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At least 433 records · Page 24

Simulation driven adaptive sampling for neutron-diffraction based strain mapping of additively manufactured parts

Neutron diffraction based strain mapping is a useful technique for measuring residual strains in additively manufactured (AM) metal parts. The measurement is traditionally done by scanning the sample in a point-wise raster pattern to extract the strain at each position. Since the overall scan can span several hours, adaptive sampling approaches using Bayesian optimization based on Gaussian process (BO-GP) regression have been introduced—demonstrating that even with a fraction of the typically made measurements the dominant strain patterns in the sample can be reconstructed. However, the parameters of the BO-GP algorithm have to be carefully chosen for best performance, and the movement time between arbitrary points can offset the time savings from a reduced number of measurement locations. In this paper, we propose algorithms to refine the BO-GP based methods by using simulations of strain patterns in AM parts based on the materials and the process used to print them. We demonstrate that the simulated strain patterns can be used to help choose better parameters for the BO-GP based framework—leading to low reconstruction error for the final strain pattern. Furthermore, we show that the strain mapping experiment can be initialized with a sampling pattern learnt from the simulation data and ordered to reduce movement time, dramatically enabling reduction in the overall time required to run the baseline BO-GP method.

Gaussian process regression↗

Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning

Motivation: Graph representation learning is a family of related approaches that learn low-dimensional vector representations of nodes and other graph elements called embeddings. Embeddings approximate characteristics of the graph and can be used for a variety of machine-learning tasks such as novel edge prediction. For many biomedical applications, partial knowledge exists about positive edges that represent relationships between pairs of entities, but little to no knowledge is available about negative edges that represent the explicit lack of a relationship between two nodes. For this reason, classification procedures are forced to assume that the vast majority of unlabeled edges are negative. Existing approaches to sampling negative edges for training and evaluating classifiers do so by uniformly sampling pairs of nodes. Results: We show here that this sampling strategy typically leads to sets of positive and negative examples with imbalanced node degree distributions. Using representative heterogeneous biomedical knowledge graph and random walk-based graph machine learning, we show that this strategy substantially impacts classification performance. If users of graph machine-learning models apply the models to prioritize examples that are drawn from approximately the same distribution as the positive examples are, then performance of models as estimated in the validation phase may be artificially inflated. We present a degree-aware node sampling approach that mitigates this effect and is simple to implement. Availability and implementation: Our code and data are publicly available at https://github.com/monarch-initiative/negativeExampleSelection.

59 BASIC BIOLOGICAL SCIENCES↗

From the inner to outer Milky Way: a photometric sample of 2.6 million red clump stars

ABSTRACT Large pristine samples of red clump stars are highly sought after given that they are standard candles and give precise distances even at large distances. However, it is difficult to cleanly select red clumps stars because they can have the same Teff and log g as red giant branch stars. Recently, it was shown that the asteroseismic parameters, $\rm {\Delta }$P and $\rm {\Delta \nu }$, which are used to accurately select red clump stars, can be derived from spectra using the change in the surface carbon to nitrogen ratio ([C/N]) caused by mixing during the red giant branch. This change in [C/N] can also impact the spectral energy distribution. In this study, we predict the $\rm {\Delta }$P, $\rm {\Delta \nu }$, Teff, and log g using 2MASS, AllWISE, Gaia, and Pan-STARRS data in order to select a clean sample of red clump stars. We achieve a contamination rate of ∼20 per cent, equivalent to what is achieved when selecting from Teff and log g derived from low-resolution spectra. Finally, we present two red clump samples. One sample has a contamination rate of ∼20 per cent and ∼405 000 red clump stars. The other has a contamination of ∼33 per cent and ∼2.6 million red clump stars that includes ∼75 000 stars at distances >10 kpc. For |b| > 30 deg, we find ∼15 000 stars with contamination rate of ∼9 per cent. The scientific potential of this catalogue for studying the structure and formation history of the Galaxy is vast, given that it includes millions of precise distances to stars in the inner bulge and distant halo where astrometric distances are imprecise.

