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At least 271 records · Page 15

Accelerated Probabilistic Marching Cubes by Deep Learning for Time-Varying Scalar Ensembles

Visualizing the uncertainty of ensemble simulations is challenging due to the large size and multivariate and temporal features of en-semble data sets. One popular approach to studying the uncertainty of ensembles is analyzing the positional uncertainty of the level sets. Probabilistic marching cubes is a technique that performs Monte Carlo sampling of multivariate Gaussian noise distributions for positional uncertainty visualization of level sets. However, the technique suffers from high computational time, making interactive visualization and analysis impossible to achieve. This paper introduces a deep-learning-based approach to learning the level-set uncertainty for two-dimensional ensemble data with a multivariate Gaussian noise assumption. We train the model using the first few time steps from time-varying ensemble data in our workflow. We demonstrate that our trained model accurately infers uncertainty in level sets for new time steps and is up to 170X faster than that of the original probabilistic model with serial computation and 10X faster than that of the original parallel computation.

Han, Mengjiao↗

Interpreting single jet measurements in Pb$+$Pb collisions at the LHC

Results are presented from a phenomenological analysis of recent measurements of jet suppression and modifications of jet fragmentation functions in Pb+Pb collisions at the LHC. Particular emphasis is placed on the impact of the differences between quark and gluon jet quenching on the transverse momentum (p jet T ) dependence of the jet R AA and on the fragmentation functions, D(z). Primordial quark and gluon parton distributions were obtained from PYTHIA8 and were parameterized using simple power-law functions and extensions to the power-law function which were found to better describe the PYTHIA8 parton spectra. A simple model for the quark energy loss based on the shift formalism is used to model R AA and D(z) using both analytic results and using direct Monte-Carlo sampling of the PYTHIA parton spectra. The model is capable of describing the full p jet T , rapidity, and centrality dependence of the measured jet R AA using three effective parameters. A key result from the analysis is that the D(z) modifications observed in the data, excluding the enhancement at low-z, may result primarily from the different quenching of the quarks and gluons. Furthermore, the model is also capable of reproducing the charged hadron R AA at high transverse momentum. Predictions are made for the jet R AA at large rapidities where it has not yet been measured and for the rapidity dependence of D(z).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Precise predictions for $V+$jets dark matter backgrounds

High-energy jets recoiling against missing transverse energy (MET) are powerful probes of dark matter at the LHC. Searches based on large MET signatures require a precise control of the $Z(\nu\bar\nu)+$jet background in the signal region. This can be achieved by taking accurate data in control regions dominated by $Z(\ell^+\ell^-)+$jet, $W(\ell\nu)+$jet and $\gamma+$jet production, and extrapolating to the $Z(\nu\bar\nu)+$jet background by means of precise theoretical predictions. In this context, recent advances in perturbative calculations open the door to significant sensitivity improvements in dark matter searches. In this spirit, we present a combination of state-of-the art calculations for all relevant $V+$jets processes, including throughout NNLO QCD corrections and NLO electroweak corrections supplemented by Sudakov logarithms at two loops. Predictions at parton level are provided together with detailed recommendations for their usage in experimental analyses based on the reweighting of Monte Carlo samples. Particular attention is devoted to the estimate of theoretical uncertainties in the framework of dark matter searches, where subtle aspects such as correlations across different $V+$jet processes play a key role. In conclusion, the anticipated theoretical uncertainty in the $Z(\nu\bar\nu)+$jet background is at the few percent level up to the TeV range.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

FuseIM: Fusing Probabilistic Traversals for Influence Maximization on Exascale Systems

