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At least 595 records · Page 33

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DOE OSTI2021

Forecasting Multi-Wave Epidemics Through Bayesian Inference

We present a simple, near-real-time Bayesian method to infer and forecast a multiwave outbreak, and demonstrate it on the COVID-19 pandemic. The approach uses timely epidemiological data that has been widely available for COVID-19. It provides short-term forecasts of the outbreak’s evolution, which can then be used for medical resource planning. The method postulates one- and multiwave infection models, which are convolved with the incubation-period distribution to yield competing disease models. The disease models’ parameters are estimated via Markov chain Monte Carlo sampling and information-theoretic criteria are used to select between them for use in forecasting. The method is demonstrated on two- and three-wave COVID-19 outbreaks in California, New Mexico and Florida, as observed during Summer-Winter 2020. We find that the method is robust to noise, provides useful forecasts (along with uncertainty bounds) and that it reliably detected when the initial single-wave COVID-19 outbreaks transformed into successive surges as containment efforts in these states failed by the end of Spring 2020.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Chapter 14: Dynamic Flux Analysis: An Experimental Approach of Fluxomics

Metabolic flux analysis represents an essential perspective to understand cellular physiology and offers quantitative information to guide pathway engineering. A valuable approach for experimental elucidation of metabolic flux is dynamic flux analysis, which estimates the relative or absolute flow rates through a series of metabolic intermediates in a given pathway. It is based on kinetic isotope labeling experiments, liquid chromatography-mass spectrometry (LC-MS), and computational analysis that relate kinetic isotope trajectories of metabolites to pathway activity. Herein, we illustrate the mathematic principles underlying the dynamic flux analysis and mainly focus on describing the experimental procedures for data generation. This protocol is exemplified using cyanobacterial metabolism as an example, for which reliable labeling data for central carbon metabolites can be acquired quantitatively. This protocol is applicable to other microbial systems as well and can be readily adapted to address different metabolic processes.

BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Understanding Spin Coherence in Polyoxometalate-Based Molecular Qubits

This research advances the understanding of spin decoherence mechanisms and addresses the grand challenges in quantum information science of generating and stabilizing quantum states that may be manipulated with single-atom precision. It is accomplished using unique capabilities developed at PNNL for ion soft landing and spatially resolved vibrational spectroscopy of well-defined supported molecular qubit (MQ) arrays. It addresses knowledge gaps impeding the development of MQ-based quantum devices by answering two scientific questions: 1) Can we minimize spin-lattice relaxation rates by tuning the substrate-MQ interface? 2) What is the optimum number of spin centers that enables sufficient coherent signal generation prior to decoherence through inter-MQ and MQ-support interactions? The objective is to develop predictive design principles for prolonging spin coherence lifetimes in arrays of optically-addressable MQs for quantum computing applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

QPress: Quantum Press for Next-Generation Quantum Information Platforms

Quantum information science (QIS) holds promise for revolutionizing computation, communication, and sensing. Of course, realizing this promise requires material platforms that can host quantum bits with pre-assigned characteristics that are uniquely attuned to such functionalities. For example, quantum bits for computation should be as immune as possible to any external perturbation, controllable on short time scales and scalable. In contrast, quantum bits for local metrology should be as small as possible and sensitive to specific fields of interest. While tremendous advances in QIS have been achieved in recent years, the underlying properties of the materials that host these quantum bits remains one of the key limitations in their performance.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Flood hazard model calibration using multiresolution model output

Riverine floods pose a considerable risk to many communities. Improving flood hazard projections has the potential to inform the design and implementation of flood risk management strategies. Current flood hazard projections are uncertain, especially due to uncertain model parameters. Calibration methods use observations to quantify model parameter uncertainty. With limited computational resources, researchers typically calibrate models using either relatively few expensive model runs at high spatial resolutions or many cheaper runs at lower spatial resolutions. This leads to an open question: is it possible to effectively combine information from the high and low resolution model runs? We propose a Bayesian emulation–calibration approach that assimilates model outputs and observations at multiple resolutions. As a case study for a riverine community in Pennsylvania, we demonstrate our approach using the LISFLOOD-FP flood hazard model. Here, the multiresolution approach results in improved parameter inference over the single resolution approach in multiple scenarios. Results vary based on the parameter values and the number of available models runs. Our method is general and can be used to calibrate other high dimensional computer models to improve projections.

