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DOE OSTI2022

Tracing and Forecasting Metabolic Indices of Cancer Patients Using Patient-Specific Deep Learning Models

We develop a patient-specific dynamical system model from the time series data of the cancer patient’s metabolic panel taken during the period of cancer treatment and recovery. The model consists of a pair of stacked long short-term memory (LSTM) recurrent neural networks and a fully connected neural network in each unit. It is intended to be used by physicians to trace back and look forward at the patient’s metabolic indices, to identify potential adverse events, and to make short-term predictions. When the model is used in making short-term predictions, the relative error in every index is less than 10% in the L ∞ norm and less than 6.3% in the L 1 norm in the validation process. Once a master model is built, the patient-specific model can be calibrated through transfer learning. As an example, we obtain patient-specific models for four more cancer patients through transfer learning, which all exhibit reduced training time and a comparable level of accuracy. This study demonstrates that this modeling approach is reliable and can deliver clinically acceptable physiological models for tracking and forecasting patients’ metabolic indices.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

An Evolve-Then-Correct Reduced Order Model for Hidden Fluid Dynamics

In this paper, we put forth an evolve-then-correct reduced order modeling approach that combines intrusive and nonintrusive models to take hidden physical processes into account. Specifically, we split the underlying dynamics into known and unknown components. In the known part, we first utilize an intrusive Galerkin method projected on a set of basis functions obtained by proper orthogonal decomposition. We then present two variants of correction formula based on the assumption that the observed data are a manifestation of all relevant processes. The first method uses a standard least-squares regression with a quadratic approximation and requires solving a rank-deficient linear system, while the second approach employs a recurrent neural network emulator to account for the correction term. We further enhance our approach by using an orthonormality conforming basis interpolation approach on a Grassmannian manifold to address off-design conditions. The proposed framework is illustrated here with the application of two-dimensional co-rotating vortex simulations under modeling uncertainty. The results demonstrate highly accurate predictions underlining the effectiveness of the evolve-then-correct approach toward real-time simulations, where the full process model is not known a priori.

long short-term memory↗

DOE OSTI2023

Spatio-Temporal Anomaly Detection with Graph Networks for Data Quality Monitoring of the Hadron Calorimeter

The Compact Muon Solenoid (CMS) experiment is a general-purpose detector for high-energy collision at the Large Hadron Collider (LHC) at CERN. It employs an online data quality monitoring (DQM) system to promptly spot and diagnose particle data acquisition problems to avoid data quality loss. In this study, we present a semi-supervised spatio-temporal anomaly detection (AD) monitoring system for the physics particle reading channels of the Hadron Calorimeter (HCAL) of the CMS using three-dimensional digi-occupancy map data of the DQM. We propose the GraphSTAD system, which employs convolutional and graph neural networks to learn local spatial characteristics induced by particles traversing the detector and the global behavior owing to shared backend circuit connections and housing boxes of the channels, respectively. Recurrent neural networks capture the temporal evolution of the extracted spatial features. We validate the accuracy of the proposed AD system in capturing diverse channel fault types using the LHC collision data sets. The GraphSTAD system achieves production-level accuracy and is being integrated into the CMS core production system for real-time monitoring of the HCAL. We provide a quantitative performance comparison with alternative benchmark models to demonstrate the promising leverage of the presented system.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Data Quality Monitoring for the Hadron Calorimeters Using Transfer Learning for Anomaly Detection

The proliferation of sensors brings an immense volume of spatio-temporal (ST) data in many domains, including monitoring, diagnostics, and prognostics applications. Data curation is a time-consuming process for a large volume of data, making it challenging and expensive to deploy data analytics platforms in new environments. Transfer learning (TL) mechanisms promise to mitigate data sparsity and model complexity by utilizing pre-trained models for a new task. Despite the triumph of TL in fields like computer vision and natural language processing, efforts on complex ST models for anomaly detection (AD) applications are limited. In this study, we present the potential of TL within the context of high-dimensional ST AD with a hybrid autoencoder architecture, incorporating convolutional, graph, and recurrent neural networks. Motivated by the need for improved model accuracy and robustness, particularly in scenarios with limited training data on systems with thousands of sensors, this research investigates the transferability of models trained on different sections of the Hadron Calorimeter of the Compact Muon Solenoid experiment at CERN. The key contributions of the study include exploring TL’s potential and limitations within the context of encoder and decoder networks, revealing insights into model initialization and training configurations that enhance performance while substantially reducing trainable parameters and mitigating data contamination effects.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Policy Innovation and Governance for Irrigation Sustainability in the Arid, Saline San Joaquin River Basin

