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At least 271 records · Page 15

An algorithm for extraction of periodic signals from sparse, irregularly sampled data

Temporal gaps in discrete sampling sequences produce spurious Fourier components at the intermodulation frequencies of an oscillatory signal and the temporal gaps, thus significantly complicating spectral analysis of such sparsely sampled data. A new fast Fourier transform (FFT)-based algorithm has been developed, suitable for spectral analysis of sparsely sampled data with a relatively small number of oscillatory components buried in background noise. The algorithm's principal idea has its origin in the so-called 'clean' algorithm used to sharpen images of scenes corrupted by atmospheric and sensor aperture effects. It identifies as the signal's 'true' frequency that oscillatory component which, when passed through the same sampling sequence as the original data, produces a Fourier image that is the best match to the original Fourier space. The algorithm has generally met with succession trials with simulated data with a low signal-to-noise ratio, including those of a type similar to hourly residuals for Earth orientation parameters extracted from VLBI data. For eight oscillatory components in the diurnal and semidiurnal bands, all components with an amplitude-noise ratio greater than 0.2 were successfully extracted for all sequences and duty cycles (greater than 0.1) tested; the amplitude-noise ratios of the extracted signals were as low as 0.05 for high duty cycles and long sampling sequences. When, in addition to these high frequencies, strong low-frequency components are present in the data, the low-frequency components are generally eliminated first, by employing a version of the algorithm that searches for non-integer multiples of the discrete FET minimum frequency.

Wilcox, J. Z.↗

Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids

Premise Recent advances in generating large‐scale phylogenies enable broad‐scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. Methods We used a supermatrix for rosids and one well‐sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). Results We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. Conclusions We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.

59 BASIC BIOLOGICAL SCIENCES↗

EXPRES. II. Searching for Planets around Active Stars: A Case Study of HD 101501

By controlling instrumental errors to below 10 cm s{sup −1}, the EXtreme PREcision Spectrograph (EXPRES) allows for a more insightful study of photospheric velocities that can mask weak Keplerian signals. Gaussian processes (GP) have become a standard tool for modeling correlated noise in radial velocity data sets. While GPs are constrained and motivated by physical properties of the star, in some cases they are still flexible enough to absorb unresolved Keplerian signals. We apply GP regression to EXPRES radial velocity measurements of the 3.5 Gyr old chromospherically active Sun-like star, HD 101501. We obtain tight constraints on the stellar rotation period and the evolution of spot distributions using 28 seasons of ground-based photometry, as well as recent Transiting Exoplanet Survey Satellite data. Light-curve inversion was carried out on both photometry data sets to reveal the spot distribution and spot evolution timescales on the star. We find that the >5 m s{sup −1} rms radial velocity variations in HD 101501 are well modeled with a GP stellar activity model without planets, yielding a residual rms scatter of 45 cm s{sup −1}. We carry out simulations, injecting and recovering signals with the GP framework, to demonstrate that high-cadence observations are required to use GPs most efficiently to detect low-mass planets around active stars like HD 101501. Sparse sampling prevents GPs from learning the correlated noise structure and can allow it to absorb prospective Keplerian signals. We quantify the moderate to high-cadence monitoring that provides the necessary information to disentangle photospheric features using GPs and to detect planets around active stars.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Adversarial methods to reduce simulation bias in neutrino interaction event filtering at liquid argon time projection chambers

For current and future neutrino oscillation experiments using large liquid argon time projection chambers (LAr-TPCs), a key challenge is identifying neutrino interactions from the pervading cosmic-ray background. Rejection of such background is often possible using traditional cut-based selections, but this typically requires the prior use of computationally expensive reconstruction algorithms. This work demonstrates an alternative approach of using a 3D submanifold sparse convolutional network trained on low-level information from the scintillation light signal of interactions inside LAr-TPCs. This technique is applied to example simulations from ICARUS, the far detector of the short baseline neutrino program at Fermilab. The results of the network, show that cosmic background is reduced by up to 76.3% whilst neutrino interaction selection efficiency remains over 98.9%. We further present a way to mitigate potential biases from imperfect input simulations by applying domain adversarial neural networks (DANNs), for which modified simulated samples are introduced to imitate real data and a small portion of them are used for adversarial training. A series of mock-data studies are performed and demonstrate the effectiveness of using DANNs to mitigate biases, showing neutrino interaction selection efficiency performances significantly better than that achieved without the adversarial training.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The Role of Lightning in Controlling Interannual Variability of Tropical Tropospheric Ozone and OH and its Implications for Climate

