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DOE OSTI2020

Preliminary Target Selection for the DESI Quasar (QSO) Sample

The DESI survey will measure large-scale structure using quasars as direct tracers of dark matter in the redshift range 0.9 < z < 2.1 and using quasar Lyα forests at z > 2.1. In this work, we present two methods to select candidate quasars for DESI based on imaging in three optical (g, r, z) and two infrared (W1, W2) bands. The first method uses traditional color cuts and the second utilizes a machine-learning algorithm.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

HIV vaccine enters human efficacy trials

The HIV mosaic vaccine was originally designed at Los Alamos National Laboratory using a machine learning algorithm designed by Bette Korber and her team. It's the first computationally designed HIV vaccine. Through a decade of testing, it has shown promise and is now in human efficacy trials. The study will evaluate whether the investigational vaccine regimen is safe and able to reduce the incidence of HIV infection among 2,600 sexually active women in sub-Saharan Africa. The new study, HVTN 705/HPX2008, is known as “Imbokodo,” the Zulu word for “rock,” from a South African saying that refers to the strength of women and their importance in the community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Predicting the proximity to macroscopic failure using local strain populations from dynamic in situ X-ray tomography triaxial compression experiments on rocks

Predicting the proximity of large-scale dynamic failure is a critical concern in the engineering and geophysical sciences. Here we use evolving contractive, dilatational, and shear strain deformation preceding failure in dynamic X-ray tomography experiments to examine which strain components best predict the proximity to failure. We develop machine learning models to predict the proximity to failure using time series of three-dimensional local incremental strain tensor fields acquired in rock deformation experiments under stress conditions of the upper crust. Three-dimensional scans acquired in situ throughout triaxial compression experiments provide a distribution of density contrasts from which we estimate the three-dimensional incremental strain that accumulates between each scan acquisition. Training machine learning models on multiple experiments of six rock types provides suites of feature importance that indicate the predictive power of each feature. Comparing the average importance of groups of features that include information about each strain component quantifies the ability of the contractive, dilatational and shear strain to predict the proximity of macroscopic failure. A total of 24 models of four machine learning algorithms with six rock types indicate that 1) the dilatational strain provides the best predictive power of the strain components, and 2) the intermediate values (25th-75th percentile) of the strain population provide the best predictive power of the statistics of the strain populations. In addition, the success of the predictions of models trained on one rock type and tested on other rock types quantifies the similarities and differences of the precursory strain accumulation process in the six rock types. These similarities suggest the potential existence of a unified theory of brittle rock deformation for a range of rock types.

58 GEOSCIENCES↗

DOE OSTI2023

Ten questions concerning reinforcement learning for building energy management

As buildings account for approximately 40% of global energy consumption and associated greenhouse gas emissions, their role in decarbonizing the power grid is crucial. The increased integration of variable energy sources, such as renewables, introduces uncertainties and unprecedented flexibilities, necessitating buildings to adapt their energy demand to enhance grid resiliency. Consequently, buildings must transition from passive energy consumers to active grid assets, providing demand flexibility and energy elasticity while maintaining occupant comfort and health. This fundamental shift demands advanced optimal control methods to manage escalating energy demand and avert power outages. Reinforcement learning (RL) emerges as a promising method to address these challenges. Here, in this paper, we explore ten questions related to the application of RL in buildings, specifically targeting flexible energy management. We consider the growing availability of data, advancements in machine learning algorithms, open-source tools, and the practical deployment aspects associated with software and hardware requirements. Our objective is to deliver a comprehensive introduction to RL, present an overview of existing research and accomplishments, underscore the challenges and opportunities, and propose potential future research directions to expedite the adoption of RL for building energy management.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

Development of an inexpensive matrix-assisted laser desorption—time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize

Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety contained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.

