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At least 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

The EFT of Large Scale Structures at all redshifts: analytical predictions for lensing

We study the prediction of the Effective Field Theory of Large Scale Structures (EFTofLSS) for the matter power spectrum at different redshifts. In previous work, we found that the two-loop prediction can match the nonlinear power spectrum measured from N -body simulations at redshift zero within approximately 2% up to k ∼ 0.6 h Mpc{sup -1} after fixing a single free parameter, the so-called 'speed of sound'. We determine the time evolution of this parameter by matching the EFTofLSS prediction to simulation output at different redshifts, and find that it is well-described by a fitting function that only includes one additional parameter. After the two free parameters are fixed, the prediction agrees with nonlinear data within approximately 2% up to at least k ∼ 1 h Mpc{sup -1} at z ≥ 1, and also within approximately 5% up to k ∼ 1.2 h Mpc{sup -1} at z =1 and k ∼ 2.3 h Mpc{sup -1} at z =3, a major improvement with respect to other perturbative techniques. We also develop an accurate way to estimate where the EFTofLSS predictions at different loop orders should fail, based on the sizes of the next-order terms that are neglected, and find agreement with the actual comparisons to data. Finally, we use our matter power spectrum results to perform analytical calculations of lensing potential power spectra corresponding to both CMB and galaxy lensing. This opens the door to future direct applications of the EFTofLSS to observations of gravitational clustering on cosmic scales.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Gyrokinetic predictions of multiscale transport in a DIII-D ITER baseline discharge

New multiscale gyrokinetic simulations predict that electron energy transport in a DIII-D ITER baseline discharge with dominant electron heating and low input torque is multiscale in nature, with roughly equal amounts of the electron energy flux Q e coming from long wavelength ion-scale (k y ρ s < 1) and short wavelength electron-scale (k y ρ s > 1) fluctuations when the gyrokinetic results match independent power balance calculations. Corresponding conventional ion-scale simulations are able to match the power balance ion energy flux Q i , but systematically underpredict Q e when doing so. We observe significant nonlinear cross-scale couplings in the multiscale simulations, but the exact simulation predictions are found to be extremely sensitive to variations of model input parameters within experimental uncertainties. Most notably, depending upon the exact value of the equilibrium E x B shearing rate γ E x B used, either enhancement or suppression of the long-wavelength turbulence and transport levels in the multiscale simulations is observed relative to what is predicted by ion-scale simulations. And while the enhancement of the long wavelength fluctuations by inclusion of the short wavelength turbulence was previously observed in similar multiscale simulations of an Alcator C-Mod L-mode discharge, these new results show for the first time a complete suppression of long-wavelength turbulence in a multiscale simulation, for parameters at which conventional ion-scale simulation predicts small but finite levels of low-k turbulence and transport consistent with the power balance Q i . Though computational resource limitations prevent a fully rigorous validation assessment of these new results, they provide significant new evidence that electron energy transport in burning plasmas is likely to have a strong multiscale character, with significant nonlinear cross-scale couplings that must be fully understood to predict the performance of those plasmas with confidence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Comparison of reduced model predictions for divertor detachment onset and reattachment timescales in ASDEX Upgrade and JET experiments

Building on prior analysis of ASDEX Upgrade (AUG) experiments (Henderson et al 2023 Nucl. Fusion63 086024), this study compares simple analytical formula predictions for divertor detachment onset and reattachment timescales in JET experiments. Detachment onset primarily scales with divertor neutral pressure, impurity concentration, power directed to the targets, machine size, and integral perpendicular power decay length. JET experiments, focusing on seeding mixtures of Ne and Ar, align with the detachment onset predictions. Radiation efficiencies among the impurities show good agreement with the model predictions, contrasting with AUG observations which suggested higher efficiency for Ar and lower efficiency for Ne. The time taken to re-ionise the neutral volume in front of the outer target in fully detached divertor conditions was measured following both abrupt increases in injected neutral beam power and, separately, cutting of the impurity gas flow. Re-ionisation of the neutrals occurs within approximately 1 s on JET, which aligns with the simple model prediction derived from AUG data. While the AUG results are not new, their comparison with the JET results enhances understanding, reinforcing confidence in using simple models to predict future reactor scenarios.