This paper provides a chronology and overview of events and policy initiatives aimed at addressing irrigation sustainability issues in the San Joaquin River Basin (SJRB) of California. Although the SJRB was selected in this case study, many of the same resource management issues are being played out in arid, agricultural regions around the world. The first part of this paper provides an introduction to some of the early issues impacting the expansion of irrigated agriculture primarily on the west side of the San Joaquin Valley and the policy and capital investments that were used to address salinity impairments to the use of the San Joaquin River (SJR) as an irrigation water supply. Irrigated agriculture requires large quantities of water if it is to be sustained, as well as supply water of adequate quality for the crop being grown. The second part of the paper addresses these supply issues and a period of excessive groundwater pumping that resulted in widespread land subsidence. A joint federal and state policy response that resulted in the facilities to import Delta water provided a remedy that lasted almost 50 years until the Sustainable Groundwater Management Act of 2014 was passed in the legislature to address a recurrence of the same issue. The paper describes the current state of basin-scale simulation modeling that many areas, including California, are using to craft a future sustainable groundwater resource management policy. The third section of the paper deals with unique water quality issues that arose in connection with the selenium crisis at Kesterson Reservoir and the significant threats to irrigation sustainability on the west side of the San Joaquin Valley that followed. The eventual policy response to this crisis was incremental, spanning two decades of University of California-led research programs focused on finding permanent solutions to the salt and selenium contamination problems constraining irrigated agriculture, primarily on the west side. Arid-zone agricultural drainage-induced water quality problems are becoming more ubiquitous worldwide. One policy approach that found traction in California is an innovative variant on the traditional Total Maximum Daily Load (TMDL) approach to salinity regulation, which has features in common with a scheme in Australia’s Hunter River Basin. The paper describes the real-time salinity management (RTSM) concept, which is geared to improving coordination of west side agricultural and wetland exports of salt load with east side tributary reservoir release flows to improve compliance with river salinity objectives. RTSM is a concept that requires access to continuous flow and electrical conductivity data from sensor networks located along the San Joaquin River and its major tributaries and a simulation model-based decision support designed to make salt load assimilative capacity forecasts. Web-based information dissemination and data sharing innovations are described with an emphasis on experience with stakeholder engagement and participation. The last decade has seen wide-scale, global deployment of similar technologies for enhancing irrigation agriculture productivity and protecting environmental resources.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Sequence-Defined Nanotubes Assembled from IR780-Conjugated Peptoids for Chemophototherapy of Malignant Glioma

Near-infrared (NIR) laser-induced phototherapy through NIR agents has demonstrated the great potential for cancer therapy. However, insufficient tumor killing due to the nonuniform heat or cytotoxic singlet oxygen ( 1 O 2 ) distribution over tumors from phototherapy results in tumor recurrence and inferior outcomes. To achieve high tumor killing efficacy, one of the solutions is to employ the combinational treatment of phototherapy with other modalities, especially with chemotherapeutic agents. In this paper, a simple and effective multimodal therapeutic system was designed via combining chemotherapy, photothermal therapy (PTT), and photodynamic therapy (PDT) to achieve the polytherapy of malignant glioma which is one of the most aggressive tumors in the brain. IR-780 (IR780) dye-labeled tube-forming peptoids (PepIR) were synthesized and self-assembled into crystalline nanotubes (PepIR nanotubes). These PepIR nanotubes showed an excellent efficacy for PDT/PTT because the IR780 photosensitizers were effectively packed and separated from each other within crystalline nanotubes by tuning IR780 density; thus, a self-quenching of these IR780 molecules was significantly reduced. Moreover, the efficient DOX loading achieved due to the nanotube large surface area contributed to an efficient and synergistic chemotherapy against glioma cells. Given the unique properties of peptoids and peptoid nanotubes, we believe that the developed multimodal DOX-loaded PepIR nanotubes in this work offer great promises for future glioma therapy in clinic.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

