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At least 1,405 records · Page 78

SARS-CoV2 billion-compound docking

Abstract This dataset contains ligand conformations and docking scores for 1.4 billion molecules docked against 6 structural targets from SARS-CoV2, representing 5 unique proteins: MPro, NSP15, PLPro, RDRP, and the Spike protein. Docking was carried out using the AutoDock-GPU platform on the Summit supercomputer and Google Cloud. The docking procedure employed the Solis Wets search method to generate 20 independent ligand binding poses per compound. Each compound geometry was scored using the AutoDock free energy estimate, and rescored using RFScore v3 and DUD-E machine-learned rescoring models. Input protein structures are included, suitable for use by AutoDock-GPU and other docking programs. As the result of an exceptionally large docking campaign, this dataset represents a valuable resource for discovering trends across small molecule and protein binding sites, training AI models, and comparing to inhibitor compounds targeting SARS-CoV-2. The work also gives an example of how to organize and process data from ultra-large docking screens.

60 APPLIED LIFE SCIENCES↗

Enhancing the Quality and Reliability of Machine Learning Interatomic Potentials through Better Reporting Practices

Recent developments in machine learning interatomic potentials (MLIPs) have empowered even nonexperts in machine learning to train MLIPs for accelerating materials simulations. However, reproducibility and independent evaluation of presented MLIP results is hindered by a lack of clear standards in current literature. In this Perspective, we aim to provide guidance on best practices for documenting MLIP use while walking the reader through the development and deployment of MLIPs including hardware and software requirements, generating training data, training models, validating predictions, and MLIP inference. We also suggest useful plotting practices and analyses to validate and boost confidence in the deployed models. Finally, we provide a step-by-step checklist for practitioners to use directly before publication to standardize the information to be reported. Altogether, we hope that our work will encourage the reliable and reproducible use of these MLIPs, which will accelerate their ability to make a positive impact in various disciplines including materials science, chemistry, and biology, among others.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stream Temperature Predictions for River Basin Management in the Pacific Northwest and Mid-Atlantic Regions Using Machine Learning

Stream temperature (Ts) is an important water quality parameter that affects ecosystem health and human water use for beneficial purposes. Accurate Ts predictions at different spatial and temporal scales can inform water management decisions that account for the effects of changing climate and extreme events. In particular, widespread predictions of Ts in unmonitored stream reaches can enable decision makers to be responsive to changes caused by unforeseen disturbances. In this study, we demonstrate the use of classical machine learning (ML) models, support vector regression and gradient boosted trees (XGBoost), for monthly Ts predictions in 78 pristine and human-impacted catchments of the Mid-Atlantic and Pacific Northwest hydrologic regions spanning different geologies, climate, and land use. The ML models were trained using long-term monitoring data from 1980–2020 for three scenarios: (1) temporal predictions at a single site, (2) temporal predictions for multiple sites within a region, and (3) spatiotemporal predictions in unmonitored basins (PUB). In the first two scenarios, the ML models predicted Ts with median root mean squared errors (RMSE) of 0.69–0.84 °C and 0.92–1.02 °C across different model types for the temporal predictions at single and multiple sites respectively. For the PUB scenario, we used a bootstrap aggregation approach using models trained with different subsets of data, for which an ensemble XGBoost implementation outperformed all other modeling configurations (median RMSE 0.62 °C).The ML models improved median monthly Ts estimates compared to baseline statistical multi-linear regression models by 15–48% depending on the site and scenario. Air temperature was found to be the primary driver of monthly Ts for all sites, with secondary influence of month of the year (seasonality) and solar radiation, while discharge was a significant predictor at only 10 sites. The predictive performance of the ML models was robust to configuration changes in model setup and inputs, but was influenced by the distance to the nearest dam with RMSE <1 °C at sites situated greater than 16 and 44 km from a dam for the temporal single site and regional scenarios, and over 1.4 km from a dam for the PUB scenario. Our results show that classical ML models with solely meteorological inputs can be used for spatial and temporal predictions of monthly Ts in pristine and managed basins with reasonable (<1 °C) accuracy for most locations.

