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At least 775 records · Page 43

Developing a SARS-CoV-2 main protease binding prediction random forest model for drug repurposing for COVID-19 treatment

The coronavirus disease 2019 (COVID-19) global pandemic resulted in millions of people becoming infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and close to seven million deaths worldwide. It is essential to further explore and design effective COVID-19 treatment drugs that target the main protease of SARS-CoV-2, a major target for COVID-19 drugs. In this study, machine learning was applied for predicting the SARS-CoV-2 main protease binding of Food and Drug Administration (FDA)-approved drugs to assist in the identification of potential repurposing candidates for COVID-19 treatment. Ligands bound to the SARS-CoV-2 main protease in the Protein Data Bank and compounds experimentally tested in SARS-CoV-2 main protease binding assays in the literature were curated. These chemicals were divided into training (516 chemicals) and testing (360 chemicals) data sets. To identify SARS-CoV-2 main protease binders as potential candidates for repurposing to treat COVID-19, 1188 FDA-approved drugs from the Liver Toxicity Knowledge Base were obtained. A random forest algorithm was used for constructing predictive models based on molecular descriptors calculated using Mold2 software. Model performance was evaluated using 100 iterations of fivefold cross-validations which resulted in 78.8% balanced accuracy. The random forest model that was constructed from the whole training dataset was used to predict SARS-CoV-2 main protease binding on the testing set and the FDA-approved drugs. Model applicability domain and prediction confidence on drugs predicted as the main protease binders discovered 10 FDA-approved drugs as potential candidates for repurposing to treat COVID-19. Our results demonstrate that machine learning is an efficient method for drug repurposing and, thus, may accelerate drug development targeting SARS-CoV-2.

Research & Experimental Medicine↗

Parameter inference from event ensembles and the top-quark mass

One of the key tasks of any particle collider is measurement. In practice, this is often done by fitting data to a simulation, which depends on many parameters. Sometimes, when the effects of varying different parameters are highly correlated, a large ensemble of data may be needed to resolve parameter-space degeneracies. An important example is measuring the top-quark mass, where other physical and unphysical parameters in the simulation must be profiled when fitting the top-quark mass parameter. We compare four different methodologies for top-quark mass measurement: a classical histogram fit similar to one commonly used in experiment augmented by soft-drop jet grooming; a 2D profile likelihood fit with a nuisance parameter; a machine-learning method called DCTR; and a linear regression approach, either using a least-squares fit or with a dense linearly-activated neural network. Despite the fact that individual events are totally uncorrelated, we find that the linear regression methods work most effectively when we input an ensemble of events sorted by mass, rather than training them on individual events. Although all methods provide robust extraction of the top-quark mass parameter, the linear network does marginally best and is remarkably simple. For the top study, we conclude that the Monte-Carlo-based uncertainty on current extractions of the top-quark mass from LHC data can be reduced significantly (by perhaps a factor of 2) using networks trained on sorted event ensembles. More generally, machine learning from ensembles for parameter estimation has broad potential for collider physics measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The Current State of High-Fidelity Simulations for Main Gas Path Turbomachinery Components and Their Industrial Impact

High-fidelity simulations have become feasible for most main gas path turbomachinery components, over the past two decades. This paper introduces the key challenges of simulating and modelling turbomachinery flows and presents an overview of possible simulation strategies. A comprehensive overview is given of which particular design challenges have to date been addressed by high-fidelity simulations, with a particular focus on high-pressure and centrifugal compressors, and high-pressure and low-pressure turbines. Recommendations are provided for how quality and accuracy can be ensured for high-fidelity simulations, using direct numerical simulations of a low-pressure turbine as a case study. It is argued that industrial impact from high-fidelity simulations can be achieved in two ways, either by conducting design-of-experiment-like studies that can provide designers with insight into certain physical mechanisms and phenomena, or by helping mature and improve lower-order models. The latter is discussed with particular emphasis on recent advances in machine learning for model assessment and improvement, and the potential of one selected data-driven approach is demonstrated on predictions of wake mixing for low-pressure and high-pressure turbines.

