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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Improved joint X-ray and neutron refinement procedure in Phenix

Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues related to poor data quality. Therefore, neutron structure determination often relies on the presence of an X-ray data set for joint X-ray and neutron (XN) refinement. In this approach, the X-ray data serve to compensate for the deficiencies of the neutron diffraction data by refining one model simultaneously against the X-ray and neutron data sets. To be applicable, it is assumed that both data sets are highly isomorphous, and preferably collected from the same crystals and at the same temperature. However, the approach has a number of limitations that are discussed in this work by comparing four separately re-refined neutron models. To address the limitations, a new method for joint XN refinement is introduced that optimizes two different models against the different data sets. This approach is tested using neutron models and data deposited in the Protein Data Bank. The efficacy of refining models with H atoms as riding or as individual atoms is also investigated.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A new method for inferring city emissions and lifetimes of nitrogen oxides from high-resolution nitrogen dioxide observations: a model study

We present a new method to infer emissions and lifetimes of nitrogen oxides (NO x ) based on tropospheric nitrogen dioxide (NO 2 ) observations together with reanalysis wind fields for cities located in polluted backgrounds. Since the accuracy of the method is difficult to assess due to lack of “true values” that can be used as a benchmark, we apply the method to synthetic NO 2 observations derived from the NASA-Unified Weather Research and Forecasting (NU-WRF) model at a high horizontal spatial resolution of 4 km × 4 km for cities over the continental United States. We compare the inferred emissions and lifetimes with the values given by the NU-WRF model to evaluate the method. The method is applicable to 26 US cities. The derived results are generally in good agreement with the values given by the model, with the relative differences of 2 % ± 17 % (mean ± standard deviation) and 15 % ± 25 % for lifetimes and emissions, respectively. Our investigation suggests that the use of wind data prior to the satellite overpass time improves the performance of the method. The correlation coefficients between inferred and NU-WRF lifetimes increase from 0.56 to 0.79 and for emissions increase from 0.88 to 0.96 when comparing results based on wind fields sampled simultaneously with satellite observations and averaged over 9 h data prior to satellite observations, respectively. We estimate that uncertainties in NO x lifetime and emissions arising from the method are approximately 15 % and 20 %, respectively, for typical (US) cities. The total uncertainties reach up to 43% (lifetimes) and 45% (emissions) by considering the additional uncertainties associated with satellite NO 2 observations and wind data. We expect this new method to be applicable to NO 2 observations from the TROPOspheric Monitoring Instrument (TROPOMI) and geostationary satellites, such as Geostationary Environment Monitoring Spectrometer (GEMS) or the Tropospheric Emissions: Monitoring Pollution (TEMPO) instrument, to estimate urban NO x emissions and lifetimes globally.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

SPARTA: A flux adjustment methodology to interpret complex experiments

For the accurate determination of reactivity from a detector count rate, correction of spatial effects is of prime importance. This spatial correction is often provided using simulation methodologies, but this may introduce a bias if the result of the experiment is also used as input data for the simulation. Here, this work presents a flux adjustment methodology able to infer experimental reactivity and correction of spatial effects without the need for a simulation. It can process the signal from a complex experiment such as a heat balance measurement in the TREAT reactor, where control rods are continuously adjusted to maintain a constant power. In the present work, this methodology successfully computed the reactivity and the local spatial variation of the flux of a generated signal. It also proved to be robust against noise and errors on kinetic parameters and provides a credible interpretation of a heat balance experiment in TREAT. Efficiency of flux adjustment methods for complex experiment enable a better experiment interpretation less reliant on nuclear data evaluation.

