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At least 343 records · Page 19

Bayesian D‐Optimal Designs for Gaussian Process Surrogate Models

Computer experiments often employ space-filling strategies to create surrogate models with strong predictive performance. The impact of model parameter estimation for Gaussian process surrogates, however, is often overlooked. Obtaining a better initial estimate of the covariance lengthscale parameter, θ, can greatly improve the resulting Gaussian process fit through more effective sequential acquisitions during active learning. In this work, we propose a novel initial design maximizing the Bayesian D-optimality criterion of the Gaussian process lengthscale parameter. Previously published results have shown the emphasis on lengthscale estimation to be promising, but relied on an empirically driven design creation process. Our Bayesian D-optimal designs are rooted in information theory and lead to more informative sequential acquisitions by improving lengthscale estimation. In many cases, these gains eventually result in better surrogates than those seeded with space-filling initial designs. Furthermore, Bayesian D-optimal designs can be tailored to either isotropic or anisotropic covariance structures, and the Bayesian framework enables the inclusion of prior knowledge in the design process, offering greater flexibility and adaptability. Through several simulation studies, we demonstrate the advantages of Bayesian D-optimal designs in terms of both lengthscale estimation accuracy and predictive performance during active learning.

Bayesian experimental design↗

Shape restricted additive hazards models: Monotone, unimodal, and U‐shape hazard functions

We consider estimation of the semiparametric additive hazards model with an unspecified baseline hazard function where the effect of a continuous covariate has a specific shape but otherwise unspecified. Such estimation is particularly useful for a unimodal hazard function, where the hazard is monotone increasing and monotone decreasing with an unknown mode. A popular approach of the proportional hazards model is limited in such setting due to the complicated structure of the partial likelihood. Our model defines a quadratic loss function, and its simple structure allows a global Hessian matrix that does not involve parameters. Thus, once the global Hessian matrix is computed, a standard quadratic programming method can be applicable by profiling all possible locations of the mode. However, the quadratic programming method may be inefficient to handle a large global Hessian matrix in the profiling algorithm due to a large dimensionality, where the dimension of the global Hessian matrix and number of hypothetical modes are the same order as the sample size. We propose the quadratic pool adjacent violators algorithm to reduce computational costs. The proposed algorithm is extended to the model with a time‐dependent covariate with monotone or U‐shape hazard function. In simulation studies, our proposed method improves computational speed compared to the quadratic programming method, with bias and mean square error reductions. We analyze data from a recent cardiovascular study.

Mathematical & Computational Biology↗

A hidden Markov model for population-level cervical cancer screening data

The Cancer Registry of Norway has been administrating a national cervical cancer screening program since 1992 by coordinating triennial cytology exam screenings for the female population between 25 and 69 years of age. Up to 80% of cancers are prevented through mass screening, but this comes at the expense of considerable screening activity and leads to overtreatment of clinically asymptomatic precancers. Here, we present a continuous-time, time-inhomogeneous hidden Markov model which was developed to understand the screening process and cervical cancer carcinogenesis in detail. By leveraging 1.7 million individual's multivariate time-series of medical exams performed over a 25-year period, we simultaneously estimate all model parameters. We show that an age-dependent model reflects the Norwegian screening program by comparing empirical survival curves from observed registry data and data simulated from the proposed model. The model can be generalized to include more detailed individual-level covariates as well as new types of screening exams. By utilizing individual screening histories and covariate data, the proposed model shows potential for improving strategies for cancer screening programs by personalizing recommended screening intervals.

59 BASIC BIOLOGICAL SCIENCES↗

Brown-York charges at null boundaries

The Brown-York stress tensor provides a means for defining quasilocal gravitational charges in subregions bounded by a timelike hypersurface. We consider the generalization of this stress tensor to null hypersurfaces. Such a stress tensor can be derived from the on-shell subregion action of general relativity associated with a Dirichlet variational principle, which fixes an induced Carroll structure on the null boundary. The formula for the mixed-index tensor T i j takes a remarkably simple form that is manifestly independent of the choice of auxiliary null vector at the null surface, and we compare this expression to previous proposals for null Brown-York stress tensors. The stress tensor we obtain satisfies a covariant conservation equation with respect to any connection induced from a rigging vector at the hypersurface, as a result of the null constraint equations. For transformations that act covariantly on the boundary structures, the Brown-York charges coincide with canonical charges constructed from a version of the Wald-Zoupas procedure. For anomalous transformations, the charges differ by an intrinsic functional of the boundary geometry, which we explicity verify for a set of symmetries associated with finite null hyper-surfaces. Applications of the null Brown-York stress tensor to symmetries of asymptotically flat spacetimes and celestial holography are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Initial value problem in string-inspired nonlocal field theory

