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At least 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Vectorization techniques for probability distribution functions using VecCore

Probability distribution functions (PDFs) are very used in modeling random processes and physics simulations. Improving the performance of algorithms that generate many random numbers under complex PDFs is often a very challenging task when methods as direct functions are not available. In this work we present general strategies on how to vectorize some PDFs using VecCore library. We show the results for the Exponential, Gaussian, discrete Poisson and Gamma probability distributions.

Chaparro Amaro, Oscar R.↗
DOE OSTI2020

How accurate is a machine learning-based wind speed extrapolation under a round-robin approach?

As the size of commercial wind turbines keeps increasing, having accurate ways to vertically extrapolate wind speed is essential to obtain a precise characterization of the wind resource for wind energy production. Recently, machine learning has been proposed and applied to extrapolate wind speed to hub heights. However, previous studies trained and tested the machine learning methods at the same site, giving them an unfair advantage over the conventional extrapolation techniques, which are instead more universal. Here, we use data from four sites in Oklahoma to test a round-robin validation approach for machine learning, under which we train a random forest at a site, and test it at a different site, where the model has no prior knowledge of the wind resource. We quantify how the accuracy of this technique varies with distance from the training site, and we find that it outperforms conventional techniques for wind extrapolation at all the considered spatial separations. We then assess how the accuracy of the machine-learning based approach varies when it is used to predict wind speed in a wind farm far wake. Finally, we explore as case study the performance of the random forest in extrapolating winds during a low-level jet event.

17 WIND ENERGY↗
DOE OSTI2024

Learning linear optical circuits with coherent states

We analyze the energy and training data requirements for supervised learning of an M-mode linear optical circuit by minimizing an empirical risk defined solely from the action of the circuit on coherent states. When the linear optical circuit acts non-trivially only on k < M unknown modes (i.e. a linear optical k-junta), we provide an energy-efficient, adaptive algorithm that identifies the junta set and learns the circuit. We compare two schemes for allocating a total energy, E, to the learning algorithm. In the first scheme, each of the T random training coherent states has energy E/T. In the second scheme, a single random MT-mode coherent state with energy E is partitioned into T training coherent states. The latter scheme exhibits a polynomial advantage in training data size sufficient for convergence of the empirical risk to the full risk due to concentration of measure on the $(2MT-1)$-sphere. Specifically, generalization bounds for both schemes are proven, which indicate that for ε-approximation of the full risk by the empirical risk with high probability, $O(E^{2/3}M^{2/3}/\epsilon^{2/3})$ training states are sufficient for the first scheme and $O(E^{1/3}M^{1/3}/\epsilon^{2/3})$ training states are sufficient for the second scheme.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Optimal calibration of gates in trapped-ion quantum computers

Abstract To harness the power of quantum computing, it is essential that a quantum computer provide maximal possible fidelity for a quantum circuit. To this end, much work has been done in the context of qubit routing or embedding, i.e., mapping circuit qubits to physical qubits based on gate performance metrics to optimize the fidelity of execution. Here, we take an alternative approach that leverages a unique capability of a trapped-ion quantum computer, i.e., the all-to-all qubit connectivity. We develop a method to determine a fixed number (budget) of quantum gates that, when calibrated, will maximize the fidelity of a batch of input quantum programs. This dynamic allocation of calibration resources on randomly accessible gates, determined using our heuristics, increases, for a wide range of calibration budget, the average fidelity from 70% or lower to 90% or higher for a typical batch of jobs on an 11-qubit device, in which the fidelity of calibrated and uncalibrated gates are taken to be 99% and 90%, respectively. Our heuristics are scalable, more than 2.5 orders of magnitude faster than a randomized method for synthetic benchmark circuits generated based on real-world use cases.