dereplication↗

DOE OSTI2023

Deep learning uncertainty quantification for clinical text classification

Machine learning algorithms are expected to work side-by-side with humans in decision-making pipelines. Thus, the ability of classifiers to make reliable decisions is of paramount importance. Deep neural networks (DNNs) represent the state-of-the-art models to address real-world classification. Although the strength of activation in DNNs is often correlated with the network’s confidence, in-depth analyses are needed to establish whether they are well calibrated. In this paper, we demonstrate the use of DNN-based classification tools to benefit cancer registries by automating information extraction of disease at diagnosis and at surgery from electronic text pathology reports from the US National Cancer Institute (NCI) Surveillance, Epidemiology, and End Results (SEER) population-based cancer registries. In particular, we introduce multiple methods for selective classification to achieve a target level of accuracy on multiple classification tasks while minimizing the rejection amount—that is, the number of electronic pathology reports for which the model’s predictions are unreliable. We evaluate the proposed methods by comparing our approach with the current in-house deep learning-based abstaining classifier. Overall, all the proposed selective classification methods effectively allow for achieving the targeted level of accuracy or higher in a trade-off analysis aimed to minimize the rejection rate. On in-distribution validation and holdout test data, with all the proposed methods, we achieve on all tasks the required target level of accuracy with a lower rejection rate than the deep abstaining classifier (DAC). Interpreting the results for the out-of-distribution test data is more complex; nevertheless, in this case as well, the rejection rate from the best among the proposed methods achieving 97% accuracy or higher is lower than the rejection rate based on the DAC. We show that although both approaches can flag those samples that should be manually reviewed and labeled by human annotators, the newly proposed methods retain a larger fraction and do so without retraining—thus offering a reduced computational cost compared with the in-house deep learning-based abstaining classifier.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Machine Learning Based Parallel I/O Predictive Modeling: A Case Study on Lustre File Systems

Parallel I/O hardware and software infrastructure is a key contributor to performance variability for applications running on large-scale HPC systems. This variability confounds efforts to predict application performance for characterization, modeling, optimization, and job scheduling. We propose a modeling approach that improves predictive ability by explicitly treating the variability and by leveraging the sensitivity of application parameters on performance to group applications with similar characteristics. We develop a Gaussian process-based machine learning algorithm to model I/O performance and its variability as a function of application and file system characteristics. We demonstrate the effectiveness of the proposed approach using data collected from the Edison system at the National Energy Research Scientific Computing Center. The results show that the proposed sensitivity-based models are better at prediction when compared with application-partitioned or unpartitioned models. We highlight modeling techniques that are robust to the outliers that can occur in production parallel file systems. Using the developed metrics and modeling approach, we provide insights into the file system metrics that have a significant impact on I/O performance.

I/O performance variability↗

DOE OSTI2023

Bayesian averaging for ground state masses of atomic nuclei in a Machine Learning approach

We present global predictions of the ground state mass of atomic nuclei based on a novel Machine Learning algorithm. We combine precision nuclear experimental measurements together with theoretical predictions of unmeasured nuclei. This hybrid data set is used to train a probabilistic neural network. In addition to training on this data, a physics-based loss function is employed to help refine the solutions. The resultant Bayesian averaged predictions have excellent performance compared to the testing set and come with well-quantified uncertainties which are critical for contemporary scientific applications. We assess extrapolations of the model’s predictions and estimate the growth of uncertainties in the region far from measurements.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Anomaly Detection and Mitigation for Dynamic Frequency Regulation in Hydropower-Battery Systems: Preprint

Hydropower operators and energy storage providers are increasingly interested in participating in frequency regulation services, driven by the incentives offered by independent system operators, such as the Pennsylvania-New Jersey-Maryland Interconnection (PJM), in a competitive electricity market. This transition, however, unfolds against the backdrop of a modernizing and rapidly digitizing power grid, exposing the integrated legacy infrastructure and vulnerable communication networks to a multitude of cybersecurity threats. These evolving threats not only endanger grid operations but also have the potential to trigger cascading disruptions across the broader grid network and influence regulation markets. This work presents an approach for developing an anomaly detection and mitigation system to address cybersecurity challenges during the participation of a hydropower-integrated battery energy storage system (BESS) in a frequency regulation market. The applied anomaly detector utilizes machine learning algorithms to provide detailed classification of cyber-physical events and provide a comprehensive situation awareness to grid operators. Later, the applied mitigation system triggers predefined corrective actions to minimize the impact of data integrity attacks on the regulation market and system stability. We evaluated the proposed approach on a fully active BESS topology using the slow regulation signal (Reg A) coming from the PJM market. Our simulation results reveal that the proposed approach performs well in detecting data integrity attacks within the allocated time frame and also minimizes the system's instability and economic loss during the participation of hydropower and BESS in the regulation market.