Lucey, Madeline↗

A comparative study of the physical properties for a representative sample of Narrow and Broad-line Seyfert galaxies

ABSTRACT We present a comparative study of the physical properties of a homogeneous sample of 144 Narrow line Seyfert 1 (NLSy1) and 117 Broad-line Seyfert 1 (BLSy1) galaxies. These two samples are in a similar luminosity and redshift range and have optical spectra available in the 16th data release of Sloan Digital Sky Survey (SDSS-DR16) and X-ray spectra in either XMM-NEWTON or ROSAT. Direct correlation analysis and a principal component analysis (PCA) have been performed using ten observational and physical parameters obtained by fitting the optical spectra and the soft X-ray photon indices as another parameter. We confirm that the established correlations for the general quasar population hold for both types of galaxies in this sample despite significant differences in the physical properties. We characterize the sample also using the line shape parameters, namely the asymmetry and kurtosis indices. We find that the fraction of NLSy1 galaxies showing outflow signatures, characterized by blue asymmetries, is higher by a factor of about 3 compared to the corresponding fraction in BLSy1 galaxies. The presence of high iron content in the broad-line region of NLSy1 galaxies in conjunction with higher Eddington ratios can be the possible reason behind this phenomenon. We also explore the possibility of using asymmetry in the emission lines as a tracer of outflows in the inner regions of Active Galactic Nuclei. The PCA results point to the NLSy1 and BLSy1 galaxies occupying different parameter spaces, which challenges the notion that NLSy1 galaxies are a subclass of BLSy1 galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

SDSS-IV MaNGA: The incidence of major mergers in type I and II AGN host galaxies in the DR15 sample

We present a study on the incidence of major mergers and their impact on the triggering of nuclear activity in 47 type I and 236 type II optically selected AGN from the MaNGA DR15 sample. From an estimate of non-parametric image predictors (Gini, M_20, concentration (C), asymmetry (A), clumpiness (S), Sérsic index (n), and shape asymmetry ()) using the SDSS images, in combination with a Linear Discriminant Analysis Method, we identified major mergers and merger stages. We reinforced our results by looking for bright tidal features in our post-processed SDSS and DESI legacy images. We find a statistically significant higher incidence of major mergers of 29 per cent ± 3 per cent in our type I+II AGN sample compared to 22 per cent ± 0.8 per cent for a non-AGN sample matched in redshift, stellar mass, colour, and morphological type, finding also a prevalence of post-coalescence (51 per cent ± 5 per cent) over pre-coalescence (23 per cent ± 6 per cent) merger stages. The levels of AGN activity among our massive major mergers are similar to those reported in other works using [O iii] tracers. However, similar levels are produced by our AGN-galaxies hosting stellar bars, suggesting that major mergers are important promoters of nuclear activity but are not the main nor the only mechanism behind the AGN triggering. The tidal strength parameter Q was considered at various scales looking for environmental differences that could affect our results on the merger incidence, finding non-significant differences. Finally, the H-H β diagram could be used as an empirical predictor for the flux coming from an AGN source, useful to correct photometric quantities in large AGN samples emerging from surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

H i -rich but low star formation galaxies in MaNGA: physical properties and comparison to control samples

ABSTRACT Gas-rich galaxies are typically star forming. We make use of H i-MaNGA, a programme of H i follow-up for the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey of the Sloan Digital Sky Surveys, to construct a sample of unusual neutral hydrogen (H i, 21 cm)-rich galaxies that have low star formation rates (SFRs), using infrared colour from the Wide-field Infrared Survey Explorer as a proxy for specific SFR. Out of a set of 1575 MaNGA galaxies with H i-MaNGA detections, we find that 83 (5 per cent) meet our selection criteria to be H i rich with low SFR. We construct two stellar mass-matched control samples: H i-rich galaxies with typical SFR (high SF control) and H i-poor galaxies with low SFR (low H i control). We investigate the properties of each of these samples, comparing physical parameters such as ionization state maps, stellar and ionized gas velocity and dispersion, environment measures, metallicity, and morphology to search for the reasons why these unusual H i-rich galaxies are not forming stars. We find evidence for recent external accretion of gas in some galaxies (via high counter-rotating fractions), along with some evidence for active galactic nucleus (AGN) feedback (from a high central low-ionization emission-line region and/or red geyser fraction), and bar quenching (via an enhanced strong bar fraction). Some galaxies in the sample are consistent with simply having their H i in a high angular momentum, large-radius, low-density disc. We conclude that no single physical process can explain all H i-rich, low-SFR galaxies.