Maksymov, Andrii (ORCID:0000000282442851)↗
DOE OSTI2024

Grover-QAOA for 3-SAT: quadratic speedup, fair-sampling, and parameter clustering

Abstract The SAT problem is a prototypical NP-complete problem of fundamental importance in computational complexity theory with many applications in science and engineering; as such, it has long served as an essential benchmark for classical and quantum algorithms. This study shows numerical evidence for a quadratic speedup of the Grover Quantum Approximate Optimization Algorithm (G-QAOA) over random sampling for finding all solutions to 3-SAT (All-SAT) and Max-SAT problems. G-QAOA is less resource-intensive and more adaptable for these problems than Grover’s algorithm, and it surpasses conventional QAOA in its ability to sample all solutions. We show these benefits by classical simulations of many-round G-QAOA on thousands of random 3-SAT instances. We also observe G-QAOA advantages on the IonQ Aria quantum computer for small instances, finding that current hardware suffices to determine and sample all solutions. Interestingly, a single-angle-pair constraint that uses the same pair of angles at each G-QAOA round greatly reduces the classical computational overhead of optimizing the G-QAOA angles while preserving its quadratic speedup. We also find parameter clustering of the angles. The single-angle-pair protocol and parameter clustering significantly reduce obstacles to classical optimization of the G-QAOA angles.

Zhang, Zewen (ORCID:000000032258613X)↗
DOE OSTI2021

Learning to Unknot

We introduce natural language processing into the study of knot theory, as made natural by the braid word representation of knots. We study the UNKNOT problem of determining whether or not a given knot is the unknot. After describing an algorithm to randomly generate N-crossing braids and their knot closures and discussing the induced prior on the distribution of knots, we apply binary classification to the UNKNOT decision problem. We find that the Reformer and shared-QK Transformer network architectures outperform fully-connected networks, though all perform at 95% accuracy. Perhaps surprisingly, we find that accuracy increases with the length of the braid word, and that the networks learn a direct correlation between the confidence of their predictions and the degree of the Jones polynomial. Finally, we utilize reinforcement learning (RL) to find sequences of Markov moves and braid relations that simplify knots and can identify unknots by explicitly giving the sequence of unknotting actions. Trust region policy optimization (TRPO) performs consistently well, reducing 80% of the unknots with up to 96 crossings we tested to the empty braid word, and thoroughly outperformed other RL algorithms and random walkers. Studying these actions, we find that braid relations are more useful in simplifying to the unknot than one of the Markov moves.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Improving Traditional Registrational Trial End Points: Development and Application of a Desirability of Outcome Ranking End Point for Complicated Urinary Tract Infection Clinical Trials

Abstract Background Traditional end points used in registrational randomized, controlled trials (RCTs) often do not allow for complete interpretation of the full range of potential clinical outcomes. Desirability of outcome ranking (DOOR) is an approach to the design and analysis of clinical trials that incorporates benefits and risks of novel treatment strategies and provides a global assessment of patient experience. Methods Through a multidisciplinary committee of experts in infectious diseases, clinical trial design, drug regulation, and patient experience, we developed a DOOR end point for infectious disease syndromes and demonstrated how this could be applied to 3 registrational drug trials (ZEUS, APEKS-cUTI, and DORI-05) for complicated urinary tract infections (cUTIs). ZEUS compared fosfomycin to piperacillin/tazobactam, APEKS-cUTI compared cefiderocol to imipenem, and DORI-05 compared doripenem to levofloxacin. Using DOOR, we estimated the probability of a more desirable outcome with each investigational antibacterial drug. Results In each RCT, the DOOR distribution was similar and the probability that a patient in the investigational arm would have a more desirable outcome than a patient in the control arm had a 95% confidence interval containing 50%, indicating no significant difference between treatment arms. DOOR facilitated improved understanding of potential trade-offs between clinical efficacy and safety. Partial credit and subgroup analyses also highlight unique attributes of DOOR. Conclusions DOOR can effectively be used in registrational cUTI trials. The DOOR end point presented here can be adapted for other infectious disease syndromes and prospectively incorporated into future clinical trials.

