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At least 199 records · Page 11

Uncertainty Estimates of Psychoacoustic Thresholds Obtained from Group Tests

Adaptive psychoacoustic test methods, in which the next signal level depends on the response to the previous signal, are the most efficient for determining psychoacoustic thresholds of individual subjects. In many tests conducted in the NASA psychoacoustic labs, the goal is to determine thresholds representative of the general population. To do this economically, non-adaptive testing methods are used in which three or four subjects are tested at the same time with predetermined signal levels. This approach requires us to identify techniques for assessing the uncertainty in resulting group-average psychoacoustic thresholds. In this presentation we examine the Delta Method of frequentist statistics, the Generalized Linear Model (GLM), the Nonparametric Bootstrap, a frequentist method, and Markov Chain Monte Carlo Posterior Estimation and a Bayesian approach. Each technique is exercised on a manufactured, theoretical dataset and then on datasets from two psychoacoustics facilities at NASA. The Delta Method is the simplest to implement and accurate for the cases studied. The GLM is found to be the least robust, and the Bootstrap takes the longest to calculate. The Bayesian Posterior Estimate is the most versatile technique examined because it allows the inclusion of prior information.

Rathsam, Jonathan↗

Model-Data for Joint Estimation of Biogeochemical Model Parameters from Multiple Experiments: A Bayesian Approach Applied to Mercury Methylation

This modeling archive supports the manuscript submitted for publication in the Environmental Modeling and Software. This study is supported by ORNL-SFA and IDEAS-Watershed. This study aims to improve calibration of complex biogeochemical models using datasets from multiple experiments targeting specific subprocesses. The proposed Bayesian joint-fitting scheme calibrates the entire biogeochemical model in one go using all the available datasets and estimate parameter uncertainties using Markov Chain Monte Carlo (MCMC). This allows for complete propagation of uncertainties and utilization of the information shared between different datasets. Mapping joint distribution of parameters guides model improvement by identifying null spaces in the parameter space. This archive contains files used to perform MCMC, post-process outputs and visualize results.

East Fork Poplar Creek↗

Quantum Model of Emerging Grammars

A special class of quantum recurrent nets simulating Markov chains with absorbing states is introduced. The absorbing states are exploited for pattern recognition: each class of patterns, each combination of patterns acquires its own meaning.

Quantum computing Markov chains↗

A hybrid full-wave Markov chain approach to calculating radio-frequency wave scattering from scrape-off layer filaments

The interaction of radio-frequency (RF) waves with edge turbulence modifies the incident wave spectrum, and can significantly affect RF heating and current drive in tokamaks. Previous lower hybrid (LH) scattering models have either used the weak-turbulence approximation, or treated more realistic, filamentary turbulence in the ray tracing limit. In this study, a new model is introduced which retains full-wave effects of RF scattering in filamentary turbulence. First, a Mie-scattering technique models the interaction of an incident wave with a single Gaussian filament. Next, an effective differential scattering width is derived for a statistical ensemble of filaments. Lastly, a Markov chain solves for the transmitted wave spectrum in slab geometry. This model is applied to LH launching for current drive. The resulting wave spectrum is asymmetrically broadened in angular wavenumber space. This asymmetry is not accounted for in previous LH scattering models. The modified wave spectrum is coupled to a ray tracing/Fokker–Planck solver (GENRAY/CQL3D) to study its impact on current drive. The resulting current profile is greatly altered, and there is significant increase in the on-axis current and decrease in the off-axis peaks. This is attributed to a portion of the modified wave spectrum that is strongly dampened on-axis during the first pass.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Adding GPU Support to the Markov Chain Monte Carlo Code Catmip