battery energy storage system↗

DOE OSTI2024

Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS

Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown. Characterizing polyketides relies on bioactivity-guided purification, which is expensive and time-consuming. To address this, we present Seq2PKS, a machine learning algorithm that predicts chemical structures derived from Type 1 polyketide synthases. Seq2PKS predicts numerous putative structures for each gene cluster to enhance accuracy. The correct structure is identified using a variable mass spectral database search. Benchmarks show that Seq2PKS outperforms existing methods. Applying Seq2PKS to Actinobacteria datasets, we discover biosynthetic gene clusters for monazomycin, oasomycin A, and 2-aminobenzamide-actiphenol.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Integrating Reanalysis and Satellite Cloud Information to Estimate Surface Downward Long-Wave Radiation

The estimation of downward long-wave radiation (DLR) at the surface is very important for the understanding of the Earth’s radiative budget with implications in surface–atmosphere exchanges, climate variability, and global warming. Theoretical radiative transfer and observationally based studies identify the crucial role of clouds in modulating the temporal and spatial variability of DLR. In this study, a new machine learning algorithm that uses multivariate adaptive regression splines (MARS) and the combination of near-surface meteorological data with satellite cloud information is proposed. The new algorithm is compared with the current operational formulation used by the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) Satellite Application Facility on Land Surface Analysis (LSA-SAF). Both algorithms use near-surface temperature and dewpoint temperature along with total column water vapor from the latest European Centre for Medium-range Weather Forecasts (ECMWF) reanalysis ERA5 and satellite cloud information from the Meteosat Second Generation. The algorithms are trained and validated using both ECMWF-ERA5 and DLR acquired from 23 ground stations as part of the Baseline Surface Radiation Network (BSRN) and the Atmospheric Radiation Measurement (ARM) user facility. Results show that the MARS algorithm generally improves DLR estimation in comparison with other model estimates, particularly when trained with observations. When considering all the validation data, root mean square errors (RMSEs) of 18.76, 23.55, and 22.08 W·m –2 are obtained for MARS, operational LSA-SAF, and ERA5, respectively. The added value of using the satellite cloud information is accessed by comparing with estimates driven by ERA5 total cloud cover, showing an increase of 17% of the RMSE. The consistency of MARS estimate is also tested against an independent dataset of 52 ground stations (from FLUXNET2015), further supporting the good performance of the proposed model.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

The structural information filtered features (SIFF) potential: Maximizing information stored in machine-learning descriptors for materials prediction

Machine learning inspired potentials continue to improve the ability for predicting structures of materials. However, many challenges still exist, particularly when calculating structures of disordered systems. These challenges are primarily due to the rapidly increasing dimensionality of the feature-vector space which in most machine-learning algorithms is dependent on the size of the structure. In this article, we present a feature-engineered approach that establishes a set of principles for representing potentials of physical structures (crystals, molecules, and clusters) in a feature space rather than a physically motivated space. Our goal in this work is to define guiding principles that optimize information storage of the physical parameters within the feature representations. In this manner, we focus on keeping the dimensionality of the feature space independent of the number of atoms in the structure. Our Structural Information Filtered Features (SIFF) potential represents structures by utilizing a feature vector of low-correlated descriptors, which correspondingly maximizes information within the descriptor. We present results of our SIFF potential on datasets composed of disordered (carbon and carbon–oxygen) clusters, molecules with C 7 O 2 H 2 stoichiometry in the GDB9-14B dataset, and crystal structures of the form (Al x Ga y In z ) 2 O 3 as proposed in the NOMAD Kaggle competition. Our potential's performance is at least comparable, sometimes significantly more accurate, and often more efficient than other well-known machine-learning potentials for structure prediction. However, primarily, we offer a different perspective on how researchers should consider opportunities in maximizing information storage for features.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Baseflow Identification via Explainable AI With Kolmogorov‐Arnold Networks