Immunology↗
DOE OSTI2023

Moving Beyond Mortality: Development and Application of a Desirability of Outcome Ranking (DOOR) Endpoint for Hospital-Acquired Bacterial Pneumonia and Ventilator-Associated Bacterial Pneumonia

Abstract Background Hospital-acquired and ventilator-associated bacterial pneumonia (HABP/VABP) are frequently caused by multidrug-resistant organisms. Patient-centered endpoints in clinical trials are needed to develop new antibiotics for HABP/VABP. Desirability of outcome ranking (DOOR) is a paradigm for the design, analysis, and interpretation of clinical trials based on a patient-centered, benefit-risk evaluation. Methods A multidisciplinary committee created an infectious diseases DOOR endpoint customized for HABP/VABP, incorporating infectious complications, serious adverse events, and mortality. We applied this to 2 previously completed, large randomized controlled trials for HABP/VABP. ZEPHyR compared vancomycin to linezolid and VITAL compared linezolid to tedizolid. For each trial, we evaluated the DOOR distribution and probability, including DOOR component and partial credit analyses. We also applied DOOR in subgroup analyses. Results In both trials, the HABP/VABP DOOR demonstrated similar overall clinical outcomes between treatment groups. In ZEPHyR, the probability that a participant treated with linezolid would have a more desirable outcome than a participant treated with vancomycin was 50.2% (95% confidence interval [CI], 45.1%­−55.3%). In VITAL, the probability that a participant treated with tedizolid would have a more desirable outcome than a participant treated with linezolid was 48.7% (95% CI, 44.8%–52.6%). The DOOR component analysis revealed that participants treated with tedizolid had a less desirable outcome than those treated with linezolid when considering clinical response alone. However, participants with decreased renal function had improved overall outcomes with tedizolid. Conclusions The HABP/VABP DOOR provided more granular information about clinical outcomes than is typically presented in clinical trials. HABP/VABP trials would benefit from prospectively using DOOR.

Immunology↗
DOE OSTI2021

Finding diverse ways to improve algebraic connectivity through multi-start optimization

The algebraic connectivity, also known as the Fiedler value, is a spectral measure of network connectivity that can be increased through edge addition. We present an algorithm for producing many diverse ways to add a fixed number of edges to a network to achieve a near optimal Fiedler value. Previous Fielder value optimization algorithms (i.e. the greedy algorithm) output only one solution. Obtaining a single solution is rarely good enough for real-world network redesign problems, as practical constraints (political, physical or financial) may prevent implementation. Our algorithm takes a multi-start optimization approach, adding a random initial edge and then applies a greedy heuristic to improve the Fiedler value. The random choice moves us to a new region of the search space, enabling discovery of diverse solutions. Additionally, we present a Determinantal Point Process framework for quantifying diversity. We then apply a Markov chain Monte Carlo technique to sift through the large number of output solutions and locate a smaller, more manageable collection of highly diverse solutions that can be presented to network redesign engineers. We demonstrate the effectiveness of our algorithm on real-world graphs with varied structures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