In geophysics, we are confronted with many under-determined inverse problems. For example, all of our observations of earthquakes are made at the Earth’s surface. So, when we try to infer how slip during an earthquake evolves in space and time, we find that there are many potential slip histories that are consistent with our limited observations and our understanding of earthquake physics. One way to approach these problems is with Bayesian analysis which allows us to infer the ensemble of all potential slip models that satisfy the observations and our prior knowledge of earthquake physics. In Bayesian analysis, our prior knowledge is known as the prior probability density function or prior PDF, the fit to the data is known as the data likelihood, and the target PDF that satisfies both the prior PDF and data likelihood is known as the posterior PDF. However, simulating the posterior PDF typically requires using Markov Chain Monte Carlo (MCMC) to draw tens of billions of random realizations of earthquake slip models, which may not be computationally feasible. To make this and similar geophysical inversions computationally tractable, we developed the Cascading Adaptive Transitional Metropolis In Parallel (CATMIP) algorithm. CATMIP is an efficient parallel Markov Chain Monte Carlo (MCMC) sampler that is used for model fitting and uncertainty quantification in geophysics. Example use cases are earthquake rupture modeling, determining mineral composition on Mars, reconstructing the history of ocean salinity, and historical earthquake relocation. CATMIP employs many parallel instances of the Metropolis algorithm for sampling in a transitioning framework. Transitioning is a process in which a set of random samples at equilibrium with a known probability density function (PDF) are used as seeds for the Markov chains to sample successive target PDFs that incrementally move the distribution from the starting seeds to the final desired PDF that describes the relative plausibility of potential values for the model parameters. The algorithm is implemented as a Master-Worker model employing MPI for communication. The worker processes are loosely coupled with global parameters periodically optimized by the master process. This provides a very high amount of parallelism with little communication between updates. During the presentation we will discuss the history of the algorithm and elaborate the earthquake rupture modeling use case for the CATMIP package. Our first step toward GPU optimization was to optimize the code for the CPU. CPU profiling revealed that most of the compute time is spent in calls to level 2 BLAS routines and calls to GSL random number generators. We revised the algorithm to employ level 3 BLAS routines instead. In our presentation we will describe how this was accomplished. Adding GPU support to CATMIP consisted mostly of replacing the calls to GSL with calls to GPU vendor-provided library routines. A small number of loops were directly implemented in CUDA. In the presentation will provide implementation details. Finally, we will discuss methods for profiling and opportunities for further optimizing GPU execution. By creating a code with the flexibility to run on either a CPU or GPU architecture, CATMIP can be used on systems ranging from large CPU-based HPC environments to single servers with GPU acceleration and everything in between.

HECC↗

EvoProtGrad (Directed Evolution for Proteins with Gradients) [SWR-23-48]

A Python package for directed evolution on a protein sequence with gradient-based discrete Markov chain monte carlo (MCMC). Users are able to compose custom models that map sequence to function with pretrained models, including protein language models (PLMs), to guide and constrain search. Our package natively integrates with the HuggingFace platform and supports PLMs from transformers. Our MCMC sampler identifies promising amino acids to mutate via model gradients taken with respect to the input (i.e., sensitivity analysis). We allow users to compose their own custom target function for MCMC by leveraging the Product of Experts MCMC paradigm. Each model is an "expert" that contributes its own knowledge about the protein's fitness landscape to the overall target function. The sampler is designed to be more efficient and effective than brute force and random search while maintaining most of the generality and flexibility. Additional information can be found in the related publication: https://iopscience.iop.org/article/10.1088/2632-2153/accacd

Emami, Patrick↗

Probabilistic Prognosis of Non-Planar Fatigue Crack Growth

Quantifying the uncertainty in model parameters for the purpose of damage prognosis can be accomplished utilizing Bayesian inference and damage diagnosis data from sources such as non-destructive evaluation or structural health monitoring. The number of samples required to solve the Bayesian inverse problem through common sampling techniques (e.g., Markov chain Monte Carlo) renders high-fidelity finite element-based damage growth models unusable due to prohibitive computation times. However, these types of models are often the only option when attempting to model complex damage growth in real-world structures. Here, a recently developed high-fidelity crack growth model is used which, when compared to finite element-based modeling, has demonstrated reductions in computation times of three orders of magnitude through the use of surrogate models and machine learning. The model is flexible in that only the expensive computation of the crack driving forces is replaced by the surrogate models, leaving the remaining parameters accessible for uncertainty quantification. A probabilistic prognosis framework incorporating this model is developed and demonstrated for non-planar crack growth in a modified, edge-notched, aluminum tensile specimen. Predictions of remaining useful life are made over time for five updates of the damage diagnosis data, and prognostic metrics are utilized to evaluate the performance of the prognostic framework. Challenges specific to the probabilistic prognosis of non-planar fatigue crack growth are highlighted and discussed in the context of the experimental results.

