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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics

Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., 10) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring the ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6/15 phylogenomic datasets. Lastly, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multivariable degradation modeling and life prediction using multivariate fractional Brownian motion

In system prognostics and health management, multivariable degradation models have been widely developed to predict the life of complex systems using degradation data of multiple Performance Characteristics (PCs). Recent studies have detected a Long-Term Memory (LTM) effect among the degradation process of various PCs, implying a strong coupling phenomenon between the future degradation behavior and historical degradation trajectory. Although the LTM has been widely integrated into single-PC-based degradation modeling, it has not been considered in multi-PC-based scenarios. To capture LTM among multiple PCs, this article proposes a novel LTM-integrated Multivariate Degradation Model (MDM) for system life prediction based on multivariate fractional Brownian motion, which simultaneously incorporates the cross-correlation among different PCs. To estimate parameters of the LTM-integrated MDM, a maximum likelihood method is developed. Here, two likelihood-ratio hypothesis tests are developed to test the existence of the overall and individual LTM effect among multiple PCs. Both simulation studies and physical experiments on the performance degradation of solar energy conversion and storage devices are conducted to validate the proposed model. Results reveal that the proposed LTM-integrated MDM significantly outperforms existing MDMs in life prediction, while the lifetime uncertainty is heavily underestimated by those traditional approaches that neglect the LTM.

42 ENGINEERING↗
DOE OSTI2021

An Indirect Search for Weakly Interacting Massive Particles in the Sun Using Upward-going Muons in NOvA

I present the first Dark Matter search results using the full data set collected with the upward-going muon trigger in NOvA. Weakly Interactive Massive Particles (WIMPs) are a theoretical non-baryonic form of Dark Matter. The nature of Dark Matter is one of the most exciting open questions in modern physics. Though its existence can be inferred by astrophysical evidence, its properties are not yet understood. If we assume that Dark Matter particles can produce Standard Model particles through their interactions, an indirect search can help shed light on this mystery.The NOvA collaboration has built a 14 kton, fine-grained, low-Z, total absorption tracking calorimeter at an off-axis angle to the NuMI neutrino beam. Even though the detector is optimized to observe electron neutrino appearance from a muon neutrino beam, it has a unique potential for more exotic searches given its excellent granularity and energy resolution and relatively low-energy neutrino thresholds. In fact, with an efficient upward-going muon trigger and sufficient background suppression offline, NOvA is capable of a competitive indirect Dark Matter search for low-mass WIMPs.The idea of the upward-going muon trigger is first to select high-quality muon tracks, then use the timing information of all of the hits of each track to estimate directionality. In this way, the background flux is suppressed by more than a factor of 10^5 at trigger level to a rate of approximately 1 Hz. To further optimize this search, we use only upward-going muons that point to the Sun, so our search occurs at night when the Sun is on the other side of the Earth. This strategy also allows us to use the time when the Sun is above the horizon as a control region to estimate the background. Ultimately, implementation of a cut based and maximum likelihood analysis provides a powerful tool for rejecting background and selecting a sample of neutrino-induced upward-going muons. The overall background rejection power achieved by the analysis is substantial and impressive. Starting with approximately 150,000 events per second, we reduced it to 40 events per year. Since no statistically significant excess was found, a 90\% C.L. upper limit on the expected muon flux of upward-going muons has been set using the upper limit on the number of events given the number of observed events in the signal region. Lastly, by assuming the theory behind the upward-going muon flux, a limit on the WIMP-nucleon spin-dependent cross-section in the Sun was estimated. Although the limits on the spin-dependent cross-section do not appear to be competitive with previous indirect Dark Matter searches, the upward-going muon flux limits are promising. The upward-going muon flux limits could extend these results to a broader class of models that are not specific to the dark matter theory but produce upward-going muons, leading to competitive results.

Principato, Cristiana↗
DOE OSTI2025

Enhancing Gaussian Process Surrogates for Optimization and Posterior Approximation via Random Exploration

This paper proposes novel noise-free Bayesian optimization strategies that rely on a random exploration step to enhance the accuracy of Gaussian process surrogate models. The new algorithms retain the ease of implementation of the classical GP-UCB algorithm, but the additional random exploration step accelerates their convergence, nearly achieving the optimal convergence rate. Furthermore, to facilitate Bayesian inference with intractable likelihoods, we propose to utilize optimization iterates for maximum a posteriori estimation to build a Gaussian process surrogate model for the unnormalized log-posterior density. We provide bounds for the Hellinger distance between the true and the approximate posterior distributions in terms of the number of design points. We demonstrate the effectiveness of our Bayesian optimization algorithms in nonconvex benchmark objective functions, in a machine learning hyperparameter tuning problem, and in a black-box engineering design problem. The effectiveness of our posterior approximation approach is demonstrated in two Bayesian inference problems for parameters of dynamical systems.