The frequency of extreme X-ray variability for radio-quiet quasars

ABSTRACT We analyse 1598 serendipitous Chandra X-ray observations of 462 radio-quiet quasars to constrain the frequency of extreme amplitude X-ray variability that is intrinsic to the quasar corona and innermost accretion flow. The quasars in this investigation are all spectroscopically confirmed, optically bright (mi ≤ 20.2), and contain no identifiable broad absorption lines in their optical/ultraviolet spectra. This sample includes quasars spanning z ≈ 0.1–4 and probes X-ray variability on time-scales of up to ≈12 rest-frame years. Variability amplitudes are computed between every epoch of observation for each quasar and are analysed as a function of time-scale and luminosity. The tail-heavy distributions of variability amplitudes at all time-scales indicate that extreme X-ray variations are driven by an additional physical mechanism and not just typical random fluctuations of the coronal emission. Similarly, extreme X-ray variations of low-luminosity quasars seem to be driven by an additional physical mechanism, whereas high-luminosity quasars seem more consistent with random fluctuations. The amplitude at which an X-ray variability event can be considered extreme is quantified for different time-scales and luminosities. Extreme X-ray variations occur more frequently at long time-scales (Δt ≳ 300 d) than at shorter time-scales and in low-luminosity quasars compared to high-luminosity quasars over a similar time-scale. A binomial analysis indicates that extreme intrinsic X-ray variations are rare, with a maximum occurrence rate of $\lt 2.4{{\ \rm per\ cent}}$ of observations. Finally, we present X-ray variability and basic optical emission-line properties of three archival quasars that have been newly discovered to exhibit extreme X-ray variability.

Timlin, III, John D.↗
DOE OSTI2020

Optimizing LSST observing strategy for weak lensing systematics

ABSTRACT The Legacy Survey of Space and Time (LSST) survey will provide unprecedented statistical power for measurements of dark energy. Consequently, controlling systematic uncertainties is becoming more important than ever. The LSST observing strategy will affect the statistical uncertainty and systematics control for many science cases; here, we focus on weak lensing (WL) systematics. The fact that the LSST observing strategy involves hundreds of visits to the same sky area provides new opportunities for systematics mitigation. We explore these opportunities by testing how different dithering strategies (pointing offsets and rotational angle of the camera in different exposures) affect additive WL shear systematics on a baseline operational simulation, using the ρ-statistics formalism. Some dithering strategies improve systematics control at the end of the survey by a factor of up to ∼3–4 better than others. We find that a random translational dithering strategy, applied with random rotational dithering at every filter change, is the most effective of those strategies tested in this work at averaging down systematics. Adopting this dithering algorithm, we explore the effect of varying the area of the survey footprint, exposure time, number of exposures in a visit, and exposure to the Galactic plane. We find that any change that increases the average number of exposures (in filters relevant to WL) reduces the additive shear systematics. Some ways to achieve this increase may not be favorable for the WL statistical constraining power or for other probes, and we explore the relative trade-offs between these options given constraints on the overall survey parameters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Optimizing automatic morphological classification of galaxies with machine learning and deep learning using Dark Energy Survey imaging

There are several supervised machine learning methods used for the application of automated morphological classification of galaxies; however, there has not yet been a clear comparison of these different methods using imaging data, or an investigation for maximizing their effectiveness. We carry out a comparison between several common machine learning methods for galaxy classification [Convolutional Neural Network (CNN), K-nearest neighbour, logistic regression, Support Vector Machine, Random Forest, and Neural Networks] by using Dark Energy Survey (DES) data combined with visual classifications from the Galaxy Zoo 1 project (GZ1). Our goal is to determine the optimal machine learning methods when using imaging data for galaxy classification. We show that CNN is the most successful method of these ten methods in our study. Using a sample of ~2800 galaxies with visual classification from GZ1, we reach an accuracy of ~0.99 for the morphological classification of ellipticals and spirals. The further investigation of the galaxies that have a different ML and visual classification but with high predicted probabilities in our CNN usually reveals the incorrect classification provided by GZ1. We further find the galaxies having a low probability of being either spirals or ellipticals are visually lenticulars (S0), demonstrating that supervised learning is able to rediscover that this class of galaxy is distinct from both ellipticals and spirals. We confirm that ~2.5 percent galaxies are misclassified by GZ1 in our study. After correcting these galaxies’ labels, we improve our CNN performance to an average accuracy of over 0.99 (accuracy of 0.994 is our best result).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Photometric cross-calibration of the SDSS Stripe 82 Standard Stars catalogue with Gaia EDR3, and comparison with Pan-STARRS1, DES, CFIS, and GALEX catalogues

