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At least 487 records · Page 27

Towards a robust out-of-the-box neural network model for genomic data

The accurate prediction of biological features from genomic data is paramount for precision medicine and sustainable agriculture. For decades, neural network models have been widely popular in fields like computer vision, astrophysics and targeted marketing given their prediction accuracy and their robust performance under big data settings. Yet neural network models have not made a successful transition into the medical and biological world due to the ubiquitous characteristics of biological data such as modest sample sizes, sparsity, and extreme heterogeneity. Here, we investigate the robustness, generalization potential and prediction accuracy of widely used convolutional neural network and natural language processing models with a variety of heterogeneous genomic datasets. Mainly, recurrent neural network models outperform convolutional neural network models in terms of prediction accuracy, overfitting and transferability across the datasets under study. While the perspective of a robust out-of-the-box neural network model is out of reach, we identify certain model characteristics that translate well across datasets and could serve as a baseline model for translational researchers.

59 BASIC BIOLOGICAL SCIENCES↗

Deep Neural Network Algorithm for CMC Microstructure Characterization and Variability Quantification

Microstructure characterization and variability quantification are crucial for understanding ceramic matrix composites (CMCs) mechanical behavior and deformation mechanisms across length scales. Traditionally, analyses of the micrographs obtained from microscopy are labor-intensive. However, with the vast improvement in computer vision (CV) and deep learning (DL), an automated algorithm can be designed to extract essential microstructure variability from micrographs which can then be used to construct a statistically representative volume element (SRVE). The DL-based algorithm spans the taxonomy of microstructure analyses, including semantic segmentation of microstructure constituents, secondary phases, matrix/fiber interface, and defects, and quantifying the microstructure variability in terms of probability distributions. In this work, C/SiNC and SiC/SiNC CMCs microstructures are semantically segmented through a deep convolutional neural network, followed by variability quantification through the implementation of a fully connected regression layer, hence forming a deep regression network. The deep regression network operates in a feedforward regime, in which the neuron output signal traverses through the network in a unidirectional manner. The weight tensor associated with each layer is updated through a backpropagation stochastic gradient descent approach. The input gray-scale image obtained through in-house scanning electron microscope and confocal microscope micrographs is augmented through affine transformations to increase the training set size, which is then processed through four strided convolutional layers. This compresses the image resolution by half at each layer while increasing the image depth by applying different filters (image encoding). The class activation maps (CAMs) corresponding to the applied filters highlight the key architectural features and assist with the semantic segmentation of the microstructure.

Hamza, Mohamed H.↗

Advancing 3D surface imaging: single-axis structured light illumination plenoptic camera with machine learning integration

Structured light illumination (SLI) is a configurable 3D surface imaging modality that can function largely independently of surface texture. At the same time, machine learning (ML) approaches are providing new ways to capture relevant information from SLI patterns, avoiding the need to develop advanced computer vision algorithms. By projecting an optical pattern onto a surface and measuring the apparent distortion of that pattern, one can determine surface topography from a single image. Common realizations of SLI 3D imaging use off-axis SLI to allow for parallax-based determination of depth; however, in constrained geometries, the ability to make single-axis measurements can be of major benefit. While plenoptic imaging (PI) cameras have long been developed for the purpose of single-axis 3D imaging, they are generally reliant on the surface texture of the measured object, thus making them unreliable in certain experimental conditions. Therefore, we present a single-axis 3D SLI plenoptic camera, which combines the single-axis benefits of PI technology while using coaxial SLI to maintain indifference to surface conditions. We also present a study of the camera capabilities paired with the development of several algorithms, including traditional feature tracking methods as well as ML methods, which are found to enhance resolution and range. We report depth sensitivity down to 0.2% $\frac{dz}{z_0}$. The single-axis SLI 3D plenoptic camera demonstrates potential applicability for in-situ topographical measurements under a wide range of conditions including, but not limited to, objects without trackable surface texture, high temperatures, and constrained geometry environments.

Imaging systems↗

Effectiveness of Deep Learning Trained on SynthCity Data for Urban Point-Cloud Classification

3D object recognition is one of the most popular areas of study in computer vision. Many of the more recent algorithms focus on indoor point clouds, classifying 3D geometric objects, and segmenting outdoor 3D scenes. One of the challenges of the classification pipeline is finding adequate and accurate training data. Hence, this article seeks to evaluate the accuracy of a synthetically generated data set called SynthCity, tested on two mobile laser-scan data sets. Varying levels of noise were applied to the training data to reflect varying levels of noise in different scanners. The chosen deep-learning algorithm was Kernel Point Convolution, a convolutional neural network that uses kernel points in Euclidean space for convolution weights.

