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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Continual Learning for Pattern Recognizers using Neurogenesis Deep Learning

Deep neural networks have emerged as a leading set of algorithms to infer information from a variety of data sources such as images and time series data. In their most basic form, neural networks lack the ability to adapt to new classes of information. Continual learning is a field of study attempting to give previously trained deep learning models the ability to adapt to a changing environment. Previous work developed a CL method called Neurogenesis for Deep Learning (NDL). Here, we combine NDL with a specific neural network architecture (the Ladder Network) to produce a system capable of automatically adapting a classification neural network to new classes of data. The NDL Ladder Network was evaluated against other leading CL methods. While the NDL and Ladder Network system did not match the cutting edge performance achieved by other CL methods, in most cases it performed comparably and is the only system evaluated that can learn new classes of information with no human intervention.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Considerations for Distributed Edge Data Centers and Use of Building Loads to Support Large Interconnections

The rapid expansion of artificial intelligence (AI) and machine learning is driving unprecedented electricity demand from data centers. It is predicted that by 2030, 90% of AI workloads will be inference-based, requiring interconnection of multiple low-latency edge data centers (<20 MW) sited closer to end users - often on already constrained distribution feeders. Although individually small, these loads can aggregate to large loads per feeder, straining infrastructure, creating multi-year interconnection delays, and driving up customer costs. This paper proposes a data center-focused grid-integration framework that combines feeder hosting capacity analysis with building energy efficiency, building load flexibility, and waste heat reuse to expand effective feeder and substation headroom. Such approaches can reduce interconnection delays, lower costs for ratepayers, and accelerate AI-ready infrastructure deployment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Enabling Robust Exoplanet Atmospheric Retrievals with Gaussian Processes

Atmospheric retrievals are essential tools for interpreting exoplanet transmission and eclipse spectra, enabling quantitative constraints on the chemical composition, aerosol properties, and thermal structure of planetary atmospheres. The James Webb Space Telescope (JWST) offers unprecedented spectral precision, resolution, and wavelength coverage, unlocking transformative insights into the formation, evolution, climate, and potential habitability of planetary systems. However, this opportunity is accompanied by challenges: modeling assumptions and unaccounted-for noise or signal sources can bias retrieval outcomes and their interpretation. To address these limitations, we introduce a Gaussian process (GP)-aided atmospheric retrieval framework that flexibly accounts for unmodeled features and correlated noise in exoplanet spectra. We validate this method on synthetic JWST observations, and show that GP-aided retrievals reduce bias in inferred abundances and better capture model–data mismatches than traditional approaches. We also introduce the concept of mean squared error to quantify the trade-off between bias and variance, arguing that this metric more accurately reflects retrieval performance than bias alone. We then reanalyze the NIRISS/SOSS JWST transmission spectrum of WASP-96 b, finding that GP-aided retrievals yield broader constraints on CO 2 and H 2 O, possibly alleviating tension between previous retrieval results and equilibrium predictions. Our GP framework provides precise and accurate constraints while highlighting regions where models fail to explain the data. As JWST matures and future facilities come online, a deeper understanding of the limitations of both data and models will be essential, and GP-enabled retrievals like the one presented here offer a principled path forward.

Rotman, Yoav [Arizona State Univ., Tempe, AZ (Unit↗
DOE OSTI2022

Autodifferentiable Spectrum Model for High-dispersion Characterization of Exoplanets and Brown Dwarfs

We present an autodifferentiable spectral modeling of exoplanets and brown dwarfs. This model enables a fully Bayesian inference of the high-dispersion data to fit the ab initio line-by-line spectral computation to the observed spectrum by combining it with the Hamiltonian Monte Carlo in recent probabilistic programming languages. An open-source code, ExoJAX, developed in this study, was written in Python using the GPU/TPU compatible package for automatic differentiation and accelerated linear algebra, JAX. We validated the model by comparing it with existing opacity calculators and a radiative transfer code and found reasonable agreements for the output. As a demonstration, we analyzed the high-dispersion spectrum of a nearby brown dwarf, Luhman 16 A, and found that a model including water, carbon monoxide, and H 2 /He collision-induced absorption was well fitted to the observed spectrum (R = 10 5 and 2.28-2.30 μm). As a result, we found that T0 = 1295$^{-32}_{+35}$ K at 1 bar and C/O = 0.62 ± 0.03, which is slightly higher than the solar value. This work demonstrates the potential of a full Bayesian analysis of brown dwarfs and exoplanets as observed by high-dispersion spectrographs and also directly imaged exoplanets as observed by high-dispersion coronagraphy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Post-irradiation Heating Tests of As-Irradiated AGR-3/4 TRISO Fuel Compacts