54 ENVIRONMENTAL SCIENCES↗

Protein sequence design with a learned potential

The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.

59 BASIC BIOLOGICAL SCIENCES↗

Estimating Watershed Subsurface Permeability From Stream Discharge Data Using Deep Neural Networks

Subsurface permeability is a key parameter in watershed models that controls the contribution from the subsurface flow to stream flows. Since the permeability is difficult and expensive to measure directly at the spatial extent and resolution required by fully distributed watershed models, estimation through inverse modeling has had a long history in subsurface hydrology. The wide availability of stream surface flow data, compared to groundwater monitoring data, provides a new data source to infer soil and geologic properties using integrated surface and subsurface hydrologic models. As most of the existing methods have shown difficulty in dealing with highly nonlinear inverse problems, we explore the use of deep neural networks for inversion owing to their successes in mapping complex, highly nonlinear relationships. We train various deep neural network (DNN) models with different architectures to predict subsurface permeability from stream discharge hydrograph at the watershed outlet. The training data are obtained from ensemble simulations of hydrographs corresponding to an permeability ensemble using a fully-distributed, integrated surface-subsurface hydrologic model. The trained model is then applied to estimate the permeability of the real watershed using its observed hydrograph at the outlet. Our study demonstrates that the permeabilities of the soil and geologic facies that make significant contributions to the outlet discharge can be more accurately estimated from the discharge data. Their estimations are also more robust with observation errors. Compared to the traditional ensemble smoother method, DNNs show stronger performance in capturing the nonlinear relationship between permeability and stream hydrograph to accurately estimate permeability. Our study sheds new light on the value of the emerging deep learning methods in assisting integrated watershed modeling by improving parameter estimation, which will eventually reduce the uncertainty in predictive watershed models.

54 ENVIRONMENTAL SCIENCES↗

From Pixels to Planets

The Kepler Mission was launched in 2009 as NASAs first mission capable of finding Earth-size planets in the habitable zone of Sun-like stars. Its telescope consists of a 1.5-m primary mirror and a 0.95-m aperture. The 42 charge-coupled devices in its focal plane are read out every half hour, compressed, and then downlinked monthly. After four years, the second of four reaction wheels failed, ending the original mission. Back on earth, the Science Operations Center developed the Science Pipeline to analyze about 200,000 target stars in Keplers field of view, looking for evidence of periodic dimming suggesting that one or more planets had crossed the face of its host star. The Pipeline comprises several steps, from pixel-level calibration, through noise and artifact removal, to detection of transit-like signals and the construction of a suite of diagnostic tests to guard against false positives. The Kepler Science Pipeline consists of a pipeline infrastructure written in the Java programming language, which marshals data input to and output from MATLAB applications that are executed as external processes. The pipeline modules, which underwent continuous development and refinement even after data started arriving, employ several analytic techniques, many developed for the Kepler Project. Because of the large number of targets, the large amount of data per target and the complexity of the pipeline algorithms, the processing demands are daunting. Some pipeline modules require days to weeks to process all of their targets, even when run on NASA's 128-node Pleiades supercomputer. The software developers are still seeking ways to increase the throughput. To date, the Kepler project has discovered more than 4000 planetary candidates, of which more than 1000 have been independently confirmed or validated to be exoplanets. Funding for this mission is provided by NASAs Science Mission Directorate.

supercomputers↗

EcoPLOT: dynamic analysis of biogeochemical data

Motivation: We have created EcoPLOT (parameterized linkage of omics-driven technologies), a web-app for the dynamic, interactive analysis of biogeochemical datasets that combines state-of-the-art analysis tools to statistically and graphically explore environmental, geochemical and microbiome datasets. Using the iterative random forest, a machine learning algorithm, EcoPLOT allows for the de novo discovery of drivers which exhibit significant impact on plant, microbial or soil dynamics. Availability and implementation: EcoPLOT is built entirely within the R language. It can be accessed through any system where R is installed, including Windows, Mac and most Linux systems. EcoPLOT is free to use and can be accessed at https://github.com/cdsanchez18/EcoPLOT.