Probabilistic breadth-first traversals (BPTs) are used in many network science and graph machine learning applications. In this paper, we are motivated by the application of BPTs in stochastic diffusion-based graph problems such as influence maximization. These applications heavily rely on BPTs to implement a Monte-Carlo sampling step for their approximations. Given the large sampling complexity, stochasticity of the diffusion process, and the inherent irregularity in real-world graph topologies, efficiently parallelizing these BPTs remains significantly challenging. In this paper, we present a new algorithm to fuse massive number of concurrently executing BPTs with random starts on the input graph. Our algorithm is designed to fuse BPTs by combining separate traversals into a unified frontier on distributed multi-GPU systems. To show the general applicability of the fused BPT technique, we have incorporated it into two state-of-the-art influence maximization parallel implementations (gIM and Ripples). Our experiments on up to 4K nodes of the OLCF Frontier supercomputer (32,768 GPUs and 196K CPU cores) show strong scaling behavior, and that fused BPTs can improve the performance of these implementations up to 34x (for gIM) and ~360x (for Ripples).

Neff, Reece W.↗

Data Assimilation for Robust UQ Within Agent-Based Simulation on HPC Systems

Agent-based simulation provides a powerful tool for in silico system modeling. However, these simulations do not provide built-in methods for uncertainty quantification (UQ). Within these types of models a typical approach to UQ is to run multiple realizations of the model then compute aggregate statistics. This approach is limited due to the compute time required for a solution. When faced with an emerging biothreat, public health decisions need to be made quickly and solutions for integrating near real-time data with analytic tools are needed. We propose an integrated Bayesian UQ framework for agent-based models based on sequential Monte Carlo sampling. Given streaming or static data about the evolution of an emerging pathogen this Bayesian framework provides a distribution over the parameters governing the spread of a disease through a population. These estimates of the spread of a disease may be provided to public health agencies seeking to abate the spread. By coupling agent-based simulations with Bayesian modeling in a data assimilation, our proposed framework provides a powerful tool for modeling dynamical systems in silico. We propose a method which reduces model error and provides a range of realistic possible outcomes. Moreover, our method addresses two primary limitations of ABMs: the lack of UQ and an inability to assimilate data. Our proposed framework combines the flexibility of an agent-based model with UQ provided by the Bayesian paradigm in a workflow which scales well to HPC systems. We provide algorithmic details and results on a simulated outbreak with both static and streaming data.

Spannaus, Adam [ORNL] (ORCID:0000000225213657)↗

Mads.jl

Mads.jl (Model analysis and decision support in Julia) is a code that streamlines the process of using data and models for analysis and decision support. It is based on another open-source code developed at LANL and written in C/C++ (MADS; http://mads.lanl.gov; LA-CC-11- 035). Mads.jl can work with external models of arbitrary complexity as well as built-in models of flow and transport in porous media. It enables a number of data- and model-based analyses including model calibration, sensitivity analysis, uncertainty quantification, and decision analysis. The code also can use a series of alternative adaptive computational techniques for Bayesian sampling, Monte Carlo, and Bayesian Information-Gap Decision Theory. The code is implemented in the Julia programming language, and has high-performance (parallel) and memory management capabilities. The code uses a series of third party modules developed by others. The code development will also include contributions to the existing third party modules written in Julia; this contributions will be important for the efficient implementation of the algorithm used by Mads.jl. The code also uses a series of LANL developed modules that are developed by Dan O'Malley; these modules will be also a part of the Mads.jl release. Mads.jl will be released under GPL V3 license. The code will be distributed as a Git repo at gitlab.com and github.com. Mads.jl manual and documentation will be posted at madsjulia.lanl.gov.

