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At least 1,189 records · Page 66

Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge

Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein–ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein–ligand interactions from cryo-EM density maps of proteins and ligands. DeepProLigand first uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein–ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps. These results demonstrate that the deep learning bioinformatics approach is a promising direction for modeling protein–ligand interactions on cryo-EM data using prior structural information.

59 BASIC BIOLOGICAL SCIENCES↗

Hierarchical Reinforcement Learning of a Short-Range Bond-Order Potential for Silica: Analytic Embedding of Coordination with Classical Efficiency

Reinforcement learning (RL) has recently emerged as a data-efficient strategy to parametrize short-range interatomic potentials. Building on our past RL optimization of pairwise silica models, we extend the framework to a bond-order (Tersoff-type) potential that provides an analytic embedding of local coordination through a three-body term. A hierarchical RL workflow combining continuous-action Monte Carlo Tree Search and property-based rewards efficiently explores the 26-dimensional parameter space, sequentially optimizing lattice parameters, densities, angles, and cohesive energies of 21 silica polymorphs. The resulting models, Q-Tersoff and ML-Tersoff, reproduce the energetic ordering of low-energy phases and capture the angular correlations and amorphous structure factors of silica with improved fidelity over pairwise force fields, while remaining orders of magnitude faster than high-dimensional machine-learned potentials. Both models underperform for elastic constants and high-energy frameworks, delineating the limits of the current analytic form. The approach establishes a general and interpretable route to angle-aware, short-range potentials that bridge physics-based and machine-learned descriptions of silicate materials.

36 MATERIALS SCIENCE↗

Battery aging mode identification across NMC compositions and designs using machine learning

A comprehensive understanding of lithium-ion battery (LiB) lifespan is the key to designing durable batteries and optimizing use protocols. Although battery lifetime prediction methods are flourishing, diagnosis of the root causes of aging and degradation have not yet been well developed nor studied for a broad mixture of designs and use cases. Here, we create a machine-learning (ML)-based framework that distinguishes aging modes using multiple electrochemical signatures recorded cycle-by-cycle. The predominant aging behaviors include a combination of loss of active materials in cathode (LAMPE) and a loss of Li inventory (LLI) in Li plating or solid electrolyte interphase (SEI) formation, manifested from 44 batteries representing two cathode chemistries, two electrode loadings, and five charging rates. Here, the aging mode classification accuracy is 86% using features within the first 50 cycles and increases to 88% beyond 225 cycles. The same features can quantify the percentage of end-of-life LAMPE with only 4.3% of error.

25 ENERGY STORAGE↗

Using electronic health record metadata to predict housing instability amongst veterans

Housing instability is considered a significant life stressor and preemptive screening should be applied to identify those at risk for homelessness as early as possible so that they can be targeted for specialized care. We developed models to classify patient outcomes for an established VA Homelessness Screening Clinical Reminder (HSCR), which identifies housing instability, in the two months prior to its administration. Logistic Regression and Random Forest models were fit to classify responses using the last 18 months of document activity. We measure concentration of risk across stratifications of predicted probability and observe an enriched likelihood of finding confirmed false negative responses from veterans with diagnosed housing instability. Positive responses were 34 times more likely to be detected within the top 1 % of patients predicted at risk than from those randomly selected. There is a 1 in 4 chance of detecting false negatives within the top 1 % of predicted risk. Machine learning methods can classify between episodes of housing instability using a data-driven approach that does not rely on variables curated from domain experts. This method has the potential to improve clinicians’ ability to identify veterans who are experiencing housing instability but are not captured by HSCR.

60 APPLIED LIFE SCIENCES↗

A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs

Tuberculosis (TB) is the deadliest infectious disease worldwide. The design of new treatments for TB is hindered by the large number of candidate drugs, drug combinations, dosing choices, and complex pharmaco-kinetics/dynamics (PK/PD). Here we study the interplay of these factors in designing combination therapies by linking a machine-learning model, INDIGO-MTB, which predicts in vitro drug interactions using drug transcriptomics, with a multi-scale model of drug PK/PD and pathogen-immune interactions called GranSim. We calculate an in vivo drug interaction score (iDIS) from dynamics of drug diffusion, spatial distribution, and activity within lesions against various pathogen sub-populations. The iDIS of drug regimens evaluated against non-replicating bacteria significantly correlates with efficacy metrics from clinical trials. Our approach identifies mechanisms that can amplify synergistic or mitigate antagonistic drug interactions in vivo by modulating the relative distribution of drugs. Our mechanistic framework enables efficient evaluation of in vivo drug interactions and optimization of combination therapies.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements

