Fractional Gaussian fields provide a rich class of spatial models and have a long history of applications in multiple branches of science. However, estimation and inference for fractional Gaussian fields present significant challenges. This book chapter investigates the use of the fractional Laplacian differencing on regular lattices to approximate to continuum fractional Gaussian fields. Emphasis is given on model based geostatistics and likelihood based computations. For a certain range of the fractional parameter, we demonstrate that there is considerable agreement between the continuum models and their lattice approximations. For that range, the parameter estimates and inferences about the continuum fractional Gaussian fields can be derived from the lattice approximations. Interestingly, regular lattice approximations facilitate fast matrix-free computations and enable anisotropic representations. We illustrate the usefulness of lattice approximations via simulation studies and by analyzing sea surface temperature on the Indian Ocean.
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Faces play a central role in the combinatorial and computational aspects of polyhedra. In this paper, we present the first formalization of faces of polyhedra in the proof assistant Coq. This builds on the formalization of a library providing the basic constructions and operations over polyhedra, including projections, convex hulls and images under linear maps. Moreover, we design a special mechanism which automatically introduces an appropriate representation of a polyhedron or a face, depending on the context of the proof. We demonstrate the usability of this approach by establishing some of the most important combinatorial properties of faces, namely that they constitute a family of graded atomistic and coatomistic lattices closed under interval sublattices. We also prove a theorem due to Balinski on the $d$-connectedness of the adjacency graph of polytopes of dimension $d$.
In this paper we generalize Dillon's switching method to characterize the exact $c$-differential uniformity of functions constructed via this method. More precisely, we modify some PcN/APcN and other functions with known $c$-differential uniformity in a controllable number of coordinates to render more such functions. We present several applications of the method in constructing PcN and APcN functions with respect to all $c\neq 1$. As a byproduct, we generalize some result of [Y. Wu, N. Li, X. Zeng, {\em New PcN and APcN functions over finite fields}, Designs Codes Crypt. 89 (2021), 2637--2651]. Computational results rendering functions with low differential uniformity, as well as, other good cryptographic properties are sprinkled throughout the paper.
Ethereum Improvement Proposal (EIP) 1559 was recently implemented to transform Ethereum's transaction fee market. EIP-1559 utilizes an algorithmic update rule with a constant learning rate to estimate a base fee. The base fee reflects prevailing network conditions and hence provides a more reliable oracle for current gas prices. Using on-chain data from the period after its launch, we evaluate the impact of EIP-1559 on the user experience and market performance. Our empirical findings suggest that although EIP-1559 achieves its goals on average, short-term behavior is marked by intense, chaotic oscillations in block sizes (as predicted by our recent theoretical dynamical system analysis [1]) and slow adjustments during periods of demand bursts (e.g., NFT drops). Both phenomena lead to unwanted inter-block variability in mining rewards. To address this issue, we propose an alternative base fee adjustment rule in which the learning rate varies according to an additive increase, multiplicative decrease (AIMD) update scheme. Our simulations show that the latter robustly outperforms the EIP-1559 protocol under various demand scenarios. These results provide evidence that variable learning rate mechanisms may constitute a promising alternative to the default EIP-1559-based format and contribute to the ongoing discussion on the design of more efficient transaction fee markets.
Linear mixed models (LMMs) are instrumental for regression analysis with structured dependence, such as grouped, clustered, or multilevel data. However, selection among the covariates--while accounting for this structured dependence--remains a challenge. We introduce a Bayesian decision analysis for subset selection with LMMs. Using a Mahalanobis loss function that incorporates the structured dependence, we derive optimal linear coefficients for (i) any given subset of variables and (ii) all subsets of variables that satisfy a cardinality constraint. Crucially, these estimates inherit shrinkage or regularization and uncertainty quantification from the underlying Bayesian model, and apply for any well-specified Bayesian LMM. More broadly, our decision analysis strategy deemphasizes the role of a single "best" subset, which is often unstable and limited in its information content, and instead favors a collection of near-optimal subsets. This collection is summarized by key member subsets and variable-specific importance metrics. Customized subset search and out-of-sample approximation algorithms are provided for more scalable computing. These tools are applied to simulated data and a longitudinal physical activity dataset, and demonstrate excellent prediction, estimation, and selection ability.
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from rapid virtual screening to detailed free energy calculations. Traditionally, MM potentials have relied on human-curated, inflexible, and poorly extensible discrete chemical perception rules or applying parameters to small molecules or biopolymers, making it difficult to optimize both types and parameters to fit quantum chemical or physical property data. Here, we propose an alternative approach that uses graph neural networks to perceive chemical environments, producing continuous atom embeddings from which valence and nonbonded parameters can be predicted using invariance-preserving layers. Since all stages are built from smooth neural functions, the entire process is modular and end-to-end differentiable with respect to model parameters, allowing new force fields to be easily constructed, extended, and applied to arbitrary molecules. We show that this approach is not only sufficiently expressive to reproduce legacy atom types, but that it can learn to accurately reproduce and extend existing molecular mechanics force fields. Trained with arbitrary loss functions, it can construct entirely new force fields self-consistently applicable to both biopolymers and small molecules directly from quantum chemical calculations, with superior fidelity than traditional atom or parameter typing schemes. When trained on the same quantum chemical small molecule dataset used to parameterize the openff-1.2.0 small molecule force field augmented with a peptide dataset, the resulting espaloma model shows superior accuracy vis-\`a-vis experiments in computing relative alchemical free energy calculations for a popular benchmark set.
