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At least 1,477 records · Page 82

Resource selection functions based on hierarchical generalized additive models provide new insights into individual animal variation and species distributions

Habitat selection studies are designed to generate predictions of species distributions or inference regarding general habitat associations and individual variation in habitat use. Such studies frequently involve either individually indexed locations gathered across limited spatial extents and analyzed using resource selection functions (RSFs) or spatially extensive locational data without individual resolution typically analyzed using species distribution models. Both analytical methodologies have certain desirable features, but analyses that combine individual- and population-level inference with flexible non-linear functions may provide improved predictions while accounting for individual variation. Here, we describe how RSFs can be fit using hierarchical generalized additive models (HGAMs) using widely available software, providing a means to explore individual variation in habitat associations and to generate species distribution maps. We used GPS tracking data from golden eagles Aquila chrysaetos from across eastern North America with four environmental predictors to generate monthly distribution models. We considered three model structures that assumed different amounts of individual variation in the functional relationship between predictors and habitat use and used k-fold cross-validation to compare model performance. Models accounting for individual variability in shape and smoothness of functional responses performed best. Eagles exhibited the least amount of individual variation in response to land cover variables during winter months, with most individuals more closely adhering to the population-level trend. During the summer months, eagles exhibited more substantial individual variation in shape and smoothness of the functional relationships, suggesting some need to account for individual variation in eagle habitat use for both inferential and predictive purposes, during this time of year. Because they allow users to blend flexible functions with random effects structures and are well-supported by a variety of software platforms, we believe that HGAMs provide a useful addition to the suite of analyses used for modeling habitat associations or predicting species distributions.

54 ENVIRONMENTAL SCIENCES↗

Impact of point spread function higher moments error on weak gravitational lensing – II. A comprehensive study

ABSTRACT Weak lensing is one of the most powerful probes for dark matter and dark energy science, although it faces increasing challenges in controlling systematic uncertainties as the statistical errors become smaller. The point spread function (PSF) needs to be precisely modeled to avoid systematic error on the weak lensing measurements. The weak lensing biases induced by errors in the PSF model second moments, i.e. its size and shape, are well-studied. However, Zhang et al. showed that errors in the higher moments of the PSF may also be a significant source of systematics for upcoming weak lensing surveys. Therefore, this work comprehensively investigate the modelling quality of PSF moments from the 3rd to 6th order, and propagate the PSFEx higher moments modelling error in the HSC survey data set to the weak lensing shear–shear correlation functions and their cosmological analyses. The overall multiplicative shear bias associated with errors in PSF higher moments can cause an ∼0.1σ shift on the cosmological parameters for LSST Y10, while the associated additive biases can induce 1σ uncertainties in cosmology parameter inference for LSST Y10, if not accounted. We compare the PSFEx model with PSF in Full FOV, and find similar performance in modelling the PSF higher moments. We conclude that PSF higher moment errors of the future PSF models should be reduced from those in current methods, otherwise needed to be explicitly modeled in the weak lensing analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

Data-driven projection pursuit adaptation of polynomial chaos expansions for dependent high-dimensional parameters

Uncertainty quantification (UQ) and inference involving a large number of parameters are valuable tools for problems associated with heterogeneous and non-stationary behaviors. The difficulty with these problems is exacerbated when these parameters are statistically dependent requiring statistical characterization over joint measures. Probabilistic modeling methodologies stand as effective tools in the realms of UQ and inference. Among these, polynomial chaos expansions (PCE), when adapted to low-dimensional quantities of interest (QoI), provide effective yet accurate approximations for these QoI in terms of an adapted orthogonal basis. These adaptation techniques have been cast as projection pursuits in Gaussian Hilbert space in what has been referred to as a projection pursuit adaptation (PPA) by Xiaoshu Zeng and Roger Ghanem (2023). The PPA method efficiently identifies an optimal low-dimensional space for representing the QoI and simultaneously evaluates an optimal PCE within that space. The quality of this approximation clearly depends on the size of the training dataset, which is typically a function of the adapted reduced dimension. Here, the complexity of the problem is thus mediated by the complexity of the low-dimensional quantity of interest and not the complexity of the high-dimensional parameter space.