Bayesian inference↗
DOE OSTI2025

An iterative CMB lensing estimator minimizing instrumental noise bias

Noise maps from cosmic microwave background (CMB) experiments are generally statistically anisotropic, due to scanning strategies, atmospheric conditions, or instrumental effects. Any mismodeling of this complex noise can bias the reconstruction of the lensing potential and the measurement of the lensing power spectrum from the observed CMB maps. We introduce a new CMB lensing estimator based on the maximum (MAP) reconstruction that is minimally sensitive to these instrumental noise biases. By modifying the likelihood to rely exclusively on correlations between CMB map splits with independent noise realizations, we minimize autocorrelations that contribute to biases. In the regime of many independent splits, this maximum closely approximates the optimal MAP reconstruction of the lensing potential. In simulations, we demonstrate that this method is able to determine lensing observables that are immune to any noise mismodeling with a negligible cost in signal-to-noise ratio. Our estimator enables unbiased and nearly optimal lensing reconstruction for next-generation CMB surveys.

Legrand, Louis [University of Cambridge (United Ki↗
DOE OSTI2024

Estimating Sparse Direct Effects in Multivariate Regression With the Spike-and-Slab LASSO

The multivariate regression interpretation of the Gaussian chain graph model simultaneously parametrizes (i) the direct effects of p predictors on q outcomes and (ii) the residual partial covariances between pairs of outcomes. We introduce a new method for fitting sparse versions of these models with spike-and-slab LASSO (SSL) priors. We develop an Expectation Conditional Maximization algorithm to obtain sparse estimates of the p × q matrix of direct effects and the q × q residual precision matrix. Our algorithm iteratively solves a sequence of penalized maximum likelihood problems with self-adaptive penalties that gradually filter out negligible regression coefficients and partial covariances. Because it adaptively penalizes individual model parameters, our method is seen to outperform fixed-penalty competitors on simulated data. We establish the posterior contraction rate for our model, buttressing our method’s excellent empirical performance with strong theoretical guarantees. Using our method, we estimated the direct effects of diet and residence type on the composition of the gut microbiome of elderly adults.

EM algorithm↗
DOE OSTI2023

Analysis of Unpolarised p+p¿ Photoproduction with the GlueX Experiment

This thesis presents measurements of spin-density matrix elements in unpolarised p+p? photoproduction on a proton target. The dominant resonance contribution to the dipion system is the r(770) meson. Due to the large production cross section for this resonance, a valid comparison can be made between the obtained final results and r(770) spin-density matrix elements measured previously with other experiments. The measurement was performed over the 3:0 ? 11:6 GeV beam energy regime, which is a more extensive energy range than has ever been studied previously for the r(770). Results were obtained by analysing data from the GlueX experiment based at Jefferson Lab. Extended maximum likelihood fits were applied to extract three spin-density matrix elements using Markov chain Monte Carlo based parameter estimations. This was performed using various binning configurations to probe the energy, mass, and four-momentum transfer dependence of the determined physics observables. Spin-density matrix elements are shown to be consistent with the model of s-channel helicity conservation at low ?t. The effects of pomeron and f2 exchanges are clearly visible in the energy dependence of the measured observables. These observations provide valuable insights into the relative strengths of both processes as a function of the photon energy, and may enable theorists to disentangle the f2=P coupling ratio. Spin-density matrix elements are seen to be highly dependent on the reconstructed resonance mass. This observation is likely to be a result of non-resonant S-wave background processes, and emphasises the need for a more detailed model of the p+p? angular distribution that considers all of the competing angular momentum components that contribute to the measured final state. The statistical precision of measurements performed for this thesis surpass what was achievable in previous studies of the r(770) by several orders of magnitude. Studies of the energy and four-momentum transfer dependence, and insights into the effects of non r(770) background contributions provide valuable input for production models. This will help inform the choice of wave-sets used for partial wave analyses, supporting GlueX in its search for exotic hybrid meson states.