ABSTRACT We extend the SDSS Stripe 82 Standard Stars catalogue with post-2007 SDSS imaging data. This improved version lists averaged SDSS ugriz photometry for nearly a million stars brighter than r ∼ 22 mag. With 2–3 times more measurements per star, random errors are 1.4–1.7 times smaller than in the original catalogue, and about three times smaller than for individual SDSS runs. Random errors in the new catalogue are $\lesssim$0.01 mag for stars brighter than 20.0, 21.0, 21.0, 20.5, and 19.0 mag in u, g, r, i, and z-bands, respectively. We achieve this error threshold by using the Gaia Early Data Release 3 (EDR3) Gmag photometry to derive grey photometric zeropoint corrections, as functions of RA and Declination, for the SDSS catalogue, and use the Gaia BP–RP colour to derive corrections in the ugiz bands, relative to the r-band. The quality of the recalibrated photometry, tested against Pan-STARRS1, DES, CFIS, and GALEX surveys, indicates spatial variations of photometric zeropoints ≦ 0.01 mag (rms), with typical values of 3–7 millimag in the RA, and 1–2 millimag in the Declination directions, except for $\lesssim$6 millimag scatter in the u-band. We also report a few minor photometric problems with other surveys considered here, including a magnitude-dependent ∼0.01 mag bias between 16 ≤ GGaia ≤ 20 in the Gaia EDR3. Our new, publicly available catalogue offers robust calibration of ugriz photometry below 1 per cent level, and will be helpful during the commissioning of the Vera C. Rubin Observatory Legacy Survey of Space and Time.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

On the discovery of stars, quasars, and galaxies in the Southern Hemisphere with S-PLUS DR2

ABSTRACT This paper provides a catalogue of stars, quasars, and galaxies for the Southern Photometric Local Universe Survey Data Release 2 (S-PLUS DR2) in the Stripe 82 region. We show that a 12-band filter system (5 Sloan-like and 7 narrow bands) allows better performance for object classification than the usual analysis based solely on broad bands (regardless of infrared information). Moreover, we show that our classification is robust against missing values. Using spectroscopically confirmed sources retrieved from the Sloan Digital Sky Survey DR16 and DR14Q, we train a random forest classifier with the 12 S-PLUS magnitudes + 4 morphological features. A second random forest classifier is trained with the addition of the W1 (3.4 $\mu\mathrm{m} $) and W2 (4.6 $\mu\mathrm{m} $) magnitudes from the Wide-field Infrared Survey Explorer (WISE). Forty-four per cent of our catalogue have WISE counterparts and are provided with classification from both models. We achieve 95.76 per cent (52.47 per cent) of quasar purity, 95.88 per cent (92.24 per cent) of quasar completeness, 99.44 per cent (98.17 per cent) of star purity, 98.22 per cent (78.56 per cent) of star completeness, 98.04 per cent (81.39 per cent) of galaxy purity, and 98.8 per cent (85.37 per cent) of galaxy completeness for the first (second) classifier, for which the metrics were calculated on objects with (without) WISE counterpart. A total of 2926 787 objects that are not in our spectroscopic sample were labelled, obtaining 335 956 quasars, 1347 340 stars, and 1243 391 galaxies. From those, 7.4 per cent, 76.0 per cent, and 58.4 per cent were classified with probabilities above 80 per cent. The catalogue with classification and probabilities for Stripe 82 S-PLUS DR2 is available for download.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Photometric redshift estimation of BASS DR3 quasars by machine learning