Type 1 diabetes (T1D) is a devastating autoimmune disease for which advanced mass spectrometry (MS) methods are increasingly used to identify new biomarkers and better understand underlying mechanisms. For example, integration of MS analysis and machine learning has identified multimolecular biomarker panels. In mechanistic studies, MS has contributed to the discovery of neoepitopes, and pathways involved in disease development and identifying therapeutic targets. However, challenges remain in understanding the role of tissue microenvironments, spatial heterogeneity, and environmental factors in disease pathogenesis. Recent advancements in MS, such as ultra-fast ion-mobility separations, and single-cell and spatial omics, can play a central role in addressing these challenges. Here, in this work, we review recent advancements in MS-based molecular measurements and their role in understanding T1D.

60 APPLIED LIFE SCIENCES↗

FAIR Surrogate Benchmarks Supporting AI and Simulation Research (Final Report)

Computational Science is being revolutionized by integrating AI and simulation and, in particular, by deep learning surrogate models that can replace all or part of traditional large‐scale HPC computations. Such surrogates can achieve remarkable performance improvements, as much as several orders of magnitude, and save both compute time and energy. The Surrogate Benchmark Initiative (SBI) project creates a community repository and FAIR (Findable, Accessible, Interoperable, and Reusable) data ecosystem for HPC application surrogate benchmarks. The SBI team comes from Argonne National Laboratory (ANL), Indiana University (IU), Rutgers University, the University of Tennessee, Knoxville (UTK), and the University of Virginia (UVA). SBI repositories include data, code, and all relevant collateral artifacts that the science and engineering community need to use and reuse these data sets and surrogates. SBI repositories generate active research from both the participants in SBI and the broad community of AI and domain scientists. This project develops surrogates that use several different neural nets to learn and quickly infer the results of simulations and data systems and captures them as surrogate benchmarks with a rich set of metadata covering: Data; Model; Metrics specification; Machine specification; and Science, Speed, and Power Results. We research FAIR metadata for these benchmarks. We develop application surrogate examples as benchmarks across many fields (ANL, UTK, IU, UVA). We also study non-Surrogate benchmarks that have many common features and similar issues as regards FAIRness. We work with MLCommons (UVA, UTK), which is a major machine learning benchmarking activity where we get metadata ontologies, software, and benchmarks, Benchmarks have datasets, models, and metadata and they need a technical framework developed by UTK and Rutgers and deployed by UVA. We study features of Surrogates including performance, training set size, and uncertainty quantification (Rutgers, UVA and IU).

97 MATHEMATICS AND COMPUTING↗

Co-Firing Switchgrass and Waste Coal in A Power Plant: A Techno-Economic and Life Cycle Evaluation for The Ohio River Valley (SWITCH) (Final Technical Report for Ohio State/FE0032204)