JET↗
DOE OSTI2024

A new data-driven map predicts substantial undocumented peatland areas in Amazonia

Tropical peatlands are among the most carbon-dense terrestrial ecosystems yet recorded. Collectively, they comprise a large but highly uncertain reservoir of the global carbon cycle, with wide-ranging estimates of their global area (441 025–1700 000 km 2 ) and below-ground carbon storage (105–288 Pg C). Substantial gaps remain in our understanding of peatland distribution in some key regions, including most of tropical South America. Here we compile 2413 ground reference points in and around Amazonian peatlands and use them alongside a stack of remote sensing products in a random forest model to generate the first field-data-driven model of peatland distribution across the Amazon basin. Our model predicts a total Amazonian peatland extent of 251 015 km 2 (95th percentile confidence interval: 128 671–373 359), greater than that of the Congo basin, but around 30% smaller than a recent model-derived estimate of peatland area across Amazonia. The model performs relatively well against point observations but spatial gaps in the ground reference dataset mean that model uncertainty remains high, particularly in parts of Brazil and Bolivia. For example, we predict significant peatland areas in northern Peru with relatively high confidence, while peatland areas in the Rio Negro basin and adjacent south-western Orinoco basin which have previously been predicted to hold Campinarana or white sand forests, are predicted with greater uncertainty. Similarly, we predict large areas of peatlands in Bolivia, surprisingly given the strong climatic seasonality found over most of the country. Very little field data exists with which to quantitatively assess the accuracy of our map in these regions. Data gaps such as these should be a high priority for new field sampling. This new map can facilitate future research into the vulnerability of peatlands to climate change and anthropogenic impacts, which is likely to vary spatially across the Amazon basin.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Deep reinforcement learning for predicting kinetic pathways to surface reconstruction in a ternary alloy

Abstract The majority of computational catalyst design focuses on the screening of material components and alloy composition to optimize selectivity and activity for a given reaction. However, predicting the metastability of the alloy catalyst surface at realistic operating conditions requires an extensive sampling of possible surface reconstructions and their associated kinetic pathways. We present CatGym, a deep reinforcement learning (DRL) environment for predicting the thermal surface reconstruction pathways and their associated kinetic barriers in crystalline solids under reaction conditions. The DRL agent iteratively changes the positions of atoms in the near-surface region to generate kinetic pathways to accessible local minima involving changes in the surface compositions. We showcase our agent by predicting the surface reconstruction pathways of a ternary Ni 3 Pd 3 Au 2 (111) alloy catalyst. Our results show that the DRL agent can not only explore more diverse surface compositions than the conventional minima hopping method, but also generate the kinetic surface reconstruction pathways. We further demonstrate that the kinetic pathway to a global minimum energy surface composition and its associated transition state predicted by our agent is in good agreement with the minimum energy path predicted by nudged elastic band calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Multi-task graph neural networks for simultaneous prediction of global and atomic properties in ferromagnetic systems *

Abstract We introduce a multi-tasking graph convolutional neural network, HydraGNN, to simultaneously predict both global and atomic physical properties and demonstrate with ferromagnetic materials. We train HydraGNN on an open-source ab initio density functional theory (DFT) dataset for iron-platinum with a fixed body centered tetragonal lattice structure and fixed volume to simultaneously predict the mixing enthalpy (a global feature of the system), the atomic charge transfer, and the atomic magnetic moment across configurations that span the entire compositional range. By taking advantage of underlying physical correlations between material properties, multi-task learning (MTL) with HydraGNN provides effective training even with modest amounts of data. Moreover, this is achieved with just one architecture instead of three, as required by single-task learning (STL). The first convolutional layers of the HydraGNN architecture are shared by all learning tasks and extract features common to all material properties. The following layers discriminate the features of the different properties, the results of which are fed to the separate heads of the final layer to produce predictions. Numerical results show that HydraGNN effectively captures the relation between the configurational entropy and the material properties over the entire compositional range. Overall, the accuracy of simultaneous MTL predictions is comparable to the accuracy of the STL predictions. In addition, the computational cost of training HydraGNN for MTL is much lower than the original DFT calculations and also lower than training separate STL models for each property.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Multimodal representation learning for predicting molecule–disease relations