We consider a nonlocal scalar field theory inspired by the tachyon action in open string field theory. The Lorentz-covariant action is characterized by a parameter ξ 2 that quantifies the amount of nonlocality. Restricting to purely time-dependent configurations, we show that a field redefinition perturbative in ξ 2 reduces the action to a local two-derivative theory with a ξ 2 -dependent potential. This picture is supported by evidence that the redefinition maps the wildly oscillating rolling tachyon solutions of the nonlocal theory to conventional rolling in the new scalar potential. For general field configurations we exhibit an obstruction to a local Lorentz-covariant formulation, but we can still achieve a formulation local in time, as well as a light-cone formulation. These constructions provide an initial value formulation and a Hamiltonian. Their causality is consistent with a lack of superluminal behavior in the nonlocal theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Conformal conserved currents in embedding space

We study conformal conserved currents in arbitrary irreducible representations of the Lorentz group using the embedding space formalism. With the help of the operator product expansion, we first show that conservation conditions can be fully investigated by considering only two- and three-point correlation functions. We then find an explicitly conformally-covariant differential operator in embedding space that implements conservation based on the standard position space operator product expansion differential operator ∂μ, although the latter does not uplift to embedding space covariantly. The differential operator in embedding space that imposes conservation is the same differential operator $D_{ijA}$ used in the operator product expansion in embedding space. We provide several examples including conserved currents in irreducible representations that are not symmetric and traceless. With an eye on four-point conformal bootstrap equations for four conserved vector currents $\langle JJJJ\rangle$ and four energy-momentum tensors $\langle TTTT\rangle$, we mostly focus on conservation conditions for $\langle JJ\mathcal{O}\rangle$ and $\langle TT\mathcal{O}\rangle$. Finally, we reproduce and extend the consequences of conformal Ward identities at coincident points by determining three-point coefficients in terms of charges.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Local SU(2) × U(1) quark flavor symmetry in the RS bulk

We propose a model of quark flavor based on an additional SU(2) × U(1) local symmetry in a warped extra dimensional bulk. In contrast to other works, we break the additional gauge symmetry in the bulk via two complex scalars which acquire bulk vevs, rather than relying on brane-localized symmetry breaking. A gauge-covariant Kaluza-Klein decomposition of a theory with a bulk spontaneously broken gauge symmetry is performed, and exact expressions for the bulk profiles of all physical particles in such systems are given. The SM quark masses and mixings are then recreated using gauge-covariant bulk quark mass terms and Yukawa-like couplings to the new bulk scalars. A numerical sampling of points in the model parameter space that recreate the quark masses and mixings is performed at a KK scale of M KK = 5 TeV. We then compute the ΔF = 2 4-quark operators arising from our new flavor gauge bosons and scalars, and those arising from Kaluza-Klein modes of SM gauge bosons. By decoupling one of our bulk scalar fields to all quark fields except the right-handed up-like sector, we find that it is possible to greatly suppress tree-level contributions to the highly constrained Kaon mixing parameters. Instead, the dominant constraints on the model emerge from neutral Bd and D meson mixing. These constraints are explored with our numerical sampling of the model parameter space, and the specific contribution of the new flavor gauge bosons and scalars is discussed. We find that for a significant range of realistic flavor gauge couplings, the new gauge bosons compete with the normally dominant gluon flavor-changing currents, but flavor-changing operators emerging from the bulk scalar fields are highly suppressed. Finally, we briefly comment on flavor constraints that are independent of the flavor gauge sector arising from the Z$\overline{b}$ L b L coupling and rare top decays.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Soft-collinear gravity beyond the leading power