Vesselinov, Velimir↗

Quantifying the Accuracy and Uncertainty of Diurnal Thermodynamic Profiles and Convection Indices Derived from the Atmospheric Emitted Radiance Interferometer

Abstract While radiosondes have provided atmospheric scientists an accurate high-vertical-resolution profile of the troposphere for decades, they are unable to provide high-temporal-resolution observations without significant recurring expenses. Remote sensing technology, however, has the ability to monitor the evolution of the atmosphere in unprecedented detail. One particularly promising tool is the Atmospheric Emitted Radiance Interferometer (AERI), a passive ground-based infrared radiometer. Through a physical retrieval, the AERI can retrieve the vertical profile of temperature and humidity at a temporal resolution on the order of minutes. The synthesis of these two instruments may provide an improved diagnosis of the processes occurring in the atmosphere. This study provides a better understanding of the capabilities of the AERI in environments supportive of deep, moist convection. Using 3-hourly radiosonde launches and thermodynamic profiles retrieved from collocated AERIs, this study evaluates the accuracy of AERI-derived profiles over the diurnal cycle by analyzing AERI profiles in both the convective and stable boundary layers. Monte Carlo sampling is used to calculate the distribution of convection indices and compare the impact of measurement errors from each instrument platform on indices. This study indicates that the nonintegrated indices (e.g., lifted index) derived from AERI retrievals are more accurate than integrated indices (e.g., CAPE). While the AERI retrieval’s vertical resolution can inhibit precise diagnoses of capping inversions, the high-temporal-resolution nature of the AERI profiles overall helps in detecting rapid temporal changes in stability.

54 ENVIRONMENTAL SCIENCES↗

A Bayesian Approach for Statistical–Physical Bulk Parameterization of Rain Microphysics. Part I: Scheme Description

A novel framework is proposed for the bulk parameterization of rain microphysics: the Bayesian Observationally Constrained Statistical–Physical Scheme (BOSS). It is designed to facilitate direct constraint by observations using Bayesian inference. BOSS combines existing process-level microphysical knowledge with flexible process rate formulations and parameters constrained by observations within a Bayesian framework. Furthermore, using a raindrop size distribution (DSD) normalization method that relates DSD moments to one another via generalized power series, generalized multivariate power expressions are derived for the microphysical process rates as functions of a set of prognostic DSD moments. The scheme is flexible and can utilize any number and combination of prognostic moments and any number of terms in the process rate formulations. This means that both uncertainty in parameter values and structural uncertainty associated with the process rate formulations can be investigated systematically, which is not possible using traditional schemes. In this paper, BOSS is compared to two- and three-moment versions of a traditional bulk rain microphysics scheme (denoted as MORR). It is demonstrated that some process formulations in MORR are analytically equivalent to the generalized power expressions in BOSS using one or two terms, while others are not. BOSS is able to replicate the behavior of MORR in idealized one-dimensional rainshaft tests, but with a much more flexible and systematic design. Part II of this study describes the application of BOSS to derive rain microphysical process rates and posterior parameter distributions in Bayesian experiments using Markov chain Monte Carlo sampling constrained by synthetic observations.

58 GEOSCIENCES↗

A Bayesian Approach for Statistical–Physical Bulk Parameterization of Rain Microphysics. Part II: Idealized Markov Chain Monte Carlo Experiments

Observationally informed development of a new framework for bulk rain microphysics, the Bayesian Observationally Constrained Statistical–Physical Scheme (BOSS; described in Part I of this study), is demonstrated. This scheme’s development is motivated by large uncertainties in cloud and weather simulations associated with approximations and assumptions in existing microphysics schemes. Here, a proof-of-concept study is introduced using a Markov chain Monte Carlo sampling algorithm with BOSS to probabilistically estimate microphysical process rates and parameters directly from a set of synthetically generated rain observations. The framework utilized is an idealized steady-state one-dimensional column rainshaft model with specified column-top rain properties and a fixed thermodynamical profile. Different configurations of BOSS—flexibility being a key feature of this approach—are constrained via synthetic observations generated from a traditional three-moment bulk microphysics scheme. The ability to retrieve correct parameter values when the true parameter values are known is illustrated. For cases when there is no set of true parameter values, the accuracy of configurations of BOSS that have different levels of complexity is compared. It is found that addition of the sixth moment as a prognostic variable improves prediction of the third moment (proportional to bulk rain mass) and rain rate. In contrast, increasing process rate formulation complexity by adding more power terms has little benefit—a result that is explained using further-idealized experiments. BOSS rainshaft simulations are shown to well estimate the true process rates from constraint by bulk rain observations, with the further benefit of rigorously quantified uncertainty of these estimates.