Nitrogen oxides (NO(x) = NO + NO2) produced by lightning make a major contribution to the production of the dominant tropospheric oxidants (OH and ozone). These oxidants control the lifetime of many trace gases including long-lived greenhouse gases, and control the source-receptor relationship of inter-hemispheric pollutant transport. Lightning is affected by meteorological variability, and therefore represents a potentially important tropospheric chemistry-climate feedback. Understanding how interannual variability (IAV) in lightning affects IAV in ozone and OH in the recent past is important if we are to predict how oxidant levels may change in a future warmer climate. However, lightning parameterizations for chemical transport models (CTMs) show low skill in reproducing even climatological distributions of flash rates from the Lightning Imaging Sensor (LIS) and the Optical Transient Detector (OTD) satellite instruments. We present an optimized regional scaling algorithm for CTMs that enables sufficient sampling of spatiotemporally sparse satellite lightning data from LIS to constrain the spatial, seasonal, and interannual variability of tropical lightning. We construct a monthly time series of lightning flash rates for 1998-2010 and 35degS-35degN, and find a correlation of IAV in total tropical lightning with El Nino. We use the IAV-constraint to drive a 9-year hindcast (1998-2006) of the GEOS-Chem 3D chemical transport model, and find the increased IAV in LNO(x) drives increased IAV in ozone and OH, improving the model fs ability to simulate both. Although lightning contributes more than any other emission source to IAV in ozone, we find ozone more sensitive to meteorology, particularly convective transport. However, we find IAV in OH to be highly sensitive to lightning NO(x), and the constraint improves the ability of the model to capture the temporal behavior of OH anomalies inferred from observations of methyl chloroform and other gases. The sensitivity of OH is explained using photochemical reaction rates which show a "magnification" effect of the initial lightning NO perturbation on OH primary production, HO(x) recycling, and OH loss frequencies. This influence on OH may represent a negative feedback, if lightning increases in a warming world..

Murray, Lee T.↗

Non-intrusive reduced-order modeling for dynamical systems with spatially localized features

This work presents a non-intrusive reduced-order modeling framework for dynamical systems with spatially localized features characterized by slow singular value decay. The proposed approach builds upon two existing methodologies for reduced and full-order non-intrusive modeling, namely Operator Inference (OpInf) and sparse Full-Order Model (sFOM) inference. We decompose the domain into two complementary subdomains that exhibit fast and slow singular value decay. The dynamics of the subdomain exhibiting slow singular value decay are learned with sFOM while the dynamics with intrinsically low dimensionality on the complementary subdomain are learned with OpInf. The resulting, coupled OpInf-sFOM formulation leverages the computational efficiency of OpInf and the high resolution of sFOM, and thus enables fast non-intrusive predictions for conditions beyond those sampled in the training data set. A novel regularization technique with a closed-form solution based on the Gershgorin disk theorem is introduced to promote stable sFOM and OpInf models. We also provide a data-driven indicator for subdomain selection and ensure solution smoothness over the interface via a post-processing interpolation step. We evaluate the efficiency of the approach in terms of offline and online speedup through a quantitative, parametric computational cost analysis. We demonstrate the coupled OpInf-sFOM formulation for two test cases: a one-dimensional Burgers’ model for which accurate predictions beyond the span of the training snapshots are presented, and a two-dimensional parametric model for the Pine Island Glacier ice thickness dynamics, for which the OpInf-sFOM model achieves an average prediction error on the order of 1% with an online speedup factor of approximately 8$\times$ compared to the numerical simulation.