Astronomy & Astrophysics↗

The spectra of IceCube Neutrino (SIN) candidate sources – III. Optical spectroscopy and source characterization of the full sample

A correlation between astrophysical high-energy neutrinos and blazars has been suggested by various authors. In particular, a likely association between IceCube events and intermediate- and high-energy peaked BL Lac objects has led to a sample of 47 objects having a high probability of being neutrino sources. In the first paper of this series we reported optical spectroscopy of 17 objects, which together with data taken from the literature covered 80 per cent of the sample. Here, we present spectroscopy obtained at large aperture telescopes of a further 17 objects (plus four additional targets), which completes the sample coverage. For 12 objects we are able to determine the redshift (0.07 < z < 1.6), while for the others we set a lower limit on it, based on either the robust detection of intervening absorption systems or on an estimation derived from the absence of spectral signatures of the host galaxy. With these new data we expand and reinforce the main results of our previous papers, namely the fact that in terms of their broad-band properties our sources appear to be indistinguishable from the rest of the blazar population and the relatively large (>34 per cent and possibly as high as 80 per cent) fraction of masquerading BL Lac objects, for which the low equivalent width of the emission lines is due to the brightness of the boosted continuum, rather than being an intrinsic property, in our sample.

79 ASTRONOMY AND ASTROPHYSICS↗

Generating mock galaxy catalogues for flux-limited samples like the DESI Bright Galaxy Survey

ABSTRACT Accurate mock galaxy catalogues are crucial to validate analysis pipelines used to constrain dark energy models. We present a fast HOD-fitting method which we apply to the AbacusSummit simulations to create a set of mock catalogues for the DESI Bright Galaxy Survey, which contain r-band magnitudes and $(g-r)$ colours. The halo tabulation method fits HODs for different absolute magnitude threshold samples simultaneously, preventing unphysical HOD crossing between samples. We validate the HOD fitting procedure by fitting to real-space clustering measurements and galaxy number densities from the MXXL BGS mock, which was tuned to the SDSS and GAMA surveys. The best-fitting clustering measurements and number densities are mostly within the assumed errors, but the clustering for the faint samples is low on large scales. The best-fitting HOD parameters are robust when fitting to simulations with different realizations of the initial conditions. When varying the cosmology, trends are seen as a function of each cosmological parameter. We use the best-fitting HOD parameters to create cubic box and cut sky mocks from the AbacusSummit simulations, in a range of cosmologies. As an illustration, we compare the ${}^{0.1}M_r\lt -20$ sample of galaxies in the mock with BGS measurements from the DESI one-percent survey. We find good agreement in the number densities, and the projected correlation function is reasonable, with differences that can be improved in the future by fitting directly to BGS clustering measurements. The cubic box and cut-sky mocks in different cosmologies are made publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗

Improving statistical precision in Monte Carlo samples with negative weights via reweighting and uncertainty quantification

High statistical precision is critical for Monte Carlo (MC) samples in high energy physics and is degraded by negatively weighted events. This paper investigates a procedure to learn the relationship between the negative and positive weight distributions of any sample, allowing the reduction of statistical uncertainty by reweighting kinematically equivalent events with the same sign. A robust uncertainty quantification method is required for the practical application of such method. Two methods for the estimation of the reweighting uncertainty are developed: one at the event and another one at the final observable level. The latter method is strongly favored. The gains in statistical precision are then quantified. The method is demonstrated on Sherpa vector boson plus jets samples when using all generated events and when restricted to the signal region of a mock analysis. It is demonstrated to significantly reduce stochastic behavior in sparse MC samples while decreasing the overall uncertainty with a sufficiently well-known reweighting function.