Data-driven↗

Application of Modified Meshgraphnets for Subsurface Prediction during CO2 Sequestration

In the face of the increasingly dire consequences of anthropogenic climate change, capturing and storing carbon dioxide is paramount. However, several impediments exist to the safe and effective subsurface storage of CO2, such as cost of transport, identification of suitable sites for subsurface storage, and assessment of long-term risk from storage in subsurface aquifers. Accurate subsurface modeling is necessary to ensure that CO2 storage is both safe and effective. Still, such modeling has traditionally required either substantial time and computational power (numerical simulation) or a substantial amount of pre-existing data for training (machine learning models). Additionally, these models lack flexibility in dealing with both changes in discretization of the input data and generalizability beyond the data on which they are trained. In order to address these issues, this research applies graph neural networks (GNNs) to predict subsurface saturation and pressure during CO₂ injection in a model of the Illinois Basin-Decatur Project (IBDP). GNNs provide a flexible, intuitive method for representing and manipulating complex unstructured data, which is often found in many practical domain problems such as fluid flow and subsurface characterization. These unstructured grids are easily represented in GNNs by representing spatially-localized features such as permeability, porosity, saturation, and pressure as nodes in a graph and relationships between these properties as edges connecting these nodes. This research applies a specific GNN model called MeshGraphNets (MGN) to model the change in CO2 saturation and pressure over a 50-month time period (36 months of injection, 14 months post-injection). The MGN model leverages a message passing process that allows the network to learn both the spatial and temporal dynamics of this system simultaneously. Additionally, training on a limited dataset (64 realizations, 20 time points each) resulted in a high degree of accuracy in saturation prediction both within the same timeframe as the training (20 months, 0.039 average RMSE) and when projecting out to the end of injection (36 months, 0.053 average RMSE). Temporal predictions such as those generated by MGNs and other similar models are prone to accumulated error over time; in order to address this, a multi-step rollout (MSR) training process was applied to calculate training loss. This method mimics the forward prediction during inference by “rolling out” multiple time points in a single training step using the previous prediction as input to the MGN model. By calculating the loss several time steps forward from the current prediction, the model is forced to find a more stable state over time. Application of MSR to the MGN model resulted in an average 15% reduction in inference error over time during forward prediction. This study showcases the immense potential of GNNs as a game-changing methodology for predicting pressure and saturation evolution in CCS projects, ultimately paving the way for more sustainable and effective carbon storage solutions. Presentation prepared for the 2024 AiChE Annual Meeting, October 27 to November 1 2024, San Diego, CA.

Holcomb, Paul↗

Causal network inference using biochemical kinetics

Motivation: Networks are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of biochemical systems are generally non-linear, suggesting that suitable non-linear formulations may offer gains with respect to causal network inference and aid in associated prediction problems. Results: We present a general framework for network inference and dynamical prediction using time course data that is rooted in nonlinear biochemical kinetics. This is achieved by considering a dynamical system based on a chemical reaction graph with associated kinetic parameters. Both the graph and kinetic parameters are treated as unknown; inference is carried out within a Bayesian framework. This allows prediction of dynamical behavior even when the underlying reaction graph itself is unknown or uncertain. Results, based on (i) data simulated from a mechanistic model of mitogen-activated protein kinase signaling and (ii) phosphoproteomic data from cancer cell lines, demonstrate that non-linear formulations can yield gains in causal network inference and permit dynamical prediction and uncertainty quantification in the challenging setting where the reaction graph is unknown. Availability and implementation: MATLAB R2014a software is available to download from warwick.ac.uk/chrisoates.

