We propose a data-driven, closure model for Reynolds-averaged Navier-Stokes (RANS) simulations that incorporates aleatoric, model uncertainty. The proposed closure consists of two parts. A parametric one, which utilizes previously proposed, neural-network-based tensor basis functions dependent on the rate of strain and rotation tensor invariants. This is complemented by latent, random variables which account for aleatoric model errors. A fully Bayesian formulation is proposed, combined with a sparsity-inducing prior in order to identify regions in the problem domain where the parametric closure is insufficient and where stochastic corrections to the Reynolds stress tensor are needed. Training is performed using sparse, indirect data, such as mean velocities and pressures, in contrast to the majority of alternatives that require direct Reynolds stress data. For inference and learning, a Stochastic Variational Inference scheme is employed, which is based on Monte Carlo estimates of the pertinent objective in conjunction with the reparametrization trick. This necessitates derivatives of the output of the RANS solver, for which we developed an adjoint-based formulation. In this manner, the parametric sensitivities from the differentiable solver can be combined with the built-in, automatic differentiation capability of the neural network library in order to enable an end-to-end differentiable framework. We demonstrate the capability of the proposed model to produce accurate, probabilistic, predictive estimates for all flow quantities, even in regions where model errors are present, on a separated flow in the backward-facing step benchmark problem.
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ACM/IEEE第23屆模型驅動工程語言和系統國際會議，是模型驅動軟件和系統工程的首要會議系列，由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來，模型涵蓋了建模的各個方面，從語言和方法到工具和應用程序。模特的參加者來自不同的背景，包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇，參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會，并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。
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Distributionally robust optimization has emerged as an attractive way to train robust machine learning models, capturing data uncertainty and distribution shifts. Recent statistical analyses have proved that robust models built from Wasserstein ambiguity sets have nice generalization guarantees, breaking the curse of dimensionality. However, these results are obtained in specific cases, at the cost of approximations, or under assumptions difficult to verify in practice. In contrast, we establish, in this article, exact generalization guarantees that cover all practical cases, including any transport cost function and any loss function, potentially non-convex and nonsmooth. For instance, our result applies to deep learning, without requiring restrictive assumptions. We achieve this result through a novel proof technique that combines nonsmooth analysis rationale with classical concentration results. Our approach is general enough to extend to the recent versions of Wasserstein/Sinkhorn distributionally robust problems that involve (double) regularizations.
In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes (SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and methodologies lead to incomparable results. We review 31 state-of-the-art methods, categorizing SVGs into three types: overall, cell-type-specific, and spatial-domain-marker SVGs. Our review explains the intuitions underlying these methods, summarizes their applications, and categorizes the hypothesis tests they use in the trade-off between generality and specificity for SVG detection. We discuss challenges in SVG detection and propose future directions for improvement. Our review offers insights for method developers and users, advocating for category-specific benchmarking.
Computability on uncountable sets has no standard formalization, unlike that on countable sets, which is given by Turing machines. Some of the approaches to define computability in these sets rely on order-theoretic structures to translate such notions from Turing machines to uncountable spaces. Since these machines are used as a baseline for computability in these approaches, countability restrictions on the ordered structures are fundamental. Here, we show several relations between the usual countability restrictions in order-theoretic theories of computability and some more common order-theoretic countability constraints, like order density properties and functional characterizations of the order structure in terms of multi-utilities. As a result, we show how computability can be introduced in some order structures via countability order density and multi-utility constraints.
This paper presents a novel simplification calculus for propositional logic derived from Peirce's existential graphs' rules of inference and implication graphs. Our rules can be applied to propositional logic formulae in nested form, are equivalence-preserving, guarantee a monotonically decreasing number of variables, clauses and literals, and maximise the preservation of structural problem information. Our techniques can also be seen as higher-level SAT preprocessing, and we show how one of our rules (TWSR) generalises and streamlines most of the known equivalence-preserving SAT preprocessing methods. In addition, we propose a simplification procedure based on the systematic application of two of our rules (EPR and TWSR) which is solver-agnostic and can be used to simplify large Boolean satisfiability problems and propositional formulae in arbitrary form, and we provide a formal analysis of its algorithmic complexity in terms of space and time. Finally, we show how our rules can be further extended with a novel n-ary implication graph to capture all known equivalence-preserving preprocessing procedures.