59 BASIC BIOLOGICAL SCIENCES↗

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Abstract Through advanced mechanistic modeling and the generation of large high-quality datasets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show that mechanistic and machine learning models can be combined to enable accurate genotype-to-phenotype predictions. We use a genome-scale model to pinpoint engineering targets, efficient library construction of metabolic pathway designs, and high-throughput biosensor-enabled screening for training diverse machine learning algorithms. From a single data-generation cycle, this enables successful forward engineering of complex aromatic amino acid metabolism in yeast, with the best machine learning-guided design recommendations improving tryptophan titer and productivity by up to 74 and 43%, respectively, compared to the best designs used for algorithm training. Thus, this study highlights the power of combining mechanistic and machine learning models to effectively direct metabolic engineering efforts.

59 BASIC BIOLOGICAL SCIENCES↗

Nanoscale defect evaluation framework combining real-time transmission electron microscopy and integrated machine learning-particle filter estimation

Observation of dynamic processes by transmission electron microscopy (TEM) is an attractive technique to experimentally analyze materials’ nanoscale phenomena and understand the microstructure-properties relationships in nanoscale. Even if spatial and temporal resolutions of real-time TEM increase significantly, it is still difficult to say that the researchers quantitatively evaluate the dynamic behavior of defects. Images in TEM video are a two-dimensional projection of three-dimensional space phenomena, thus missing information must be existed that makes image’s uniquely accurate interpretation challenging. Therefore, even though they are still a clustering high-dimensional data and can be compressed to two-dimensional, conventional statistical methods for analyzing images may not be powerful enough to track nanoscale behavior by removing various artifacts associated with experiment; and automated and unbiased processing tools for such big-data are becoming mission-critical to discover knowledge about unforeseen behavior. We have developed a method to quantitative image analysis framework to resolve these problems, in which machine learning and particle filter estimation are uniquely combined. The quantitative and automated measurement of the dislocation velocity in an Fe-31Mn-3Al-3Si autunitic steel subjected to the tensile deformation was performed to validate the framework, and an intermittent motion of the dislocations was quantitatively analyzed. The framework is successfully classifying, identifying and tracking nanoscale objects; these are not able to be accurately implemented by the conventional mean-path based analysis.

36 MATERIALS SCIENCE↗

Influence of Ga doping on magnetic properties, magnetocaloric effect, and electronic structure of pseudobinary GdZn 1 - x Ga x ( x = 0 - 0.1 )

Here, we explore the impact of introducing IIIA-group element Ga in place of IIB-group element Zn in binary intermetallic GdZn on its magnetic and magnetocaloric properties, as well as explicate the modified electronic band structure of the compound. The magnetic transition temperature of the compound decreases with the increase of Ga concentration in GdZn 1-x ⁢Ga x ⁢(x = 0–0.1) while the crystal structure (CsCl prototype) and lattice parameters remain unchanged. Our detailed analysis of magnetization and magnetocaloric data conclusively proves that long-ranged magnetic ordering exists in the sample, despite the magnetic interaction considerably weakening with the increase of Ga. The experimental data are rationalized using both a theoretical machine-learning model and first-principle density functional theory. The electronic band structure of GdZn is manifested with some unusual complex features which gradually diminish with Ga doping and the conventional sinusoidal feature of Ruderman-Kittel-Kasuya-Yosida-type interactions also disappears. A mean-field theory model is developed and can successfully describe the overall magnetocaloric behavior of the GdZn 1-x⁢ Ga x series of samples.