Four post-irradiation heating tests of fuel compacts from the U.S. Advanced Gas Reactor (AGR)-3/4 irradiation experiment were completed. In addition to tristructural isotropic (TRISO)-coated driver fuel, each compact contained designed-to-fail (DTF) particles with fuel kernels coated only in pyrocarbon so as to simulate exposed kernels. Tests at 1600/1700°C, 1400°C, and 1200°C were performed to measure fission product release as a function of time and temperature. Silver release was highest in the 1200°C test, supporting the observation that silver release rates are highest in the 1100–1300°C range. Compared to tests of AGR-1 compacts with no exposed kernels, the Cs-134 and Kr-85 releases were noticeably higher in AGR-3/4. The exposed kernels’ contributions to Eu and Sr release are inconclusive, due to the difficulty in distinguishing among the combined effects of higher irradiation temperatures in these particular AGR-3/4 compacts, the presence of the DTF particles, and the Fuel Accident Condition Simulator (FACS) test temperatures. These data can be used to make inferences about fission product retention in exposed kernels as a function of time and temperature.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

First Estimation of Model Parameters for Neutrino-Induced Nucleon Knockout Using Simulation-Based Inference

To enable an accurate determination of oscillation parameters, accelerator-based neutrino experiments require detailed simulations of nuclear interaction physics in the GeV regime. While substantial effort from both theory and experiment is currently being invested to improve the fidelity of these simulations, their present deficiencies typically oblige experimental collaborations to resort to empirical tuning of simulation model parameters. As the precision requirements of the field continue to become more stringent, machine learning techniques may provide a powerful means of handling corresponding growth in the complexity of future neutrino interaction model tuning exercises. To study the suitability of simulation-based inference (SBI) for this physics application, in this paper we revisit a tuned configuration of the GENIE neutrino event generator that was originally developed by the MicroBooNE collaboration. Despite closely reproducing the adopted values of four physics parameters when confronted with the tuned cross-section predictions as input, we find that our trained SBI algorithm prefers modestly different values (within MicroBooNE's assigned uncertainties) and achieves slightly better goodness-of-fit when inference is run on the experimental data set originally used by MicroBooNE. We also find that our trained algorithm can create a fair approximation of an alternative neutrino scattering simulation, NuWro, that shares only a subset of its physics model parameters with GENIE.

Tame-Narvaez, Karla [Fermilab] (ORCID:000000022249↗
DOE OSTI2023

Locating Operational Events of the Cooling Tower of a Nuclear Reactor with a Very Local Seismic Network

Geolocation of emergent seismic signals is challenging at close distances. Here, we used three-component data from a seismic network and a targeted experiment at a research nuclear reactor to locate seismic sources. Utilizing known events collected during the targeted experiment, we were able to infer source locations with seismic amplitudes and polarization characteristics of the data. Although the resolution of the source location is not perfect, the seismic amplitudes and polarization analysis offer useful constraints. For the known events, the source region inferred with our analysis includes the true source locations. Synthetic tests indicate the resolution is largely due to limited data coverage and measurement uncertainties because the synthetic tests show similar results compared with the field data. We identified the source of the unknown event through spectrum cross correlation between the signals from the known events and an unknown event. Our findings were confirmed by operational staff at the facility. When the propagation medium properties (i.e., seismic velocity and quality factor for attenuation) are known, our analysis can be applied to continuous data from a seismic array to infer both source amplitude and location. If the medium properties are not known, a targeted experiment can be conducted to estimate them.