Motivation: Predicting molecule–disease indications and side effects is important for drug development and pharmacovigilance. Comprehensively mining molecule–molecule, molecule–disease and disease–disease semantic dependencies can potentially improve prediction performance. Methods: We introduce a Multi-Modal REpresentation Mapping Approach to Predicting molecular-disease relations (M2REMAP) by incorporating clinical semantics learned from electronic health records (EHR) of 12.6 million patients. Specifically, M2REMAP first learns a multimodal molecule representation that synthesizes chemical property and clinical semantic information by mapping molecule chemicals via a deep neural network onto the clinical semantic embedding space shared by drugs, diseases and other common clinical concepts. To infer molecule–disease relations, M2REMAP combines multimodal molecule representation and disease semantic embedding to jointly infer indications and side effects. Results: We extensively evaluate M2REMAP on molecule indications, side effects and interactions. Results show that incorporating EHR embeddings improves performance significantly, for example, attaining an improvement over the baseline models by 23.6% in PRC-AUC on indications and 23.9% on side effects. Further, M2REMAP overcomes the limitation of existing methods and effectively predicts drugs for novel diseases and emerging pathogens. Availability and implementation: The code is available at https://github.com/celehs/M2REMAP, and prediction results are provided at https://shiny.parse-health.org/drugs-diseases-dev/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples

Microbial communities play important roles in the function and maintenance of various biosystems, ranging from the human body to the environment. A major challenge in microbiome research is the classification of microbial communities of different environments or host phenotypes. The most common and cost-effective approach for such studies to date is 16S rRNA gene sequencing. Recent falls in sequencing costs have increased the demand for simple, efficient and accurate methods for rapid detection or diagnosis with proved applications in medicine, agriculture and forensic science. We describe a reference- and alignment-free approach for predicting environments and host phenotypes from 16S rRNA gene sequencing based on k-mer representations that benefits from a bootstrapping framework for investigating the sufficiency of shallow sub-samples. Deep learning methods as well as classical approaches were explored for predicting environments and host phenotypes. A k-mer distribution of shallow sub-samples outperformed Operational Taxonomic Unit (OTU) features in the tasks of body-site identification and Crohn’s disease prediction. Aside from being more accurate, using k-mer features in shallow sub-samples allows (i) skipping computationally costly sequence alignments required in OTU-picking and (ii) provided a proof of concept for the sufficiency of shallow and short-length 16S rRNA sequencing for phenotype prediction. In addition, k-mer features predicted representative 16S rRNA gene sequences of 18 ecological environments, and 5 organismal environments with high macro-F1 scores of 0.88 and 0.87. For large datasets, deep learning outperformed classical methods such as Random Forest and Support Vector Machine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

SIFTER search: a web server for accurate phylogeny-based protein function prediction

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Predictive models of the genetic bases underlying budding yeast fitness in multiple environments

Abstract The ability of organisms to adapt and survive depends on the effects of genes and the environment on fitness. However, the multigenic nature of fitness and genotype-by-environment interactions hinder our understanding of the genetic basis of fitness. Here, we established fitness prediction models for 35 environments using machine learning and existing fitness data and different genetic variant types for a Saccharomyces cerevisiae population. Models revealed that the predictive ability of genetic variants varied across environments, with copy number variants explaining the majority of fitness variation in most cases. Model interpretation showed that different variant types identified distinct gene sets associated with predictive variants. These gene sets were significantly enriched in experimentally validated genes affecting fitness in only a subset of environments, indicating that many genes influencing fitness remain unexplored. Notably, non-experimentally validated genes were more important than validated ones for fitness predictions. Gene contributions to predictions were both isolate- and environment-dependent, pointing to gene-by-gene and gene-by-environment interactions. Furthermore, models uncovered experimentally validated and novel candidate genetic interactions for a well-characterized stress, the fungicide benomyl. These findings highlight the feasibility of identifying the genetic basis of fitness by using different genetic variant types and offer novel targets for future functional analysis.