An experimental process parameter study on the identification of defects in additively fabricated Al6061 with laser powder bed fusion

Additively fabricated metal parts using laser powder bed fusion (L-PBF) possess sophisticated morphology due to the recurrent use of laser-induced metal powder melting and solidification. The surface and 3D morphology of these parts often include defects in the form of protrusions, depressions, pores, voids, keyholes, or cracks that are known to be influenced by laser scanning paths and layer-to-layer processing. Such inconsistent part quality hampers the extensive adoption of L-PBF. Pores and cracks are detrimental to the fatigue life of the parts and components. Quantifying and controlling part defects and optimizing processing and scanning strategy parameters adaptively in real-time through in situ monitoring systems are highly desired. This study investigates the optimization of experimental process parameters (power, scan velocity, and hatch spacing) and their effects on the cracking and porosity of Al6061 alloy using machine learning techniques. Multi-objective optimization is formulated and conducted to determine the L-PBF parameters that minimize both porosity and crack densities.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Lithium in T Coronae Borealis

T Coronae Borealis is a recurrent, symbiotic nova system currently in quiescence between its periodic ≈80 yr cycle of eruptions. Observations during inter-outburst epochs provide an opportunity to study properties of the accretion disk and the M red giant. Here we present new irradiated (blackbody veiling) models, incorporating modern molecular opacities and line lists, of spectra derived from high-resolution (22,000 ≲ R ≲ 120,000) optical echelle observations obtained at two epochs, one prior to and one post the 2015 rebrightening event at similar spectroscopic system phase. We find a lithium abundance in the secondary at both epochs to be comparable. The non-irradiated (classical) model atmospheres yield a lithium abundance, A(Li) = 1.3 ± 0.1. The irradiated model (veiled) atmospheres, which are likely a better representation of the system in which the white dwarf and accretion disk illuminate the red giant, give A(Li) = 2.4 ± 0.1.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Photometry as a Proxy for Stellar Activity in Radial Velocity Analyses

Stellar activity remains a limiting factor in measuring precise planet parameters from radial velocity spectroscopy, not least in the search for Earth-mass planets orbiting in the habitable zones of Sun-like stars. One approach to mitigate stellar activity is to use combined analyses of both radial velocity and time-series photometry. We present an analysis of simultaneous disk-integrated photometry and radial velocity data of the Sun in order to determine the useful limits of a combined analysis. We find that simple periodogram or autocorrelation analysis of solar photometry give the correct rotation period <50% of the time. We therefore use a Gaussian process to investigate the time variability of solar photometry and to directly compare simultaneous photometry with radial velocity data. We find that the hyperparameter posteriors are relatively stable over 70 yr of solar photometry and the amplitude tracks the solar cycle. We observe good agreement between the hyperparameter posteriors for the simultaneous photometry and radial velocity data. Our primary conclusion is a recommendation to include an additional prior in Gaussian process fits to constrain the evolutionary timescale to be greater than the recurrence timescale (i.e., the rotation period) to recover more physically plausible and useful results. Our results indicate that such simultaneous monitoring may be a useful tool in enhancing the precision of radial velocity surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

KELT-11 b: Abundances of Water and Constraints on Carbon-bearing Molecules from the Hubble Transmission Spectrum