We construct “soft-collinear gravity”, the effective field theory which describes the interaction of collinear and soft gravitons with matter (and themselves), to all orders in the soft-collinear power expansion. Despite the absence of collinear divergences in gravity at leading power, the construction exhibits remarkable similarities with soft-collinear effective theory of QCD (gauge fields). It reveals an emergent soft background gauge symmetry, which allows for a manifestly gauge-invariant representation of the interactions in terms of a soft covariant derivative, the soft Riemann tensor, and a covariant generalisation of the collinear light-cone gauge metric field. The gauge symmetries control both the unsuppressed collinear field components and the inherent inhomogeneity in λ of the invariant objects to all orders, resulting in a consistent expansion.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Functional methods for Heavy Quark Effective Theory

We use functional methods to compute one-loop effects in Heavy Quark Effective Theory. The covariant derivative expansion technique facilitates the efficient extraction of matching coefficients and renormalization group evolution equations. This paper pro- vides the first demonstration that such calculations can be performed through the algebraic evaluation of the path integral for the class of effective field theories that are (i) constructed using a non-trivial one-to-many mode decomposition of the UV theory, and (ii) valid for non-relativistic kinematics. We discuss the interplay between operators that appear at intermediate steps and the constraints imposed by the residual Lorentz symmetry that is encoded as reparameterization invariance within the effective description. The tools presented here provide a systematic approach for computing corrections to higher order in the heavy mass expansion; precision applications include predictions for experimental data and connections to theoretical tests via lattice QCD. A set of pedagogical appendices comprehensively reviews modern approaches to performing functional calculations algebraically, and derives contributions from a term with open covariant derivatives for the first time.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Spectral fluctuations in the Sachdev-Ye-Kitaev model

We present a detailed quantitative analysis of spectral correlations in the Sachdev-Ye-Kitaev (SYK) model. We find that the deviations from universal Random Matrix Theory (RMT) behavior are due to a small number of long-wavelength fluctuations (of the order of the number of Majorana fermions N ) from one realization of the ensemble to the next one. These modes can be parameterized effectively in terms of Q-Hermite orthogonal polynomials, the main contribution being due to scale fluctuations for which we give a simple analytical estimate. Our numerical results for N = 32 show that only the lowest eight polynomials are needed to eliminate the nonuniversal part of the spectral fluctuations. The covariance matrix of the coefficients of this expansion can be obtained analytically from low-order double-trace moments. We evaluate the covariance matrix of the first six moments and find that it agrees with the numerics. We also analyze the spectral correlations in terms of a nonlinear σ-model, which is derived through a Fierz transformation, and evaluate the one and two-point spectral correlation functions to two-loop order. The wide correlator is given by the sum of the universal RMT result and corrections whose lowest-order term corresponds to scale fluctuations. However, the loop expansion of the σ-model results in an ill-behaved expansion of the resolvent, and it gives universal RMT fluctuations not only for q= 4 or higher even q-body interactions, but also for the q= 2 SYK model albeit with a much smaller Thouless energy while the correct result in this case should have been Poisson statistics. In our numerical studies we analyze the number variance and spectral form factor for N = 32 and q = 4. We show that the quadratic deviation of the number variance for large energies appears as a peak for small times in the spectral form factor. After eliminating the long-wavelength fluctuations, we find quantitative agreement with RMT up to an exponentially large number of level spacings for the number variance or exponentially short times in the case of the spectral form factor.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Energy momentum tensor on and off the light cone: exposition with scalar Yukawa theory

Abstract We compute the gravitational form factorsA i ,D i and$$ {\overline{c}}_i $$ c ¯ i of the scalar Yukawa theory using both the light-cone and covariant perturbation theory at the one-loop level. The light-cone formalism provides a potential approach to access these form factors beyond the perturbative regime. However, unlike the covariant formulation, the Poincaré symmetry on the light cone is not manifest. In this work, we use perturbation theory as a benchmark to extract the gravitational form factors from the light-front energy-momentum tensor. By comparing results on and off the light cone, we identifyT ++ ,T +a ,T +− ,T 12 as the “good currents” that are properly renormalized and can be used to extract the gravitational form factors.