Geology↗

A Systematic Interpretation of Subsurface Proppant Concentration from Drilling Mud Returns: Case Study from Hydraulic Fracturing Test Site (HFTS-2) in Delaware Basin

The aim of this study is generation and validation of a proppant log using analysis of drilling mud returns for child wells. Proppant log provides qualitative as well as quantitative insights into spatial distribution of proppant sand particles from prior stimulation of parent wells. While the basic methodology was developed and formalized during analysis of material collected from through fracture cores at Hydraulic Fracturing Test Site in Midland Basin (HFTS – 1), the test wells at HFTS – 2 in the neighboring Delaware Basin allowed the opportunity to validate the workflow on actual mud return samples from subsurface. As a child well is being drilled, periodic mud return samples are collected at the rig site and preserved for analysis. The workflow involves systematic cleaning of the samples including various steps such as washing, drying and segregation of samples into relevant size fractions of interest (< Mesh 20) based on specifications of pumped sand during stimulation of the parent well. Clean samples are imaged using high resolution transparency scanning. Scan images are then systematically analyzed for particles of interest using computer vision techniques. Sample counts are further validated using elemental analysis of smaller sub-samples at various depths of interest. This step is necessary to isolate proppant versus other naturally occurring minerals such as sulphates and carbonates which show similar optical properties. We successfully correlated proppant distribution against the existing parent well and validated propped versus relatively un-propped zones for a child well at the test site. The advantage of testing the proppant log concept at the HFTS – 2 site is the plethora of additional diagnostic data that is available to validate our primary observations. We can correlate spatial proppant distribution against variability in stimulation response based on independent observations such as image logs, microseismic attributes as well as DAS response, all of which tend to corroborate one another. One of our significant successes was being able to describe varying degrees of impact of the parent well along the lateral length of a stimulated child well. Our workflow represents a systematic and one-of-a-kind interpretation of spatial proppant distribution while drilling child wells. This provides unique opportunities to better understand the current state of the Downloaded from http://onepetro.org/URTECONF/proceedings-pdf/21URTC/2-21URTC/D021S031R003/2477415/urtec-2021-5189-ms.pdf/1 by Carol Worster on 28 February 2022 URTeC 5189 2 reservoir being targeted including zones which are likely more drained relative to others and how the planned completion of the child well can be improved. Lastly, this log can be useful is validating optimal well spacing in relatively new fields under development.

58 GEOSCIENCES↗

Successful cleanroom installation of PIP-II SSR2 coupler using robotic arm

To minimize the contamination of SRF cavities, remote installation techniques are needed during the installation of components. Recent work at Fermilab has been performed to begin the process of developing techniques for assembling cavities using robotics. Multiple alignment methods were prototyped including alignment and computer vision methods. Using a remotely controlled robotic arm, the alignment and installation of couplers have been successfully performed on prototype PIP-II SSR2 cavities in a cleanroom. The installation process will be shown to show to demonstrate the potential of future installations on other cavities and cavity ancillaries.

43 PARTICLE ACCELERATORS↗

Novel Proppant Logging Technique for Infill Drilling of Unconventional Shale Wells

Summary During the development of an unconventional play, wells are drilled and completed in batches, and depending on the development plans, current and expected energy market trends, as well as other developmental considerations, new wells are drilled and hydraulically fractured later near existing producing laterals. This creates challenges in terms of optimizing resource recovery and reducing interwell communication. A novel approach is proposed that utilizes systematic composite sampling and analysis of drilling mud returns to look for and quantitatively identify sand particles. The workflow involves cleaning, drying, and segregation of samples into sizes of interest to us (size distribution of pumped proppant in offset parent wells). These samples are imaged at a very high resolution and analyzed for grains using characteristic optical imaging properties to classify proppant sand particles using computer vision algorithms. Further analysis, such as elemental compositional analysis, is used to validate the results from the imaging workflow. We present a case study from the Permian Basin, where a new child well was used as a test case to prove this technology at the Hydraulic Fracturing Test Site (HFTS-2) in Delaware Basin. We introduce new proppant parameters that help identify sustained proppant zones vs. localized propped fractures. We have used additional diagnostics and data collected at the test site to validate observations from the proppant log and have successfully interpreted significantly propped vs. unpropped zones. A key finding from this test has been the significant proppant transport distances observed away from parent wells. Observable proppant was found at a lateral distance of approximately 425 m for one set of parent wells and more than 915 m for another set of parent wells. While a major limitation of this technique is the sampling rate, given adequate sampling, the proposed technology represents a systematic and one-of-a-kind interpretation of spatial proppant distribution while drilling infill wells. It provides us with unique opportunities to better understand the current state of the reservoir being targeted, including zones that are likely highly drained relative to others, and how the planned hydraulic fracturing of child wells can be improved.