Many unconventional computing models, including some that appear to be quite different from traditional ones such as Turing machines, happen to characterise either the complexity class P or PSPACE when working in deterministic polynomial time (and in the maximally parallel way, where this applies). We discuss variants of cellular automata and membrane systems that escape this dichotomy and characterise intermediate complexity classes, usually defined in terms of Turing machines with oracles, as well as some possible reasons why this happens.
Detecting differences in gene expression is an important part of single-cell RNA sequencing experiments, and many statistical methods have been developed for this aim. Most differential expression analyses focus on comparing expression between two groups (e.g., treatment vs. control). But there is increasing interest in multi-condition differential expression analyses in which expression is measured in many conditions, and the aim is to accurately detect and estimate expression differences in all conditions. We show that directly modeling single-cell RNA-seq counts in all conditions simultaneously, while also inferring how expression differences are shared across conditions, leads to greatly improved performance for detecting and estimating expression differences compared to existing methods. We illustrate the potential of this new approach by analyzing data from a single-cell experiment studying the effects of cytokine stimulation on gene expression. We call our new method "Poisson multivariate adaptive shrinkage", and it is implemented in an R package available online at //github.com/stephenslab/poisson.mash.alpha.
This paper focuses on the numerical scheme for delay-type stochastic McKean-Vlasov equations (DSMVEs) driven by fractional Brownian motion with Hurst parameter $H\in (0,1/2)\cup (1/2,1)$. The existence and uniqueness of the solutions to such DSMVEs whose drift coefficients contain polynomial delay terms are proved by exploting the Banach fixed point theorem. Then the propagation of chaos between interacting particle system and non-interacting system in $\mathcal{L}^p$ sense is shown. We find that even if the delay term satisfies the polynomial growth condition, the unmodified classical Euler-Maruyama scheme still can approximate the corresponding interacting particle system without the particle corruption. The convergence rates are revealed for $H\in (0,1/2)\cup (1/2,1)$. Finally, as an example that closely fits the original equation, a stochastic opinion dynamics model with both extrinsic memory and intrinsic memory is simulated to illustrate the plausibility of the theoretical result.
This paper proposes two innovative vector transport operators, leveraging the Cayley transform, for the generalized Stiefel manifold embedded with a non-standard metric. Specifically, it introduces the differentiated retraction and an approximation of the Cayley transform to the differentiated matrix exponential. These vector transports are demonstrated to satisfy the Ring-Wirth non-expansive condition under non-standard metrics, and one of them is also isometric. Building upon the novel vector transport operators, we extend the modified Polak-Ribi$\grave{e}$re-Polyak (PRP) conjugate gradient method to the generalized Stiefel manifold. Under a non-monotone line search condition, we prove our algorithm globally converges to a stationary point. The efficiency of the proposed vector transport operators is empirically validated through numerical experiments involving generalized eigenvalue problems and canonical correlation analysis.
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.
We present a new technique for visualizing high-dimensional data called cluster MDS (cl-MDS), which addresses a common difficulty of dimensionality reduction methods: preserving both local and global structures of the original sample in a single 2-dimensional visualization. Its algorithm combines the well-known multidimensional scaling (MDS) tool with the $k$-medoids data clustering technique, and enables hierarchical embedding, sparsification and estimation of 2-dimensional coordinates for additional points. While cl-MDS is a generally applicable tool, we also include specific recipes for atomic structure applications. We apply this method to non-linear data of increasing complexity where different layers of locality are relevant, showing a clear improvement in their retrieval and visualization quality.
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