Mechanics↗

Physics-Guided Continual Learning for Predicting Emerging Aqueous Organic Redox Flow Battery Material Performance

Aqueous organic redox flow batteries (AORFBs) have gained popularity in renewable energy storage due to their low cost, environmental friendliness and scalability. The rapid discovery of aqueous soluble organic (ASO) redox-active materials necessitates efficient machine learning surrogates for predicting battery performance. The physics-guided continual learning (PGCL) method proposed in this study can incrementally learn data from new ASO electrolytes while addressing catastrophic forgetting issues in conventional machine learning. Using a AORFB database with a thousand potential materials generated by a 780 $\text{cm}^2$ interdigitated cell model, PGCL incorporates AORFB physics to optimize the continual learning task formation and training strategies to retain previously learned battery material knowledge. Finally, the trained PGCL demonstrates its capability in assessing emerging ASO materials within the established parameter space when evaluated with the dihydroxyphenazine isomers.

25 ENERGY STORAGE↗

Perspectives on Systematic Cloud Microphysics Scheme Development With Machine Learning

Cloud microphysics—the collection of processes that govern the small‐scale formation, evolution, and interactions of liquid droplets and ice crystals in clouds and precipitation—remains a major source of uncertainty in weather and climate models. Although too small in scale to be explicitly resolved in any large‐eddy simulation, weather, or climate model, the representation of cloud microphysical processes has significant impact at the climate scale. Current microphysical schemes are limited by both parametric uncertainty, linked to uncertainty in physical parameter values, and structural uncertainty, arising from incomplete physical understanding of the processes at play or approximations made for computational efficiency. Recent advances in the application of machine learning (ML) to the physical sciences show significant potential for minimizing these limitations by leveraging high‐fidelity simulations and observations. Here we outline the challenges that must be addressed to apply ML toward cloud microphysics scheme development. This perspectives paper synthesizes recent progress in using data‐driven methods, including ML, to improve cloud microphysics parameterizations and highlights opportunities to address key uncertainties. We discuss the roles of aleatoric (irreducible, or statistical) and epistemic (reducible, or systematic) errors in contributing to microphysics parameterization uncertainty. ML can leverage observations to improve microphysical schemes via bottom‐up and top‐down constraints. Methods such as differentiable programming and ML‐enhanced sampling strategies and the creation of large scale benchmark data sets promise to bridge the gap between observations and models and to improve the consistency of cloud microphysical representation across temporal and spatial scales.

Lamb, Kara D. [Columbia Univ., New York, NY (Unite↗

Many-body expansion based machine learning models for octahedral transition metal complexes

Abstract Graph-based machine learning (ML) models for material properties show great potential to accelerate virtual high-throughput screening of large chemical spaces. However, in their simplest forms, graph-based models do not include any 3D information and are unable to distinguish stereoisomers such as those arising from different orderings of ligands around a metal center in coordination complexes. In this work we present a modification to revised autocorrelation descriptors, a molecular graph featurization method, for predicting spin state dependent properties of octahedral transition metal complexes (TMCs). Inspired by analytical semi-empirical models for TMCs, the new modeling strategy is based on the many-body expansion (MBE) and allows one to tune the captured stereoisomer information by changing the truncation order of the MBE. We present the necessary modifications to include this approach in two commonly used ML methods, kernel ridge regression and feed-forward neural networks. On a test set composed of all possible isomers of binary TMCs, the best MBE models achieve mean absolute errors (MAEs) of 2.75 kcal mol −1 on spin-splitting energies and 0.26 eV on frontier orbital energy gaps, a 30%–40% reduction in error compared to models based on our previous approach. We also observe improved generalization to previously unseen ligands where the best-performing models exhibit MAEs of 4.00 kcal mol −1 (i.e. a 0.73 kcal mol −1 reduction) on the spin-splitting energies and 0.53 eV (i.e. a 0.10 eV reduction) on the frontier orbital energy gaps. Because the new approach incorporates insights from electronic structure theory, such as ligand additivity relationships, these models exhibit systematic generalization from homoleptic to heteroleptic complexes, allowing for efficient screening of TMC search spaces.

