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DOE OSTI2022

Case studies in bias reduction and inference for electronic health record data with selection bias and phenotype misclassification

Electronic health records (EHR) are not designed for population‐based research, but they provide easy and quick access to longitudinal health information for a large number of individuals. Many statistical methods have been proposed to account for selection bias, missing data, phenotyping errors, or other problems that arise in EHR data analysis. However, addressing multiple sources of bias simultaneously is challenging. We developed a methodological framework (R package, SAMBA ) for jointly handling both selection bias and phenotype misclassification in the EHR setting that leverages external data sources. These methods assume factors related to selection and misclassification are fully observed, but these factors may be poorly understood and partially observed in practice. As a follow‐up to the methodological work, we demonstrate how to apply these methods for two real‐world case studies, and we evaluate their performance. In both examples, we use individual patient‐level data collected through the University of Michigan Health System and various external population‐based data sources. In case study (a), we explore the impact of these methods on estimated associations between gender and cancer diagnosis. In case study (b), we compare corrected associations between previously identified genetic loci and age‐related macular degeneration with gold standard external summary estimates. These case studies illustrate how to utilize diverse auxiliary information to achieve less biased inference in EHR‐based research.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Bayesian learning with Gaussian processes for low-dimensional representations of time-dependent nonlinear systems

This work presents a data-driven method for learning low-dimensional time-dependent physics-based surrogate models whose predictions are endowed with uncertainty estimates. We use the operator inference approach to model reduction that poses the problem of learning low-dimensional model terms as a regression of state space data and corresponding time derivatives by minimizing the residual of reduced system equations. Standard operator inference models perform well with accurate training data that are dense in time, but producing stable and accurate models when the state data are noisy and/or sparse in time remains a challenge. Another challenge is the lack of uncertainty estimation for the predictions from the operator inference models. Our approach addresses these challenges by incorporating Gaussian process surrogates into the operator inference framework to (1) probabilistically describe uncertainties in the state predictions and (2) procure analytical time derivative estimates with quantified uncertainties. The formulation leads to a generalized least-squares regression and, ultimately, reduced-order models that are described probabilistically with a closed-form expression for the posterior distribution of the operators. The resulting probabilistic surrogate model propagates uncertainties from the observed state data to reduced-order predictions. Furthermore, we demonstrate the method is effective for constructing low-dimensional models of two nonlinear partial differential equations representing a compressible flow and a nonlinear diffusion–reaction process, as well as for estimating the parameters of a low-dimensional system of nonlinear ordinary differential equations representing compartmental models in epidemiology.

Data-driven model reduction↗

DOE OSTI2016

Detection of enhancement in number densities of background galaxies due to magnification by massive galaxy clusters

We present a detection of the enhancement in the number densities of background galaxies induced from lensing magnification and use it to test the Sunyaev-Zel'dovich effect (SZE-) inferred masses in a sample of 19 galaxy clusters with median redshift z similar or equal to 0.42 selected from the South Pole Telescope SPT-SZ survey. These clusters are observed by the Megacam on the Magellan Clay Telescope though gri filters. Two background galaxy populations are selected for this study through their photometric colours; they have median redshifts zmedian similar or equal to 0.9 (low-z background) and z(median) similar or equal to 1.8 (high-z background). Stacking these populations, we detect the magnification bias effect at 3.3 sigma and 1.3 sigma for the low-and high-z backgrounds, respectively. We fit Navarro, Frenk and White models simultaneously to all observed magnification bias profiles to estimate the multiplicative factor. that describes the ratio of the weak lensing mass to the mass inferred from the SZE observable-mass relation. We further quantify systematic uncertainties in. resulting from the photometric noise and bias, the cluster galaxy contamination and the estimations of the background properties. The resulting. for the combined background populations with 1 sigma uncertainties is 0.83 +/- 0.24(stat) +/- 0.074(sys), indicating good consistency between the lensing and the SZE-inferred masses. We use our best-fitting eta to predict the weak lensing shear profiles and compare these predictions with observations, showing agreement between the magnification and shear mass constraints. This work demonstrates the promise of using the magnification as a complementary method to estimate cluster masses in large surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Estimating the Timing of Early Simian-Human Immunodeficiency Virus Infections: a Comparison between Poisson Fitter and BEAST