42 ENGINEERING↗

Initial Validation and Results of Geoscience Laser Altimeter System Optical Properties Retrievals

Verification of Geoscience Laser Altimeter System (GLAS) optical retrievals is . problematic in that passage over ground sites is both instantaneous and sparse plus space-borne passive sensors such as MODIS are too frequently out of sync with the GLAS position. In October 2003, the GLAS Validation Experiment was executed from NASA Dryden Research Center, California to greatly increase validation possibilities. The high-altitude NASA ER-2 aircraft and onboard instrumentation of Cloud Physics Lidar (CPL), MODIS Airborne Simulator (MAS), and/or MODIS/ASTER Airborne Simulator (MASTER) under-flew seven orbit tracks of GLAS for cirrus, smoke, and urban pollution optical properties inter-comparisons. These highly calibrated suite of instruments are the best data set yet to validate GLAS atmospheric parameters. In this presentation, we will focus on the inter-comparison with GLAS and CPL and draw preliminary conclusions about the accuracies of the GLAS 532nm retrievals of optical depth, extinction, backscatter cross section, and calculated extinction-to-backscatter ratio. Comparisons to an AERONET/MPL ground-based site at Monterey, California will be attempted. Examples of GLAS operational optical data products will be shown.

Hlavka, Dennis L.↗

Assessing Version 4 of the SMAP L4_SM Data Product

Version 4 of the SMAP Level 4 Surface and Root Zone Soil Moisture (L4_SM) product benefits from an improved land surface modeling system. Surface soil moisture is typically drier by several volumetric percent in Version 4 compared to Version 3, whereas root zone soil moisture is wetter in Version 4 in some regions and drier in others. Results from core validation site comparisons show that Version 4 of the L4_SM data product meets the accuracy requirement, which is formulated in terms of the RMSE after removal of the long-term mean difference (ubRMSE). The overall ubRMSE of the 3-hourly L4_SM data at the 9 km scale is 0.039 m3 m-3 for surface soil moisture and 0.029 m3 m-3 for root zone soil moisture, below the 0.04 m3 m-3 requirement. L4_SM surface and root zone soil moisture estimates are more skillful than model-only simulation estimates that are not informed by SMAP brightness temperature observations, with statistically significant improvements at the 5% level for surface soil moisture R and anomaly R values. Results from comparisons of the L4_SM product to in situ measurements from more than 400 sparse network sites corroborate the core validation site results.

Reichle, R.↗

Sparse Linear Algebra Toolkit for Computational Aerodynamics

Finding solutions to sparse linear systems of equations is an essential step in Computational Engineering applications of interest to NASA. Linear systems of equations are composed and solved in almost every computational engineering application. The characteristics of linear systems vary greatly from one application to another. Accordingly, there are a wide variety of methods for the solution of linear systems of equations. The operations and methods prepared by the authors are focused on linear systems of interest to NASA, primarily those associated with Computational Fluid Dynamics (CFD), Aeroelasticity, and Aeroacoustics. The Sparse Linear Algebra Toolkit (SLAT) is a coordinated collection of software featuring operations, methods, and data structures that are useful when solving sparse linear systems of equations on modern computer architectures. The implemented operations and methods are designed and tuned for parallelism in shared memory, in distributed memory, and across the hybrid combination of distributed-shared memory. The toolkit includes novel methods and implementations for modern architectures and facilitates development of new approaches for meeting NASA’s evolving computational engineering challenges using evolving computer architectures that are not available in vendor libraries. In this paper, significant features and interfaces within SLAT are presented and verified for simulations performed with NASA’s CFD solver, FUN3D. The runtime and scaling performance of the Generalized Minimum Residual (GMRES) method implemented in SLAT is analyzed for the linear subproblems within the solution of turbulent Navier-Stokes equations employed in the simulation of high-lift configurations. Prior to this work, the SPARSKIT GMRES implementation was the only Krylov subspace method available within FUN3D. A strong scaling study shows the SLAT GMRES implementation facilitates accurate Reynolds-averaged Navier-Stokes CFD solutions between 15% and 56% faster than the SPARSKIT GMRES implementation.