Meyer, Ralf (ORCID:0000000322360261)↗

Model-Free Probabilistic Forecasting of Nodal Voltages in Distribution Systems

As the penetration of distributed energy resources (DERs) into distribution systems increases, so does the interest in forecasting relevant system variables to help mitigate the associated challenges. One such challenge is the more frequent occurrence of excessive voltages in distribution systems with higher shares of DERs. Accurate and reliable estimates together with forecasts of system states (i.e., nodal voltages) will therefore play a key role in improving the utilization of these variable and uncertain sources while mitigating potential operational risks. Whilst recent literature has explored machine learning (ML) methods for voltage estimation and their extrapolation for a short-time period into the future, few have taken uncertainty quantification into account, and these methods have not yet been translated into operations. This paper discusses the advantages offered by probabilistic voltage forecasts and proposes a non-parametric Bayesian method suitable for forecasting nodal voltages at short-term time horizons while accounting for uncertainties in load and distributed photovoltaic (PV) generation. We demonstrate the value of the proposed Gaussian process (GP) model for a case study using historical forecasts and observation data.

distribution system↗

Process Image Analysis using Big Data, Machine Learning, and Computer Vision

The development of algorithms for machine learning and data analysis for the 3013 MIS corrosion surveillance program is a collaborative effort by SRNL, USC and GT. For corrosion detection, LCM image data is extracted from large binary files, with software written to convert the data to physical attributes (i.e. height, color and grayscale values; all as functions of a location in a plane projection). The user interface for the software permits selective downloading of binary data and interrogation of attributes. User input thresholds are used to flag attributes of interest. Machine learning algorithms, developed for this application, are used to determine whether the features are the result of corrosion. To address the fundamental mechanisms of corrosion, machine learning algorithms are being developed to derive interatomic potential force-fields from ab-initio DFT calculations. The goal is to apply molecular modeling on a large enough scale to guide the design of resistant materials.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Predicting Short-Term Deformation in the Central Valley Using Machine Learning

Land subsidence caused by excessive groundwater pumping in Central Valley, California, is a major issue that has several negative impacts such as reduced aquifer storage and damaged infrastructures which, in turn, produce an economic loss due to the high reliance on crop production. This is why it is of utmost importance to routinely monitor and assess the surface deformation occurring. Two main goals that this paper attempts to accomplish are deformation characterization and deformation prediction. The first goal is realized through the use of Principal Component Analysis (PCA) applied to a series of Interferomtric Synthetic Aperture Radar (InSAR) images that produces eigenimages displaying the key characteristics of the subsidence. Water storage changes are also directly analyzed by the use of data from the Gravity Recovery and Climate Experiment (GRACE) twin satellites and the Global Land Data Assimilation System (GLDAS). The second goal is accomplished by building a Long Short-Term Memory (LSTM) model to predict short-term deformation after developing an InSAR time series using LiCSBAS, an open-source InSAR time series package. The model is applied to the city of Madera and produces better results than a baseline averaging model and a one dimensional convolutional neural network (CNN) based on a mean squared error metric showing the effectiveness of machine learning in deformation prediction as well as the potential for incorporation in hazard mitigation models. The model results can directly aid policy makers in determining the appropriate rate of groundwater withdrawal while maintaining the safety and well-being of the population as well as the aquifers’ integrity.