Many HIV prevention strategies are currently under consideration where it is highly informative to know the study participants’ times of infection. These can be estimated using viral sequence data sampled early in infection. However, there are several scenarios that, if not addressed, can skew timing estimates. These include multiple transmitted/founder (TF) viruses, APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like)-mediated mutational enrichment, and recombination. Here, we suggest a pipeline to identify these problems and resolve the biases that they introduce. We then compare two modeling strategies to obtain timing estimates from sequence data. The first, Poisson Fitter (PF), is based on a Poisson model of random accumulation of mutations relative to the TF virus (or viruses) that established the infection. The second uses a coalescence-based phylogenetic strategy as implemented in BEAST. The comparison is based on timing predictions using plasma viral RNA (cDNA) sequence data from 28 simian-human immunodeficiency virus (SHIV)-infected animals for which the exact day of infection is known. In this particular setting, based on nucleotide sequences from samples obtained in early infection, the Poisson method yielded more accurate, more precise, and unbiased estimates for the time of infection than did the explored implementations of BEAST. The inference of the time of infection is a critical parameter in testing the efficacy of clinical interventions in protecting against HIV-1 infection. For example, in clinical trials evaluating the efficacy of passively delivered antibodies (Abs) for preventing infections, accurate time of infection data are essential for discerning levels of the Abs required to confer protection, given the natural Ab decay rate in the human body. In such trials, genetic sequences from early in the infection are regularly sampled from study participants, generally prior to immune selection, when the viral population is still expanding and genetic diversity is low. In this particular setting of early viral growth, the Poisson method is superior to the alternative approach based on coalescent methods. This approach can also be applied in human vaccine trials, where accurate estimates of infection times help ascertain if vaccine-elicited immune protection wanes over time.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

An optimization approach to design monitoring schemes for CO 2 leakage detection

This paper demonstrates an approach to identify optimal monitoring designs that minimize the time to first detection of CO 2 leakage from a subsurface storage formation. This research is part of the National Risk Assessment Partnership (NRAP), a DOE project tasked with conducting risk and uncertainty analysis in the areas of reservoir performance, natural leakage pathways, wellbore integrity, groundwater protection, monitoring, and systems level modeling. Our approach applies a simulated annealing algorithm that searches the solution space by iteratively mutating potential monitoring designs. An example application is provided to demonstrate the effectiveness and efficiency of this method compared to an exhaustive search of the entire solution space. We took into account uncertainty by evaluating the performance of potential monitoring designs across a set of simulated leakage realization. A flexible two-tiered signature was implemented to infer that CO 2 leakage had occurred. This approach was ~50 times faster than an exhaustive search. A user-friendly tool, MDLD, is being developed for use on personal computers to make this method available to stakeholders, regulators, and researchers.

03 NATURAL GAS↗

DOE OSTI2023

Early Alarm: Robust Event Analysis for Power Systems using 1-D Fully Convolutional Network

This work presents a novel deep learning model for early, accurate, and robust detection, recognition, and temporal localization of multi-type events in large-scale power systems. The proposed method develops a unified 1-D fully convolutional network (FCN) model that takes time series of raw frequency signals measured from a power system as input, extracts distinguishing features, and predicts at every temporal point in the time series if an event is happening and what the type of the event is. Compared to existing methods, the proposed model eliminates the necessity for hand-crafted feature extraction or complicated data pre-processing, can flexibly handle input signals of arbitrary length, and precisely infer the event occurrence time. Most importantly, the model is intentionally trained with incomplete patterns, such that it is more robust to partial features of an event which is common in real-world online recognition, resulting in early alarm for power system failures. Extensive experimental results demonstrate that the proposed method achieves superior performance to the state-of-the-art, and also shows strong robustness to noise and system oscillations.

Li, Chengcheng↗

NASA NTRS1975

Prediction of oxidation performance of reinforced carbon-carbon material for Space Shuttle leading edges

A method was developed for predicting oxidation performance, in an earth atmospheric entry environment, of reinforced carbon-carbon material, coated for oxidation resistance. A model was developed which describes oxidation control mechanisms, and the equations defining these mechanisms were derived. These relations were used to correlate oxidation test data, and to infer pertinent rate constants. Predictions were made of material oxidation performance in a representative entry environment, and the predictions were compared with ground test data. Results indicate that the method can be successfully used for predicting material oxidation performance.