Stephen L Wood↗

Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning

Computational methods have demonstrated success in identifying virucidal agents, effectively contributing to the discovery of novel virucidal molecules. In this study, we developed a machine learning (ML) model, trained on a small dataset, to predict inhibitors of human enterovirus 71 (EV71), a pathological agent that causes severe disease in children and immunocompromised adults. Despite the dataset’s limitation, comprising of only 36 compounds tested, our ML framework demonstrated significant predictive capability. Notably, experimental validation revealed that five out of the eight compounds predicted by our model from the Chinese cosmetic material list exhibited virucidal activity. The inhibitor effects displayed by the main active compounds were further confirmed by molecular dynamics simulation. This underscores the potential of our AI-driven approach to bypass data constraints in identifying active molecules against viral pathogens.

60 APPLIED LIFE SCIENCES↗

Data for: A hybrid biophysical-machine learning framework for diurnal surface energy flux estimation using proximal sensing

Thermal-based remote sensing of surface energy fluxes has traditionally relied on high spatial resolution satellite data with revisit frequencies on the order of weeks. In this study, we evaluate a biophysics-based analytical surface energy balance model for predicting latent energy (LE) and sensible heat (H) fluxes using proximal sensing observations. The Surface Temperature Initiated Closure (STIC1.2) model has been extensively validated across a wide range of spatial and temporal scales using various satellite-derived thermal datasets. Here we extend this validation by applying STIC at sub-hourly temporal resolution over multiple growing seasons for four distinct agricultural systems. We further develop and evaluate novel STIC variants that incorporate machine learning (ML) techniques to eliminate the need for specific surface energy balance observations, specifically net radiation and soil heat flux, thereby enhancing model applicability in data-sparse settings. The integration of an ML component to estimate surface available energy is shown to have strong predictive performance for both LE (R2 = 0.81-0.94) and H (R2 = 0.46-0.72) across all agricultural systems examined here, demonstrating the potential of hybrid biophysical – machine learning approaches for surface energy balance modeling with minimal data requirements. This study concludes with a novel application of explainable machine learning (exML) to diagnose sources of model error. This exML framework attributes residual prediction errors to both model input variables and environmental drivers not explicitly included in the simulation experiments. This approach provides a new pathway for improving model design and integrating previously overlooked yet influential variables into future model iterations.

Agricultural Sciences↗

Operator learning for predicting multiscale bubble growth dynamics

We report simulating and predicting multiscale problems that couple multiple physics and dynamics across many orders of spatiotemporal scales is a great challenge that has not been investigated systematically by deep neural networks (DNNs). Herein, we develop a framework based on operator regression, the so-called deep operator network (DeepONet), with the long-term objective to simplify multiscale modeling by avoiding the fragile and time-consuming “hand-shaking” interface algorithms for stitching together heterogeneous descriptions of multiscale phenomena. To this end, as a first step, we investigate if a DeepONet can learn the dynamics of different scale regimes, one at the deterministic macroscale and the other at the stochastic microscale regime with inherent thermal fluctuations. Specifically, we test the effectiveness and accuracy of the DeepONet in predicting multirate bubble growth dynamics, which is described by a Rayleigh–Plesset (R–P) equation at the macroscale and modeled as a stochastic nucleation and cavitation process at the microscale by dissipative particle dynamics (DPD). First, we generate data using the R–P equation for multirate bubble growth dynamics caused by randomly time-varying liquid pressures drawn from Gaussian random fields (GRFs). Our results show that properly trained DeepONets can accurately predict the macroscale bubble growth dynamics and can outperform long short-term memory networks. We also demonstrate that the DeepONet can extrapolate accurately outside the input distribution using only very few new measurements. Subsequently, we train the DeepONet with DPD data corresponding to stochastic bubble growth dynamics. Although the DPD data are noisy and we only collect sparse data points on the trajectories, the trained DeepONet model is able to predict accurately the mean bubble dynamics for time-varying GRF pressures. Taken together, our findings demonstrate that DeepONets can be employed to unify the macroscale and microscale models of the multirate bubble growth problem, hence providing new insight into the role of operator regression via DNNs in tackling realistic multiscale problems and in simplifying modeling with heterogeneous descriptions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A phase transition for finding needles in nonlinear haystacks with LASSO artificial neural networks