Leser, Patrick E.↗

Pulsar Emission Geometry and Accelerating Field Strength

The high-quality Fermi LAT observations of gamma-ray pulsars have opened a new window to understanding the generation mechanisms of high-energy emission from these systems, The high statistics allow for careful modeling of the light curve features as well as for phase resolved spectral modeling. We modeled the LAT light curves of the Vela and CTA I pulsars with simulated high-energy light curves generated from geometrical representations of the outer gap and slot gap emission models. within the vacuum retarded dipole and force-free fields. A Markov Chain Monte Carlo maximum likelihood method was used to explore the phase space of the magnetic inclination angle, viewing angle. maximum emission radius, and gap width. We also used the measured spectral cutoff energies to estimate the accelerating parallel electric field dependence on radius. under the assumptions that the high-energy emission is dominated by curvature radiation and the geometry (radius of emission and minimum radius of curvature of the magnetic field lines) is determined by the best fitting light curves for each model. We find that light curves from the vacuum field more closely match the observed light curves and multiwavelength constraints, and that the calculated parallel electric field can place additional constraints on the emission geometry

DeCesar, Megan E.↗

Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification

To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. HIV biomarkers are measurable biological quantities that have some relationship to the amount of time someone has been infected with HIV. To train our model, we used five biomarkers based on real data from serological assays, HIV sequence data, and target cell counts in longitudinally followed, untreated patients with known infection times. The biomarkers were modeled with a mixed effects framework to allow for patient specific variation and general trends, and fit to patient data using Markov Chain Monte Carlo (MCMC) methods. Subsequently, the density of the unobserved infection time conditional on observed biomarkers were obtained by integrating out the random effects from the model fit. This probabilistic information about infection times was incorporated into the likelihood function for the transmission history and phylogenetic tree reconstruction, informed by the HIV sequence data. To critically test our methodology, we developed a coalescent-based simulation framework that generates phylogenies and biomarkers given a specific or general transmission history. Testing on many epidemiological scenarios showed that biomarker augmented phylogenetics can reach 90% accuracy under idealized situations. Under realistic within-host HIV-1 evolution, involving substantial within-host diversification and frequent transmission of multiple lineages, the average accuracy was at about 50% in transmission clusters involving 5–50 hosts. Realistic biomarker data added on average 16 percentage points over using the phylogeny alone. Using more biomarkers improved the performance. Shorter temporal spacing between transmission events and increased transmission heterogeneity reduced reconstruction accuracy, but larger clusters were not harder to get right. More sequence data per infected host also improved accuracy. We show that the method is robust to incomplete sampling and that adding biomarkers improves reconstructions of real HIV-1 transmission histories. The technology presented here could allow for better prevention programs by providing data for locally informed and tailored strategies.

60 APPLIED LIFE SCIENCES↗

Advancing earth system model calibration: a diffusion-based method

Understanding of climate impact on ecosystems globally requires site-specific model calibration. Here we introduce a novel diffusion-based uncertainty quantification (DBUQ) method for efficient model calibration. DBUQ is a score-based diffusion model that leverages Monte Carlo simulation to estimate the score function and evaluates a simple neural network to quickly generate samples for approximating parameter posterior distributions. DBUQ is stable, efficient, and can effectively calibrate the model given diverse observations, thereby enabling rapid and site-specific model calibration on a global scale. This capability significantly advances Earth system modeling and our understanding of climate impacts on Earth systems. We demonstrate DBUQ's capability in E3SM land model calibration at the Missouri Ozark AmeriFlux forest site. Both synthetic and real-data applications indicate that DBUQ produces accurate parameter posterior distributions similar to those generated by Markov Chain Monte Carlo sampling but with 30X less computing time. This efficiency marks a significant stride in model calibration, paving the way for more effective and timely climate impact analyses.

Liu, Yanfang↗

Modular techniques for dynamic fault-tree analysis

It is noted that current approaches used to assess the dependability of complex systems such as Space Station Freedom and the Air Traffic Control System are incapable of handling the size and complexity of these highly integrated designs. A novel technique for modeling such systems which is built upon current techniques in Markov theory and combinatorial analysis is described. It enables the development of a hierarchical representation of system behavior which is more flexible than either technique alone. A solution strategy which is based on an object-oriented approach to model representation and evaluation is discussed. The technique is virtually transparent to the user since the fault tree models can be built graphically and the objects defined automatically. The tree modularization procedure allows the two model types, Markov and combinatoric, to coexist and does not require that the entire fault tree be translated to a Markov chain for evaluation. This effectively reduces the size of the Markov chain required and enables solutions with less truncation, making analysis of longer mission times possible. Using the fault-tolerant parallel processor as an example, a model is built and solved for a specific mission scenario and the solution approach is illustrated in detail.