Fitches, James↗
DOE OSTI2022

Comparative Study of Wind Energy Potential Estimation Methods for Wind Sites in Togo and Benin (West Sub-Saharan Africa)

The characterization of wind speed distribution and the optimal assessment of wind energy potential are critical factors in selecting a suitable site for wind power plants (WPP). The Weibull distribution law has been used extensively to analyze the wind characteristics of candidate WPP sites, and to estimate the available and deliverable energy. This paper presents a comparative study of five wind energy resource assessment methods as they applied to the context of wind sites in West Sub-Saharan Africa. We investigated three numerical approaches, namely, the adaptive neuro-fuzzy inference system (ANFIS), the multilayer perceptron method (MLP), and support vector regression (SVR), to derive the distribution law of wind speeds and to optimally quantify the corresponding wind energy potential. Next, we compared these three approaches to two well-known Weibull distribution law-based methods: the empirical method of Justus (EMJ) and the maximum likelihood method (MLM). Case study results indicated that the neural network-based methods, ANFIS and MLP, yielded the most accurate distribution fits and wind energy potential estimates, and consequently, are the most recommended methods for the wind sites in Togo and Benin. The orders of magnitude of the root mean squared error (RMSE) in estimating the recoverable energy using ANFIS were, respectively, 10-4 and 10-5 for Lomé and Cotonou, while MLP achieved an RMSE order of magnitude of 10-3 for both sites.

17 WIND ENERGY↗
DOE OSTI2021

Solving inverse problems in stochastic models using deep neural networks and adversarial training

Inverse problems associated with stochastic models constitute a significant portion of scientific and engineering applications. In such cases the unknown quantities are distributions. The applicability of traditional methods is limited because of their demanding assumptions or prohibitive computational consumption; for example, maximum likelihood methods require closed-form density functions, and Markov Chain Monte Carlo needs a large number of simulations. We propose a new method that estimates the unknown distribution by matching the statistical properties between observed and simulated random processes. We leverage the expressive power of neural networks to approximate the unknown distribution and use a discriminative neural network for computing the statistical discrepancies between the observed and simulated random processes. Here we demonstrated numerically that the proposed methods can estimate both the model parameters and learn complicated unknown distributions.

42 ENGINEERING↗
DOE OSTI2024

Early-time γ -ray constraints on cosmic-ray acceleration in the core-collapse SN 2023ixf with the Fermi Large Area Telescope

Context. While supernova remnants (SNRs) have been considered the most relevant Galactic cosmic ray (CR) accelerators for decades, core-collapse supernovae (CCSNe) could accelerate particles during the earliest stages of their evolution and hence contribute to the CR energy budget in the Galaxy. Some SNRs have indeed been associated with TeV γ -rays, yet proton acceleration efficiency during the early stages of an SN expansion remains mostly unconstrained. Aims. The multi-wavelength observation of SN 2023ixf, a Type II supernova (SN) in the nearby galaxy M 101 (at a distance of 6.85 Mpc), opens the possibility to constrain CR acceleration within a few days after the collapse of the red super-giant stellar progenitor. With this work, we intend to provide a phenomenological, quasi-model-independent constraint on the CR acceleration efficiency during this event at photon energies above 100 MeV. Methods. We performed a maximum-likelihood analysis of γ -ray data from the Fermi Large Area Telescope up to one month after the SN explosion. We searched for high-energy, non-thermal emission from its expanding shock, and estimated the underlying hadronic CR energy reservoir assuming a power-law proton distribution consistent with standard diffusive shock acceleration. Results. We do not find significant γ -ray emission from SN 2023ixf. Nonetheless, our non-detection provides the first limit on the energy transferred to the population of hadronic CRs during the very early expansion of a CCSN. Conclusions. Under reasonable assumptions, our limits would imply a maximum efficiency on the CR acceleration of as low as 1%, which is inconsistent with the common estimate of 10% in generic SNe. However, this result is highly dependent on the assumed geometry of the circumstellar medium, and could be relaxed back to 10% by challenging spherical symmetry. Consequently, a more sophisticated, inhomogeneous characterisation of the shock and the progenitor’s environment is required before establishing whether or not Type II SNe are indeed efficient CR accelerators at early times.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples

The accurate identification of SARS-CoV-2 (SC2) variants and estimation of their abundance in mixed population samples (e.g., air or wastewater) is imperative for successful surveillance of community level trends. Assessing the performance of SC2 variant composition estimators (VCEs) should improve our confidence in public health decision making. Here, we introduce a linear regression based VCE and compare its performance to four other VCEs: two re-purposed DNA sequence read classifiers (Kallisto and Kraken2), a maximum-likelihood based method (Lineage deComposition for Sars-Cov-2 pooled samples (LCS)), and a regression based method (Freyja). We simulated DNA sequence datasets of known variant composition from both Illumina and Oxford Nanopore Technologies (ONT) platforms and assessed the performance of each VCE. We also evaluated VCEs performance using publicly available empirical wastewater samples collected for SC2 surveillance efforts. Bioinformatic analyses were performed with a custom NextFlow workflow (C-WAP, CFSAN Wastewater Analysis Pipeline). Relative root mean squared error (RRMSE) was used as a measure of performance with respect to the known abundance and concordance correlation coefficient (CCC) was used to measure agreement between pairs of estimators. Based on our results from simulated data, Kallisto was the most accurate estimator as it had the lowest RRMSE, followed by Freyja. Kallisto and Freyja had the most similar predictions, reflected by the highest CCC metrics. We also found that accuracy was platform and amplicon panel dependent. For example, the accuracy of Freyja was significantly higher with Illumina data compared to ONT data; performance of Kallisto was best with ARTICv4. However, when analyzing empirical data there was poor agreement among methods and variations in the number of variants detected (e.g., Freyja ARTICv4 had a mean of 2.2 variants while Kallisto ARTICv4 had a mean of 10.1 variants). This work provides an understanding of the differences in performance of a number of VCEs and how accurate they are in capturing the relative abundance of SC2 variants within a mixed sample (e.g., wastewater). Such information should help officials gauge the confidence they can have in such data for informing public health decisions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Bayesian operator inference for data-driven reduced-order modeling

This work proposes a Bayesian inference method for the reduced-order modeling of time-dependent systems. Informed by the structure of the governing equations, the task of learning a reduced-order model from data is posed as a Bayesian inverse problem with Gaussian prior and likelihood. The resulting posterior distribution characterizes the operators defining the reduced-order model, hence the predictions subsequently issued by the reduced-order model are endowed with uncertainty. The statistical moments of these predictions are estimated via a Monte Carlo sampling of the posterior distribution. Since the reduced models are fast to solve, this sampling is computationally efficient. Furthermore, the proposed Bayesian framework provides a statistical interpretation of the regularization term that is present in the deterministic operator inference problem, and the empirical Bayes approach of maximum marginal likelihood suggests a selection algorithm for the regularization hyperparameters. The proposed method is demonstrated on two examples: the compressible Euler equations with noise-corrupted observations, and a single-injector combustion process.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A Measurement of the Largest-scale CMB E -mode Polarization with CLASS

We present measurements of large-scale cosmic microwave background E-mode polarization from the Cosmology Large Angular Scale Surveyor 90 GHz data. Using 115 det-yr of observations collected through 2024 with a variable-delay polarization modulator, we achieved a polarization sensitivity of 82 μK arcimin, comparable to Planck at similar frequencies (100 and 143 GHz ). The analysis demonstrates effective mitigation of systematic errors and addresses challenges to large-angular-scale power recovery posed by time-domain filtering in maximum-likelihood map-making. A novel implementation of the pixel-space transfer matrix is introduced, which enables efficient filtering simulations and bias correction in the power spectrum using the quadratic cross-spectrum estimator. Overall, we achieved an unbiased time-domain filtering correction to recover the largest angular scale polarization, with the only power deficit, arising from map-making nonlinearity, being characterized as <3%. Through cross-correlation with Planck, we detected the cosmic reionization at 99.4% significance and measured the reionization optical depth τ = $0.053^{+0.018}_{-0.019}$, marking the first ground-based attempt at such a measurement. At intermediate angular scales (ℓ > 30), our results, both independently and in cross-correlation with Planck, remain fully consistent with Planck’s measurements.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Measurements of W + W − production cross-sections in pp collisions at $\sqrt{s}=13$ TeV with the ATLAS detector