36 MATERIALS SCIENCE↗

On the vulnerability of data-driven structural health monitoring models to adversarial attack

Many approaches at the forefront of structural health monitoring rely on cutting-edge techniques from the field of machine learning. Recently, much interest has been directed towards the study of so-called adversarial examples; deliberate input perturbations that deceive machine learning models while remaining semantically identical. This article demonstrates that data-driven approaches to structural health monitoring are vulnerable to attacks of this kind. In the perfect information or ‘white-box’ scenario, a transformation is found that maps every example in the Los Alamos National Laboratory three-storey structure dataset to an adversarial example. Also presented is an adversarial threat model specific to structural health monitoring. The threat model is proposed with a view to motivate discussion into ways in which structural health monitoring approaches might be made more robust to the threat of adversarial attack.

60 APPLIED LIFE SCIENCES↗

Evapotranspiration partitioning estimates from 8 methods from 47 NEON sites, 2019-2021

This dataset provides daily estimates of evapotranspiration (ET) and the transpiration-to-evapotranspiration ratio (T/ET) across 47 terrestrial National Ecological Observatory Network (NEON) sites spanning diverse environmental and biome conditions in the United States across three years of data (2019-2021). Daily ET is reported in both energy units (MJ m⁻² day⁻¹) and equivalent water depth (mm day⁻¹), assuming a constant latent heat of vaporization of 2.45 MJ/kg. The primary method uses a hybrid recurrent neural network–Penman–Monteith framework (RNN-PM), which integrates physically based surface energy balance constraints with data-driven learning to partition ET into transpiration and evaporation components. Model inputs include in situ meteorological observations (air temperature, vapor pressure deficit, wind speed, and radiation) combined with satellite-derived land surface temperature, leaf area index, and soil moisture. For benchmarking and uncertainty assessment, T/ET estimates from seven additional models are included: Priestley-Taylor Jet Propulsion Laboratory (PT-JPL), Penman-Monteith (P-M), Two-Source Energy Balance (TSEB), Support Vector Regression (SVR), and Categorical Boosting (CatBoost), among others—spanning empirical, machine-learning, and process-based approaches (see methods section or linked publication for detailed descriptions). Data Package Contents: The dataset a csv files containing daily ET and T/ET estimates for each site and model, along with associated metadata files these variables. Data can be accessed using common spreadsheet software (e.g., Microsoft Excel, LibreOffice) or programming environments such as R or Python. Together, these data support cross-site comparisons of ecosystem water use, evaluation of ET partitioning methods, and development of improved land–atmosphere exchange models.

EARTH SCIENCE > ATMOSPHERE↗

Predictive Data Analytics Framework Using Advanced Test Reactor Acoustic Data

Although a nuclear reactor is a hostile environment for sensing and electrical communications, the reactor core is amenable to acoustic communication. An acoustic measurement infrastructure (AMI) has been installed at the Advanced Test Reactor (ATR) nozzle trench area to record acoustic signals that has the ability to capture different operating regime of the reactor. This AMI includes ATR in-pile structural components, coolant, acoustic receivers, primary coolant pumps (PCP) as signal sources, a data acquisition system, and signal-processing algorithms, enabling real-time. This report will discusses development of recursive Fast Fourier Transform approach to process in real-time acoustic signals, application of short time Fast Fourier Transform to the ATR brush data to understand the vibration level and to develop spectrograms for different primary coolant pump combinations. The combination of primary coolant pumps for normal and power axial locator mechanism of ATR are different and generates different signatures. These acoustic signatures were used to develop machine learning approaches to automatically classify different operating regimes. This lay the foundation for predictive analytic framework that can be leverage by ATR to optimize their operation and maintenance. The path forward involves continued engagement with ATR and expanded implementation of AMI and predictive framework at ATR and other facilities within INL and at other experimental reactors.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Considerations regarding the Use of Computer Vision Machine Learning in Safety-Related or Risk-Significant Applications in Nuclear Power Plants