Abstract Hydrological models often involve constitutive laws that may not be optimal in every application. We propose to replace such laws with the Kolmogorov‐Arnold networks (KANs), a class of neural networks designed to identify symbolic expressions. We demonstrate KAN's potential on the problem of baseflow identification, a notoriously challenging task plagued by significant uncertainty. KAN‐derived functional dependencies of the baseflow components on the aridity index outperform their original counterparts; they demonstrate that water availability, rather than potential evapotranspiration, drives baseflow by constraining actual evapotranspiration under arid conditions. On a test set, they increase the Nash‐Sutcliffe efficiency (NSE) by 65%, decrease the root mean squared error by 29%, and increase the Kling‐Gupta efficiency by 34%. This superior performance is achieved while reducing the number of fitting parameters from three to two. Next, we use data from 378 catchments across the continental United States to refine the water‐balance equation at the mean‐annual scale. The KAN‐derived equations based on the refined water balance outperform both the current aridity index model, with up to a 105% increase in NSE, and the KAN‐derived equations based on the original water balance. While the performance of our model and tree‐based machine learning methods is similar, KANs offer the advantage of simplicity and transparency and require no specific software or computational tools. This case study focuses on the aridity index formulation, but the approach is flexible and transferable to other hydrological processes. Plain Language Summary Equations used in hydrologic model are often suboptimal, resulting in reduced prediction accuracy and efficiency. We implemented Kolmogorov‐Arnold networks (KAN), a machine learning algorithm for deriving symbolic formulations, to estimate groundwater recharge and showed that it outperforms an existing state‐of‐the‐art semi‐empirical formulation. In hydrology, Nash‐Sutcliffe efficiency (NSE), root mean squared error (RMSE), and Kling‐Gupta efficiency (KGE) are commonly used to evaluate model performance. Higher NSE and KGE values indicate better performance, while lower RMSE values are preferable. Our results show that NSE increased by 71%, RMSE decreased by 32%, and KGE improved by 25%. In addition, KAN identifies an optimal functional form and can be used to derive new analytical formulas using the prior knowledge. The KAN‐inspired equation outperformed the original formulation and reduced the fitting parameters. Furthermore, we refined the water‐balance equation at the mean‐annual scale and showed that, based on the new water‐balance equation, KAN can derive new formulations that are superior to the original aridity index formulations (up to 105% increase in NSE) and KAN‐derived equations based on the original water balance. These findings highlight the significant potential of KAN to advance the scientific understanding of a wide range of hydrologic processes. Key Points Kolmogorov‐Arnold networks (KANs) enhance interpretability of machine‐learned hydrological models KAN‐derived symbolic formulations outperform state‐of‐the‐art semi‐empirical aridity indices KAN‐identified functional form yields an analytical index with fewer fitting parameters and improved performance

baseflow↗

DOE OSTI2024

Characterization of Fuel Cladding Chemical Interaction on a High Burnup U-10Zr Metallic Fuel via Electron Energy Loss Spectroscopy Enhanced by Machine Learning

Fuel cladding chemical interaction (FCCI) is one of the main performance limiting factors for metallic nuclear fuels. The interaction destabilizes the martensitic microstructure and deteriorates mechanical properties of HT-9 cladding. The detection of low atomic number elements (Z<10) and overlapping of elemental peaks can be problematic in interpreting energy dispersive X-ray spectroscopy (EDS) data. Electron energy loss spectroscopy (EELS) provides precise elemental edge energy values and can detect elements with a low atomic number. This work utilizes EELS to study the distribution of lanthanides and light elements at the interaction region. The sample was prepared from the FCCI region of a U-10Zr (wt.%) solid fuel with HT-9 cladding, irradiated to a burnup of 13.2 at.%. Processing the EELS data included three major steps: 1) enhance the signal to noise ratio by denoising the spectrum with principal component analysis (PCA) method, removing background and performing deconvolution; 2) identify chemical elements with core energy loss edges; 3) confirm different phases using a popular machine learning method, K-means. This work presents qualitative assessment of lanthanides and light elements like carbon (C) and oxygen (O) enhanced by the application of machine learning algorithms. By comparing with EDS elemental maps, EELS provides higher resolution chemical maps, reveals the distribution of carbon at the interaction region supporting the formation of zirconium carbide, a rind-like microstructure feature that was proposed to mitigate the chemical interaction. Furthermore, the plasmon peak map was also found to indicate an energy shift associated with the formation of phases/compounds. K-means clustering method was used on the processed electron energy loss (EEL) spectrum to automatically reveal different phases. The resulting clustered maps from K-means clustering align well with elemental maps confirming certain phases, especially Fe-Ce and Zr-C, in the FCCI region.