60 APPLIED LIFE SCIENCES↗

MHz free electron laser x-ray diffraction and modeling of pulsed laser heated diamond anvil cell

A new diamond anvil cell experimental approach has been implemented at the European x-ray Free Electron Laser, combining pulsed laser heating with MHz x-ray diffraction. In this report we use this setup to determine liquidus temperatures under extreme conditions, based on the determination of time-resolved crystallization. The focus is on a Fe-Si-O ternary system, relevant for planetary cores. This time-resolved diagnostic is complemented by a finite-element model, reproducing temporal temperature profiles measured experimentally using streaked optical pyrometry. This model calculates the temperature and strain fields by including (i) pressure and temperature dependencies of material properties, and (ii) the heat-induced thermal stress, including feedback effect on material parameter variations. Making our model more realistic, these improvements are critical as they give 7000 K temperature differences compared to previous models. Laser intensities are determined by seeking minimal deviation between measured and modeled temperatures. Combining models and streak optical pyrometry data extends temperature determination below detection limit. The presented approach can be used to infer the liquidus temperature by the appearance of SiO 2 diffraction spots. In addition, temperatures obtained by the model agree with crystallization temperatures reported for Fe–Si alloys. Our model reproduces the planetary relevant experimental conditions, providing temperature, pressure, and volume conditions. Those predictions are then used to determine liquidus temperatures at experimental timescales where chemical migration is limited. This synergy of novel time-resolved experiments and finite-element modeling pushes further the interpretation capabilities in diamond anvil cell experiments.

36 MATERIALS SCIENCE↗

Bridging the Gap Between Astronomical Datasets: From Proof-of-Concept to AI Model Deployment with Domain Adaptation

Artificial Intelligence is transforming astrophysics, from studying stars and galaxies to analyzing cosmic large-scale structures. However, a critical challenge arises when AI models trained on simulations or past observational data are applied to new observation— leading to domain shifts, reduced robustness, and increased uncertainty of model predictions. This talk will explore these issues, highlighting examples such as galaxy morphology classification and cosmological parameter inference, where AI struggles to adapt across different datasets. We will discuss domain adaptation as a strategy to improve model generalization and mitigate biases—essential for making AI-driven discoveries reliable. Notably, these challenges extend beyond astrophysics, affecting AI applications across physics and other scientific domains. Addressing them is essential for maximizing AI’s impact in advancing scientific research.

Ćiprijanović, Aleksandra [Fermilab]↗

A Nonparametric Method for the Inference of Halo Occupation Distributions

The galaxy–halo connection traces processes by which galaxies form and evolve. The halo occupation distribution (HOD) describes the relationship between galaxies and their host dark matter haloes. Measurements of the galaxy two-point correlation function (2PCF) allow us to extract information about the HODs of observed galaxy samples. Several parametric HOD models have been proposed in the literature, but the choice of parameterization restricts the space of possible HODs. To resolve this issue, we introduce a nonparametric HOD fitting method in which we train an emulator to learn the mappings among the galaxy 2PCF, physical properties used to select galaxy samples, and the HOD, all obtained from simulated past light cones constructed with the Santa Cruz semianalytic model. Implementing this emulator within a likelihood analysis framework, we derive constraints on the HOD of a galaxy sample when provided with a measurement of its 2PCF. Using the emulator to accelerate likelihood evaluations, we test the nonparametric HOD approach on a set of 2PCFs for mock galaxy samples drawn from the TNG100-1 simulation and selected above threshold values of stellar mass and star formation rate. Our framework is able to recover TNG100-1 HODs within 0.2 dex. We use the TNG100-1 mocks to tune the reported uncertainties to estimate those expected in the analysis of observations. Comparing to parametric HOD modelling routines applied to the same mock galaxy samples, our approach consistently infers the HOD with comparable or greater precision and accuracy.