Abandoned coal mine lands (AMLs) represent one of the most persistent environmental challenges in the United States. Prior to the enactment of the Surface Mining Control and Reclamation Act (SMCRA) in 1977, coal mining operations were not legally required to reclaim disturbed lands, leaving behind approximately 500,000 AML sites nationwide. These sites pose severe environmental and health risks, including acid mine drainage, soil and water contamination, and spontaneous combustion of waste coal piles. Millions of Americans live within one mile of these AMLs, underscoring the urgency of remediation. Traditional reclamation practices, such as planting cool-season grasses, often fail to fully restore ecological function or leverage the economic potential of these lands. This project addressed these challenges by developing integrated strategies for resource recovery, land reclamation, and sustainable energy production. This project evaluated an integrated strategy to convert this liability into an opportunity by recovering waste coal and co-firing it with switchgrass (Panicum virgatum L.) cultivated on reclaimed or marginal AML areas in existing coal-fired power plants. Switchgrass not only provides a renewable feedstock but also aids in land reclamation and carbon sequestration. 1) Remote Sensing and Machine Learning for Waste Coal Identification Using Sentinel-2 satellite imagery and supervised classification, we applied four machine learning models to detect historical waste coal piles. Random Forest achieved the highest accuracy (precision: 86%, recall: 77%). Time-series analysis revealed gradual vegetation recovery since 1986, indicating natural reclamation processes in historical sites, while active mining areas showed ongoing disturbance. This workflow enables scalable monitoring and prioritization of reclamation efforts. 2) UAS-Based Stockpile Volume Estimation To quantify recoverable waste coal, we evaluated Unmanned Aerial Systems (UAS) equipped with Light Detection and Ranging (LiDAR) and multispectral sensors. Structure-from-Motion (SfM) photogrammetry combined with interpolated Digital Terrain Models (DTMs) achieved strong agreement with LiDAR reference volumes (Root Mean Square Error (RMSE) ≈147 m 3 , Mean Absolute Percentage Error (MAPE) ≈2%). Sensitivity analysis confirmed that spatial resolution significantly influences accuracy, emphasizing the need for high-resolution data for precise volume estimation. This approach offers a scalable, cost-effective, and accurate alternative to conventional ground-based surveys. 3) Switchgrass Cultivation for Bioenergy and Water Quality Improvement We assessed the hydrological and water quality impacts of converting AMLs to switchgrass production areas using the Soil and Water Assessment Tool (SWAT). Results showed that converting 10% of the watershed area into the switchgrass production zone reduced streamflow by 3.1%, total suspended solids by 18.1%, total nitrogen by 7.6%, and total phosphorus by 6.2%, while achieving biomass yields of 8.6–9.2 metric tons per hectare. These findings highlight switchgrass as a dual-benefit strategy for land reclamation and bioenergy feedstock production. 4) Integrated Co-Firing and CCS for Carbon-Negative Power Generation We modeled co-firing scenarios using the Power Plant Flexible Model (PPFM) to evaluate plant efficiency, greenhouse gas (GHG) emissions, and levelized cost of electricity (LCOE). Without carbon capture and storage (CCS), increasing switchgrass co-firing ratios reduced LCOE from $\$$150/MWh at 0% biomass to $\$$110/MWh at full substitution. Under CCS, costs remained higher (~$\$$250/MWh at 0% biomass) but decreased to $\$$200/MWh at 100% biomass, while enabling net-zero or carbon-negative electricity due to switchgrass sequestration benefits. Although CCS introduced efficiency penalties, pairing it with biomass co-firing offset these impacts and maximized climate benefits. Overall, optimizing co-firing ratios between 60-100%, supported by reliable logistics and storage strategies, emerged as a practical pathway to balance affordability, sustainability, and net-zero or negative GHG emissions while promoting productive reuse of AMLs.

01 COAL, LIGNITE, AND PEAT↗

Towards developing multiscale-multiphysics models and their surrogates for digital twins of metal additive manufacturing

Artificial intelligence (AI) embedded within digital models of manufacturing processes can be used to improve process productivity and product quality significantly. The application of such advanced capabilities particularly to highly digitalized processes such as metal additive manufacturing (AM) is likely to make those processes commercially more attractive. AI capabilities will reside within Digital Twins (DTs) which are living virtual replicas of the physical processes. DTs will be empowered to operate autonomously in a diagnostic control capacity to supervise processes and can be interrogated by the practitioner to inform the optimal processing route for any given product. The utility of the information gained from the DTs would depend on the quality of the digital models and, more importantly, their faster-solving surrogates which dwell within DTs for consultation during rapid decision-making. In this article, we point out the exceptional value of DTs in AM and focus on the need to create high-fidelity multiscale-multiphysics models for AM processes to feed the AI capabilities. We identify technical hurdles for their development, including those arising from the multiscale and multiphysics characteristics of the models, the difficulties in linking models of the subprocesses across scales and physics, and the scarcity of experimental data. We discuss the need for creating surrogate models using machine learning approaches for real-time problem-solving. We further identify non-technical barriers, such as the need for standardization and difficulties in collaborating across different types of institutions. We offer potential solutions for all these challenges, after reflecting on and researching discussions held at an international symposium on the subject in 2019. Here, we argue that a collaborative approach can not only help accelerate their development compared with disparate efforts, but also enhance the quality of the models by allowing modular development and linkages that account for interactions between the various sub-processes in AM. A high-level roadmap is suggested for starting such a collaboration.

36 MATERIALS SCIENCE↗

The development of an augmented machine learning approach for the additive manufacturing of thermoelectric materials

Through the integration of machine learning (ML) techniques alongside additive manufacturing (AM) experimentation, we demonstrate an iterative process to rapidly predict laser-material interactions and melt pool geometries throughout the build parameter space for a bismuth telluride thermoelectric (TE) material. In doing so, we determined process parameters that created crack-free, highly dense (>99 %) n-type bismuth telluride (Bi 2 Te 2.7 Se 0.3 ) parts through laser powder bed fusion (LPBF). Furthermore, the ML-assisted understanding of the processing space allowed for the identification of build parameters that successfully yielded geometrically enhanced Bi 2 Te 2.7 Se 0.3 parts with reduced build times and no increase in experimental effort.