EELS↗

DOE OSTI2018

Geologic CO 2 sequestration monitoring design: A machine learning and uncertainty quantification based approach

Monitoring is a crucial aspect of geologic carbon dioxide (CO 2 ) sequestration risk management. Effective monitoring is critical to ensure CO 2 is safely and permanently stored throughout the life-cycle of a geologic CO 2 sequestration project. Effective monitoring involves deciding: (i) where is the optimal location to place the monitoring well(s), and (ii) what type of data (pressure, temperature, CO 2 saturation, etc.) should be measured taking into consideration the uncertainties at geologic sequestration sites. We have developed a filtering-based data assimilation procedure to design effective monitoring approaches. To reduce the computational cost of the filtering-based data assimilation process, a machine-learning algorithm: Multivariate Adaptive Regression Splines is used to derive computationally effcient reduced order models from results of full-physics numerical simulations of CO 2 injection in saline aquifer and subsequent multi-phase fluid flow. We use example scenarios of CO 2 leakage through legacy wellbore and demonstrate a monitoring strategy can be selected with the aim of reducing uncertainty in metrics related to CO 2 leakage. We demonstrate the proposed framework with two synthetic examples: a simple validation case and a more complicated case including multiple monitoring wells. The examples demonstrate that the proposed approach can be effective in developing monitoring approaches that take into consideration uncertainties.

58 GEOSCIENCES↗

DOE OSTI2019

An application of survival analysis to disruption prediction via Random Forests</strong

We report one of the most pressing challenges facing the fusion community is adequately mitigating or, even better, avoiding disruptions of tokamak plasmas. However, before this can be done, disruptions must first be predicted with sufficient warning time to actuate a response. The established field of survival analysis provides a convenient statistical framework for time-to-event (i.e. time-to-disruption) studies. This paper demonstrates the integration of an existing disruption prediction machine learning algorithm with the Kaplan–Meier estimator of survival probability. Specifically discussed are the implied warning times from binary classification of disruption databases and the interpretation of output signals from Random Forest algorithms trained and tested on these databases. This survival analysis approach is applied to both smooth and noisy test data to highlight important features of the survival and hazard functions. In addition, this method is applied to three Alcator C-Mod plasma discharges and compared to a threshold-based scheme for triggering alarms. In one case, both techniques successfully predict the disruption; although, in another, neither warns of the impending disruption with enough time to mitigate. For the final discharge, the survival analysis approach could avoid the false alarm triggered by the threshold method. Limitations of this analysis and opportunities for future work are also presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Predictive Models of Genetic Redundancy in Arabidopsis thaliana

Abstract Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene pairs, but a predictive model of genetic redundancy incorporating a wide variety of features derived from accumulating omics and mutant phenotype data is yet to be established. In addition, the relative importance of these features for genetic redundancy remains largely unclear. Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including posttranslational modifications, gene expression, and gene network properties. The definition of redundancy, data transformations, feature subsets, and machine learning algorithms used significantly affected model performance based on holdout, testing phenotype data. Among the most important features in predicting gene pairs as redundant were having a paralog(s) from recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and having similar expression patterns under stress conditions. We also explored the potential reasons underlying mispredictions and limitations of our studies. This genetic redundancy model sheds light on characteristics that may contribute to long-term maintenance of paralogs, and will ultimately allow for more targeted generation of functionally informative double mutants, advancing functional genomic studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Fine-tuning machine-learned particle-flow reconstruction for new detector geometries in future colliders

We demonstrate transfer learning capabilities in a machine-learned algorithm trained for particle-flow reconstruction in high energy particle colliders. This paper presents a cross-detector fine-tuning study, where we initially pretrain the model on a large full simulation dataset from one detector design, and subsequently fine-tune the model on a sample with a different collider and detector design. Specifically, we use the Compact Linear Collider detector (CLICdet) model for the initial training set and demonstrate successful knowledge transfer to the CLIC-like detector (CLD) proposed for the Future Circular Collider in electron-positron mode. We show that with an order of magnitude less samples from the second dataset, we can achieve the same performance as a costly training from scratch, across particle-level and event-level performance metrics, including jet and missing transverse momentum resolution. Furthermore, we find that the fine-tuned model achieves comparable performance to the traditional rule-based particle-flow approach on event-level metrics after training on 100,000 CLD events, whereas a model trained from scratch requires at least 1 million CLD events to achieve similar reconstruction performance. To our knowledge, this represents the first full-simulation cross-detector transfer learning study for particle-flow reconstruction. These findings offer valuable insights towards building large foundation models that can be fine-tuned across different detector designs and geometries, helping to accelerate the development cycle for new detectors and opening the door to rapid detector design and optimization using machine learning.

43 PARTICLE ACCELERATORS↗