Kennedy, Jacob [Rutgers Univ., Piscataway, NJ (Uni↗

DGaaS: GPU as a Service on Distributed Computing System

In the rapidly evolving landscape of scientific computing, Graphics Processing Units (GPUs) have become indispensable for their unparalleled ability to handle parallel tasks in complex calculations, simulations, and data analysis. Their utility is further magnified in machine learning and AI applications, where they significantly accelerate model training and predictive analytics. Within this context, the Triton Inference Server emerges as a pivotal open-source tool, specializing in AI inferencing and optimizing GPU utilization across various platforms and frameworks. This paper presents an in-depth study on distributed High Throughput Computing (HTC), specifically focusing on the HTCondor framework and its resource provisioning tools, GlideinWMS and HEPCloud. These systems enable large-scale scientific experiments like CMS and DUNE to efficiently access and utilize vast computational resources. The paper explores the core architectural components of GlideinWMS, including jobs, user pools, and worker nodes, and discusses their integration with GPUs and the Triton server. The primary aim of this research is to develop a solution that optimizes GPU utilization by leveraging Glideins and containers. This approach allows computational jobs, particularly those involving AI models, to use GPUs only when essential, thereby facilitating efficient sharing of limited GPU resources. To validate this architecture, the study conducted three key tests involving custom scripts, container-based servers, and Triton server deployments. However, the study faces challenges, notably in locating the Triton server and ensuring secure remote access. To address these issues, future work will focus on developing a proxy mechanism and enhancing security protocols. In conclusion, this study offers a comprehensive roadmap for effective and efficient GPU utilization in distributed High Throughput Computing. It aims to contribute significantly to the scientific community by solving pressing problems and implementing robust solutions in collaboration with the GlideinWMS and HEPCloud teams. The research sets the stage for a more efficient, scalable, and cost-effective paradigm in scientific computing.

97 MATHEMATICS AND COMPUTING↗

A High-Rate, Single-Crystal Model for Cyclotrimethylene Trinitramine including Phase Transformations and Plastic Slip

A continuum model for the high-rate, thermo-mechanical deformation of single-crystal cyclotrimethylene trinitramine (RDX) is developed. The model includes the effects of anisotropy, large deformations, nonlinear thermo-elasticity, phase transformations, and plastic slip. A multiplicative decomposition of the deformation gradient is used. The volumetric elastic component of the deformation is accounted for through a free-energy based equation of state for the low- (α) and high-pressure (γ) polymorphs of RDX. Crystal plasticity is addressed using a phenomenological thermal activation model. The deformation gradient for the phase transformation is based on an approach that has been applied to martensitic transformations. Simulations were conducted and compared to high-rate, impact loading of oriented RDX single crystals. The simulations considered multiple orientations of the crystal relative to the direction of shock loading and multiple sample thicknesses. Thirteen slip systems, which were inferred from indentation and x-ray topography, were used to model the α-polymorph. It is shown that by increasing the number of slip systems from the previously considered number of six (6) to thirteen (13) in the α-polymorph, better comparisons with data may be obtained. Simulations of impact conditions in the vicinity of the α- to γ-polymorph transformation (3.8 GPa) are considered. Eleven of the simulations, which were at pressures below the transformation value (3.0 GPa), were compared to experimental data. Comparison of the model was also made with available data for one experiment above the transformation pressure (4.4 GPa). Also, simulations are provided for a nominal pressure of 7.5 GPa to demonstrate the effect of the transformation kinetics on the deformation of a high-rate plate impact problem.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Simultaneous global and local clustering in multiplex networks with covariate information

Understanding both global and layer-specific group structures is useful for uncovering complex patterns in networks with multiple interaction types. In this work, we introduce a new model, the hierarchical multiplex stochastic blockmodel, which simultaneously detects communities within individual layers of a multiplex network while inferring a global node clustering across the layers. A stochastic blockmodel is assumed in each layer, with probabilities of layer-level group memberships determined by a node’s global group assignment. Our model uses a Bayesian framework, employing a probit stick-breaking process to construct node-specific mixing proportions over a set of shared Griffiths–Engen–McCloseky distributions. These proportions determine layer-level community assignment, allowing for an unknown and varying number of groups across layers, while incorporating nodal covariate information to inform the global clustering. We propose a scalable variational inference procedure with parallelisable updates for application to large networks. Extensive simulation studies demonstrate our model’s ability to accurately recover both global and layer-level clusters in complicated settings, and applications to real data showcase the model’s effectiveness in uncovering interesting latent network structure.

community detection↗

Bridging Hydrological Ensemble Simulation and Learning Using Deep Neural Operators

