as the nonlinear Vlasov-Poisson system.

We consider the problem of finite-time identification of linear dynamical systems from $T$ samples of a single trajectory. Recent results have predominantly focused on the setup where no structural assumption is made on the system matrix $A^* \in \mathbb{R}^{n \times n}$, and have consequently analyzed the ordinary least squares (OLS) estimator in detail. We assume prior structural information on $A^*$ is available, which can be captured in the form of a convex set $\mathcal{K}$ containing $A^*$. For the solution of the ensuing constrained least squares estimator, we derive non-asymptotic error bounds in the Frobenius norm that depend on the local size of $\mathcal{K}$ at $A^*$. To illustrate the usefulness of these results, we instantiate them for four examples, namely when (i) $A^*$ is sparse and $\mathcal{K}$ is a suitably scaled $\ell_1$ ball; (ii) $\mathcal{K}$ is a subspace; (iii) $\mathcal{K}$ consists of matrices each of which is formed by sampling a bivariate convex function on a uniform $n \times n$ grid (convex regression); (iv) $\mathcal{K}$ consists of matrices each row of which is formed by uniform sampling (with step size $1/T$) of a univariate Lipschitz function. In all these situations, we show that $A^*$ can be reliably estimated for values of $T$ much smaller than what is needed for the unconstrained setting.

With the recent success of generative models in image and text, the evaluation of generative models has gained a lot of attention. Whereas most generative models are compared in terms of scalar values such as Frechet Inception Distance (FID) or Inception Score (IS), in the last years (Sajjadi et al., 2018) proposed a definition of precision-recall curve to characterize the closeness of two distributions. Since then, various approaches to precision and recall have seen the light (Kynkaanniemi et al., 2019; Naeem et al., 2020; Park & Kim, 2023). They center their attention on the extreme values of precision and recall, but apart from this fact, their ties are elusive. In this paper, we unify most of these approaches under the same umbrella, relying on the work of (Simon et al., 2019). Doing so, we were able not only to recover entire curves, but also to expose the sources of the accounted pitfalls of the concerned metrics. We also provide consistency results that go well beyond the ones presented in the corresponding literature. Last, we study the different behaviors of the curves obtained experimentally.

We discuss the design of an invariant measure-preserving transformed dynamics for the numerical treatment of Langevin dynamics based on rescaling of time, with the goal of sampling from an invariant measure. Given an appropriate monitor function which characterizes the numerical difficulty of the problem as a function of the state of the system, this method allows the stepsizes to be reduced only when necessary, facilitating efficient recovery of long-time behavior. We study both the overdamped and underdamped Langevin dynamics. We investigate how an appropriate correction term that ensures preservation of the invariant measure should be incorporated into a numerical splitting scheme. Finally, we demonstrate the use of the technique in several model systems, including a Bayesian sampling problem with a steep prior.

We establish a connection between problems studied in rigidity theory and matroids arising from linear algebraic constructions like tensor products and symmetric products. A special case of this correspondence identifies the problem of giving a description of the correctable erasure patterns in a maximally recoverable tensor code with the problem of describing bipartite rigid graphs or low-rank completable matrix patterns. Additionally, we relate dependencies among symmetric products of generic vectors to graph rigidity and symmetric matrix completion. With an eye toward applications to computer science, we study the dependency of these matroids on the characteristic by giving new combinatorial descriptions in several cases, including the first description of the correctable patterns in an (m, n, a=2, b=2) maximally recoverable tensor code.

We study the canonical variables based numerical schemes of a hybrid model with kinetic ions and mass-less electrons. Two equivalent formulations of the hybrid model are presented with the vector potentials in different gauges and the distribution functions depending on canonical momentum (not velocity), which constitutes a pair of canonical variables with the position variable. Particle-in-cell methods are used for the distribution functions, and the vector potentials are discretized by the finite element methods in the framework of finite element exterior calculus. Splitting methods are used for the time discretizations. It is illustrated that the second formulation is numerically superior and the schemes constructed based on the anti-symmetric bracket proposed have better conservation properties and lower noise, although the filters can be used to improve the schemes of the first formulation.

Capturing the extremal behaviour of data often requires bespoke marginal and dependence models which are grounded in rigorous asymptotic theory, and hence provide reliable extrapolation into the upper tails of the data-generating distribution. We present a toolbox of four methodological frameworks, motivated by modern extreme value theory, that can be used to accurately estimate extreme exceedance probabilities or the corresponding level in either a univariate or multivariate setting. Our frameworks were used to facilitate the winning contribution of Team Yalla to the EVA (2023) Conference Data Challenge, which was organised for the 13$^\text{th}$ International Conference on Extreme Value Analysis. This competition comprised seven teams competing across four separate sub-challenges, with each requiring the modelling of data simulated from known, yet highly complex, statistical distributions, and extrapolation far beyond the range of the available samples in order to predict probabilities of extreme events. Data were constructed to be representative of real environmental data, sampled from the fantasy country of "Utopia"

We develop an inferential toolkit for analyzing object-valued responses, which correspond to data situated in general metric spaces, paired with Euclidean predictors within the conformal framework. To this end we introduce conditional profile average transport costs, where we compare distance profiles that correspond to one-dimensional distributions of probability mass falling into balls of increasing radius through the optimal transport cost when moving from one distance profile to another. The average transport cost to transport a given distance profile to all others is crucial for statistical inference in metric spaces and underpins the proposed conditional profile scores. A key feature of the proposed approach is to utilize the distribution of conditional profile average transport costs as conformity score for general metric space-valued responses, which facilitates the construction of prediction sets by the split conformal algorithm. We derive the uniform convergence rate of the proposed conformity score estimators and establish asymptotic conditional validity for the prediction sets. The finite sample performance for synthetic data in various metric spaces demonstrates that the proposed conditional profile score outperforms existing methods in terms of both coverage level and size of the resulting prediction sets, even in the special case of scalar and thus Euclidean responses. We also demonstrate the practical utility of conditional profile scores for network data from New York taxi trips and for compositional data reflecting energy sourcing of U.S. states.