In the past decade, the analysis of exoplanet atmospheric spectra has revealed the presence of water vapor in almost all the planets observed, with the exception of a fraction of overcast planets. Indeed, water vapor presents a large absorption signature in the wavelength coverage of the Hubble Space Telescope’s (HST) Wide Field Camera 3 (WFC3), which is the main space-based observatory for atmospheric studies of exoplanets, making its detection very robust. However, while carbon-bearing species such as methane, carbon monoxide, and carbon dioxide are also predicted from current chemical models, their direct detection and abundance characterization has remained a challenge. Here we analyze the transmission spectrum of the puffy, clear hot-Jupiter KELT-11 b from the HST WFC3 camera. We find that the spectrum is consistent with the presence of water vapor and an additional absorption at longer wavelengths than 1.5 μm, which could well be explained by a mix of carbon bearing molecules. CO{sub 2}, when included is systematically detected. One of the main difficulties to constrain the abundance of those molecules is their weak signatures across the HST WFC3 wavelength coverage, particularly when compared to those of water. Through a comprehensive retrieval analysis, we attempt to explain the main degeneracies present in this data set and explore some of the recurrent challenges that are occurring in retrieval studies (e.g., the impact of model selection, the use of free versus self-consistent chemistry, and the combination of instrument observations). Our results make this planet an exceptional example of a chemical laboratory to test current physical and chemical models of the atmospheres of hot Jupiters.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

A Systematic Search for Outbursting AM CVn Systems with the Zwicky Transient Facility

AM CVn systems are a rare type of accreting binary that consists of a white dwarf and a helium-rich, degenerate donor star. Using the Zwicky Transient Facility (ZTF), we searched for new AM CVn systems by focusing on blue, outbursting stars. We first selected outbursting stars using the ZTF alerts. We cross matched the candidates with Gaia and Pan-STARRS catalogs. The initial selection of candidates based on the Gaia BP-RP contains 1751 unknown objects. We used the Pan-STARRS g-r and r-i color in combination with the Gaia color to identify 59 strong AM CVn candidates. We obtained identification spectra of 35 sources, of which 18 are high-priority candidates, and discovered nine new AM CVn systems and one magnetic CV that shows only He-ii lines. Using the outburst recurrence time, we estimate the orbital periods of the nine new AM CVn systems that are in the range of 29–50 minutes. We conclude that targeted follow up of blue, outbursting sources is an efficient method to find new AM CVn systems and we plan to follow up all candidates we identified to systematically study the population of outbursting AM CVn systems.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

First Impressions: Early-time Classification of Supernovae Using Host-galaxy Information and Shallow Learning

Substantial effort has been devoted to the characterization of transient phenomena from photometric information. Automated approaches to this problem have taken advantage of complete phase coverage of an event, limiting their use for triggering rapid follow-up of ongoing phenomena. In this work, we introduce a neural network with a single recurrent layer designed explicitly for early photometric classification of supernovae (SNe). Our algorithm leverages transfer learning to account for model misspecification, host-galaxy photometry to solve the data-scarcity problem soon after discovery, and a custom weighted loss to prioritize accurate early classification. We first train our algorithm using state-of-the-art transient and host-galaxy simulations, then adapt its weights and validate it on the spectroscopically confirmed SNe Ia, SNe II, and SNe Ib/c from the Zwicky Transient Facility Bright Transient Survey. On observed data, our method achieves an overall accuracy of 82% ± 2% within 3 days of an event’s discovery, and an accuracy of 87% ± 5% within 30 days of discovery. At both early and late phases, our method achieves comparable or superior results to the leading classification algorithms with a simpler network architecture. These results help pave the way for rapid photometric and spectroscopic follow-up of scientifically valuable transients discovered in massive synoptic surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

A Model for Pair Production Limit Cycles in Pulsar Magnetospheres

Abstract It was recently proposed that the electric field oscillation as a result of self-consistent e ± pair production may be the source of coherent radio emission from pulsars. Direct particle-in-cell simulations of this process have shown that the screening of the parallel electric field by this pair cascade manifests as a limit cycle, as the parallel electric field is recurrently induced when pairs produced in the cascade escape from the gap region. In this work, we develop a simplified time-dependent kinetic model of e ± pair cascades in pulsar magnetospheres that can reproduce the limit-cycle behavior of pair production and electric field screening. This model includes the effects of a magnetospheric current, the escape of e ± , as well as the dynamic dependence of pair production rate on the plasma density and energy. Using this simple theoretical model, we show that the power spectrum of electric field oscillations averaged over many limit cycles is compatible with the observed pulsar radio spectrum.