58 GEOSCIENCES↗

A Machine Learning–Based Approach to Time-series Wave Identification in the Solar Wind

The Wind spacecraft has yielded several decades of high-resolution magnetic field data, a large fraction of which displays small-scale structures. In particular, the solar wind is full of wavelike fluctuations that appear in both the field magnitude and its components. The nature of these fluctuations can be tied to the properties of other structures in the solar wind, such as shocks, that have implications for the time evolution of the solar wind. As such, having a large collection of wave events would facilitate further study of the effects that these fluctuations have on solar wind evolution. Given the large volume of magnetic field data available, machine learning is the most practical approach to classifying the myriad small-scale structures observed. To this end, a subset of Wind data is labeled and used as a training set for a multibranch 1D convolutional neural network aimed at classifying circularly polarized wave modes. Using this algorithm, a preliminary statistical study of 1 yr of data is performed, yielding about 300,000 wave intervals out of about 5,000,000 solar wind intervals. The wave intervals come about more often in the fast solar wind and at higher temperatures, and the number of waves per day is highly periodic. This machine learning–based approach to wave detection has the potential to be a powerful, inexpensive way to catalog waves throughout decades of spacecraft data.

79 ASTRONOMY AND ASTROPHYSICS↗

Advanced Offshore Hazard Forecasting to Enable Resilient Offshore Operations

Paper prepared for the Offshore Technology Conference, 2024. Hazards in the offshore environment can imperil successful energy operations, whether those operations are conventional, renewable, or for decarbonization. The expanding accessibility of data science and the advanced applications of machine learning (ML) models creates an opportunity to assess potential hazards and the infrastructure they impact. We present a use case demonstrating the combined application of published ML tools to U.S. federal waters of the Gulf of Mexico, an actively explored region for offshore energy that is affected by variable metocean conditions and geologic processes contributing to potential hazards.

Mark-Moser, Mackenzie K.↗

Underground hydrogen storage leakage detection and characterization based on machine learning of sparse seismic data

Underground hydrogen storage (UHS) is considered as a scalable approach for massive storage and seasonal extraction of hydrogen (H 2 ). Although conventional leakage detection and characterization methods based on time-lapse seismic imaging and inversion generally apply to H 2 leakage detection problem, a high-fidelity yet cost effective geophysics approach is still missing to reliably inform leakage location and properties based on very sparse data. In response, we develop a novel supervised machine learning method to detect and characterize H 2 leakage from UHS. The input to our neural network are sparse time-lapse seismic waveforms, while the output from the neural network includes the spatial location and physical properties of a H 2 leakage. Here, we generate high-quality time-lapse waveforms using the elastic-wave equations to train the neural network. We train and validate our machine learning model and find that it attains high accuracy in using extremely sparse time-lapse seismic data to detect and characterize H 2 leakage. Our investigation is the first systematic study that focuses on applying machine learning to subsurface H 2 leakage detection and characterization and could potentially serve as a cost-effective geophysical tool for underground hydrogen leakage detection and characterization with high fidelity.

08 HYDROGEN↗

Towards provably efficient quantum algorithms for large-scale machine-learning models

Large machine learning models are revolutionary technologies of artificial intelligence whose bottlenecks include huge computational expenses, power, and time used both in the pre-training and fine-tuning process. In this work, we show that fault-tolerant quantum computing could possibly provide provably efficient resolutions for generic (stochastic) gradient descent algorithms, scaling as $\mathcal{O}$(T 2 x polylog($n$)), where n is the size of the models and T is the number of iterations in the training, as long as the models are both sufficiently dissipative and sparse, with small learning rates. Based on earlier efficient quantum algorithms for dissipative differential equations, we find and prove that similar algorithms work for (stochastic) gradient descent, the primary algorithm for machine learning. In practice, we benchmark instances of large machine learning models from 7 million to 103 million parameters. We find that, in the context of sparse training, a quantum enhancement is possible at the early stage of learning after model pruning, motivating a sparse parameter download and re-upload scheme. Our work shows solidly that fault-tolerant quantum algorithms could potentially contribute to most state-of-the-art, large-scale machine-learning problems.