To fit sparse linear associations, a LASSO sparsity inducing penalty with a single hyperparameter provably allows to recover the important features (needles) with high probability in certain regimes even if the sample size is smaller than the dimension of the input vector (haystack). More recently learners known as artificial neural networks (ANN) have shown great successes in many machine learning tasks, in particular fitting nonlinear associations. Small learning rate, stochastic gradient descent algorithm and large training set help to cope with the explosion in the number of parameters present in deep neural networks. Yet few ANN learners have been developed and studied to find needles in nonlinear haystacks. Driven by a single hyperparameter, our ANN learner, like for sparse linear associations, exhibits a phase transition in the probability of retrieving the needles, which we do not observe with other ANN learners. To select our penalty parameter, we generalize the universal threshold of Donoho and Johnstone (Biometrika 81(3):425–455, 1994) which is a better rule than the conservative (too many false detections) and expensive cross-validation. In the spirit of simulated annealing, we propose a warm-start sparsity inducing algorithm to solve the high-dimensional, non-convex and non-differentiable optimization problem. We perform simulated and real data Monte Carlo experiments to quantify the effectiveness of our approach.

97 MATHEMATICS AND COMPUTING↗

Peak2Patch: High-Fidelity Functional Group Identification through Attention-Based Fusion of Infrared and Mass Spectra

Identifying molecular structure based on spectroscopic readings is a key task in a variety of chemical and biological applications. Common spectroscopy techniques, such as Infrared (IR) Spectroscopy and Mass Spectrometry (MS), provide detailed information on the structure of molecular compounds but nonetheless require expert-level knowledge to decode. Machine learning has emerged as a potential solution for automating structure prediction from chemical spectra; however, current approaches generally focus on single sensor modalities, neglecting to leverage the complementary information contained within differing spectra. In this paper, we introduce Peak2Patch, a novel approach to fusion-enhanced prediction of functional groups from IR and mass spectra. First, we perform a detailed comparison of backbone networks for encoding both sparse mass spectra and dense IR spectra and demonstrate the superior performance of transformer neural networks over current state-of-the-art convolutional neural networks. Second, we evaluate three broad categories of fusion: early (raw feature), middle (deep feature), and late (decision) fusion, demonstrating the potential of a deep feature fusion-based approach. Lastly, we present Peak2Patch, our attention-based fusion scheme, which leverages cross-attention to mix features between encoded tokens of the two modalities. We validate our approach on a publicly available multimodal spectroscopic data set of 790k simulated molecules, demonstrating a large improvement in functional group prediction over both the previous state-of-the-art and our own strong single-modal baselines.

Jacobson, Philip [Sandia National Laboratories (SN↗

Validation of Fault Displacements from Dynamic Rupture Simulations against the Observations from the 1992 Landers Earthquake

ABSTRACT Coseismic fault displacements in large earthquakes have caused significant damage to structures and lifelines on and near fault lines. Coseismic displacements represent a real threat, especially to distributed infrastructure systems. For infrastructure systems that can not avoid active faults, engineering displacement demands are defined using probabilistic fault-displacement hazard analyses (PFDHA). However, PFDHA models are sparse and poorly constrained partly due to the scarcity of detailed fault-displacement observations. Advancements in dynamic rupture simulation methods make them an attractive approach to address this important issue. Because fault displacements can be simulated for various geologic conditions as constrained by current knowledge about earthquake processes, they can be used to supplement the observation datasets. In addition to providing on-fault displacements, when used with appropriate constitutive models for the bulk medium, they can capture off-fault distributed inelastic deformations as well. For viable extrapolation, simulations must first be validated against data. In this article, we summarize the calibration and validation of the dynamic rupture model against the observations of the well-documented 1992 Landers earthquake. We defined a preferred model that reproduces several first-order fault-displacement metrics such as the on-fault partition of the total displacement, the mean fault-zone width, and the location of the peak displacement. Simulated ground motions consistent with the observations ensure that all physics important to modeling have been properly parameterized. For the extrapolation, we generated a suite of dynamic rupture models to quantify expected fault-displacement metrics, their intercorrelations, and magnitude dependencies, which are in part supported by the Landers and other recent earthquakes. Our validation and extrapolation exercise paves the way for using dynamic rupture modeling to quantitatively address fault-displacement hazard on a broader scale. The results are promising and are expected to be useful to inform PFDHA model development.