Physics↗

Higher-derivative relations between scalars and gluons

We extend the covariant color-kinematics duality introduced by Cheung and Mangan to effective field theories. We focus in particular on relations between the effective field theories of gluons only and of gluons coupled to bi-adjoint scalars. Maps are established between their respective equations of motion and between their tree-level scattering amplitudes. An additional rule for the replacement of flavor structures by kinematic factors realizes the map between higher-derivative amplitudes. As an example of new relations, the pure-gluon amplitudes of mass dimension up to eight, featuring insertions of the F 3 and F 4 operators which satisfy the traditional color-kinematics duality, can be generated at all multiplicities from just renormalizable amplitudes of gluons and bi-adjoint scalars. We also obtain closed-form expressions for the kinematic numerators of the dimension-six gluon effective field theory, which are valid in D space-time dimensions. Finally, we find strong evidence that this extended covariant color-kinematics duality relates the (DF) 2 +YM(+Φ 3 ) theories which, at low energies, generate infinite towers of operators satisfying the traditional color-kinematics duality, beyond aforementioned F 3 and F 4 ones.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Renormalizing two-fermion operators in the SMEFT via supergeometry

We extend the geometric framework of field-space covariance for loop computations, thereby unifying the treatment of scalars, fermions, and gauge bosons in effective field theories. This allows us to derive a manifestly covariant formula for one-loop UV divergences that includes contributions from mixed boson-fermion graphs. The result is expressed in terms of geometric invariants of the field-space supermanifold. As a demonstration of this formula, we compute the renormalization group equations for two-fermion operators at the dimension-eight level in the Standard Model Effective Field Theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Physicochemical and Performance Characterization of Six Commercial Organic Solvent Nanofiltration Membranes

This work introduces a novel, gradient-free metamaterial design method based on Gaussian process regression to represent the density field of a unit cell. The dimension of the design space is determined by the covariance matrix dimension in the Gaussian process regression. We propose compressing this matrix using an autoencoder, enabling the decoder to generate the density field and effectively reduce the originally large design space to a lower-dimensional subspace. In this compressed space, we employ an active learning method, Bayesian Adaptive Direct Search (BADS), for efficient exploration of the design space. We demonstrate that for simple 2D designs aimed at maximizing unit cell stiffness, our method yields results comparable to those of standard topology optimization. Furthermore, we extend our approach to various mechanical problems, from linear elasticity to hyperelastic large deformation and elasto-plasticity under finite deformation, to 3D metamaterial design. This illustrates the method’s versatility and effectiveness across a range of applications.

Wu, Haoran↗

Divergent controls of soil organic carbon between observations and process-based models

Abstract The storage and cycling of soil organic carbon (SOC) are governed by multiple co-varying factors, including climate, plant productivity, edaphic properties, and disturbance history. Yet, it remains unclear which of these factors are the dominant predictors of observed SOC stocks, globally and within biomes, and how the role of these predictors varies between observations and process-based models. Here we use global observations and an ensemble of soil biogeochemical models to quantify the emergent importance of key state factors – namely, mean annual temperature, net primary productivity, and soil mineralogy – in explaining biome- to global-scale variation in SOC stocks. We use a machine-learning approach to disentangle the role of covariates and elucidate individual relationships with SOC, without imposing expected relationships a priori . While we observe qualitatively similar relationships between SOC and covariates in observations and models, the magnitude and degree of non-linearity vary substantially among the models and observations. Models appear to overemphasize the importance of temperature and primary productivity (especially in forests and herbaceous biomes, respectively), while observations suggest a greater relative importance of soil minerals. This mismatch is also evident globally. However, we observe agreement between observations and model outputs in select individual biomes – namely, temperate deciduous forests and grasslands, which both show stronger relationships of SOC stocks with temperature and productivity, respectively. This approach highlights biomes with the largest uncertainty and mismatch with observations for targeted model improvements. Understanding the role of dominant SOC controls, and the discrepancies between models and observations, globally and across biomes, is essential for improving and validating process representations in soil and ecosystem models for projections under novel future conditions.