97 MATHEMATICS AND COMPUTING↗

Machine Learning-Based PV Reserve Determination Strategy for Frequency Control on the WECC System

Frequency control from photovoltaic (PV) power plants has great potential to address the frequency response challenge of the power system with high penetrations of renewable generation. Using model-based approaches to determine the optimal PV headroom reserve, however, requires significant online computation and is intractable for an interconnection level system. This paper proposes a machine learning based strategy, that is suitable for real-time operation, to determine the optimal PV reserve for frequency control. The proposed machine learning algorithm is trained and tested on 1,987 offline simulations of a 60% renewable penetration Western Electricity Coordinating Council (WECC) system. Furthermore, the proposed reserve determination strategy is applied on a realistic 1-day operation profile of the WECC system and demonstrates a savings of more than 40% PV headroom compared to a conservative approach. It is evident that the proposed strategy can efficiently and effectively determine the optimal PV frequency control reserve for realistic interconnection systems.

frequency control↗

J-PLUS: Support vector machine applied to STAR-GALAXY-QSO classification

Context. In modern astronomy, machine learning has proved to be efficient and effective in mining big data from the newest telescopes. Aims. In this study, we construct a supervised machine-learning algorithm to classify the objects in the Javalambre Photometric Local Universe Survey first data release (J-PLUS DR1). Methods. The sample set is featured with 12-waveband photometry and labeled with spectrum-based catalogs, including Sloan Digital Sky Survey spectroscopic data, the Large Sky Area Multi-Object Fiber Spectroscopic Telescope, and VERONCAT – the Veron Catalog of Quasars & AGN. The performance of the classifier is presented with the applications of blind test validations based on RAdial Velocity Extension, the Kepler Input Catalog, the Two Micron All Sky Survey Redshift Survey, and the UV-bright Quasar Survey. A new algorithm was applied to constrain the potential extrapolation that could decrease the performance of the machine-learning classifier. Results. The accuracies of the classifier are 96.5% in the blind test and 97.0% in training cross-validation. The F1-scores for each class are presented to show the balance between the precision and the recall of the classifier. We also discuss different methods to constrain the potential extrapolation.

79 ASTRONOMY AND ASTROPHYSICS↗

The Lund jet plane

Lund diagrams, a theoretical representation of the phase space within jets, have long been used in discussing parton showers and resummations. We point out that they can be created for individual jets through repeated Cambridge/Aachen declustering, providing a powerful visual representation of the radiation within any given jet. Concentrating here on the primary Lund plane, we outline some of its analytical properties, highlight its scope for constraining Monte Carlo simulations and comment on its relation with existing observables such as the zg variable and the iterated soft-drop multiplicity. We then examine its use for boosted electroweak boson tagging at high momenta. It provides good performance when used as an input to machine learning. Much of this performance can be reproduced also within a transparent log-likelihood method, whose underlying assumption is that different regions of the primary Lund plane are largely decorrelated. This suggests a potential for unique insight and experimental validation of the features being used by machine-learning approaches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Overcoming sparse datasets with multi-task learning as applied to high entropy alloys

Abstract The design of novel High Entropy Alloys for use in high-temperature applications is an area of active interest due to their potential to provide exceptional properties compared to conventional alloys. Since the increased popularity of machine learning, an important cog in the design process has been training surrogate models on alloy properties. However, these Single-Task models are trained on individual mechanical properties and do not take advantage of the relatedness between properties. Multi-Task models can capture the interdependencies between tasks, leading to potentially more accurate predictions for all tasks. In this paper, we investigate if Multi-Task models can show improvement over Single-Task models when used for predicting the mechanical properties of these alloys. To ensure fair evaluation between the models, we apply L 0 regularization and skip connections to the models, which allows them to adjust the number of model parameters and depth for optimal performance. We find that the Multi-Task models can leverage task relationships to perform better than Single-Task models, especially for high amounts of missing data in the tasks. Furthermore, adding simple auxiliary targets can boost Multi-Task performance even further despite not being effective as input descriptors to single-task models themselves. We anticipate that the proposed strategies can achieve more accurate predictions and consequently enable better design capabilities for such data-constrained domains without incurring much additional computational cost.

Debnath, Arindam (ORCID:0000000194274499)↗

MBX V1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations

The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the "gold standard" coupled-cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. In conclusion, these advancements enable simulations on nanosecond time scales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