58 GEOSCIENCES↗

Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone

Allosteric regulation is a key component of cellular communication, but the way in which information is passed from one site to another within a folded protein is not often clear. While backbone motions have long been considered essential for long-range information conveyance, side-chain motions have rarely been considered. In this work, we demonstrate their potential utility using Monte Carlo sampling of side-chain torsional angles on a fixed backbone to quantify correlations amongst side-chain inter-rotameric motions. Results indicate that long-range correlations of side-chain fluctuations can arise independently from several different types of interactions: steric repulsions, implicit solvent interactions, or hydrogen bonding and salt-bridge interactions. These robust correlations persist across the entire protein (up to 60 Å in the case of calmodulin) and can propagate long-range changes in side-chain variability in response to single residue perturbations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A modified Susceptible-Infected-Recovered model for observed under-reported incidence data

Fitting Susceptible-Infected-Recovered (SIR) models to incidence data is problematic when not all infected individuals are reported. Assuming an underlying SIR model with general but known distribution for the time to recovery, this paper derives the implied differential-integral equations for observed incidence data when a fixed fraction of newly infected individuals are not observed. The parameters of the resulting system of differential equations are identifiable. Using these differential equations, we develop a stochastic model for the conditional distribution of current disease incidence given the entire past history of reported cases. We estimate the model parameters using Bayesian Markov Chain Monte-Carlo sampling of the posterior distribution. We use our model to estimate the transmission rate and fraction of asymptomatic individuals for the current Coronavirus 2019 outbreak in eight American Countries: the United States of America, Brazil, Mexico, Argentina, Chile, Colombia, Peru, and Panama, from January 2020 to May 2021. Our analysis reveals that the fraction of reported cases varies across all countries. For example, the reported incidence fraction for the United States of America varies from 0.3 to 0.6, while for Brazil it varies from 0.2 to 0.4.

60 APPLIED LIFE SCIENCES↗

Official data release for Bayes 2022 paper, arXiv:2311.07835

Official data release to accompany the first NOvA Bayesian results paper, https://arxiv.org/abs/2311.07835. The included `README.md` below describes the contents more fully, but in short, included here are: * A `README.md` describing the files * Four `.root` files containing marginal posterior densities in neutrino oscillation parameters, and associated 1D and 2D credible regions derived from them * One `.root` file containing a `TTree` with Markov Chain Monte Carlo samples, which can be used to recreate the posteriors above. **Please use the URL below to download this large (2GB) file** https://mod.fnal.gov/cwsmod/n/nova_docdb_ext/arxiv-2311.07835.data-release.mcmcsamples.root * One Jupyter notebook giving extensive examples how the MCMC samples above can be used

Collaboration, NOvA↗

Stan : A Probabilistic Programming Language

Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm. Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectation propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible. Stan can also be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.

97 MATHEMATICS AND COMPUTING↗

Learning the ground state of a non-stoquastic quantum Hamiltonian in a rugged neural network landscape

Strongly interacting quantum systems described by non-stoquastic Hamiltonians exhibit rich low-temperature physics. Yet, their study poses a formidable challenge, even for state-of-the-art numerical techniques. Here, we investigate systematically the performance of a class of universal variational wave-functions based on artificial neural networks, by considering the frustrated spin- 1/2 1 / 2 J_1-J_2 J 1 − J 2 Heisenberg model on the square lattice. Focusing on neural network architectures without physics-informed input, we argue in favor of using an ansatz consisting of two decoupled real-valued networks, one for the amplitude and the other for the phase of the variational wavefunction. By introducing concrete mitigation strategies against inherent numerical instabilities in the stochastic reconfiguration algorithm we obtain a variational energy comparable to that reported recently with neural networks that incorporate knowledge about the physical system. Through a detailed analysis of the individual components of the algorithm, we conclude that the rugged nature of the energy landscape constitutes the major obstacle in finding a satisfactory approximation to the ground state wavefunction, and prevents learning the correct sign structure. In particular, we show that in the present setup the neural network expressivity and Monte Carlo sampling are not primary limiting factors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantifying the Impact of Single Bit Flips on Floating Point Arithmetic