Medford, J. E.↗

DOE OSTI2020

Inferring transmission heterogeneity using virus genealogies: estimation and targeted prevention

Spread of HIV typically involves uneven transmission patterns where some individuals spread to a large number of individuals while others to only a few or none. Such transmission heterogeneity can impact how fast and how much an epidemic spreads. Further, more efficient interventions may be achieved by taking such transmission heterogeneity into account. To address these issues, we developed two phylogenetic methods based on virus sequence data: 1) to generally detect if significant transmission heterogeneity is present, and 2) to pinpoint where in a phylogeny high-level spread is occurring. We derive inference procedures to estimate model parameters, including the amount of transmission heterogeneity, in a sampled epidemic. We show that it is possible to detect transmission heterogeneity under a wide range of simulated situations, including incomplete sampling, varying levels of heterogeneity, and including within-host genetic diversity. When evaluating real HIV-1 data from different epidemic scenarios, we found a lower level of transmission heterogeneity in slowly spreading situations and a higher level of heterogeneity in data that included a rapid outbreak, while R0 and Sackin’s index (overall tree shape statistic) were similar in the two scenarios, suggesting that our new method is able to detect transmission heterogeneity in real data. We then show by simulations that targeted prevention, where we pinpoint high-level spread using a coalescence measurement, is efficient when sequence data are collected in an ongoing surveillance system. Such phylogeny-guided prevention is efficient under both single-step contact tracing as well as iterative contact tracing as compared to random intervention.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Bayesian inference for high confidence signal validation and sensor calibration assessment - 328

Online Monitoring (OLM) systems has been investigated for applications in the nuclear industry for the past two decades. These systems offer economic and technological advantages over the currently implemented time based testing methods for sensors and associated instrumentations. The advantages offered not only augment economic viability of current nuclear reactors but will be an inevitable change called for to suit the technologies of the advanced reactors (Gen III+). Irrespective, the acceptance of OLM into the regulatory structure in the U.S. is still hindered by technical and structural clarity on uncertainty quantification used by these systems. A Bayesian inference technique is implemented in the form of a residual model to quantify uncertainty in OLM predictions. The developed system used Gaussian processes to represent the OLM predictions and model inadequacy, the stationary representation of model based uncertainty. In addition, model selection techniques are used in conjunction with numerical methods such as Genetic Algorithm (GA) and Gibb's sampler to add robustness to the estimation model inadequacy, particularly in the presence of drifts and faulted conditions. The prediction model developed herein find applicability in fault detection, obtaining real values of processes after the onset of faults etc. Further development looks into the extension of current method for a multiple output scale implementation. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NASA NTRS2004

Feasibility of Sensing Tropospheric Ozone with MODIS 9.6 Micron Observations

With the infrared observations made by the Moderate Resolution Imaging Spectrometer (MODIS) on board the EOS-Aqua satellite, which include the 9.73 micron channel, a method is developed to deduce horizontal patterns of tropospheric ozone in cloud free conditions on a scale of about 100 km. It is assumed that on such small scale, at a given instant, horizontal changes in stratospheric ozone are small compared to that in the troposphere. From theoretical simulations it is found that uncertainties in the land surface emissivity and the vertical thermal stratification in the troposphere can lead to significant errors in the inferred tropospheric ozone. Because of this reason in order to derive horizontal patterns of tropospheric ozone in a given geographic area a tuning of this method is necessary with the help of a few dependent cases. After tuning, this method is applied to independent cases of MODIS data taken over Los Angeles basin in cloud free conditions to derive horizontal distribution of ozone in the troposphere. Preliminary results indicate that the derived patterns of ozone resemble crudely the patterns of surface ozone reported by EPA.

Prabhakara, C.↗

NASA NTRS2019

New Estimates of Ice and Oxygen Fluxes Across the Entire Lid of Lake Vostok From Observations of Englacial Radio Wave Attenuation

Over deep Antarctic subglacial lakes, spatially varying ice thickness and the pressure‐dependent melting point of ice result in distinct areas of melting and freeze‐on at the ice‐water interface, that is, at the lake lid. These ice mass fluxes drive lake circulation and, because basal Antarctic ice contains air clathrate, affect the input of oxygen to the lake, with implications for subglacial life. Inferences of rates of melting and freeze‐on, that is, accretion rates, from radar layer tracking and geodesy are limited in spatial coverage and resolution. Here we develop a new method to estimate accretion rate, and the resulting oxygen input at a lake lid, using airborne radar data over Lake Vostok together with ice‐temperature and chemistry data from the Vostok ice core. Because the lake lid is a coherent reflector of known reflectivity (at our radar frequency), we can infer depth‐averaged radio wave attenuation in the ice, with a spatial resolution of ~1 km along flight lines. Spatial variation in attenuation depends mostly on variation in ice temperature near the lid, which in turn varies strongly with ice mass flux at the lid. We model ice temperature versus depth with ice mass flux as a parameter, thus linking that flux to observed depth‐averaged attenuation. The resulting map of melt and accretion rates independently reproduces features known from earlier studies but now covers the entire lid. We find that freeze‐on is dominant when integrated over the lid, with an ice imbalance of 0.05 to 0.07 cu.km/year, which is robust against uncertainties.