Energy & Fuels↗

Canopy 2.1 User Guide

Canopy is a visual analytic software suite, developed by researchers at the Pacific Northwest National Laboratory (PNNL), to support intelligence analysts’ ability to efficiently analyze massive amounts of multimedia data. Canopy incorporates state-of-the-art computer vision algorithms and interactive visualizations so that analysts can comprehend and articulate the big picture, thereby reducing their workload and ultimately the effort of identifying the critical intelligence for decision makers.

Canopy↗

Muon Neutrino Disappearance in NOvA with a Deep Convolutional Neural Network Classifier

The NuMI Off-axis Neutrino Appearance Experiment (NOvA) is designed to study neutrino oscillation in the NuMI (Neutrinos at the Main Injector) beam. NOvA observes neutrino oscillation using two detectors separated by a baseline of 810 km; a 14 kt Far Detector in Ash River, MN and a functionally identical 0.3 kt Near Detector at Fermilab. The experiment aims to provide new measurements of Δm 2 and θ23 and has potential to determine the neutrino mass hierarchy as well as observe CP violation in the neutrino sector. Essential to these analyses is the classification of neutrino interaction events in NOvA detectors. Raw detector output from NOvA is interpretable as a pair of images which provide orthogonal views of particle interactions. A recent advance in the field of computer vision is the advent of convolutional neural networks, which have delivered top results in the latest image recognition contests. This work presents an approach novel to particle physics analysis in which a convolutional neural network is used for classification of particle interactions. The approach has been demonstrated to improve the signal efficiency and purity of the event selection, and thus physics sensitivity. Early NOvA data has been analyzed (2.74×10 20 POT, 14 kt equivalent) to provide new best- fit measurements of sin 2 (θ23) = 0.43 (with a statistically-degenerate compliment near 0.60) and |Δm2 | = 2.48 × 10 -3 eV 2 .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NOvA Reconstruction using Deep Learning [Slides]

The NOvA experiment has made measurements of the disappearance of νμ and the appearance of νe in the NuMI beam at Fermilab. Key to these measurements is the identification of the neutrino flavor and measurement of the neutrino energy, for which NOvA has implemented deep learning algorithms utilizing tools from the field of computer vision. These algorithms, first applied to NOvA's 2016 results, showed significant improvement over previous reconstruction methods. I will present NOvA's implementation of deep learning algorithms using convolutional neural networks for identification of event neutrino flavor and single particles used in the 2018 analysis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The MicroBooNE Search For Anomalous Electron Neutrino Appearance Using Image Based Data Reconstruction

This thesis presents the MicroBooNE search for the MiniBooNE low energy excess using a fully automated image based data reconstruction scheme. A suite of traditional and deep learning computer vision algorithms are developed for identication of charge current quasi-elastic (CCQE) like muon and electron neutrino interactions using the MicroBooNE detector. Given a model of the MiniBooNE low energy excess as due to an enhancement of electron neutrino type events, this analysis predicts a combined statistical and systematic 3.8 low energy signal in 13:2 1020 POT of MicroBooNE data. When interpreted in the context of ! e 3 + 1 sterile neutrino oscillations a best t point of (m2 41; sin2 2e) = (0:063; 0:794) is found with a 90% condence allowed region consistent with > 0:1 eV2 oscillations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Reinforcement Learning-based Traffic Control to Optimize Energy Usage and Throughput (CRADA report)

The US roadways are critical to meeting the mobility and economic needs of the nation. The United States uses 28% of its energy in moving goods and people, with approximately 60% of that utilized by cars, light trucks, and motorcycles. Thus, improved transportation efficiency is vital to America’s economic progress. The increasing congestion and energy resource requirements of transportation systems for metropolitan areas require research in methods to improve and optimize control methods. Coordinating and optimizing traffic in urban areas may introduce hundreds of thousands of vehicles and traffic management systems, which can require high performance computing (HPC) resources to model and manage. In this work, we seek to use machine learning, computer vision, and HPC to improve the energy efficiency aspects of traffic control by leveraging GRIDSMART traffic cameras as sensors for adaptive traffic control, with a sensitivity to the fuel consumption characteristics of the traffic in the camera’s visual field. Traffic control use cases using reinforcement learning have been published and achieved good results. Surveys from DOE national laboratories estimate that the fuel cost of idling is 6 billion gallons wasted annually [Argonne National Laboratory, 2019]. GRIDSMART cameras—an existing, fielded commercial product—sense the presence of vehicles at intersections and replace more conventional sensors (such as inductive loops) to issue calls to traffic control. These cameras, which have horizon-to-horizon view, offer the potential for an improved view of the traffic environment which can be used to generate better control algorithms.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Congestion Estimation Using Traffic Cameras