Patterson-Hine, F. A.↗

Bayesian Exploration of Phenomenological EoS of Neutron/Hybrid Stars with Recent Observations

The description of the stellar interior of compact stars remains as a big challenge for the nuclear astrophysics community. The consolidated knowledge is restricted to density regions around the saturation of hadronic matter ρ 0 =2.8 × 10 14 g cm -3 , regimes where our nuclear models are successfully applied. As one moves towards higher densities and extreme conditions up to the quark/gluons deconfinement, little can be said about the microphysics of the equation of state (EoS). Here, we employ a Markov Chain Monte Carlo (MCMC) strategy to access the variability at high density regions of polytropic piecewise models for neutron star (NS) EoS or possible hybrid stars, i.e., a NS with a small quark-matter core. With a fixed description of the hadronic matter for low density, below the nuclear saturation density, we explore a variety of models for the high density regimes leading to stellar masses near to 2.5 M ⊙ , in accordance with the observations of massive pulsars. The models are constrained, including the observation of the merger of neutrons stars from VIRGO-LIGO and with the pulsar observed by NICER. In addition, we also discuss the possibility of the use of a Bayesian power regression model with heteroscedastic error. The set of EoS from the Laser Interferometer Gravitational-Wave Observatory (LIGO) was used as input and treated as the data set for the testing case.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

First measurement in a magnetic confinement fusion experiment of the H 3 + H 3 → He 5 + n intermediate two-body resonant reaction

We report on the first experimental measurements made at a magnetic confinement fusion device of the tritium(T)-tritium(T) reaction T + T → He 4 + 2 n indicating the presence of the intermediate two-body resonant reaction T + T → He 5 + n . During the second deuterium-tritium campaign (DTE2) at the Joint European Torus, measurements of fusion plasmas with high tritium concentrations, n T / ( n T + n D ) ≈ 0.99 , heated with tritium neutral beam injection, were performed using the neutron time-of-flight (TOF) spectrometer TOFOR. We detect a peak in the neutron emission TOF spectrum consistent with the two-body resonant reaction. The TT neutron emission energy spectrum is modeled using an R -matrix framework where the distributions of the most likely model parameters given our experimental TOF data are determined utilizing a Markov chain Monte Carlo approach. We compare our best estimate of the T + T neutron emission energy spectrum with results obtained at inertial confinement fusion experiments at the OMEGA facility and find a spectral shape that is consistent with the energy dependency in the neutron spectrum observed at OMEGA. Published by the American Physical Society 2024

Physics↗

Planck constraints and gravitational wave forecasts for primordial black hole dark matter seeded by multifield inflation

Here, we perform a Markov Chain Monte Carlo analysis of a simple yet generic multifield inflation model characterized by two scalar fields coupled to each other and nonminimally coupled to gravity, fit to Planck 2018 cosmic microwave background (CMB) data. In particular, model parameters are constrained by data on the amplitude of the primordial power spectrum of scalar curvature perturbations on CMB scales A s , the spectral index n s , and the ratio of power in tensor to scalar modes r, with a prior that the primordial power spectrum should also lead to primordial black hole (PBH) production sufficient to account for the observed dark matter abundance. We find that n s in particular controls the constraints on our model. Whereas previous studies of PBH formation from an ultraslow-roll phase of inflation have highlighted the need for at least one model parameter to be highly fine-tuned, we identify a degeneracy direction in parameter space such that shifts by ~10% of one parameter can be compensated by comparable shifts in other parameters while preserving a close fit between model predictions and observations. Furthermore, we find this allowed parameter region produces observable gravitational wave signals in the frequency ranges to which upcoming experiments are projected to be sensitive, including Advanced LIGO and Virgo, the Einstein Telescope, Cosmic Explorer, DECIGO, and LISA.

79 ASTRONOMY AND ASTROPHYSICS↗

Impact of a midband gravitational wave experiment on detectability of cosmological stochastic gravitational wave backgrounds

In this report we make forecasts for the impact a future “midband” space-based gravitational wave experiment, most sensitive to 10 -2 - 10Hz,could have on potential detections of cosmological stochastic gravitational wave backgrounds (SGWBs). Specific proposed midband experiments considered are TianGo, B-DECIGO, and AEDGE. We propose a combined power-law integrated sensitivity (CPLS) curve combining GW experiments over different frequency bands, which shows the midband improves sensitivity to SGWBs by up to two orders of magnitude at 10 -2 - 10 Hz . We consider GW emission from cosmic strings and phase transitions as benchmark examples of cosmological SGWBs. We explicitly model various astrophysical SGWB sources, most importantly from unresolved black hole mergers. Using Markov Chain Monte Carlo, we demonstrated that midband experiments can, when combined with LIGO A+ and LISA, significantly improve sensitivities to cosmological SGWBs and better separate them from astrophysical SGWBs. In particular, we forecast that a midband experiment improves sensitivity to cosmic string tension G μ by up to a factor of 10, driven by improved component separation from astrophysical sources. For phase transitions, a midband experiment can detect signals peaking at 0.1–1 Hz, which for our fiducial model corresponds to early Universe temperatures of T * ~10 4 – 10 6 GeV , generally beyond the reach of LIGO and LISA. The midband closes an energy gap and better captures characteristic spectral shape information. It thus substantially improves measurement of the properties of phase transitions at lower energies of T * ~ O(10 3 ) GeV , potentially relevant to new physics at the electroweak scale, whereas in this energy range LISA alone will detect an excess but not effectively measure the phase transition parameters. Our modeling code and chains are publicly available.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analyzing rotational bands in odd-mass nuclei using effective field theory and Bayesian methods