multiresolution↗

DOE OSTI2022

Grassmannian Shape Representations for Aerodynamic Applications

Airfoil shape design is a classical problem in engineering, science, and manufacturing. Our motivation is to combine principled physics-based considerations for the shape design problem with modern computational techniques informed by a data-driven approach. Traditional analyses of airfoil shapes emphasize a flow-based sensitivity to deformations which can be represented generally by affine transformations (rotation, scaling, shearing, shifting). We present a novel representation of shapes which decouples affine-style deformations from a rich set of data-driven deformations over a submanifold of the Grassmannian. The Grassmannian representation, informed by a database of physically relevant airfoils, offers (i) a rich set of novel 2D airfoil deformations not previously captured in the data, (ii) improved low-dimensional parameter domain for inferential statistics, and (iii) consistent 3D blade representation and perturbation over a sequence of nominal shapes.

blade representation↗

DOE OSTI2024

L-PBF High-Throughput Data Pipeline Approach for Multi-modal Integration

Abstract Metal-based additive manufacturing requires active monitoring solutions for assessing part quality. Multiple sensors and data streams, however, generate large heterogeneous data sets that are impractical for manual assessment and characterization. In this work, an automated pipeline is developed that enables feature extraction from high-speed camera video and multi-modal data analysis. The framework removes the need for manual assessment through the utilization of deep learning techniques and training models in a weakly supervised paradigm. We demonstrate this pipeline’s capability over 700,000 high-speed camera frames. The pipeline successfully extracts melt pool and spatter geometries and links them to corresponding pyrometry, radiography, and processparameter information. 715 individual prints are examined to reveal melt pool areas that exceeds 0.07 mm 2 and pyrometry signal over a threshold (375 pyrometry units) were more likely to have defects. These automated processes enable massive throughput of characterization techniques.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Grassmannian Shape Representations for Aerodynamic Applications: Preprint

blade representation↗

DOE OSTI2026

Global Explainability of A Deep Abstaining Classifier for Cancer Pathology Reports

We present a global explainability method to characterize sources of errors in a real-world multitask deep abstaining classifier (DAC), in the context of cancer histology prediction. Our multitask classifier, currently deployed for automated annotation of cancer pathology reports from NCI-SEER registries, was trained and evaluated on 1.04 million hand-annotated samples and makes simultaneous predictions of cancer site, subsite, histology, laterality, and behavior for each report. The DAC framework enables the model to abstain on ambiguous reports and confusing classes to achieve the target accuracy on the retained (non-abstained) samples, but at the cost of decreased coverage. Requiring 97% accuracy on the histology task caused our model to retain only 22% of all samples, mostly the less ambiguous and common classes. Local explainability with the GradInp technique provided a computationally efficient way of obtaining contextual reasoning for hundreds of thousands of individual predictions. Our method, involving dimensionality reduction of approximately 13000 aggregated local explanations (ALE), offers a tractable path to true global explainability. It enabled identification of sources of errors in histology classification, globally, as hierarchical complexity among classes, label noise, insufficient information, and conflicting evidence. This suggests several strategies for iterative improvement of our DAC, including well-designed exclusion criteria, focused annotation, and reduced penalties for errors involving hierarchically related classes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Model-free estimation of completeness, uncertainties, and outliers in atomistic machine learning using information theory

Abstract An accurate description of information is relevant for a range of problems in atomistic machine learning (ML), such as crafting training sets, performing uncertainty quantification (UQ), or extracting physical insights from large datasets. However, atomistic ML often relies on unsupervised learning or model predictions to analyze information contents from simulation or training data. Here, we introduce a theoretical framework that provides a rigorous, model-free tool to quantify information contents in atomistic simulations. We demonstrate that the information entropy of a distribution of atom-centered environments explains known heuristics in ML potential developments, from training set sizes to dataset optimality. Using this tool, we propose a model-free UQ method that reliably predicts epistemic uncertainty and detects out-of-distribution samples, including rare events in systems such as nucleation. This method provides a general tool for data-driven atomistic modeling and combines efforts in ML, simulations, and physical explainability.