With the advancements made to date in the field of artificial intelligence (AI), significant potential exists to utilize AI capabilities for nuclear power plant (NPP) applications. AI can replicate human decision making and it is usually faster and more accurate than humans. For implementations that impact critical NPP applications (e.g., safety-related or non-safety systems that potentially affect overall plant risk), a deeper safety analysis of the AI methods is necessary. AI applied to NPP operations could resemble the use of digital I&C (DI&C) because such applications involve digital computer hardware and custom-designed software that input plant data, execute complex software algorithms, and output the results to a system or licensed human operator to potentially provoke an action. For AI methods to be compliant with current safety requirements for DI&C, AI compatibility must be evaluated, and AI-related gaps may exist that prevent the prompt deployment of AI in NPPs. This effort aims to evaluate how example AI technologies align with the DI&C safety framework, and discusses how they could be analyzed, modeled, tested, and validated in a manner similar to typical DI&C technologies. Because AI is a broad field that encompasses areas such as machine learning (ML), natural language processing, and computer vision, this research focused on a subset of methods categorized as the computer vision ML (CVML) methods. This report explores two CVML use cases, gauge reading and fire watch, considered relevant to the DI&C standards, as they could play a safety-critical role. For the gauge reading use case, a CVML-enabled technology that can read gauges at oblique angles is utilized. For the fire watch use case, a CVML-enabled technology is utilized that migrates fire watch from a manual (human) approach to automated fire detection. These use cases are mainly intended to give context to the CVML system discussion. This effort assumes the worst-case scenario, with the CVML system being used to replace a safety-related or risk-significant system, thus requiring evaluation. Evaluating CVML against most of the relevant safety requirements for DI&C yielded several CVML-specific considerations due to the uniqueness of its characteristics in comparison with typical DI&C systems. For example, CVML models often employ commonly used (open-source) datasets, and it is not always possible to determine the level of overlap among open-source datasets. Therefore, the independence of the developed CVML models when demonstrating diversity is questionable, therefore creating vulnerability to common cause failure (CCF). The design verification process is also impacted since the data overlap could result in overestimation of the software validation and verification (V&V) performance results. Section 2 of this report evaluates a list of the identified CVML-specific characteristics and discusses the resulting considerations and potential solutions in the context of each referenced requirement. A summation is provided in Section 3. This report is not to be used as a guideline. It was developed to identify and consider issues in the implementation of ML technologies used to augment activities that may have a bearing on plant operation. The report draws parallels to the use of DI&C technologies, for which many standards are available to guide their use in nuclear plant operation. It considers the technologies and some of the potential implications of their use in safety-related applications but is not intended to address regulatory or licensing related issues.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The IPAC Image Subtraction and Discovery Pipeline for the Intermediate Palomar Transient Factory

We describe the near real-time transient-source discovery engine for the intermediate Palomar Transient Factory (iPTF), currently in operations at the Infrared Processing and Analysis Center (IPAC), Caltech. We coin this system the IPAC/iPTF Discovery Engine (or IDE). We review the algorithms used for PSF-matching, image subtraction, detection, photometry, and machine-learned (ML) vetting of extracted transient candidates. We also review the performance of our ML classifier. For a limiting signal-to-noise ratio of 4 in relatively unconfused regions, bogus candidates from processing artifacts and imperfect image subtractions outnumber real transients by approximately equal to 10:1. This can be considerably higher for image data with inaccurate astrometric and/or PSF-matching solutions. Despite this occasionally high contamination rate, the ML classifier is able to identify real transients with an efficiency (or completeness) of approximately equal to 97% for a maximum tolerable false-positive rate of 1% when classifying raw candidates. All subtraction-image metrics, source features, ML probability-based real-bogus scores, contextual metadata from other surveys, and possible associations with known Solar System objects are stored in a relational database for retrieval by the various science working groups. We review our efforts in mitigating false-positives and our experience in optimizing the overall system in response to the multitude of science projects underway with iPTF.