We recently developed an Effective Field Theory (EFT) for rotational bands in odd-mass nuclei. Here we use EFT expressions to perform a Bayesian analysis of data on the rotational energy levels of 99 Tc, 155,157 Gd, 159 Dy, 167,169 Er, 167,169 Tm, 183 W, 235 U and 239 Pu. The error model in our Bayesian analysis includes both experimental and EFT truncation uncertainties. It also accounts for the fact that low-energy constants (LECs) at even and odd orders are expected to have different sizes. We use Markov Chain Monte Carlo (MCMC) sampling to explore the joint posterior of the EFT and error-model parameters and show both the LECs and the breakdown scale can be reliably determined. We extract the LECs up to fourth order in the EFT and find that, provided we correctly account for EFT truncation errors in our likelihood, results for lower-order LECs are stable as we go to higher orders. LEC results are also stable with respect to the addition of higher-energy data. We extract the expansion parameter for all the nuclei listed above and find a clear correlation between the extracted and the expected value of the inverse breakdown scale, W, based on the single-particle and vibrational energy scales. However, the W that actually determines the convergence of the EFT expansion is markedly smaller than would be naively expected based on those scales.

EFT↗

A Diffusion‐Based Uncertainty Quantification Method to Advance E3SM Land Model Calibration

Abstract Calibrating land surface models and accurately quantifying their uncertainty are crucial for improving the reliability of simulations of complex environmental processes. This, in turn, advances our predictive understanding of ecosystems and supports climate‐resilient decision‐making. Traditional calibration methods, however, face challenges of high computational costs and difficulties in accurately quantifying parameter uncertainties. To address these issues, we develop a diffusion‐based uncertainty quantification (DBUQ) method. Unlike conventional generative diffusion methods, which are computationally expensive and memory‐intensive, DBUQ innovates by formulating a parameterized generative model and approximates this model through supervised learning, which enables quick generation of parameter posterior samples to quantify its uncertainty. DBUQ is effective, efficient, and general‐purpose, making it suitable for site‐specific ecosystem model calibration and broadly applicable for parameter uncertainty quantification across various earth system models. In this study, we applied DBUQ to calibrate the Energy Exascale Earth System Model land model at the Missouri Ozark AmeriFlux forest site. Results indicated that DBUQ produced accurate parameter posterior distributions similar to those from Markov Chain Monte Carlo sampling but with 30 times less computing time. This significant improvement in efficiency suggests that DBUQ can enable rapid, site‐level model calibration at a global scale, enhancing our predictive understanding of climate impacts on terrestrial ecosystems.

54 ENVIRONMENTAL SCIENCES↗

Alma Images the Eccentric HD 53143 Debris Disk

We present ALMA 1.3 mm observations of the HD 53143 debris disk—the first infrared or millimeter image produced of this ∼1 Gyr old solar analog. Previous HST STIS coronagraphic imaging did not detect flux along the minor axis of the disk, which could suggest a face-on geometry with two clumps of dust. These ALMA observations reveal a disk with a strikingly different structure. In order to fit models to the millimeter visibilities and constrain the uncertainties on the disk parameters, we adopt a Markov Chain Monte Carlo approach. This is the most eccentric debris disk observed to date with a forced eccentricity of 0.21 ± 0.02, nearly twice that of the Fomalhaut debris disk, and also displays an apocenter glow. Although this eccentric model fits the outer debris disk well, significant interior residuals remain, which may suggest a possible edge-on inner disk, which remains unresolved in these observations. Combined with the observed structure difference between HST and ALMA, these results suggest a potential previous scattering event or dynamical instability in this system. We also note that the stellar flux changes considerably over the course of our observations, suggesting flaring at millimeter wavelengths. Using simultaneous TESS observations, we determine the stellar rotation period to be 9.6 ± 0.1 days.

Radio astronomy↗