Astronomy & Astrophysics↗

DOE OSTI2022

Supernova-driven Turbulent Metal Mixing in High-redshift Galactic Disks: Metallicity Fluctuations in the Interstellar Medium and its Imprints on Metal-poor Stars in the Milky Way

The extent to which turbulence mixes gas in the face of recurrent infusions of fresh metals by supernovae (SN) could help provide important constraints on the local star formation conditions. This includes predictions of the metallicity dispersion among metal-poor stars, which suggests that the interstellar medium was not very well mixed at these early times. The purpose of this Letter is to help isolate, via a series of numerical experiments, some of the key processes that regulate turbulent mixing of SN elements in galactic disks. We study the gas interactions in small simulated patches of a galaxy disk with the goal of resolving the small-scale mixing effects of metals at parsec scales, which enables us to measure the turbulent diffusion coefficient in various galaxy environments. By investigating the statistics of variations of α elements in these simulations, we are able to derive constraints not only on the allowed range of intrinsic yield variations in SN explosions but also on the star formation history of the Milky Way. We argue that the observed dispersion of [Mg/Fe] in metal-poor halo stars is compatible with the star-forming conditions expected in dwarf satellites or in an early low-star-forming Milky Way progenitor. In particular, metal variations in stars that have not been phase-mixed can be used to infer the star-forming conditions of disrupted dwarf satellites.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Development of a Machine-Learned Cruise Guide Indicator for Rotorcraft

This paper presents a machine-learned virtual cruise guide indicator (vCGI) for Chinook helicopters. Two temporal neural networks were trained and evaluated on measured data from 55 flight tests, one for the fore rotor and another for the aft rotor, to predict a vCGI value, which protects 23 components from fatigue damage during steady-state conditions. Three different classes of machine learning architectures were evaluated for prediction of the vCGI from time sequences: a temporal convolutional neural network with 1D dilated causal convolutions, a long short-term memory recurrent neural network, and an attention-based transformer architecture. The final average model accuracy on unseen flight data is currently greater than 93% for CGI values which could result in fatigue damage and 90% for normal operation CGI values. Model accuracy was improved through a series of advancements in:(1) selection of optimal training data using temporal collective variables and unsupervised learning, (2) dataset augmentation with maximum-entropy temporal collective variables, and (3) implementation of a mixture-of-experts classification- regression approach using an adversarial classification approach to assign maneuver labels. The results are presented for each advancement in model development along with lessons learned in training machine learning models on real- world, time-dependent rotorcraft data.

Boyer, Mathew↗

DOE OSTI2022

KGML-ag: a modeling framework of knowledge-guided machine learning to simulate agroecosystems: a case study of estimating N<sub>2</sub>O emission using data from mesocosm experiments

Abstract. Agricultural nitrous oxide (N2O) emission accounts for a non-trivial fraction of global greenhouse gas (GHG) budget. To date, estimating N2O fluxes from cropland remains a challenging task because the related microbial processes (e.g., nitrification and denitrification) are controlled by complex interactions among climate, soil, plant and human activities. Existing approaches such as process-based (PB) models have well-known limitations due to insufficient representations of the processes or uncertainties of model parameters, and due to leverage recent advances in machine learning (ML) a new method is needed to unlock the “black box” to overcome its limitations such as low interpretability, out-of-sample failure and massive data demand. In this study, we developed a first-of-its-kind knowledge-guided machine learning model for agroecosystems (KGML-ag) by incorporating biogeophysical and chemical domain knowledge from an advanced PB model, ecosys, and tested it by comparing simulating daily N2O fluxes with real observed data from mesocosm experiments. The gated recurrent unit (GRU) was used as the basis to build the model structure. To optimize the model performance, we have investigated a range of ideas, including (1) using initial values of intermediate variables (IMVs) instead of time series as model input to reduce data demand; (2) building hierarchical structures to explicitly estimate IMVs for further N2O prediction; (3) using multi-task learning to balance the simultaneous training on multiple variables; and (4) pre-training with millions of synthetic data generated from ecosys and fine-tuning with mesocosm observations. Six other pure ML models were developed using the same mesocosm data to serve as the benchmark for the KGML-ag model. Results show that KGML-ag did an excellent job in reproducing the mesocosm N2O fluxes (overall r2=0.81, and RMSE=3.6 mgNm-2d-1 from cross validation). Importantly, KGML-ag always outperforms the PB model and ML models in predicting N2O fluxes, especially for complex temporal dynamics and emission peaks. Besides, KGML-ag goes beyond the pure ML models by providing more interpretable predictions as well as pinpointing desired new knowledge and data to further empower the current KGML-ag. We believe the KGML-ag development in this study will stimulate a new body of research on interpretable ML for biogeochemistry and other related geoscience processes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Technical note: Using long short-term memory models to fill data gaps in hydrological monitoring networks