36 MATERIALS SCIENCE↗

DOE OSTI2020

General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part II

X-ray Bragg coherent diffraction imaging (BCDI) has been demonstrated as a powerful 3D microscopy approach for the investigation of sub-micrometre-scale crystalline particles. The approach is based on the measurement of a series of coherent Bragg diffraction intensity patterns that are numerically inverted to retrieve an image of the spatial distribution of the relative phase and amplitude of the Bragg structure factor of the diffracting sample. This 3D information, which is collected through an angular rotation of the sample, is necessarily obtained in a non-orthogonal frame in Fourier space that must be eventually reconciled. To deal with this, the approach currently favored by practitioners (detailed in Part I) is to perform the entire inversion in conjugate non-orthogonal real- and Fourier-space frames, and to transform the 3D sample image into an orthogonal frame as a post-processing step for result analysis. In this article, which is a direct follow-up of Part I, two different transformation strategies are demonstrated, which enable the entire inversion procedure of the measured data set to be performed in an orthogonal frame. The new approaches described here build mathematical and numerical frameworks that apply to the cases of evenly and non-evenly sampled data along the direction of sample rotation ( i.e. the rocking curve). The value of these methods is that they rely on the experimental geometry, and they incorporate significantly more information about that geometry into the design of the phase-retrieval Fourier transformation than the strategy presented in Part I. Finally, two important outcomes are (1) that the resulting sample image is correctly interpreted in a shear-free frame and (2) physically realistic constraints of BCDI phase retrieval that are difficult to implement with current methods are easily incorporated. Computing scripts are also given to aid readers in the implementation of the proposed formalisms.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Facility Location Optimization Model for COVID-19 Resources

In response to anticipated resource shortfalls related to the treatment and testing of COVID-19, many communities are planning to build additional facilities to increase capacity. These facilities include field hospitals, testing centers, mobile manufacturing units, and distribution centers. In many cases, these facilities are intended to be temporary and are designed to meet an immediate need. When deciding where to place new facilities many factors need to be considered, including the feasibility of potential locations, existing resource availability, anticipated demand, and accessibility between patients and the new facility. In this project, a facility location optimization model was developed to integrate these key pieces of information to help decision makers identify the best place, or places, to build a facility to meet anticipated resource demands. The facility location optimization model uses the location of existing resources and the anticipated resource demand at each location to minimize the distance a patient must travel to get to the resource they need. The optimization formulation is presented below. The model was designed to operate at the county scale, where patients are grouped per county. This assumption can be modified to integrate other scales or include individual patients.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Network analysis of memristive device circuits: dynamics, stability and correlations

Abstract Networks with memristive devices are a potential basis for the next generation of computing devices. They are also an important model system for basic science, from modeling nanoscale conductivity to providing insight into the information-processing of neurons. The resistance in a memristive device depends on the history of the applied bias and thus displays a type of memory. The interplay of this memory with the dynamic properties of the network can give rise to new behavior, offering many fascinating theoretical challenges. But methods to analyze general memristive circuits are not well described in the literature. In this paper we develop a general circuit analysis for networks that combine memristive devices alongside resistors, capacitors and inductors and under various types of control. We derive equations of motion for the memory parameters of these circuits and describe the conditions for which a network should display properties characteristic of a resonator system. For the case of a purely memresistive network, we derive Lyapunov functions, which can be used to study the stability of the network dynamics. Surprisingly, analysis of the Lyapunov functions show that these circuits do not always have a stable equilibrium in the case of nonlinear resistance and window functions. The Lyapunov function allows us to study circuit invariances, wherein different circuits give rise to similar equations of motion, which manifest through a gauge freedom and node permutations. Finally, we identify the relation between the graph Laplacian and the operators governing the dynamics of memristor networks operators, and we use these tools to study the correlations between distant memristive devices through the effective resistance.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Science-informed Machine Learning to Increase Recovery Efficiency in Unconventional Reservoirs

Production of hydrocarbons from fractured, unconventional reservoirs is inherently inefficient. But machine learning offers a pathway both to increasing recovery efficiency at a site and to improving forecasts of production, thereby improving the economics of operations in unconventional reservoirs. Los Alamos—in partnership with DOE, NETL, and WVU—has been developing a science-informed workflow and platform for optimizing pressure-drawdown at a site, which will allow an operator to make reservoir-management decisions that optimize recovery in consideration of future production. This work relies on a hybridization of physics-based prediction and machine learning, whereby accurate synthetic data (in combination with available site data) can enable the application of machine learning methods for rapid forecasting and optimization. The physics-based prediction is built upon experimental and theoretical work to determine transport characteristics in shale at various scales, with an emphasis on materials from MSEEL-I; this fundamental shale R&D was conducted in partnership with DOE, NETL, and several other national labs. This work has resulted from a coordinated leveraging of developments across several projects within DOE FE30, along with internal investments from Los Alamos via LDRD. The development has utilized data from the MSEEL–I site for calibration and demonstration; however, the workflow and platform are readily extendable to operations at other sites, plays, and basins. This machine-learning method can aid operators to improve both recovery efficiency and competitiveness; to this end, future work would quantify processes for other plays/basins and integrate production details with economics.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2025