73 - NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Comparing Automated Posterior Estimation Techniques for Modeling Strong Lenses In Ground-based Survey Data

Current and future ground-based cosmological surveys, such as the Dark Energy Survey (DES), and the Vera Rubin Observatory Legacy Survey of Space and Time (LSST), are predicted to discover thousands to tens of thousands of strong gravitational lenses. The large number of strong lenses discoverable in future surveys will make strong lensing a highly competitive and complementary cosmic probe. However, conventional lens modeling techniques are unable to scale up to the sheer number of lenses that will be discovered through upcoming surveys. Therefore, the use of automated lens analysis techniques is necessary. We demonstrate that machine learning methods can be used to automate the inference of informative model posteriors of strong lensing systems in ground-based surveys with credible uncertainty estimation. We present two Simulation-Based Inference (SBI) approaches for lens parameter estimation of galaxy-galaxy lenses. We demonstrate applications of Neural Posteriors Estima tors (NPEs) and Bayesian Neural Network (BNNs) to automate the inference of a 12-parameter lensing system for DES-like ground-based imaging data. We apply a suite of diagnostics (e.g., posterior coverage and SBC) to validate the performance of our methods. We find that NPEs outperform the BNN, producing posterior distributions that are for the most part both more accurate and more precise; in particular, several source-light model parameters are systematically biased in the BNN implementation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

The DECADE cosmic shear project III: validation of analysis pipeline using spatially inhomogeneous data

We present the pipeline for the cosmic shear analysis of the Dark Energy Camera All Data Everywhere (DECADE) weak lensing dataset: a catalog consisting of 107 million galaxies observed by the Dark Energy Camera (DECam) in the northern Galactic cap. The catalog derives from a large number of disparate observing programs and is therefore more inhomogeneous across the sky compared to existing lensing surveys. First, we use simulated data-vectors to show the sensitivity of our constraints to different analysis choices in our inference pipeline, including sensitivity to residual systematics. Next we use simulations to validate our covariance modeling for inhomogeneous datasets. Finally, we show that our choices in the end-to-end cosmic shear pipeline are robust against inhomogeneities in the survey, by extracting relative shifts in the cosmology constraints across different subsets of the footprint/catalog and showing they are all consistent within 1σ to 2σ. This is done for forty-six subsets of the data and is carried out in a fully consistent manner: for each subset of the data, we re-derive the photometric redshift estimates, shear calibrations, survey transfer functions, the data vector, measurement covariance, and finally, the cosmological constraints. Our results show that existing analysis methods for weak lensing cosmology can be fairly resilient towards inhomogeneous datasets. This also motivates exploring a wider range of image data for pursuing such cosmological constraints.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

PacBio high‐throughput multi‐locus sequencing reveals high genetic diversity in mushroom‐forming fungi

Abstract Multi‐locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi‐locus pooled sequencing method using PacBio long‐read high‐throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein‐coding genesrpb1,rpb2 andtef1. Within‐sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants ofrpb2 andtef1 from corticioid Cantharellales. Our method is a cost‐effective approach for generating accurate multi‐locus sequence data coupled with recovery of alleles from polymorphic samples and multi‐organism specimens. These results have important implications for understanding intra‐individual genomic variation among genetic loci commonly used in species delimitation of fungi.

Biochemistry & Molecular Biology↗
DOE OSTI2024

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↗
DOE OSTI2021

Extract useful information from building permits data to profile a city’s building retrofit history

Building retrofit is one of the key strategies for cities to reduce energy use and GHG emissions. The historical information about changes to buildings is crucial to infer the buildings’ current energy system efficiency levels and to identify candidate buildings for retrofit. In general, a building permit is required before the start of any construction activity of a building, such as changing building structure, remodeling, or installing new equipment. Moreover, many large cities provide public datasets of building permits in history. Therefore, the permits are a potentially good resource for mining information on the city’s retrofit history. In this study, we use the permit dataset from the city of San Francisco as a case study. Location and time information from the dataset is also used to depict the retrofit timeline of each building and the whole building stock. The type of work of the permit is inferred from the descriptive text by a machine learning model. At last, the limitations of the current permit dataset and potential improvements on the permit data management are discussed to better utilize the information in the future.