Dale P. Winebrenner↗

DOE OSTI2021

EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning

Characterizing the functional properties of plant acyl-ACP thioesterases (TEs), a key enzyme class used in the production of renewable oleochemicals in microbial hosts, experimentally, can be an expensive and time consuming process since it requires manual screening of thousands of candidates in a database. Using amino acid sequence to computationally predict an enzyme’s function might accelerate this process; however obtaining the necessary amount of information on previously characterized enzymes and their respective sequences required by standard Machine Learning (ML) based approaches to accurately infer sequence-function relationships can be prohibitive, especially with a low-throughput testing cycle. Experimental noise, unbalanced dataset where high sequence similarity does not always imply identical functional properties will further prevent robust prediction performance. Herein we present a ML method, Ensemble method for enZyme Classification (EnZymClass), that is specifically designed to address these issues. We used EnZymClass to classify TEs into short, long and mixed free fatty acid substrate specificity categories. While general guidelines for inferring substrate specificity have been proposed before, prediction of chain-length preference from primary sequence has remained elusive for plant acyl-ACP TEs. By applying EnZymClass to a subset of TEs in the ThYme database, we identified two medium chain TEs, ClFatB3 and CwFatB2, with previously uncharacterized activity in E. coli fatty acid production hosts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

deeprob/ThioesteraseEnzymeSpecificity: EnZymClass-first-release

Banerjee, Deepro↗

NASA NTRS2009

Comparison of Image Restoration Methods for Lunar Epithermal Neutron Emission Mapping

Orbital measurements of neutrons by the Lunar Exploring Neutron Detector (LEND) onboard the Lunar Reconnaissance Orbiter are being used to quantify the spatial distribution of near surface hydrogen (H). Inferred H concentration maps have low signal-to-noise (SN) and image restoration (IR) techniques are being studied to enhance results. A single-blind. two-phase study is described in which four teams of researchers independently developed image restoration techniques optimized for LEND data. Synthetic lunar epithermal neutron emission maps were derived from LEND simulations. These data were used as ground truth to determine the relative quantitative performance of the IR methods vs. a default denoising (smoothing) technique. We review and used factors influencing orbital remote sensing of neutrons emitted from the lunar surface to develop a database of synthetic "true" maps for performance evaluation. A prior independent training phase was implemented for each technique to assure methods were optimized before the blind trial. Method performance was determined using several regional root-mean-square error metrics specific to epithermal signals of interest. Results indicate unbiased IR methods realize only small signal gains in most of the tested metrics. This suggests other physically based modeling assumptions are required to produce appreciable signal gains in similar low SN IR applications.

McClanahan, T. P.↗

DOE OSTI2024

Analytic Neural Network Gaussian Process Enabled Chance-Constrained Voltage Regulation for Active Distribution Systems with PVs, Batteries and EVs

This paper proposes an analytic neural network Gaussian process (NNGP)-based chance-constrained real-time voltage regulation method for active distribution systems with photovoltaics (PVs), batteries, and electric vehicles (EVs). NNGP can utilize historical measurement data to achieve real-time probabilistic node voltage estimation through Bayesian inference. Then, NNGP is fully analytically embedded into the optimal power flow model to perform voltage regulation and adapt to various topological changes. The uncertainties of voltage estimations are easily considered via the chance constraint, and it has been shown that the adoption of this chance constraint can significantly improve the reliability of voltage regulation under various scenarios. The comparison results with other methods, carried out on a real 759-node distribution system located in western Colorado, U.S., show that the proposed method can achieve accurate voltage estimation across different topologies and reliably perform voltage regulation considering PVs, batteries, and EVs.