Abstract. Quantifying the spatiotemporal dynamics in subsurface hydrological flows over a long time window usually employs a network of monitoring wells. However, such observations are often spatially sparse with potential temporal gaps due to poor quality or instrument failure. In this study, we explore the ability of recurrent neural networks to fill gaps in a spatially distributed time-series dataset. We use a well network that monitors the dynamic and heterogeneous hydrologic exchanges between the Columbia River and its adjacent groundwater aquifer at the U.S. Department of Energy's Hanford site. This 10-year-long dataset contains hourly temperature, specific conductance, and groundwater table elevation measurements from 42 wells with gaps of various lengths. We employ a long short-term memory (LSTM) model to capture the temporal variations in the observed system behaviors needed for gap filling. The performance of the LSTM-based gap-filling method was evaluated against a traditional autoregressive integrated moving average (ARIMA) method in terms of error statistics and accuracy in capturing the temporal patterns of river corridor wells with various dynamics signatures. Our study demonstrates that the ARIMA models yield better average error statistics, although they tend to have larger errors during time windows with abrupt changes or high-frequency (daily and subdaily) variations. The LSTM-based models excel in capturing both high-frequency and low-frequency (monthly and seasonal) dynamics. However, the inclusion of high-frequency fluctuations may also lead to overly dynamic predictions in time windows that lack such fluctuations. The LSTM can take advantage of the spatial information from neighboring wells to improve the gap-filling accuracy, especially for long gaps in system states that vary at subdaily scales. While LSTM models require substantial training data and have limited extrapolation power beyond the conditions represented in the training data, they afford great flexibility to account for the spatial correlations, temporal correlations, and nonlinearity in data without a priori assumptions. Thus, LSTMs provide effective alternatives to fill in data gaps in spatially distributed time-series observations characterized by multiple dominant frequencies of variability, which are essential for advancing our understanding of dynamic complex systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Micro- and nano-porosity of the active Alpine Fault zone, New Zealand

Porosity reduction in rocks from a fault core can cause elevated pore fluid pressures and consequently influence the recurrence time of earthquakes. We investigated the porosity distribution in the New Zealand's Alpine Fault core in samples recovered during the first phase of the Deep Fault Drilling Project (DFDP-1B) by using two-dimensional nanoscale and three-dimensional microscale imaging. Synchrotron X-ray microtomography-derived analyses of open pore spaces show total microscale porosities in the range of 0.1 %–0.24 %. These pores have mainly non-spherical, elongated, flat shapes and show subtle bipolar orientation. Scanning and transmission electron microscopy reveal the samples' microstructural organization, where nanoscale pores ornament grain boundaries of the gouge material, especially clay minerals. Our data imply that (i) the porosity of the fault core is very small and not connected; (ii) the distribution of clay minerals controls the shape and orientation of the associated pores; (iii) porosity was reduced due to pressure solution processes; and (iv) mineral precipitation in fluid-filled pores can affect the mechanical behavior of the Alpine Fault by decreasing the already critically low total porosity of the fault core, causing elevated pore fluid pressures and/or introducing weak mineral phases, and thus lowering the overall fault frictional strength. We conclude that the current state of very low porosity in the Alpine Fault core is likely to play a key role in the initiation of the next fault rupture.

58 GEOSCIENCES↗