DNA copy number variations↗
DOE OSTI2020

Enzyme activities predicted by metabolite concentrations and solvent capacity in the cell

Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we use two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. The first predictive method uses a statistical thermodynamics and metabolic control theory framework while the second method is performed using a hybrid optimization–reinforcement learning approach. Efficient regulation schemes were learned from experimental data that either agree with theoretical calculations or result in a higher cell fitness using maximum useful work as a metric. As previously hypothesized, regulation is herein shown to control the concentrations of both immediate and downstream product concentrations at physiological levels. Model predictions provide the following two novel general principles: (1) the regulation itself causes the reactions to be much further from equilibrium instead of the common assumption that highly non-equilibrium reactions are the targets for regulation; and (2) the minimal regulation needed to maintain metabolite levels at physiological concentrations maximizes the free energy dissipation rate instead of preserving a specific energy charge. The resulting energy dissipation rate is an emergent property of regulation which may be represented by a high value of the adenylate energy charge. In addition, the predictions demonstrate that the amount of regulation needed can be minimized if it is applied at the beginning or branch point of a pathway, in agreement with common notions. The approach is demonstrated for three pathways in the central metabolism of E. coli (gluconeogenesis, glycolysis-tricarboxylic acid (TCA) and pentose phosphate-TCA) that each require different regulation schemes. It is shown quantitatively that hexokinase, glucose 6-phosphate dehydrogenase and glyceraldehyde phosphate dehydrogenase, all branch points of pathways, play the largest roles in regulating central metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Robust ab initio prediction of nuclear electric quadrupole observables by scaling to the charge radius

Meaningful predictions for electric quadrupole (E2) observables from ab initio nuclear theory are necessary, if the ab initio description of collective correlations is to be confronted with experiment, as well as to provide predictive power for unknown E2 observables. However, converged results for E2 observables are notoriously challenging to obtain in ab initio no-core configuration interaction (NCCI) approaches. Matrix elements of the E2 operator are sensitive to the large-distance tails of the nuclear wave function, which converge slowly in an oscillator basis expansion. Similar convergence challenges beset ab initio prediction of the nuclear charge radius. We demonstrate that the convergence patterns of the E2 and radius observables are strongly correlated, and that meaningful predictions for the absolute scale of E2 observables may be made by calibrating to the experimentally-known ground-state charge radius. Here, we illustrate by providing robust ab initio predictions for several E2 transition strengths and quadrupole moments in p-shell nuclei, in cases where experimental results are available for comparison.

6 ≤ A ≤ 19↗
DOE OSTI2019

CMB lensing bispectrum: Assessing analytical predictions against full-sky lensing simulations

We report that cosmic microwave background (CMB) lensing is an integrated effect whose kernel is greater than half the peak value in the range 1 < z < 5. Measuring this effect offers a powerful tool to probe the large-scale structure of the Universe at high redshifts. With the increasing precision of ongoing CMB surveys, other statistics than the lensing power spectrum, in particular the lensing bispectrum, will be measured at high statistical significance. This will provide ways to improve the constraints on cosmological models and lift degeneracies. Following up on an earlier paper, we test analytical predictions of the CMB lensing bispectrum against full-sky lensing simulations, and we discuss their validity and limitation in detail. The tree-level prediction of perturbation theory agrees with the simulation only up to ℓ ~ 200 , but the one-loop order allows capturing the simulation results up to ℓ ~ 600 . We also show that analytical predictions based on fitting formulas for the matter bispectrum agree reasonably well with simulation results, although the precision of the agreement depends on the configurations and scales considered. For instance, the agreement is at the 10% level for the equilateral configuration at multipoles up to ℓ ~ 2000 , but the difference in the squeezed limit increases to more than a factor of 2 at ℓ ~ 2000 . This discrepancy appears to come from limitations in the fitting formula of the matter bispectrum. We also find that the analytical prediction for the post-Born correction to the bispectrum is in good agreement with the simulation. Finally, we conclude by discussing the bispectrum prediction in some theories of modified gravity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Neural network–based pore flow field prediction in porous media using super resolution