Zhang, Wanni↗
DOE OSTI2023

The Ontology of Biological Attributes (OBA)—computational traits for the life sciences

Abstract Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Software-Hardware Co-design of Heterogeneous SmartNIC System for Recommendation Models Inference and Training

Deep Learning Recommendation Models (DLRMs) are critical applications in various domains and have evolved as one of the single largest machine learning applications. Trillions of DLRM parameters exceed the on-chip memory capacity of GPUs. Large-scale multi-node systems are required for distributed DLRM inference and training, which suffer from the all-to-all communication bottleneck, mainly limiting the scalability of ever-growing DLRMs. In recent years, SmartNICs have evolved with coupled computation and communication capabilities providing opportunities for a powerful heterogeneous device in the system. However, there isn't such a distributed system that fully leverages the abundant smartNIC resources that resolve the scalability issue of DLRMs. In this work, we proposed a software-hardware co-design of a heterogeneous smartNIC system that resolves the communication bottleneck of distributed DLRMs, mitigates the memory bandwidth pressure, and improves computation efficiency. We provide a set of smartNIC designs of cache systems (including local cache and remote cache) and smartNIC computation kernels which reduce data movement, relieve memory lookup intensity, and improve the GPU's computation efficiency. In addition, we propose a graph algorithm that improves the data locality of queries within batches which optimizes the overall system performance with higher data reuse. Our evaluation shows that our system achieves 2.1x latency speedup for inference and 1.6x throughput speedup for training.

Guo, Anqi↗
DOE OSTI2022

A Step in Understanding the Hubble Tension

As cosmological data have improved, tensions have arisen. One such tension is the difference between the locally measured Hubble constant H 0 and the value inferred from the cosmic microwave background (CMB). Interacting radiation has been suggested as a solution, but studies show that conventional models are precluded by high-ℓ CMB polarization data. It seems at least plausible that a solution may be provided by related models that distinguish between high- and low-ℓ multipoles. When interactions of strongly-coupled radiation are mediated by a force-carrier that becomes non-relativistic, the dark radiation undergoes a "step" in which its relative energy density increases as the mediator deposits its entropy into the lighter species. If this transition occurs while CMB-observable modes are inside the horizon, high- and low-ℓ peaks are impacted differently, corresponding to modes that enter the horizon before or after the step. Here, these dynamics are naturally packaged into the simplest supersymmetric theory, the Wess-Zumino model, with the mass of the scalar mediator near the eV-scale. We investigate the cosmological signatures of such "Wess-Zumino Dark Radiation" (WZDR) and find that it provides an improved fit to the CMB alone, favoring larger values of H 0 . If supernovae measurements from the SH0ES collaboration are also included in the analysis, the inferred value of H 0 is yet larger, but the preference for dark radiation and the location of the transition is left nearly unchanged. Utilizing a standardized set of measures, we compare to other models and find that WZDR is among the most successful at addressing the H 0 tension and the best of those with a Lagrangian formulation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Forecasting Dark Matter Subhalo Constraints from Stellar Streams using Implicit Likelihood Inference

The evidence for dark matter (DM) remains compelling, although attempts to understand its particle nature remain inconclusive. One promising method to study DM is detecting DM subhalos through their gravitational interactions with stellar streams. In this study, we apply Neural Posterior Estimation (NPE) to constrain subhalo interaction parameters, including mass, scale radius, velocity, and encounter geometry, from stellar stream kinematics. We generate particle spray simulations based on the Lagrange Cloud stripping technique, focusing on the ATLAS-Aliqa Uma stream as a test case. We train multiple NPE models across multiple observational scenarios, quantifying how kinematic completeness affects inference and forecasting constraints from upcoming surveys including LSST, 4MOST, and 10-year Gaia data. Our results demonstrate that NPE can produce accurate and well-calibrated posteriors. In the idealized case with full 6D coordinates, we achieve subhalo mass uncertainties of 15-20% for a $10^7 \, \mathrm{M_\odot}$ subhalo, with 5D coordinates (excluding radial velocities) achieving similar performance. Under realistic observational conditions, mass uncertainties range from 50% (present-day) to 20-40% (future scenarios), with comparable performance between the photometric-only LSST sample and a smaller sample that includes Gaia proper motions and 4MOST radial velocities. Most notably, we find that velocity bimodality emerges when phase space is poorly sampled, whether due to missing kinematic information or limited stellar tracers. Combining large photometric samples with targeted spectroscopic follow-up can effectively resolves this degeneracy. These results demonstrate the power of implicit likelihood inference for optimizing stellar stream observational strategies and forecasting DM subhalo constraints from upcoming surveys.