58 GEOSCIENCES↗
DOE OSTI2024

Increasing the power of weak lensing data with multipole-based intrinsic alignment estimators

ABSTRACT It has long been known that galaxy shapes align coherently with the large-scale density field. Characterizing this effect is essential to interpreting measurements of weak gravitational lensing, the deflection of light from distant galaxies by matter overdensities along the line of sight, as it also produces coherent galaxy alignments that we wish to interpret in terms of a cosmological model. Existing direct measurements of intrinsic alignments using galaxy samples with high-quality shape and redshift measurements typically use well-understood but sub-optimal projected estimators, which do not make good use of the information in the data when comparing those estimators to theoretical models. We demonstrate a more optimal estimator, based on a multipole expansion of the correlation functions or power spectra, for direct measurements of galaxy intrinsic alignments. We show that even using the lowest order multipole alone increases the significance of inferred model parameters using simulated and real data, without any additional modelling complexity. We apply this estimator to measurements of parameters of the non-linear alignment model using data from the Sloan Digital Sky survey, demonstrating consistent results with a factor of ∼2 greater precision in parameter fits to intrinsic alignments models. This result is functionally equivalent to quadrupling the survey area, but without the attendant costs – thereby demonstrating the value in using this new estimator in current and future intrinsic alignments measurements using spectroscopic galaxy samples.

Astronomy & Astrophysics↗
DOE OSTI2026

On-chip probabilistic inference for charged-particle tracking at the sensor edge

Modern scientific instruments operate under increasingly extreme constraints on bandwidth, latency, and power. Inference at the sensor edge determines experimental data collection efficiency by deciding which information to save for further analysis. Particle tracking detectors at the Large Hadron Collider exemplify this challenge: pixelated silicon sensors generate rich spatiotemporal ionization patterns, yet most of this information is discarded due to data-rate limitations. Concurrently, advancements in co-design tools provide rapid turn-around for incorporating machine learning into application-specific integrated circuits, motivating designs for particle detectors with new integrated technologies. We demonstrate that neural networks embedded in the front-end electronics can infer charged-particle kinematic parameters from a single silicon layer. We regress hit positions and incident angles with calibrated uncertainties, while satisfying stringent constraints on numerical precision, latency, and silicon area. Our results establish a path toward probabilistic inference directly at the edge, opening new opportunities for intelligent sensing in high-rate scientific instruments.

Das, Arghya Ranjan [Purdue U.] (ORCID:000000018451↗
DOE OSTI2021

Bayesian learning of orthogonal embeddings for multi-fidelity Gaussian Processes

Uncertainty propagation in complex engineering systems often poses significant computational challenges related to modeling and quantifying probability distributions of model outputs, as those emerge as the result of various sources of uncertainty that are inherent in the system under investigation. Gaussian Processes regression (GPs) is a robust meta-modeling technique that allows for fast model prediction and exploration of response surfaces. Multi-fidelity variations of GPs further leverage information from cheap and low fidelity model simulations in order to improve their predictive performance on the high fidelity model. In order to cope with the high volume of data required to train GPs in high dimensional design spaces, a common practice is to introduce latent design variables that are typically projections of the original input space to a lower dimensional subspace, and therefore substitute the problem of learning the initial high dimensional mapping, with that of training a GP on a low dimensional space. Here in this paper, we present a Bayesian approach to identify optimal transformations that map the input points to low dimensional latent variables. The \projection" mapping consists of an orthonormal matrix that is considered a priori unknown and needs to be inferred jointly with the GP parameters, conditioned on the available training data. The proposed Bayesian inference scheme relies on a two-step iterative algorithm that samples from the marginal posteriors of the GP parameters and the projection matrix respectively, both using Markov Chain Monte Carlo (MCMC) sampling. In order to take into account the orthogonality constraints imposed on the orthonormal projection matrix, a Geodesic Monte Carlo sampling algorithm is employed, that is suitable for exploiting probability measures on manifolds. We extend the proposed framework to multi-fidelity models using GPs including the scenarios of training multiple outputs together. We validate our framework on three synthetic problems with a known lower-dimensional subspace. The benefits of our proposed framework, are illustrated on the computationally challenging aerodynamic optimization of a last-stage blade for an industrial gas turbine, where we study the effect of an 85-dimensional shape parameterization of a three-dimensional airfoil on two output quantities of interest, specifically on the aerodynamic efficiency and the degree of reaction