Monte Carlo methods↗

Importance of nonuniform Brillouin zone sampling for ab initio Bethe-Salpeter equation calculations of exciton binding energies in crystalline solids

Excitons are prevalent in semiconductors and insulators, and their binding energies are critical for optoelectronic applications. The state-of-the-art method for first-principles calculations of excitons in extended systems is the ab initio GW-Bethe-Salpeter equation (BSE) approach, which can require a fine sampling of reciprocal space to accurately resolve solid-state exciton properties. Here, in this study, we show, for a range of semiconductors and insulators, that the commonly employed approach of uniformly sampling the Brillouin zone can lead to underconverged exciton binding energies, as impractical grid sizes are required to achieve adequate convergence. We further show that nonuniform sampling of the Brillouin zone, focused on the region of reciprocal space where the exciton wave function resides, enables efficient rapid numerical convergence of exciton binding energies at a given level of theory. We propose a well-defined convergence procedure, which can be carried out at relatively low computational cost and which in some cases leads to a correction of previous best theoretical estimates by almost a factor of 2, qualitatively changing the predicted exciton physics. These results call for the adoption of nonuniform sampling methods for ab initio GW-BSE calculations and for revisiting previously computed values for exciton binding energies of many systems.

36 MATERIALS SCIENCE↗

A fully contained sample holder capable of electron-yield detection at soft X-ray energies

A holder has been developed that enables electron yield-detected soft X-ray spectroscopy of fully contained samples at low temperature. Crucially, this design uses elements of the sample containment to collect ejected electrons, removing the need to expose samples directly to the vacuum environment of the spectrometer. The design is modular and should be adaptable to a number of different endstation configurations, enabling spectroscopy of air-sensitive, radioactive and vacuum-sensitive (biological) samples.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Sampling on NISQ Devices: "Who’s the Fairest One of All?"

Modern NISQ devices are subject to a variety of biases and sources of noise that degrade the solution quality of computations carried out on these devices. A natural question that arises in the NISQ era, is how fairly do these devices sample ground state solutions. To this end, we run five fair sampling problems (each with at least three ground state solutions) that are based both on quantum annealing and, on the Grover Mixer, -QAOA algorithm for gate-based NISQ hardware. In particular, we use seven IBM Q devices, the Aspen-9 Rigetti device, the IonQ device, and three D-Wave quantum annealers. For each of the fair sampling problems, we measure the ground state probability, the relative fairness of the frequency of each ground state solution with respect to the other ground state solutions, and the aggregate error as given by each hardware provider. Overall, our results show that NISQ devices do not achieve fair sampling yet. Furthermore, we also observe differences in the software stack with a particular focus on compilation techniques that illustrate what work will still need to be done to achieve a seamless integration of frontend (i.e., quantum circuit description) and backend compilation.

Computer Science↗

Sampling in Long-Screened Wells: Issues, Misconceptions, and Solutions

The issues associated with long-screened wells (LSWs) (and open boreholes) at contaminated sites are well documented in the groundwater literature but are still not fully appreciated in practice. As established in seminal and review papers going back over three decades, the interpretation of sampling results from LSWs is challenging in the presence of vertical hydraulic gradients and borehole flow; furthermore, LSWs allow for vertical redistribution of contamination between aquifer layers. Acknowledgment of these issues has led to the development of new technologies and well designs to enable discrete-zone monitoring (DZM), yet LSWs remain common for many reasons, for example, as multipurpose wells, for geophysical logging, and (or) as legacy installations. Despite the literature on LSWs and despite the adoption of DZM at many sites, the use of LSWs persists and the challenges of interpreting sampling results from LSWs remain. In this issue paper, we provide a conceptual overview of the problems posed by LSWs and review existing literature and past work to improve the interpretation of sampling in LSWs. We draw on experience from previous studies at the Hanford Site in eastern WA, USA, and use synthetic examples to illustrate key concepts and challenges for interpretation. A recently published analytical modeling framework is used to develop illustrative synthetic examples and demonstrate a workflow for building scientific intuition to understand issues around interpreting samples from LSWs, which is critical to effective characterization and groundwater remediation at sites with LSWs.