Nguyen, Tri [Northwestern U. (main); SkAI, Chicago↗
DOE OSTI2020

A Measurement of the CMB E-mode Angular Power Spectrum at Subdegree Scales from 670 Square Degrees of POLARBEAR Data

In this work, we report a measurement of the E-mode polarization power spectrum of the cosmic microwave background (CMB) using 150 GHz data taken from 2014 July to 2016 December with the POLARBEAR experiment. We reach an effective polarization map noise level of 32 μK-arcmin across an observation area of 670 square degrees. We measure the EE power spectrum over the angular multipole range 500 ≤ ℓ < 3000, tracing the third to seventh acoustic peaks with high sensitivity. The statistical uncertainty on E-mode bandpowers is ~2.3 μK 2 at ℓ ~ 1000, with a systematic uncertainty of 0.5 mK 2 . Furthermore, the data are consistent with the standard ΛCDM cosmological model with a probability-to-exceed of 0.38. We combine recent CMB E-mode measurements and make inferences about cosmological parameters in ΛCDM as well as in extensions to ΛCDM. Adding the ground-based CMB polarization measurements to the Planck data set reduces the uncertainty on the Hubble constant by a factor of 1.2 to H0 = 67.20 ±0.57 km s -1 Mpc -1 . When allowing the number of relativistic species (Neff ) to vary, we find N eff = 2.94 ±0.16, which is in good agreement with the standard value of 3.046. Instead allowing the primordial helium abundance (Y He ) to vary, the data favor Y He = 0.248 ±0.012. This is very close to the expectation of 0.2467 from big bang nucleosynthesis. When varying both Y He and N eff , we find N eff = 2.70 ±0.26 and Y He = 0.262 ±0.015.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Robust Importance Sampling for Bayesian Model Calibration with Spatio-Temporal Data

This paper addresses two challenges in Bayesian calibration: 1) computational speed of existing sampling algorithms, and 2) calibration with spatio-temporal responses. The commonly used Markov Chain Monte Carlo (MCMC) approaches require many sequential model evaluations making the computational expense prohibitive. This paper proposes an efficient sampling algorithm: iterative importance sampling with genetic algorithm (IISGA). While iterative importance sampling enables computational efficiency, the genetic algorithm enables robustness by preventing sample degeneration and avoids getting stuck in multimodal search spaces. An inflated likelihood further enables robustness in high-dimensional parameter spaces by enlarging the target distribution. Spatio-temporal data complicate both surrogate modeling, which is necessary for expensive computational models, and the likelihood estimation. In this work, singular value decomposition is investigated for reducing the high-dimensional field data to a lower-dimensional space prior to Bayesian calibration. Then the likelihood is formulated and Bayesian inference is performed in the lower-dimension, latent space. An illustrative example is provided to demonstrate IISGA relative to existing sampling methods, and then IISGA is employed to calibrate a thermal battery model with 26 uncertain calibration parameters and spatio-temporal response data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Measurement of the time-integrated 𝐶⁢𝑃 asymmetry in 𝐷 0 → 𝐾$^{0}_{S}$𝐾$^{0}_{S}$ decays using opposite-side flavor tagging at Belle and Belle II

We measure the time-integrated 𝐶⁢𝑃 asymmetry in 𝐷 0 → 𝐾$^{0}_{S}$𝐾$^{0}_{S}$ decays reconstructed in 𝑒 + ⁢𝑒 − → $c\bar{c}$ events collected by the Belle and Belle II experiments. The corresponding data samples have integrated luminosities of 980 and 428 fb −1 , respectively. To infer the flavor of the 𝐷 0 meson, we exploit the correlation between the flavor of the reconstructed decay and the electric charges of particles reconstructed in the rest of the 𝑒 + ⁢𝑒 − → $c\bar{c}$ event. This results in a sample which is independent from any other previously used at Belle or Belle II. The result, 𝐴 𝐶⁢𝑃 ⁡(𝐷 0 → 𝐾$^{0}_{S}$𝐾$^{0}_{S}$)=(1.3±2.0±0.2)%, where the first uncertainty is statistical and the second systematic, is consistent with previous determinations and with 𝐶⁢𝑃 symmetry.