In high-end computing, the collective surface area, smaller fabrication sizes, and increasing density of components have led to an increase in the number of observed bit flips. If mechanisms are not in place to detect them, such flips produce silent errors, i.e. the code returns a result that deviates from the desired solution by more than the allowed tolerance and the discrepancy cannot be distinguished from the standard numerical error associated with the algorithm. These phenomena are believed to occur more frequently in DRAM, but logic gates, arithmetic units, and other circuits are also susceptible to bit flips. Previous work has focused on algorithmic techniques for detecting and correcting bit flips in specific data structures, however, they suffer from lack of generality and often times cannot be implemented in heterogeneous computing environment. Our work takes a novel approach to this problem. We focus on quantifying the impact of a single bit flip on specific floating-point operations. We analyze the error induced by flipping specific bits in the most widely used IEEE floating-point representation in an architecture-agnostic manner, i.e., without requiring proprietary information such as bit flip rates and the vendor-specific circuit designs. We initially study dot products of vectors and demonstrate that not all bit flips create a large error and, more importantly, expected value of the relative magnitude of the error is very sensitive on the bit pattern of the binary representation of the exponent, which strongly depends on scaling. Our results are derived analytically and then verified experimentally with Monte Carlo sampling of random vectors. Furthermore, we consider the natural resilience properties of solvers based on the fixed point iteration and we demonstrate how the resilience of the Jacobi method for linear equations can be significantly improved by rescaling the associated matrix.

Elliott, James J.↗

Design Optimization of Structural Health Monitoring Systems

Sensor networks drive decisions. Approach: Design networks to minimize the expected total cost (in a statistical sense, i.e. Bayes Risk) associated with making wrong decisions and with installing maintaining and running the sensor network itself. Search for optimal solutions using Monte-Carlo-Sampling-Adapted Genetic Algorithm. Applications include structural health monitoring and surveillance.

42 ENGINEERING↗

A Practical Framework for Sharing and Rendering Real-World Bidirectional Scattering Distribution Functions

The utilization of real-world materials has been hindered by a lack of standards for sharing and interpreting measured data. This paper presents an XML representation and an Open Source C library to support bidirectional scattering distribution functions (BSDFs) in data-driven lighting simulation and rendering applications.The library provides for the efficient representation, query, and Monte Carlo sampling of arbitrary BSDFs in amodel-free framework. Currently, we support two BSDF data representations: one using a fixed subdivision of thehemisphere, and one with adaptive density. The fixed type has advantages for certain matrix operations, while theadaptive type can more accurately represent highly peaked data. We discuss advanced methods for data-drivenBSDF rendering for both types, including the proxy of detailed geometry to enhance appearance and accuracy.We also present an advanced interpolation method to reduce measured data into these standard representations.We end with our plan for future extensions and sharing of BSDF data.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Infiltration Time Profiles for E-Area LLWF Intact and Subsidence Scenarios

To support future Unreviewed Disposal Question Evaluations (UDQEs), Special Analyses (SAs) and/or Performance Assessments (PAs) for the E-Area Low-Level Waste Facility (LLWF) at the Savannah River Site (SRS), the Hydrologic Evaluation of Landfill Performance (HELP) model and a newly developed, Python-based, probabilistic model employing a Monte Carlo sampling technique were used together to generate infiltration degradation curves over a 10,000-year simulation period for both intact and subsided slit- and engineered-trench closure-cap scenarios. The results will be used in PORFLOW transport model simulations of the E-Area LLWF trench units.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