Entanglement engineering of optomechanical systems by reinforcement learning

Entanglement is fundamental to quantum information science and technology, yet controlling and manipulating entanglement—so-called entanglement engineering—for arbitrary quantum systems remains a formidable challenge. There are two difficulties: the fragility of quantum entanglement and its experimental characterization. We develop a model-free deep reinforcement-learning (RL) approach to entanglement engineering, in which feedback control together with weak continuous measurement and partial state observation is exploited to generate and maintain desired entanglement. We employ quantum optomechanical systems with linear or nonlinear photon–phonon interactions to demonstrate the workings of our machine-learning-based entanglement engineering protocol. In particular, the RL agent sequentially interacts with one or multiple parallel quantum optomechanical environments, collects trajectories, and updates the policy to maximize the accumulated reward to create and stabilize quantum entanglement over an arbitrary amount of time. The machine-learning-based model-free control principle is applicable to the entanglement engineering of experimental quantum systems in general.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Development of a Miniaturized Mobile Mapping System for In-Row, Under-Canopy Phenotyping

This paper focuses on the development of a miniaturized mobile mapping platform with advantages over current agricultural phenotyping systems in terms of acquiring data that facilitate under-canopy plant trait extraction. The system is based on an unmanned ground vehicle (UGV) for in-row, under-canopy data acquisition to deliver accurately georeferenced 2D and 3D products. The paper addresses three main aspects pertaining to the UGV development: (a) architecture of the UGV mobile mapping system (MMS), (b) quality assessment of acquired data in terms of georeferencing information as well as derived 3D point cloud, and (c) ability to derive phenotypic plant traits using data acquired by the UGV MMS. The experimental results from this study demonstrate the ability of the UGV MMS to acquire dense and accurate data over agricultural fields that would facilitate highly accurate plant phenotyping (better than above-canopy platforms such as unmanned aerial systems and high-clearance tractors). Plant centers and plant count with an accuracy in the 90% range have been achieved.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

High Performance Computing Traffic Simulations for Real-Time Traffic Control of Mobility in Chattanooga Region

In 2019, highway congestion wasted over 3 billion gallons of fuel and caused 8.8 billion hours of lost productivity.1 Research has shown that introducing near-real time traffic controls can significantly reduce congestion. Validated and calibrated traffic simulations enable the modeling of transportation systems and the evaluation of different traffic control actions and schemes given a variety of circumstances that represent likely future scenarios. The developed scenarios can inform the deployment of controls in near real-time to improve freight and passenger vehicle congestion and energy use. In this work, we present simulations used to model the traffic in the Chattanooga, Tennessee, metropolitan area. Simulations were constructed and calibrated using a variety of local, data science enhanced, data sources utilizing open source software including the Simulation of Urban Mobility (SUMO) simulator. High-Performance Computing (HPC) provides a scalable platform with enough computing for the high-fidelity simulation of many scenarios and the application of advance data science especially for large-scale systems. Our simulations include microscopic simulations at a corridor level for traffic signal control, and mesoscopic simulations to evaluate regional operational controls and infrastructure.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

A High-level Design for Bidirectional Data Streaming to High-Performance Computing Systems from External Science Facilities

Cutting-edge science is increasingly data-driven due to the emergence of scientific machine learning models that can guide scientists toward fruitful areas of exploration. Experimental science facilities such as light and neutron sources, particle colliders, and radio astronomy telescopes are also producing raw measurement data at rates that exceed available data storage and computing capacity at those facilities. As a result, scientific workflows are being developed that concurrently couple experiments at science facilities with high-performance computing (HPC) facilities to enable analysis of experimental data while the experiment is ongoing, and where analysis results are potentially fed back to the experiment for use in experimental control and/or steering in a time-sensitive manner. Our goal is to design, prototype, and deploy a new capability for the Oak Ridge Leadership Computing Facility (OLCF) that enables such workflows through support for bidirectional, memory-based streaming of data from external experiments into and out of OLCF HPC systems. This high-level design document describes the related work and motivating use cases that inform our understanding of the technical requirements for this capability, and describes a proposed architectural solution that meets these requirements and our plans for demonstrating the capability.

97 MATHEMATICS AND COMPUTING↗