CP violation↗
DOE OSTI2025

Characterization of DESI fiber assignment incompleteness effect on 2-point clustering and mitigation methods for DR1 analysis

We present an in-depth analysis of the fiber assignment incompleteness in the Dark Energy Spectroscopic Instrument (DESI) Data Release 1 (DR1). This incompleteness is caused by the restricted mobility of the robotic fiber positioner in the DESI focal plane, which limits the number of galaxies that can be observed at the same time, especially at small angular separations. As a result, the observed clustering amplitude is suppressed in a scale-dependent manner, which, if not addressed, can severely impact the inference of cosmological parameters. We discuss the methods adopted for simulating fiber assignment on mocks and data. In particular, we introduce the fast fiber assignment (FFA) emulator, which was employed to obtain the power spectrum covariance adopted for the DR1 full-shape analysis. We present the mitigation techniques, organised in two classes: measurement stage and model stage. We then use high fidelity mocks as a reference to quantify both the accuracy of the FFA emulator and the effectiveness of the different measurement-stage mitigation techniques. This complements the studies conducted in a parallel paper for the model-stage techniques, namely the θ-cut approach. We find that pairwise inverse probability (PIP) weights with angular upweighting recover the “true” clustering in all the cases considered, in both Fourier and configuration space. Notably, we present the first ever power spectrum measurement with PIP weights from real data.

cosmological simulations↗
DOE OSTI2021

Hierarchical Inference with Bayesian Neural Networks: An Application to Strong Gravitational Lensing

In the past few years, approximate Bayesian Neural Networks (BNNs) have demonstrated the ability to produce statistically consistent posteriors on a wide range of inference problems at unprecedented speed and scale. However, any disconnect between training sets and the distribution of real-world objects can introduce bias when BNNs are applied to data. This is a common challenge in astrophysics and cosmology, where the unknown distribution of objects in our universe is often the science goal. In this work, we incorporate BNNs with flexible posterior parameterizations into a hierarchical inference framework that allows for the reconstruction of population hyperparameters and removes the bias introduced by the training distribution. We focus on the challenge of producing posterior PDFs for strong gravitational lens mass model parameters given Hubble Space Telescope–quality single-filter, lens-subtracted, synthetic imaging data. We show that the posterior PDFs are sufficiently accurate (statistically consistent with the truth) across a wide variety of power-law elliptical lens mass distributions. We then apply our approach to test data sets whose lens parameters are drawn from distributions that are drastically different from the training set. We show that our hierarchical inference framework mitigates the bias introduced by an unrepresentative training set's interim prior. Simultaneously, we can precisely reconstruct the population hyperparameters governing our test distributions. Our full pipeline, from training to hierarchical inference on thousands of lenses, can be run in a day. The framework presented here will allow us to efficiently exploit the full constraining power of future ground- and space-based surveys (https://github.com/swagnercarena/ovejero).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Real-Time event reconstruction for Nuclear Physics Experiments using Artificial Intelligence

Charged track reconstruction is a critical task in nuclear physics experiments, enabling the identification and analysis of particles produced in high-energy collisions. Machine learning (ML) has emerged as a powerful tool for this purpose, addressing the challenges posed by complex detector geometries, high event multiplicities, and noisy data. Traditional methods rely on pattern recognition algorithms like the Kalman filter, but ML techniques, such as neural networks, graph neural networks (GNNs), and recurrent neural networks (RNNs), offer improved accuracy and scalability. By learning from simulated and real detector data, ML models can identify and classify tracks, predict trajectories, and handle ambiguities caused by overlapping or missing hits. Moreover, ML-based approaches can process data in near-real-time, enhancing the efficiency of experiments at large-scale facilities like the Large Hadron Collider (LHC) and Jefferson Lab (JLAB). As detector technologies and computational resources evolve, ML-driven charged track reconstruction continues to push the boundaries of precision and discovery in nuclear physics. In these proceedings, we highlight advancements in charged track identification leveraging Artificial Intelligence within the CLAS12 detector, achieving a notable enhancement in experimental statistics compared to traditional methods. Additionally, we showcase real-time event reconstruction capabilities, including the inference of charged particle properties, such as momentum, direction, and species identification, at speeds matching data acquisition rates. These innovations enable the extraction of physics observables directly from the experiment in real-time.

Gavalian, Gagik (ORCID:0000000267385457)↗