36 MATERIALS SCIENCE↗

DPM: A deep learning PDE augmentation method with application to large-eddy simulation

A framework is introduced that leverages known physics to reduce overfitting in machine learning for scientific applications. The partial differential equation (PDE) that expresses the physics is augmented with a neural network that uses available data to learn a description of the corresponding unknown or unrepresented physics. Training within this combined system corrects for missing, unknown, or erroneously represented physics, including discretization errors associated with the PDE's numerical solution. For optimization of the network within the PDE, an adjoint PDE is solved to provide high-dimensional gradients, and a stochastic adjoint method (SAM) further accelerates training. Additionally, the approach is demonstrated for large-eddy simulation (LES) of turbulence. High-fidelity direct numerical simulations (DNS) of decaying isotropic turbulence provide the training data used to learn sub-filter-scale closures for the filtered Navier–Stokes equations. Out-of-sample comparisons show that the deep learning PDE method outperforms widely-used models, even for filter sizes so large that they become qualitatively incorrect. It also significantly outperforms the same neural network when a priori trained based on simple data mismatch, not accounting for the full PDE. Measures of discretization errors, which are well-known to be consequential in LES, point to the importance of the unified training formulation's design, which without modification corrects for them. For comparable accuracy, simulation runtime is significantly reduced. A relaxation of the typical discrete enforcement of the divergence-free constraint in the solver is also successful, instead allowing the DPM to approximately enforce incompressibility physics. Since the training loss function is not restricted to correspond directly to the closure to be learned, training can incorporate diverse data, including experimental data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Improve the Search of Very Metal-poor Stars Using the Deep Learning Method

Very metal-poor (VMP) stars have [Fe/H] < -2.0 dex. They are among the oldest stars in the universe, and their unique metallicity can help explore the enrichment mechanism and evolutionary history of the chemical elements of stars in the early universe. However, most current stellar parameter estimation methods do not perform well in determining the stellar parameters of VMP stars, which limits our ability to discover and exploit the properties of VMP stars. In this study, we propose a new model based on a convolutional neural network to determine the stellar atmospheric parameters of VMP stars. We tested our model on the LAMOST spectra; our model can determine the effective temperature (T {sub eff}), surface gravity (log g), metallicity ([Fe/H]), and carbon abundance ([C/Fe]) of the LAMOST spectra with precisions σ(T {sub eff}) = 134.82 K, σ(log g) = 0.33 dex, σ ([Fe/H]) = 0.20 dex, and σ([C/Fe]) = 0.35 dex. Furthermore, our model can distinguish VMP stars from normal stars with an accuracy of 88.65%. We also compared this model with other widely used methods, and found that this method performs better than other methods. It can be applied to the stellar parameter pipelines of upcoming large surveys such as 4MOST, WEAVES, and MOONS to search for VMP stars and identify carbon-enhanced metal-poor stars.

36 MATERIALS SCIENCE↗

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD–ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

60 APPLIED LIFE SCIENCES↗

Toward a Climate OSSE Framework for Satellite Mission Design

The rich history of observing system simulation experiments (OSSEs) does not yet include a well-established framework for using climate models. The need for a climate OSSE is triggered by the need to quantify the value of a particular measurement for reducing the uncertainty in climate predictions, which differ from numerical weather predictions in that they depend on future atmospheric composition rather than the current state of the weather. However, both weather and climate modeling communities share a need for motivating major observing system investments. Here, we outline a new framework for climate OSSEs that leverages the use of machine learning to calibrate climate model physics against existing satellite data. We demonstrate its application using NASA’s GISS-E3 model to objectively quantify the value of potential future improvements in spaceborne measurements of Earth’s planetary boundary layer. A mature climate OSSE framework should be able to quantitatively compare the ability of proposed observing system architectures to answer a climate-related question, thus offering added value throughout the mission design process, which is subject to increasingly rapid advances in instrument and satellite technology. Technical considerations include selection of observational benchmarks and climate projection metrics, approaches to pinpoint the sources of model physics uncertainty that dominate uncertainty in projections, and the use of instrument simulators. Community and policy-making considerations include the potential to interface with an established culture of model intercomparison projects and a growing need to economically assess the value-driven efficiency of social spending on Earth observations.