Ensemble-based simulation and learning (ESnL) has long been used in hydrology for parameter inference, but computational demands of process-based ESnL can be quite high. To address this issue, we propose a deep neural operator learning approach. Neural operators are generic machine learning algorithms that can learn functional mappings between infinite-dimensional spaces, providing a highly flexible tool for scientific machine learning. Our approach is built upon DeepONet, a specific deep neural operator, and is designed to address several common problems in hydrology, namely, model parameter estimation, prediction at ungaged locations, and uncertainty quantification. Here we demonstrate the effectiveness of our DeepONet-based workflow using an existing large model ensemble created for an eastern U.S. watershed that is instrumented with 10 streamflow gages. Results suggest DeepONet achieves high efficiency in learning an ML surrogate model from the model ensemble, with the modified Kling-Gupta Efficiency exceeding 0.9 on holdout test sets. Parameter inference, carried out using the trained DeepONet surrogate model and genetic algorithm, also yields robust results. Additionally, we formulate and train a separate DeepONet model for physics-informed, seq-to-seq streamflow forecasting, which further reduces biases in the pre-trained DeepONet surrogate model. While this study focuses primarily on a single watershed, our approach is general and may be extended to enable learning from model ensembles across multiple basins or models. Thus, this research represents a significant contribution to the application of hybrid machine learning in hydrology.

54 ENVIRONMENTAL SCIENCES↗

Weak Lensing And Cosmology In The Dark Energy Survey

In this PhD Thesis, we present studies which aim at understanding and testing the fundamental assumptions of the $\Lambda$CDM cosmological model. We initially show that weak gravitational lensing can be derived as a consequence of General Relativity, and that it can be applied to astronomical data from the Dark Energy Survey (DES) in order to constrain the amplitude of matter fluctuations in the universe. This constraint can be used as an end-to-end cosmological test when it is compared to inferences from the Cosmic Microwave Background. We further extend the cosmological model to account for non-standard parameters which can point to novel physics, and use DES data to assess their statistical significance. We finally show that the Cold Dark Matter (CDM) paradigm can also be fundamentally tested with observational data using morphological signatures of disk galaxies in cluster environments if CDM is self-interacting.

79 ASTRONOMY AND ASTROPHYSICS↗

Hierarchical Bayesian modeling for Inverse Uncertainty Quantification of system thermal-hydraulics code using critical flow experimental data

The best estimate plus uncertainty methodology in nuclear system thermal-hydraulic studies necessitates a comprehensive understanding of uncertainties in system code predictions. The forward uncertainty quantification (UQ) process involves the propagation of input uncertainties through the computational models to obtain uncertainties in the outputs. To this end, achieving an accurate estimation of input uncertainties is important, which is the focus of inverse UQ (IUQ). Traditionally, research in Bayesian IUQ within the nuclear engineering domain has largely relied on single-level Bayesian inference. While being effective for relatively small datasets, this approach encounters limitations for cases with large datasets. The use of a single-level model may prove inefficient, as the resultant posterior distributions can significantly differ when distinct subsets of data are employed. To address this issue, we employ an hierarchical Bayesian model for IUQ. Furthermore, this approach involves organizing observations into different groups based on the test conditions, thereby accommodating varying calibration parameters across these distinct groups. In this study, we developed and implemented a hierarchical Bayesian IUQ method to consider the grouping effect of critical flow measurement data from various geometries. Comparing the outcomes of IUQ under different selections of test data using hierarchical Bayesian IUQ against those obtained from single-level Bayesian IUQ, the forward propagation of hierarchical Bayesian IUQ results demonstrates a notably improved agreement with the experimental data.

42 ENGINEERING↗

A signature of anisotropic cosmic-ray transport in the gamma-ray sky

A crucial process in Galactic cosmic-ray (CR) transport is the spatial diffusion due to the interaction with the interstellar turbulent magnetic field. Usually, CR diffusion is assumed to be uniform and isotropic all across the Galaxy. However, this picture is clearly inaccurate: several data-driven and theoretical arguments, as well as dedicated numerical simulations, show that diffusion exhibits highly anisotropic properties with respect to the direction of a background (ordered) magnetic field (i.e., parallel or perpendicular to it). In this paper we focus on a recently discovered anomaly in the hadronic CR spectrum inferred by the Fermi-LAT gamma-ray data at different positions in the Galaxy, i.e. the progressive hardening of the proton slope at low Galactocentric radii. We propose the idea that this feature can be interpreted as a signature of anisotropic diffusion in the complex Galactic magnetic field: in particular, the harder slope in the inner Galaxy is due, in our scenario, to the parallel diffusive escape along the poloidal component of the large-scale, regular, magnetic field. We implement this idea in a numerical framework, based on the DRAGON code, and perform detailed numerical tests on the accuracy of our setup. We discuss how the effect proposed depends on the relevant free parameters involved. Based on low-energy extrapolation of the few focused numerical simulations aimed at determining the scalings of the anisotropic diffusion coefficients, we finally present a set of plausible models that reproduce the behavior of the CR proton slopes inferred by gamma-ray data.