42 ENGINEERING↗
DOE OSTI2023

classLog: Logistic regression for the classification of genetic sequences

Introduction Sequencing and phylogenetic classification have become a common task in human and animal diagnostic laboratories. It is routine to sequence pathogens to identify genetic variations of diagnostic significance and to use these data in realtime genomic contact tracing and surveillance. Under this paradigm, unprecedented volumes of data are generated that require rapid analysis to provide meaningful inference. Methods We present a machine learning logistic regression pipeline that can assign classifications to genetic sequence data. The pipeline implements an intuitive and customizable approach to developing a trained prediction model that runs in linear time complexity, generating accurate output rapidly, even with incomplete data. Our approach was benchmarked against porcine respiratory and reproductive syndrome virus (PRRSv) and swine H1 influenza A virus (IAV) datasets. Trained classifiers were tested against sequences and simulated datasets that artificially degraded sequence quality at 0, 10, 20, 30, and 40%. Results When applied to a poor-quality sequence data, the classifier achieved between >85% to 95% accuracy for the PRRSv and the swine H1 IAV HA dataset and this increased to near perfect accuracy when using the full dataset. The model also identifies amino acid positions used to determine genetic clade identity through a feature selection ranking within the model. These positions can be mapped onto a maximum-likelihood phylogenetic tree, allowing for the inference of clade defining mutations. Discussion Our approach is implemented as a python package with code available at https://github.com/flu-crew/classLog .

Zeller, Michael A.↗
DOE OSTI2020

The GABLE Report: Garbled Autonomous Bots Leveraging Ethereum

Simple but mission-critical internet-based applications that require extremely high reliability and availability could potentially benefit from running on robust public programmable blockchain platforms such as Ethereum. Unfortunately, program code running on such blockchains is ordinarily publicly viewable, rendering these platforms unsuitable for applications requiring strict privacy of application code, data, and results. However, might it be possible to encode an application's business logic and data for these platforms in such a way that it becomes impossible for unauthorized parties to infer any meaningful information whatsoever about the semantics of the data, and the operations being performed on that data? In this report, we describe GABLE (Garbled Autonomous Bots Leveraging Ethereum), a system concept developed at Sandia that achieves this security goal in a limited, but still useful range of circumstances. GABLE, uses simple but effective algorithms to permit secure private execution of garbled state machines (and more efficient garbled circuits) on public computing resources. We give an example working implementation for garbled state machines, written using the Python and Solidity programming languages, and outline how our methods can be extended to support a more powerful garbled universal circuit model of computation. The capability embodied by the GABLE, system has significant potential applications, a few of which we discuss in this report.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Robust Carbon Dioxide Plume Imaging Using Joint Tomographic Inversion of Seismic Onset Time and Distributed Pressure and Temperature Measurements (Final Report)