methods: analytical – methods: data analysis –↗

Scientific machine learning for modeling and simulating complex fluids

The formulation of rheological constitutive equations—models that relate internal stresses and deformations in complex fluids—is a critical step in the engineering of systems involving soft materials. While data-driven models provide accessible alternatives to expensive first-principles models and less accurate empirical models in many engineering disciplines, the development of similar models for complex fluids has lagged. The diversity of techniques for characterizing non-Newtonian fluid dynamics creates a challenge for classical machine learning approaches, which require uniformly structured training data. Consequently, early machine-learning based constitutive equations have not been portable between different deformation protocols or mechanical observables. Here, we present a data-driven framework that resolves such issues, allowing rheologists to construct learnable models that incorporate essential physical information, while remaining agnostic to details regarding particular experimental protocols or flow kinematics. These scientific machine learning models incorporate a universal approximator within a materially objective tensorial constitutive framework. By construction, these models respect physical constraints, such as frame-invariance and tensor symmetry, required by continuum mechanics. We demonstrate that this framework facilitates the rapid discovery of accurate constitutive equations from limited data and that the learned models may be used to describe more kinematically complex flows. This inherent flexibility admits the application of these “digital fluid twins” to a range of material systems and engineering problems. We illustrate this flexibility by deploying a trained model within a multidimensional computational fluid dynamics simulation—a task that is not achievable using any previously developed data-driven rheological equation of state.

Science & Technology - Other Topics↗

Fast neutron leakage spectra of the EUCLID experiment

Special nuclear material in sub-critical and critical configurations measured in integral experiments are important for validation and adjustment of nuclear data. Many different evaluations of nuclear data exist, and these different evaluations can provide different values for individual cross sections that vary due to the uncertainties in differential experiments or lack of such data. For integral experiments, differences in these individual cross sections can have compensating errors, which lead to the same answer. One example of this is the Jezebel critical assembly, where k eff of the system is correctly computed by both ENDF/B-VIII.0 and JEFF-3.3, despite having substantially different underlying evaluated values for specific reactions (such as elastic and inelastic cross sections). To reduce compensating errors in nuclear data, the Experiments Underpinned by Computational Learning for Improvements in Nuclear Data (EUCLID) project has utilized machine learning to design a set of sub-critical and critical experiments. These experiments include slab- and cube-like configurations of 239 Pu in the form of the ZPPR plates. Six different responses were measured on a total of thirteen different configurations. One of these responses, the neutron leakage spectrum, was measured using an EJ301D detector. Finally, the results of the neutron leakage spectra show good agreement (within 1–2 σ ) with the expected spectrum from simulations and will be used in the subsequent nuclear data adjustment done by the EUCLID team.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Considerations for Introducing Artificial Intelligence into Nuclear Power Plants

Advanced computational tools and techniques such as artificial intelligence and machine learning (AI/ML) can transform the nuclear power industry. This is necessary given that the economic viability of the existing fleet is in jeopardy and its labor-centric approach to operations and maintenance. Currently, AI/ML research is being undertaken for reactor system design and analysis including fault and accident prognosis, nuclear risk analysis such as plant safety and security evaluation, and plant operations and maintenance including predictive maintenance. Applications include both existing and advanced reactor technologies with the aim of improving operational and business efficiencies. Most every aspect of the organization can benefit, from instrumentation and control, to work planning, to human-machine interactions and business management. AI/ML in nuclear can simplify complex problems and produce more effective decision-making. Nonetheless, careful consideration must be given to the implementation of an AI/ML initiative. The aims of this research are to 1) review barriers to AI/ML adoption within the nuclear power industry, and 2) suggest potential solutions. These barriers are organized along five distinct categories (Figure 1) that are interconnected. The first are historical barriers that track the industry’s development over the decades including worldwide nuclear events that shaped public perceptions. The resulting federal scrutiny and intense safety culture that emerged are discussed. Technical barriers to AI/ML adoption are considerable, and include data privacy concerns, data governance, and the current lack of AI/ML expert knowledge at the plants. The main business case barrier remains cost, but an absence of an industry-wide vision and wide-scale adoption also produces reluctance. Stakeholder readiness is reviewed with special attention given to regulatory readiness. The 5-year strategic plan for AI readiness recently published by the U.S. Nuclear Regulatory Commission is highlighted. Last, adoption barriers at the user level are addressed including the importance of user experience and explainable AI. The AI adoption barriers described here are inter-related and ideally should be addressed in a holistic fashion.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