Traffic cameras are becoming a popular form of surveillance in traffic bodies across the country. With recent advances in computer vision and deep learning, there is a great opportunity to leverage these images to provide real-time traffic estimates and other public services. In this report, we detail some of the challenges, current interests of the research community, and our early efforts in using traffic cameras for vehicle detection and traffic estimation. We also discuss a benchmark traffic dataset that we are assembling and plan to release to the research community to motivate further work in this area.

42 ENGINEERING↗

DeepMerge: Studying Distant Merging Galaxies with Deep Neural Networks

The hierarchical merging of galaxies is a probe of the cosmos to test the canonical ?CDM cosmology paradigm. A particularly interesting period is "cosmic high noon" at redshifts z? 2?3, during which star formation rates were the highest, and significant amounts of stellar mass assembled into galaxy-scale bodies. Detecting galaxy mergers in observations by conventional automated methods (which use extracted parameters of galaxy structure - asymmetry, clumpiness, concentration etc.) or by visual inspection has proven to be quite time-consuming and prone to errors. Convolutional Neural Network (CNNs) are a primary representative of deep learning algorithms which are used in computer vision tasks by training to detect features in images. CNNs were already used for classification of low-redshift merging galaxies [1, 2]. Here we will use CNN to to learn directly from images (without the need to extract morphology parameters) of distant merging galaxies in order to distinguish between merging and non-merging objects.

79 ASTRONOMY AND ASTROPHYSICS↗

All-Atom Simulation of 3D Hot Spot Formation in Shocked TATB Explosive

TATB is an insensitive high explosive (IHE) critical to the stockpile that is challenging to model at the continuum scale. Advanced detonation models in the Cheetah high explosive chemistry code require validation though subscale simulations. High explosive initiation is determined by micron-scale physics of hot spots formed a shock-collapsed pores. Pore sizes between 100 nm and 1 μm are believed to be the most important for determining the shock sensitivity of TATB. This range of pore sizes is difficult to access at the atomic scale through allatom molecular dynamics (MD) simulations, even with Sierra-class computers. Quasi-2D simulations are widely used and allow much larger pore sizes (up to 400 nm) to be studied, but the applicability of 2D simulations to the actual 3D pore response is not understood. Resolving these uncertainties through “full physics” MD modeling is key for generalizing, parameterizing, and validating the kinds of continuum models used to inform design, safety, and performance. This work was a continuation of FY20 efforts pushing simulations to full 3D with the largest-ever all-atom simulations of an explosive. These were the first all-atom full-3D simulations of large hot spots thought to govern explosive detonation and required over a billion atoms. Simulations were performed using LAMMPS, an open SNL science code. MD explosive models present unique challenges, even for established codes such as LAMMPS. Their model forms are more complex than typical models for metals, while simulating high temperature-pressure conditions is demanding and increases computational cost. Scaling problems in GPU-enabled MD algorithms initially limited simulations to <100 million atoms but were resolved through collaboration with SNL. An overall 24x speedup was obtained relative to CPU machines. Specialized analysis of these simulations required a bottom-up refactoring and algorithm parallelization of in-house codes and application of computer vision algorithms to extract meaningful information.

36 MATERIALS SCIENCE↗

Introduction to Special Section: Machine Learning for Image-based Geologic Interpretation

Image-based geological interpretation has been a labor-intensive and time-consuming process because it requires well-trained geoscientists to identify geological structures, features, and textures from various types of images. These images include scanning electron microscopic images, optical microscopic images, optical photos, resistivity images, seismic volumes, remote-sensing images, etc. With fast-evolving machine learning (ML) technology and computing power in recent decades, computers can achieve nearhuman-level to super-human-level performance with scalable high efficiency in the computer vision field. These technological revolutions facilitated image-based geological interpretation in petroleum exploration and production. For example, a fault picking method applied to 3-D seismic volume data using deep learning can achieve superior performance in comparison to conventional auto-picking methods. In addition, under the new normal of low oil prices, the petroleum industry seeks cost-effective strategies such as automating traditionally labor-intensive processes. Nevertheless, the potential of applying ML to geological image interpretation is still facing a few key challenges including data scarcity, data distribution, poor data and/or label quality, data leakage, learning algorithms, model architecture, training methodologies, testing and evaluation metrics, hyper-parameters optimization, model drift, production deployment, and the like.