54 ENVIRONMENTAL SCIENCES↗

Earth as a Proxy Exoplanet: Deconstructing and Reconstructing Spectrophotometric Light Curves

Point-source spectrophotometric (single-point) light curves of Earth-like planets contain a surprising amount of information about the spatial features of those worlds. Spatially resolving these light curves is important for assessing time-varying surface features and the existence of an atmosphere, which in turn is critical to life on Earth and significant for determining habitability on exoplanets. Given that Earth is the only celestial body confirmed to harbor life, treating it as a proxy exoplanet by analyzing time-resolved spectral images provides a benchmark in the search for habitable exoplanets. The Earth Polychromatic Imaging Camera (EPIC) on the Deep Space Climate Observatory (DSCOVR) provides such an opportunity, with observations of ∼5000 full-disk sunlit Earth images each year at 10 wavelengths with high temporal frequency. We disk-integrate these spectral images to create single-point light curves and decompose them into principal components (PCs). Using machine-learning techniques to relate the PCs to six preselected spatial features, we find that the first and fourth PCs of the single-point light curves, contributing ∼83.23% of the light-curve variability, contain information about low and high clouds, respectively. Surface information relevant to the contrast between land and ocean reflectance is contained in the second PC, while individual land subtypes are not easily distinguishable (<0.1% total light-curve variation). We build an Earth model by systematically altering the spatial features to derive causal relationships to the PCs. This model can serve as a baseline for analyzing Earth-like exoplanets and guide wavelength selection and sampling strategies for future observations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Constrained non-negative matrix factorization enabling real-time insights of in situ and high-throughput experiments

Non-negative matrix factorization (NMF) is an appealing class of methods for performing unsupervised learning on streaming spectral data, particularly in time-sensitive applications such as in situ characterization of materials. These methods seek to decompose a dataset into a small number of components and weights that can compactly represent the underlying signal while effectively reconstructing the observations with minimal error. However, canonical NMF methods have no underlying requirement that the reconstruction uses components or weights that are representative of the true physical processes. In this work, we demonstrate how constraining a subset of the NMF weights or components as rigid priors, provided as known or assumed values, can provide significant improvement in revealing true underlying phenomena. We present a PyTorch-based method for efficiently applying constrained NMF and demonstrate its application to several synthetic examples. Our implementation allows an expert researcher-in-the-loop to provide and dynamically adjust the constraints during a live experiment involving streaming spectral data. Such interactive priors allow researchers to specify known or identified independent components, as well as functional expectations about the mixing or transitions between the components. We further demonstrate the application of this method to measured synchrotron x-ray total scattering data from in situ beamline experiments. In such a context, constrained NMF can result in a more interpretive and scientifically relevant decomposition than canonical NMF or other decomposition techniques. As a result, the details of the method are provided, along with general guidance for employing constrained NMF in the extraction of critical information and insights during time-sensitive experimental applications.

36 MATERIALS SCIENCE↗

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

In vitro antibiotic susceptibility testing often fails to accurately predict in vivo drug efficacies, in part due to differences in the molecular composition between standardized bacteriologic media and physiological environments within the body. Here, we investigate the interrelationship between antibiotic susceptibility and medium composition in Escherichia coli K-12 MG1655 as contextualized through machine learning of transcriptomics data. Application of independent component analysis, a signal separation algorithm, shows that complex phenotypic changes induced by environmental conditions or antibiotic treatment are directly traced to the action of a few key transcriptional regulators, including RpoS, Fur, and Fnr. Integrating machine learning results with biochemical knowledge of transcription factor activation reveals medium-dependent shifts in respiration and iron availability that drive differential antibiotic susceptibility. By extension, the data generation and data analytics workflow used here can interrogate the regulatory state of a pathogen under any measured condition and can be applied to any strain or organism for which sufficient transcriptomics data are available.

59 BASIC BIOLOGICAL SCIENCES↗

Selecting durable building envelope systems with machine learning assisted hygrothermal simulations database

Hygrothermal simulations provide insight into the energy performance and moisture durability of building envelope components under dynamic conditions. The inputs required for hygrothermal simulations are extensive, and carrying out simulations and analyses requires expert knowledge. An expert system, the Building Science Advisor (BSA), has been developed to predict the performance and select the energy-efficient and durable building envelope systems for different climates. The BSA consists of decision rules based on expert opinions and thousands of parametric simulation results for selected wall systems. The number of potential wall systems results in millions, too many to simulate all of them. We present how machine learning can help predict durability data, such as mold growth, while minimizing the number of simulations needed to run. The simulation results are used for training and validation of machine learning tools for predicting wall durability. We tested Artificial Neural Network (ANN) and Gradient Boosted Decision Trees (GBDT) for their applicability and model accuracy. Models developed with both methods showed adequate prediction performance (root mean square error of 0.195 and 0.209, respectively). Finally, we introduce how the information supports guidance for envelope design via an easy-to-use web-based tool that does not require the end-user to run hygrothermal simulations.

Salonvaara, Mikael↗