58 GEOSCIENCES↗

Unraveling the effects of management and climate on carbon fluxes of U.S. croplands using the USDA Long-Term Agroecosystem (LTAR) network

Understanding the carbon fluxes and dynamics from a broad range of agricultural systems has the potential to improve our ability to increase carbon sequestration while maintaining crop yields. Short-term, single-location studies have limited applicability, but long-term data from a network of many locations can provide a broader understanding across gradients of climate and management choices. Here we examine eddy covariance measured carbon dioxide (CO 2 ) fluxes from cropland sites across the United States Department of Agriculture's Long-Term Agroecosystem Research (LTAR) network. The dataset was collected between 2001 and 2020, spanning 13 sites for a total of 182 site-years. Average seasonal patterns of net ecosystem CO 2 exchange (NEE), gross primary productivity (GPP), and ecosystem respiration (R eco ) were determined, and subsequent regression analysis on these “flux climatologies” was used to identify relationships to mean annual temperature (MAT), mean annual precipitation (MAP), cropping systems, and management practices. At rainfed sites, carbon fluxes were better correlated with MAP (r2 ≤ 0.5) than MAT (r2 ≤ 0.22). Net carbon balance was different among cropping systems (p < 0.001), with the greatest net carbon uptake occurring in sugarcane (Saccharum spp. hybrids) and the least in soybean (Glycine max) fields. Crop type had a greater effect on carbon balance than irrigation management at a Nebraska site. Across cropping systems, grain crops often had higher GPP and were more likely to have net uptake when compared to legume crops. This multi-site analysis highlights the potential of the LTAR network to further carbon flux research using eddy covariance measurements.

54 ENVIRONMENTAL SCIENCES↗

Allosteric prediction via convolutional neural networks and protein structural and dynamical features

Allostery is the phenomenon whereby a binding event or covalent modification at one site in a protein modulates function at a distal site, thus changing a protein’s functional state. As such, it is a ubiquitous aspect of protein functional regulation. Computationally predicting allosteric states is important as part of the broader challenge of functional annotation, but it also has practical implications for drug development, as targeting an allosteric site often affords greater specificity compared with targeting an orthosteric site. This study introduces a machine learning approach to predict the allosteric functional state using the small G-protein KRas as the model system, due to its implication in many types of cancer and being well studied as a result with many x-ray crystallographic structures of KRas available with different mutations and ligands bound. Using structural and dynamical features that can be cast as images, namely interatomic distances, contact maps, covariance, and mutual information, supervised learning was performed using convolutional neural networks. Two pretrained convolutional neural network architectures, GoogLeNet and ResNet18, were fine-tuned to classify KRas into active or inactive states based on these features. Across training regimes, atomic contact maps emerged as the most effective structural feature, whereas linearized mutual information outperformed covariance in capturing dynamical correlations relevant to allostery. Models achieved significant validation accuracy, with atomic contact maps yielding up to 90% accuracy. In conclusion, the findings suggest that integrating global structural rearrangements and correlated motion patterns with deep learning can reliably predict protein allosteric states, offering a promising framework for understanding allosteric regulation and developing targeted therapeutics.

Rajeshwar T., Rajitha [Oak Ridge National Laborato↗

Conditional Karhunen–Loève regression model with Basis Adaptation for high-dimensional problems: Uncertainty quantification and inverse modeling

Here, we propose a methodology for improving the accuracy of surrogate models of the observable response of physical systems as a function of the systems’ spatially heterogeneous parameter fields, with applications to uncertainty quantification and parameter estimation in high-dimensional problems. Practitioners often formulate finite-dimensional representations of spatially heterogeneous parameter fields using truncated unconditional Karhunen–Loève expansions (KLEs) for a certain choice of unconditional covariance kernel and construct surrogate models of the observable response with respect to the KLE coefficients. When direct measurements of the parameter fields are available, we propose improving the accuracy of these surrogate models by representing the parameter fields via conditional Karhunen-Loève expansions (CKLEs). CKLEs are constructed by conditioning the covariance kernel of the unconditional expansion on the direct measurements of the parameter field via Gaussian process regression, and then truncating the corresponding KLE. We apply the proposed methodology to constructing surrogate models via the Basis Adaptation (BA) method of the stationary hydraulic head response, measured at spatially discrete observation locations, of a groundwater flow model of the Hanford Site, as a function of the 1000-dimensional representation of the model’s log-transmissivity field. We find that BA surrogate models of the hydraulic head based on CKLEs are more accurate than BA surrogate models based on unconditional expansions for forward uncertainty quantification tasks. Furthermore, we find that inverse estimates of the hydraulic transmissivity field computed using CKLE-based BA surrogate models are more accurate than those computed using unconditional BA surrogate models.

97 MATHEMATICS AND COMPUTING↗