Geochemistry & Geophysics↗

A Hybrid Biophysical‐Machine Learning Framework for Diurnal Surface Energy Flux Estimation Using Proximal Sensing

Thermal infrared-based remote sensing of surface energy fluxes has traditionally relied on high spatial resolution satellite data with revisit frequencies on the order of weeks. In this study, we evaluate a biophysics-based analytical surface energy balance model for predicting latent energy ( LE ) and sensible heat ( H ) fluxes using proximal sensing observations. The Surface Temperature Initiated Closure (STIC1.2) model has been extensively validated across a wide range of spatial and temporal scales using various satellite-derived thermal infrared data sets. Here we extend this validation by applying STIC at sub-hourly temporal resolution over multiple growing seasons for four distinct agricultural systems. We further develop and evaluate novel STIC variants that incorporate machine learning (ML) techniques to eliminate the need for surface energy balance observations, specifically net radiation and soil heat flux, thereby enhancing model applicability in data-sparse settings. The integration of a ML component to estimate surface available energy is shown to have strong predictive performance for both LE (R 2 = 0.81–0.94) and H (R 2 = 0.46–0.72) across all agricultural systems examined here, demonstrating the potential of hybrid biophysical-machine learning approaches for surface energy balance modeling with minimal data requirements. This study concludes with a novel application of explainable machine learning (exML) to diagnose sources of model error. This exML framework attributes residual prediction errors to both model input variables and environmental drivers not explicitly included in the simulation experiments. This approach provides a new pathway for improving model design and integrating previously overlooked yet influential variables into future model iterations.

evapotranspiration↗

Efficient numerical methods to solve sparse linear equations with application to PageRank

Over the last two decades, the PageRank problem has received increased interest from the academic community as an efficient tool to estimate web-page importance in information retrieval. Despite numerous developments, the design of efficient optimization algorithms for the PageRank problem is still a challenge. Here, we propose three new algorithms with a linear time complexity for solving the problem over a bounded-degree graph. The idea behind them is to set up the PageRank as a convex minimization problem over a unit simplex, and then solve it using iterative methods with small iteration complexity. Our theoretical results are supported by an extensive empirical justification using real-world and simulated data.

97 MATHEMATICS AND COMPUTING↗

Modeling the Impacts of Material Properties on Oscillatory Neuron Behavior

In this study, neuromorphic computing, which mimics the functions of biological brains, offers improvements in both latency and energy efficiency over typical von Neumann computing architectures. Spiking neural networks can be especially power-efficient because they encode information temporally and can use more sparse electrical inputs. Here, we study the design of volatile memristors (variable resistors with memory) for neuronal devices, with particular consideration toward the feasibility of all-on-chip oscillation using built-in capacitance. We use circuit simulations to model the behavior of oscillator neurons with a range of realistic material properties. We find that energy inputs increase with insulating-phase resistivity, thermal conductivity, and device aspect ratio. However, we also find that the minimum capacitance needed for oscillation decreases with increasing insulating-phase resistivity, which opposes the constraints for power efficiency. Based on published data on NbO 2 , VO 2 , and EuNiO 3 , we find that existing materials can be engineered for all-on-chip spiking using their parasitic capacitance.

36 MATERIALS SCIENCE↗