ABSTRACT Correlating Beijing–Arizona Sky Survey (BASS) data release 3 (DR3) catalogue with the ALLWISE data base, the data from optical and infrared information are obtained. The quasars from Sloan Digital Sky Survey are taken as training and test samples while those from LAMOST are considered as external test sample. We propose two schemes to construct the redshift estimation models with XGBoost, CatBoost, and Random Forest. One scheme (namely one-step model) is to predict photometric redshifts directly based on the optimal models created by these three algorithms; the other scheme (namely two-step model) is to first classify the data into low- and high-redshift data sets, and then predict photometric redshifts of these two data sets separately. For one-step model, the performance of these three algorithms on photometric redshift estimation is compared with different training samples, and CatBoost is superior to XGBoost and Random Forest. For two-step model, the performances of these three algorithms on the classification of low and high redshift subsamples are compared, and CatBoost still shows the best performance. Therefore, CatBoost is regarded as the core algorithm of classification and regression in two-step model. In contrast to one-step model, two-step model is optimal when predicting photometric redshift of quasars, especially for high-redshift quasars. Finally, the two models are applied to predict photometric redshifts of all quasar candidates of BASS DR3. The number of high-redshift quasar candidates is 3938 (redshift ≥3.5) and 121 (redshift ≥4.5) by two-step model. The predicted result will be helpful for quasar research and follow-up observation of high-redshift quasars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Scheduling strategies for the ESPRESSO follow-up of TESS targets

ABSTRACT Radial-velocity follow-up of stars harbouring transiting planets detected by TESS is expected to require very large amounts of expensive telescope time in the next few years. Therefore, scheduling strategies should be implemented to maximize the amount of information gathered about the target planetary systems. We consider myopic and non-myopic versions of a novel uniform-in-phase scheduler, as well as a random scheduler, and compare these scheduling strategies with respect to the bias, accuracy and precision achieved in recovering the mass and orbital parameters of transiting and non-transiting planets. This comparison is carried out based on realistic simulations of radial-velocity follow-up with ESPRESSO of a sample of 50 TESS target stars, with simulated planetary systems containing at least one transiting planet with a radius below 4R⊕. Radial-velocity data sets were generated under reasonable assumptions about their noise component, including that resulting from stellar activity, and analysed using a fully Bayesian methodology. We find the random scheduler leads to a more biased, less accurate, and less precise, estimation of the mass of the transiting exoplanets. No significant differences are found between the results of the myopic and non-myopic implementations of the uniform-in-phase scheduler. With only about 22 radial velocity measurements per data set, our novel uniform-in-phase scheduler enables an unbiased (at the level of 1 per cent) measurement of the masses of the transiting planets, while keeping the average relative accuracy and precision around 16 per cent and 23 per cent, respectively. The number of non-transiting planets detected is similar for all the scheduling strategies considered, as well as the bias, accuracy and precision with which their masses and orbital parameters are recovered.

Cabona, L.↗
DOE OSTI2022

Map-based cosmology inference with lognormal cosmic shear maps

ABSTRACT Most cosmic shear analyses to date have relied on summary statistics (e.g. ξ+ and ξ−). These types of analyses are necessarily suboptimal, as the use of summary statistics is lossy. In this paper, we forward-model the convergence field of the Universe as a lognormal random field conditioned on the observed shear data. This new map-based inference framework enables us to recover the joint posterior of the cosmological parameters and the convergence field of the Universe. Our analysis properly accounts for the covariance in the mass maps across tomographic bins, which significantly improves the fidelity of the maps relative to single-bin reconstructions. We verify that applying our inference pipeline to Gaussian random fields recovers posteriors that are in excellent agreement with their analytical counterparts. At the resolution of our maps – and to the extent that the convergence field can be described by the lognormal model – our map posteriors allow us to reconstruct all summary statistics (including non-Gaussian statistics). We forecast that a map-based inference analysis of LSST-Y10 data can improve cosmological constraints in the σ8–Ωm plane by $\approx\!{30}{{\ \rm per\ cent}}$ relative to the currently standard cosmic shear analysis. This improvement happens almost entirely along the $S_8=\sigma _8\Omega _{\rm m}^{1/2}$ directions, meaning map-based inference fails to significantly improve constraints on S8.

79 ASTRONOMY AND ASTROPHYSICS↗