58 GEOSCIENCES↗

Image Classification Using Convolutional Neural Networks to Automate Visual Inspection of CCO Containers (Rev. 1)

The Savannah River Site is automating the receipt and inspection of Criticality Control Overpack drums to aid in nuclear waste disposal. The Advanced Engineering group is automating this receipt and inspection process to assist the site’s goals. Part of this process includes visually inspecting CCO drums to ensure that no defects or security risks are present. This research focuses on developing a machine learning model to automatically classify drums as passing or failing inspection. The machine learning model was implemented using the open-source Tensorflow library and uses a Convolutional Neural Network architecture to extract features and differentiate between images. The model was able to achieve an average of 85% accuracy on a dataset of 288 drums. This project’s goal was to prove the validity of computer vision in an automation process and provide a starting place for continued research.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Quarterly Research Performance Progress Report (Q8)

As part of Task 1, we have started by testing our modeling capabilities by reproducing isothermal DFIT simulations presented in the literature. Once satisfied with the results we have started by targeting the modeling of the DFITs at conducted at well 58-32. We have a identified a specific test (cycle 4 in zone 2) as the most interesting to be model with GEOS hydraulic fracturing module. Thus, we have first produced results with an isothermal model and adjusted model parameters to get a satisfying match with field pressure data. The, we have added thermal effects and compared the modeling results with and without thermal effects to estimate how thermal effects may influence test interpretation. Models seem to suggest that, for small volumes of fluid, thermal effects are moderate. In Task 2, we have adapted GEOS phase-field formulation to be able to simulate near-wellbore hydraulic fracture nucleation and propagation. We have devised a novel formulation that, compared to other existing ones, incorporates rock strengths. We have submitted a journal publication about our work. We are currently employing this phase-field formulation to model the experiments taking place at U Pitt and help us understand the effect of various parameters. In Task 3, we have built a model of the region surround well 16A and have started modeling stage 3 stimulation because of its simpler planar geometry. After calibrating simulation parameters using known analytical solutions, we have simulated the stage 3 stimulation using our isothermal hydraulic fracturing module, varying the permeability field, the stress conditions including different physics to get a better understanding of the numerical challenges and of the effects of varying these parameters on the simulation results. In Task 4 laboratory experimentation, a set of specialized drilling and injection tools has been customized and constructed to accommodate an inclined well with an orientation of up to 30 degrees relative to material anisotropy or principal stress axes. These inclined samples have also undergone thermal stress and hydraulic fracturing at a temperature of 190 degrees Celsius. Furthermore, both vertical and deviated sampling testing setups enable an extended analysis of post-peak pressure behaviors, facilitating post-test pressure analyses such as the G-function, step rate, and fracture reopening measurements. Thus, the key components of in-situ stress estimation can be extracted and validated through our experiment, providing a solid foundation for validating existing in-situ stress estimation theories or proposing new ones. Simultaneously, we are integrating computer vision techniques with traditional experimental fracture observation methods such as multi-overcore/slicing and water-penetration fracture observation. This combination will prove beneficial in populating the hydraulic fracture patterns database, generated under challenging EGS conditions. This approach aims to deepen our understanding of the complexities in EGS reservoirs and pave the way for future data-driven investigations. Additionally, PITT has also equipped the ELE International compression machine, which is now prepared for conducting indirect tensile and fracture toughness tests. These tests will aid in characterizing how rock fabrics influence the resulting fracture patterns. Additionally, we have completed the required personnel training and gained access to Scanning Electron Microscopy (SEM) and Energy Dispersive Spectroscopy (EDS) for conducting more detailed characterization and analysis of rock fabrics, as well as the examination of thermal and hydraulically induced fracture patterns. Thus, the PITT team has effectively demonstrated the capabilities of our experimental apparatuses in exploring the thermal effects, well deviation angles, material anisotropy, and operational choices (such as circulation rate, injection fluid viscosity, and injection rate) and their impact on pressure responses and fracture trajectories under the Utah FORGE conditions.

15 GEOTHERMAL ENERGY↗