Measurements of W + W − → e ± νμ ∓ ν production cross-sections are presented, providing a test of the predictions of perturbative quantum chromodynamics and the electroweak theory. The measurements are based on data from pp collisions at $\sqrt{s}$ = 13 TeV recorded by the ATLAS detector at the Large Hadron Collider in 2015–2018, corresponding to an integrated luminosity of 140 fb −1 . The number of events due to top-quark pair production, the largest background, is reduced by rejecting events containing jets with b-hadron decays. An improved methodology for estimating the remaining top-quark background enables a precise measurement of W + W − cross-sections with no additional requirements on jets. The fiducial W + W − cross-section is determined in a maximum-likelihood fit with an uncertainty of 3.1%. The measurement is extrapolated to the full phase space, resulting in a total W + W − cross-section of 127 ± 4 pb. Differential cross-sections are measured as a function of twelve observables that comprehensively describe the kinematics of W + W − events. The measurements are compared with state-of-the-art theory calculations and excellent agreement with predictions is observed. A charge asymmetry in the lepton rapidity is observed as a function of the dilepton invariant mass, in agreement with the Standard Model expectation. A CP-odd observable is measured to be consistent with no CP violation. Limits on Standard Model effective field theory Wilson coefficients in the Warsaw basis are obtained from the differential cross-sections.

Accelerator Physics↗
DOE OSTI2022

Earthquake Phase Association Using a Bayesian Gaussian Mixture Model

Earthquake phase association algorithms aggregate picked seismic phases from a network of seismometers into individual seismic events and play an important role in earthquake monitoring and research. Dense seismic networks and improved phase picking methods produce massive seismic phase datasets, particularly for earthquake swarms and aftershocks occurring closely in time and space, making phase association a challenging problem. Here, we present a new association method, the Gaussian Mixture Model Association (GaMMA), that combines the Gaussian mixture model with earthquake location, origin time, and magnitude estimation. We treat earthquake phase association as an unsupervised clustering problem in a probabilistic framework, where each earthquake corresponds to a cluster of P and S phases with a hyperbolic moveout of arrival times and a decay of amplitude with distance. We use the multivariate Gaussian distribution to model the collection of phase picks of an event; and the mean of the multivariate Gaussian distribution is given by the predicted arrival time and amplitude from the causative event. We carry out the pick assignment to each earthquake and determine earthquake source parameters (i.e., earthquake location, origin time, and magnitude) under the maximum likelihood criterion using the Expectation-Maximization algorithm. The GaMMA method does not require typical association steps of other algorithms, such as grid-search or supervised training. The results for both synthetic tests and for the 2019 Ridgecrest earthquake sequence show that GaMMA effectively associates phases from a temporally and spatially dense earthquake sequence while producing useful estimates of earthquake location and magnitude.

58 GEOSCIENCES↗
DOE OSTI2023

Simulation Based Inference with Domain Adaptation for Strong Gravitational Lensing

Simulation based inference leverages machine learning to carry out Bayesian inference for systems with intractable likelihoods. However, transitioning a network trained on simulated data to real data runs the risk of encountering domain shift, leading to performance losses. We attempt to implement domain adaptation into the sbi neural posterior estimation framework using the Maximum Mean Discrepancy as an additional network loss. We test two network architectures and use masked autoregressive flow for density estimation. We test the network on a set of 400,000 simulated strong gravitational lensing images generated using deeplenstronomy. The source domain is defined as low noise whereas the target domain has a noise profile sampled from experimentally derived DES survey conditions. We find that, while DA does lead to performance improvements, they are marginal at ~6% less inference error. We also find a similar marginal improvement in uncertainty calibration at around 8%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Simulation based inference with domain adaptation for strong gravitational lensing

Simulation based inference leverages machine learning to carry out Bayesian inference in systems with intractable likelihoods. However, transitioning a network trained on simulated data to real data runs the risk of encountering domain shift, leading to performance losses. We attempt to implement domain adaptation into the sbi neural posterior estimation framework using the Maximum Mean Discrepancy as an additional network loss, using masked autoregressive fow (MAF) as our density estimator. We test the network on a set of 400,000 simulated strong gravitational lensing images generated using deeplenstronomy. The source domain is defined as low noise whereas the target domain has a noise profile sampled from experimentally derived DES survey conditions. We find that SBI appears robust against small changes in the data with similar performance on source and target. Moreover, while DA does lead to performance improvements, they are marginal at 6% less inference error.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