79 ASTRONOMY AND ASTROPHYSICS↗

Electronic density response of warm dense matter

Matter at extreme temperatures and pressures—commonly known as warm dense matter (WDM)—is ubiquitous throughout our Universe and occurs in astrophysical objects such as giant planet interiors and brown dwarfs. Moreover, WDM is very important for technological applications such as inertial confinement fusion and is realized in the laboratory using different techniques. A particularly important property for the understanding of WDM is given by its electronic density response to an external perturbation. Such response properties are probed in x-ray Thomson scattering (XRTS) experiments and are central for the theoretical description of WDM. In this work, we give an overview of a number of recent developments in this field. To this end, we summarize the relevant theoretical background, covering the regime of linear response theory and nonlinear effects, the fully dynamic response and its static, time-independent limit, and the connection between density response properties and imaginary-time correlation functions (ITCF). In addition, we introduce the most important numerical simulation techniques, including path-integral Monte Carlo simulations and different thermal density functional theory (DFT) approaches. From a practical perspective, we present a variety of simulation results for different density response properties, covering the archetypal model of the uniform electron gas and realistic WDM systems such as hydrogen. Moreover, we show how the concept of ITCFs can be used to infer the temperature from XRTS measurements of arbitrary complex systems without the need for any models or approximations. Finally, we outline a strategy for future developments based on the close interplay between simulations and experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophages

Bacteriophage auxiliary metabolic genes (AMGs) alter host metabolism by hijacking reactions, but previous studies mostly inferred their roles from annotations, ignoring system-wide impacts and phage production. Here we integrate AMGs and phage assembly into a genome-scale metabolic model of Prochloroccocus marinus MED4 infected by P-HM2. We show that 17 directly hijacked reactions substantially affect more than 30% of the reactions in MED4 metabolism, including carbon fixation, photosynthesis, and nucleotide synthesis, distinguishing these AMGs as either phage aligned—shifting feasible reaction velocities in accordance with maximal phage production—or phage antialigned. Pareto optimization reveals that phage-aligned reactions alter phage-host growth trade-offs, while phage-antialigned reactions do not. We experimentally validate our predictions of system-level AMG impacts by measuring the N-dependent effect of P-HM2 cp12 expression on growth in a model relative of the genetically intractable MED4, Synechococcus elongatus. We also show that AMGs’ indirect impacts are synergistically and antagonistically coupled, providing systems-level insight into AMG perturbations and highlighting how nontrivial cascading effects shape host metabolism.

Rozum, Jordan C. [Pacific Northwest National Labor↗

Charge-screening role of c-axis atomic displacements in YBa 2 Cu 3 O 6+x and related superconductors

Here, the importance of charge reservoir layers for supplying holes to the CuO 2 planes of cuprate superconductors has long been recognized. Less attention has been paid to the screening of the charge transfer by the intervening ionic layers. We address this issue in the case of YBa 2 Cu 3 O 6+x , where CuO chains supply the holes for the planes. We present a simple dielectric-screening model that gives a linear correlation between the relative displacements of ions along the c axis, determined by neutron powder diffraction, and the hole density of the planes. Applying this model to the temperature-dependent shifts of ions along the c axis, we infer a charge transfer of 5–10% of the hole density from the planes to the chains on warming from the superconducting transition to room temperature. Given the significant coupling of c-axis displacements to the average charge density, we point out the relevance of local displacements for screening charge modulations and note recent evidence for dynamic screening of in-plane quasiparticles. This line of argument leads us to a simple model for atomic displacements and charge modulation that is consistent with images from scanning-tunneling microscopy for underdoped Bi 2 Sr 2 CaCu 2 O 8+δ .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