54 ENVIRONMENTAL SCIENCES↗

The iron oxidation state of Ryugu samples

The Hayabusa2 mission sampled Ryugu, an asteroid that did not suffer extensive thermal metamorphism, and returned rocks to the Earth with no significant air exposure. It therefore offers a unique opportunity to study the redox state of carbonaceous Cb-type asteroids and evaluate the overall redox state of the most primitive rocks of the solar system. An analytical framework was developed to investigate the iron mineralogy and valence state in extraterrestrial material at the micron scale by combining x-ray diffraction, conventional Mössbauer (MS), and nuclear forward scattering (NFS) spectroscopies. An array of standard minerals was analyzed and cross-calibrated between MS and NFS. Then, MS and NFS spectra on three Ryugu grains were collected at the bulk and the micron scales. In Ryugu samples, iron is essentially accommodated in magnetite, clay minerals (serpentine–smectite), and sulfides. Only a single set of Mössbauer parameters was necessary to account for the entire variability observed in MS and NFS spectra, at all spatial scales investigated. These parameters therefore make up a fully consistent iron mineralogical model for the Ryugu samples. As far as MS and NFS spectroscopies are concerned, Ryugu grains are overall similar to each other and share most of their mineralogical features with CI-type chondrites. In detail however, no ferrihydrite is found in Ryugu particles even at the very sensitive scale of Mössbauer spectroscopy. The typical Fe 3+ /Fe tot of clay minerals is much lower than typical redox ratios measured in CI chondrites (Fe 3+ /Fe tot = 85%–90%). Furthermore, magnetite from Ryugu is stoichiometric with no significant maghemite component, whereas up to 12% of maghemite was previously identified in the Orgueil's so-called magnetite. These differences suggest that most CI meteorites suffered terrestrial alteration and that the preterrestrial composition of these carbon-rich samples was less oxidized than previously measured. However, it is not clear yet whether or not the parent bodies of CI chondrites were as reduced as Ryugu. Finally, the high spatial resolution of NFS allows to disentangle the redox state and the crystal chemistry of iron accommodated in serpentine and smectite. The most likely polytype of serpentine is lizardite, containing <35% of Fe 3+ , a fraction of which being tetrahedrally coordinated. Smectite is more oxidized (Fe 3+ /Fe tot > 65%) and mainly contains octahedral ferric iron. In conclusion, this finding implies that these clays formed from highly alkaline fluids and the spatial variability highlighted here may suggest a temporal evolution or a spatial variability of the nature of this fluid.

58 GEOSCIENCES↗

Efficient sampling of constrained high-dimensional theoretical spaces with machine learning

Abstract Models of physics beyond the Standard Model often contain a large number of parameters. These form a high-dimensional space that is computationally intractable to fully explore. Experimental results project onto a subspace of parameters that are consistent with those observations, but mapping these constraints to the underlying parameters is also typically intractable. Instead, physicists often resort to scanning small subsets of the full parameter space and testing for experimental consistency. We propose an alternative approach that uses generative models to significantly improve the computational efficiency of sampling high-dimensional parameter spaces. To demonstrate this, we sample the constrained and phenomenological Minimal Supersymmetric Standard Models subject to the requirement that the sampled points are consistent with the measured Higgs boson mass. Our method achieves orders of magnitude improvements in sampling efficiency compared to a brute force search.