I/O efficiency is crucial to productivity in scientific computing, but the increasing complexity of the system and the applications makes it difficult for practitioners to understand and optimize I/O behavior at scale. Data-driven machine learning-based I/O throughput models offer a solution: they can be used to identify bottlenecks, automate I/O tuning, or optimize job scheduling with minimal human intervention. Unfortunately, current state-of-the-art I/O models are not robust enough for production use and underperform after being deployed. We analyze multiple years of application, scheduler, and storage system logs on two leadership-class HPC platforms to understand why I/O models underperform in practice. We propose a taxonomy consisting of five categories of I/O modeling errors: poor application and system modeling, inadequate dataset coverage, I/O contention, and I/O noise. We develop litmus tests to quantify each category, allowing researchers to narrow down failure modes, enhance I/O throughput models, and improve future generations of HPC logging and analysis tools.
The geometric high-order regularization methods such as mean curvature and Gaussian curvature, have been intensively studied during the last decades due to their abilities in preserving geometric properties including image edges, corners, and image contrast. However, the dilemma between restoration quality and computational efficiency is an essential roadblock for high-order methods. In this paper, we propose fast multi-grid algorithms for minimizing both mean curvature and Gaussian curvature energy functionals without sacrificing the accuracy for efficiency. Unlike the existing approaches based on operator splitting and the Augmented Lagrangian method (ALM), no artificial parameters are introduced in our formulation, which guarantees the robustness of the proposed algorithm. Meanwhile, we adopt the domain decomposition method to promote parallel computing and use the fine-to-coarse structure to accelerate the convergence. Numerical experiments are presented on both image denoising and CT reconstruction problem to demonstrate the ability to recover image texture and the efficiency of the proposed method.
In the storied Colonel Blotto game, two colonels allocate $a$ and $b$ troops, respectively, to $k$ distinct battlefields. A colonel wins a battle if they assign more troops to that particular battle, and each colonel seeks to maximize their total number of victories. Despite the problem's formulation in 1921, the first polynomial-time algorithm to compute Nash equilibrium (NE) strategies for this game was discovered only quite recently. In 2016, \citep{ahmadinejad_dehghani_hajiaghayi_lucier_mahini_seddighin_2019} formulated a breakthrough algorithm to compute NE strategies for the Colonel Blotto game\footnote{To the best of our knowledge, the algorithm from \citep{ahmadinejad_dehghani_hajiaghayi_lucier_mahini_seddighin_2019} has computational complexity $O(k^{14}\max\{a,b\}^{13})$}, receiving substantial media coverage (e.g. \citep{Insider}, \citep{NSF}, \citep{ScienceDaily}). In this work, we present the first known $\epsilon$-approximation algorithm to compute NE strategies in the two-player Colonel Blotto game in runtime $\widetilde{O}(\epsilon^{-4} k^8 \max\{a,b\}^2)$ for arbitrary settings of these parameters. Moreover, this algorithm computes approximate coarse correlated equilibrium strategies in the multiplayer (continuous and discrete) Colonel Blotto game (when there are $\ell > 2$ colonels) with runtime $\widetilde{O}(\ell \epsilon^{-4} k^8 n^2 + \ell^2 \epsilon^{-2} k^3 n (n+k))$, where $n$ is the maximum troop count. Before this work, no polynomial-time algorithm was known to compute exact or approximate equilibrium (in any sense) strategies for multiplayer Colonel Blotto with arbitrary parameters. Our algorithm computes these approximate equilibria by a novel (to the author's knowledge) sampling technique with which we implicitly perform multiplicative weights update over the exponentially many strategies available to each player.
The fruits of science are relationships made comprehensible, often by way of approximation. While deep learning is an extremely powerful way to find relationships in data, its use in science has been hindered by the difficulty of understanding the learned relationships. The Information Bottleneck (IB) is an information theoretic framework for understanding a relationship between an input and an output in terms of a trade-off between the fidelity and complexity of approximations to the relationship. Here we show that a crucial modification -- distributing bottlenecks across multiple components of the input -- opens fundamentally new avenues for interpretable deep learning in science. The Distributed Information Bottleneck throttles the downstream complexity of interactions between the components of the input, deconstructing a relationship into meaningful approximations found through deep learning without requiring custom-made datasets or neural network architectures. Applied to a complex system, the approximations illuminate aspects of the system's nature by restricting -- and monitoring -- the information about different components incorporated into the approximation. We demonstrate the Distributed IB's explanatory utility in systems drawn from applied mathematics and condensed matter physics. In the former, we deconstruct a Boolean circuit into approximations that isolate the most informative subsets of input components without requiring exhaustive search. In the latter, we localize information about future plastic rearrangement in the static structure of a sheared glass, and find the information to be more or less diffuse depending on the system's preparation. By way of a principled scheme of approximations, the Distributed IB brings much-needed interpretability to deep learning and enables unprecedented analysis of information flow through a system.
The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.
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