We develop and demonstrate rapid and cost-effective methodologies for spatiotemporal tracking of CO2 plumes during geologic sequestration using joint inversion of seismic data and distributed pressure and temperature measurements. Key elements of our methodology are: (a) a computationally efficient approach to pressure and temperature propagation, (b) analysis of time lapse seismic data using a novel ‘seismic onset time’ approach to detect fluid front propagation, and (c) data assimilation and uncertainty assessment via joint inversion of pressure, temperature and time lapse seismic data, and (d) validating the numerical tomographic inversion using a CO2 injection demonstration projects, specifically data collected from the from the Petra Nova Parish Holdings CCUS project in the West Ranch Field, Texas and the Chester-16 reef CO2 injection site in Northern Michigan which is part of the DOE Midwestern Carbon Sequestration Project. The research team is led by Texas A&M University and includes Battelle as a subcontractor with support from Shell, Anadarko, Chevron and JX Nippon. A carbon dioxide (CO2) water-alternating-gas (WAG) pilot was conducted to gain insights into tertiary oil recovery potential via CO2 flood in the West Ranch Field as part of the Petra Nova project, the world’s largest post-combustion CO2 capture and utilization initiative. With a fluvial formation geology and large contrasts in permeability, this is a challenging and novel application of CO2 enhanced oil recovery (EOR). We build a predictive dynamic model of the subsurface that incorporates the multiphase and compositional data acquired during the pilot operation. The calibrated model is used for the carbon dioxide plume imaging. The study began with an initialization of the pilot sector model extracted from a calibrated full-field model. The pilot model calibration follows a two-step hierarchical workflow. First, we performed a large-scale update of the permeability distribution by integrating available bottomhole pressure and multiphase production data. In the second step, local permeability field is fine-tuned using a streamline-based method to match CO2 breakthrough times at the producers. The predictive capability of the calibrated model was verified through two blind validation tests: (1) the model showed good agreement with saturation logs acquired at two observation wells; and (2) the model reproduced the CO2 recovery as a fraction of the injected CO2. The use of seismic onset times has shown great promise for integrating near-continuous seismic surveys for updating geologic models. In this study, we analyze the impact of seismic survey frequency on the onset time approach aiming to extend the application of onset time to infrequent seismic surveys. In addition, we quantitatively examine the nonlinearity of the onset time method and compare it to the commonly used amplitude inversion method. We carry out a sensitivity analysis of seismic survey frequency based on the complete seismic survey data (over 175 surveys) of steam injection in a heavy oil reservoir (Peace River Unit) in Canada. Our results show that an adequate onset time map can be obtained from the infrequent seismic surveys by interpolation between seismic surveys as long as there is no change in the dominant underlying physics between the successive surveys. The study also shows that nonlinearity of the onset time method can be -smaller than that of the amplitude inversion method by several orders of magnitude. Application to the Brugge benchmark case shows that the onset time method obtains comparable permeability update as the traditional seismic amplitude inversion method with faster computation and improved convergence characteristics. We extend the streamline-based data integration approach to incorporate distributed temperature sensor (DTS) data using the concept of thermal tracer travel time. Then, a hierarchical workflow composed of evolutionary and streamline methods is employed to jointly history match the DTS and pressure data. Finally, CO2 saturation and streamline maps are used to visualize the CO2 plume movement during the sequestration process. The hierarchical workflow is applied to a carbon sequestration project in a carbonate reef reservoir within the Northern Niagaran Pinnacle Reef Trend in Michigan, USA. The monitoring data set consists of distributed temperature sensing (DTS) data acquired at the injection well and a monitoring well, flowing bottom-hole pressure data at the injection well, and time-lapse pressure measurements at several locations along the monitoring well. The history matching results indicate that the CO2 movement is mostly restricted to the intended zones of injection which is consistent with an independent warm-back analysis of the temperature data. In addition to employing simulation models and inverse methods for CO2 plume imaging, we also initialized a data-driven technology for detecting inter-well connectivity based on production and pressure data. Our machine-learning framework is built on the statistical recurrent unit (SRU) model and interprets well-based injection/production data into inter-well connectivity without relying on a geologic model. We test it on synthetic and field-scale CO2 EOR projects utilizing the water-alternating-gas (WAG) process. The validation of the proposed data-driven inter-well connectivity assessment is performed using synthetic data from simulation models where inter-well connectivity can be easily measured using the streamline-based flux allocation. The SRU model is shown to offer excellent prediction performance on the synthetic case. Despite significant measurement noise and frequent well shut-ins imposed in the field-scale case, the SRU model offers good prediction accuracy, the overall relative error of the phase production rates at most producers ranges from 10% to 30%. It is shown that the dominant connections identified by the data-driven method and streamline method are in close agreement. Texas A&M University, the lead organization in the project, was primarily responsible for the development of tomographic approaches for CO2 plume mapping in conjunction with distributed pressure, temperature and seismic onset time data. Battelle, as a subcontractor, was primarily responsible for the development of analytical and empirical methods for analyzing transient injection rate and pressure data from point/line sources such as injection and monitoring wells. An additional area of emphasis for Battelle was the use of machine learning for such tasks as inferring reservoir connectivity information from injection-production data, and identifying variable importance for machine learning-based proxy models developed from full-physics simulations. The two organizations also collaborated on the application of the tomographic inversion methodology for a field data set.

02 PETROLEUM↗
DOE OSTI2026

Seismic Elastic Double-Beam Characterization of Faults and Fractures for CO₂ Storage Site Selection