Hollingsworth, Jacob↗

Standard experimental paradigm designs and data exclusion practices in cognitive psychology can inadvertently introduce systematic “shadow” biases in participant samples

Abstract Standard cognitive psychology research practices can introduce inadvertent sampling biases that reduce the reliability and generalizability of the findings. Researchers commonly acknowledge and understand that any given study sample is not perfectly generalizable, especially when implementing typical experimental constraints (e.g., limiting recruitment to specific age ranges or to individuals with normal color vision). However, less obvious systematic sampling constraints, referred to here as “shadow” biases, can be unintentionally introduced and can easily go unnoticed. For example, many standard cognitive psychology study designs involve lengthy and tedious experiments with simple, repetitive stimuli. Such testing environments may 1) be aversive to some would-be participants (e.g., those high in certain neurodivergent symptoms) who may self-select not to enroll in such studies, or 2) contribute to participant attrition, both of which reduce the sample’s representativeness. Likewise, standard performance-based data exclusion efforts (e.g., minimum accuracy or response time) or attention checks can systematically remove data from participants from subsets of the population (e.g., those low in conscientiousness). This commentary focuses on the theoretical and practical issues behind these non-obvious and often unacknowledged “shadow” biases, offers a simple illustration with real data as a proof of concept of how applying attention checks can systematically skew latent/hidden variables in the included population, and then discusses the broader implications with suggestions for how to manage and reduce, or at a minimum acknowledge, the problem.

Siritzky, Emma M.↗

Untargeted, tandem mass spectrometry (LC/MS-MS) metaproteomes from soil samples in control and warming plots in Blodgett Forest, CA (2014-2021)

The pathways of carbon transport and loss through and from soils—soil organic matter (SOM) depolymerization to dissolved organic carbon and mineralization to carbon dioxide (CO2)—are fundamentally driven by microbial activity, which is strongly regulated by environmental conditions. As part of Lawrence Berkeley National Laboratory (LBNL) Terrestrial Ecosystem Science (TES) Belowground Biogeochemistry Science Focus Area (SFA), we have established a novel whole-soil long-term warming experiment at the University of California (UC) Blodgett Forest Research Station (Sierra Nevada) in 2014, where we study the role of biogeochemical, microbial and geochemical process interactions in SOM decomposition and stabilization. This package contains soil metaproteomics data in the context of site specific metagenomes from soil depth profiles in three paired control and warming plots from a temperate mixed forest in Northern California. Each paired plot had been subjected to experimental warming since June 2014 to simulate a predicted climate change scenario for northern California. These metaproteomes were collected in 2018 after 4.5 years of warming from five depth intervals (0-10 cm, 10-30 cm, 30-45 cm, 45-60 cm, 60-80 cm). For protein identification, the collected spectra were searched following a target-decoy search strategy against a database of metagenome predicted proteins (covering 96 samples from 2014 to 2021) representing the complete sequence diversity at the site. Data was searched with mass spectrometry database search tool (MS-GF+) using Pacific Northwest National Laboratory (PNNL)'s Data Management System (DMS) Processing pipeline. The metagenomes are published as part of another data package. Raw metaproteomic data and the data products from MS-GF+ are deposited in the Mass Spectrometry Interactive Virtual Environment (MassIVE) database under accession no. MSV000097826. Here we present a dataset that includes spectral counts for the detected proteins across samples (EMSL50964_BrodieAllMAGs_Globals_SC.txt), the sequences of the detected proteins, and sample metadata file that contains site information for the soil metaproteome samples.

Belowground Biogeochemistry Science Focus Area↗

A Provably Accurate Randomized Sampling Algorithm for Logistic Regression

In statistics and machine learning, logistic regression is a widely-used supervised learning technique primarily employed for binary classification tasks. When the number of observations greatly exceeds the number of predictor variables, we present a simple, randomized sampling-based algorithm for logistic regression problem that guarantees high-quality approximations to both the estimated probabilities and the overall discrepancy of the model. Our analysis builds upon two simple structural conditions that boil down to randomized matrix multiplication, a fundamental and well-understood primitive of randomized numerical linear algebra. We analyze the properties of estimated probabilities of logistic regression when leverage scores are used to sample observations, and prove that accurate approximations can be achieved with a sample whose size is much smaller than the total number of observations. To further validate our theoretical findings, we conduct comprehensive empirical evaluations. Overall, our work sheds light on the potential of using randomized sampling approaches to efficiently approximate the estimated probabilities in logistic regression, offering a practical and computationally efficient solution for large-scale datasets.

Chowdhury, Agniva↗