active distribution systems↗

DOE OSTI2013

Measurements of emittance at low energy

Ideally, experimental measurements of all beam parameters should be made at the exit of the injector. This has not been possible on DARHT Axis-II for various practical reasons. In particular, the emittance has not been measured there. This note reviews the methods we have used for emittance measurements on the linear induction accelerator (LIA) at low-energy (< 10 MeV). It includes a discussion of some of the issues associated with making those measurements on a beam from the injector. A successful plan for emittance measurements at any energy should incorporate measures to deal with these issues. To begin with, it should be recognized that emittance measurements at the injector are not critical for beam physics in the accelerator. The emittance at the injector has very little effect on accelerator beam dynamics except for an increase in size near the end, where the beam becomes emittance dominated. Therefore, imperfect knowledge has little effect on the design and implementation of a tune. This point is illustrated in Fig. 1, which shows beam envelope calculations for our present tune over a wide range of emittances. Compare this with using the wrong diode voltage in the tune design. Figure 2 shows the effect on the beam envelope of a 2% error in the measurement of diode voltage. Therefore, a few years ago, when we made plans for beam measurements at the diode while we were upgrading the injector cells, our highest priority was on magnetic spectrometer measurements of energy. These measurements were to be used to cross calibrate the diode-voltage monitor, so that accurate diode voltage measurements could be made on every shot after the spectrometer was removed. If emittance measurements at the injector are required, then three widely used methods should be considered. These are focusing magnet scans, the use of an emittance mask (pepper pot), and optical transition radiation (OTR). We have used all three of these on our accelerators. These are invasive methods. There are noninvasive methods that we have not yet used. For example, under some conditions the beam size obtained with diamagnetic loops can be used in conjunction with the envelope equation to infer emittance. To date our diamagnetic loop data has not been of sufficient quality to do this. Another technique is to measure the beam-distribution quadrupole moment with BPMs dispersed in a quadrupole magnet lattice. Our BPMs have this capability, but the only quad lattice is in the downstream transport (DST), so this method is deferred until we operate the DST. All three methods reviewed here are invasive, and require the insertion of a target into the beam. Therefore, there is always the accompanying risk of inadvertent destruction of the target, and scattering of target material throughout the accelerator or injector. The target damage mechanism is target heating to a temperature hot enough to evolve gas, which is impact ionized by the beam, which is then ion focused to a small enough spot for the energy density to damage the target material, often destructively. Target heating is directly proportional to beam current density and pulse length. Therefore, the key to minimizing risk of target damage is to design for a large beam at the target, low current from the diode, and the shortest possible current pulse. The large-beam requirement compromises emittance measurements with OTR or focal scans, but not with the pepper pot technique. Finally, to ensure a short pulse even if the crowbar fails, the Marx generator should be reconfigured to produce the shortest possible pulse.

43 PARTICLE ACCELERATORS↗

DOE OSTI2014

Understanding the formation and evolution of interstellar ices: a Bayesian approach

Understanding the physical conditions of dark molecular clouds and star-forming regions is an inverse problem subject to complicated chemistry that varies nonlinearly with both time and the physical environment. In this paper, we apply a Bayesian approach based on a Markov chain Monte Carlo (MCMC) method for solving the nonlinear inverse problems encountered in astrochemical modeling. We use observations for ice and gas species in dark molecular clouds and a time-dependent, gas-grain chemical model to infer the values of the physical and chemical parameters that characterize quiescent regions of molecular clouds. We show evidence that in high-dimensional problems, MCMC algorithms provide a more efficient and complete solution than more classical strategies. The results of our MCMC method enable us to derive statistical estimates and uncertainties for the physical parameters of interest as a result of the Bayesian treatment.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Retracted: Monitoring Hatchery Broodstock Composition and Genetic Variation of Spring/Summer Chinook Salmon in the Columbia River Basin with Multigeneration Pedigrees

Abstract Hatchery production of Chinook Salmon Oncorhynchus tshawytscha in the Columbia River basin comprises most of the anadromous salmonid production in this region. Hatchery facilities and programs serve to mitigate for impacts to salmonids due to the construction and operation of hydropower dams and habitat impacts from development in addition to the conservation and restoration of natural populations. A genetic method referred to as parentage-based tagging (PBT) enables highly reliable detection of hatchery-origin fish and inference of multigeneration pedigrees. This study compiles 11 years of PBT data from nearly 125,000 interior stream-type Chinook Salmon from 24 spawning hatcheries located in tributaries of the mid- and upper Columbia River as well as the Salmon, Clearwater, and Grande Ronde River subbasins. Multigenerational pedigrees allowed investigation of the proportion of natural- and hatchery-origin broodstock (pNOB and pHOB, respectively) for each hatchery and enumeration of the scale of production between segregated and integrated programs. We then compared how pHOB and the scale of production influenced the number of stray fish observed, genetic diversity, relatedness, and age-class compositions within broodstocks. Over 91.0% of hatchery broodstock could be assigned back to their parents, and there was an overall rate of less than 1.0% of broodstock that were unintentionally incorporated into nonnatal hatchery programs. We evaluated 14 segregated programs with 0.0–10.0% pNOB, 7 intermediate programs (10.1–50.0% pNOB), and 3 integrated programs (>50.0% pNOB). There was no correlation between the scale of production or pNOB with the level of genetic diversity, but as production size increased, so did the effective number of breeders. This study demonstrates the utility of PBT as a monitoring tool for hatchery broodstocks, and results suggest that segregated and integrated programs have tradeoffs that generally align with their intended broodstock management purpose of providing fish for harvest and/or fish for supplementation or reintroduction.

Horn, Rebekah L.↗