Site characterization for underground injection and storage of gigatonne-scale CO₂ requires reliable and cost-effective methods to detect and characterize faults and fractures and to assess their stress state and fault activation potential. This is critical, as wastewater injection and disposal have been shown to activate faults and induce earthquakes, and CO₂ leakage remains a key concern for long-term storage. In this project, we developed seismic methods to detect and characterize large-scale sedimentary and crystalline basement faults and associated small-scale fractures below conventional seismic imaging resolution using multicomponent (9C) surface seismic data. Machine learning was used to automatically interpret large-scale faults, providing key information for estimating the maximum magnitude of potential induced earthquakes. High-fidelity imaging was achieved by exploiting redundancy across multiple elastic wave modes, where independent images from different modes and frequencies cross-validate each other. We also used our nonlinear signal comparison (NLSC) method for ground roll removal, improving data quality in complex near-surface conditions. The methods were validated using field data acquired in central Montana. Results show that basement faults extend into the sedimentary section and that small-scale fractures are widespread above the basement. The inferred stress orientation is consistent with regional stress data, and the estimated maximum induced earthquake magnitude is small (Mw ~2.3). The developed workflow provides a practical approach for fault and fracture characterization and for assessing induced seismicity and leakage risk. It is directly applicable to CO₂ storage site selection and to other subsurface systems.

02 PETROLEUM↗
DOE OSTI2021

A crystal plasticity finite element model embedding strain-rate sensitivities inherent to deformation mechanisms: Application to alloy AZ31

We report the fundamental power-law relationship representing the flow rule in crystal visco-plasticity ensures uniqueness in the selection of slip systems accommodating imposed plastic strain-rates. The power-law relationship also introduces an artificially high strain-rate sensitivity in crystal plasticity simulations, unless a high value of the power-law exponent is used. However, the use of high values for the exponent is limited by numerical tractability. This paper presents a numerical method implemented in a crystal plasticity finite element (CPFE) model for embedding any value of the power-law exponent reflecting the true material strain-rate sensitivity. Importantly, the method does not increase computation time involved in the simulations. The enhanced CPFE model is used to interpret and predict a complex strain-rate sensitive response and microstructural evolution of AZ31 Mg alloy. Measured values of strain-rate sensitivity for slip and twinning modes are used in the simulations. Calculations show that the model successfully captures the phenomena pertaining to the effect of changing applied strain-rate on the mechanical response including flow stress and evolution of texture and twinning for a broad range of strain-rates ranging from 10 -3 s -1 to 10 3 s -1 and loading orientations in tension and compression. It is shown that such predictions are a consequence of not only relative amounts of slip and twinning activities driven by a set of accurately characterized hardening law parameters but also values of the strain-rate sensitivities inherent to individual deformation mechanisms. Besides, the model validates the measured strain-rate dependency of deformation mechanisms while accurately reproducing the mechanical data. Hence, the model can be used to verify and further refine or infer measured strain-rate sensitivity per deformation mechanism by reproducing experimental data.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Abstract Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A computational pipeline to generate a synthetic dataset of metal ion sorption to oxides for AI/ML exploration

The charged mineral/electrolyte interfaces are ubiquitous in the surface and subsurface–including the surroundings of the geological disposal sites for radioactive waste. Therefore, understanding how ions interact with charged surfaces is critically important for predicting radionuclide mobility in the case of waste leakage. At present, the Surface Complexation Models (SCMs) are the most successful thermodynamic frameworks to describe ion retention by mineral surfaces. SCMs are interfacial speciation models that account for the effect of the electric field generated by charged surfaces on sorption equilibria. These models have been successfully used to analyze and interpret a broad range of experimental observations including potentiometric and electrokinetic titrations or spectroscopy. Unfortunately, many of the current procedures to solve and fit SCM to experimental data are not optimal, which leads to a non-transferable or non-unique description of interfacial electrostatics and consequently of the strength and extent of ion retention by mineral surfaces. Recent developments in Artificial Intelligence (AI) offer a new avenue to replace SCM solvers and fitting algorithms with trained AI surrogates. Unfortunately, there is a lack of a standardized dataset covering a wide range of SCM parameter values available for AI exploration and training–a gap filled by this study. Here, we described the computational pipeline to generate synthetic SCM data and discussed approaches to transform this dataset into AI-learnable input. First, we used this pipeline to generate a synthetic dataset of electrostatic properties for a broad range of the prototypical oxide/electrolyte interfaces. The next step is to extend this dataset to include complex radionuclide sorption and complexation, and finally, to provide trained AI architectures able to infer SCMs parameter values rapidly from experimental data. Here, we illustrated the AI-surrogate development using the ensemble learning algorithms, such as Random Forest and Gradient Boosting. These surrogate models allow a rapid prediction of the SCM model parameters, do not rely on an initial guess, and guarantee convergence in all cases.

Li, Chunhui↗