Direct pore-scale simulations of fluid flow through porous media are computationally expensive to perform for realistic systems. Previous works have demonstrated using the geometry of the microstructure of porous media to predict the velocity fields therein based on neural networks. However, such trained neural networks do not perform well for unseen porous media with a large degree of heterogeneity. In this study we propose that incorporating a coarse velocity field in the input of neural networks is an effective way to improve the prediction performance. The coarse velocity field can be simulated with a low computational cost and provides global information to regularize the ill-posedness of the learning problem, which is usually caused by the use of local geometries due to the computational resource constraints. We show that incorporating the coarse-mesh velocity field significantly improves the prediction accuracy of the fine-mesh velocity field by comparison to the prediction that relies on geometric information alone, especially for the porous medium with a large interior vuggy pore space. We also show the flexibility of training the network in using coarse velocity fields with various resolutions. The results suggest that even using coarse velocity field with a very low resolution, the predictions are still enhanced and close to the ground truths. The feasibility of the method is further demonstrated by testing the trained network on real rocks. This study highlights the merits of incorporating a coarse-mesh velocity field into the input for neural networks, which provides global, physics-based information for the model, thereby improving the model's generalization capability.

42 ENGINEERING↗
DOE OSTI2026

Predicting Adaptively Chosen Observables in Quantum Systems

Recent advances have demonstrated that 𝒪⁡(log 𝑀) measurements suffice to predict 𝑀 properties of arbitrarily large quantum many-body systems. However, these remarkable findings assume that the properties to be predicted are chosen independently of the data. This assumption can be violated in practice, where scientists adaptively select properties after looking at previous predictions. This work investigates the adaptive setting for three classes of observables: local, Pauli, and bounded-Frobenius-norm observables. We prove that Ω⁡(√𝑀) samples of an arbitrarily large unknown quantum state are necessary to predict expectation values of 𝑀 adaptively chosen local and Pauli observables, where the system size scales exponentially and polynomially in 𝑀, respectively. We also present computationally efficient algorithms that achieve this information-theoretic lower bound. In contrast, for bounded-Frobenius-norm observables, we devise an algorithm requiring only 𝒪⁡(log 𝑀) samples, independent of system size. These results highlight the potential pitfalls of adaptivity in analyzing data from quantum experiments and provide algorithmic tools to safeguard against erroneous predictions in quantum experiments.

Machine learning↗
DOE OSTI2024

The seventh blind test of crystal structure prediction: structure generation methods

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.

Chemistry↗
DOE OSTI2019

Learning to Predict Material Structure from Neutron Scattering Data

Understanding structural properties of materials and how they relate to its atomic structure, while extremely challenging, is a key scientific quest that has dominated the landscape of materials research for decades. Neutron and X-ray scattering is a state-of-the-art method to investigate material structure on the atomic scale. Traditional methods of processing neutron scattering data to decipher the structure of target materials have relied on computing scattering patterns using physics-based forward models and comparing them with experimentally gathered scattering profiles within a computationally expensive optimization loop. Here, we report an initial design of a data-driven machine learning pipeline for material structure prediction that is computationally faster (once trained) and potentially more accurate. We describe the architecture of the ML pipeline and a preliminary benchmarking study of shallow machine learning models in terms of their prediction accuracy and limitations. We show that material structure prediction from neutron scattering data using shallow learning models is feasible to within 90% prediction accuracy for certain classes of materials but deeper models are required for more general material structure predictions.

Garcia Cardona, Cristina↗
DOE OSTI2023

Uncertainty Aware Deep Learning for Fault Prediction Using Multivariate Time Series Signals

The superconducting radio-frequency cavities are a crucial component of the Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab. When a cavity faults, beam delivery to experimental end users is disrupted. Prediction of cavity faults prior to onset is essential to reduce operation and maintenance costs. In this work, a parallel long short-term memory (LSTM)-convolution neural network (CNN)-based deep learning (DL) model is proposed to predict impending faults using pre-fault signals. Further, we introduce an uncertainty quantification approach using Monte Carlo dropout with the LSTM-CNN model to ascertain confidence in the prediction. The model was tested using multivariate time series signals from stable cavity operations and before faults. Initial results show that on the test dataset, the model can identify impending faults before their onset with an average 10-fold cross validation accuracy of 97.39% and a standard deviation of 0.12% using a 100-ms time window. It is also observed that the model performs better as the prediction time moves closer to the fault onset. For additional context, we compare the performance of the model with three machine-learning-based (ML) fault prediction models. Our proposed parallel LSTM-CNN-based DL method shows better performance than the ML-based methods.

Rahman, Md Monibor↗