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Results for “Custom Correlation Coefficient”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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14 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Parallel accelerated Custom Correlation Coefficient calculations for genomics applications

The massive quantities of genomic data being made available through gene sequencing techniques are enabling breakthroughs in genomic science in many areas such as medical advances in the diagnosis and treatment of diseases. Analyzing this data, however, is a computational challenge insofar as the computational costs of the relevant algorithms can grow with quadratic, cubic or higher complexity—leading to the need for leadership scale computing. In this paper we describe a new approach to calculations of the Custom Correlation Coefficient (CCC) between Single Nucleotide Polymorphisms (SNPs) across a population, suitable for parallel systems equipped with graphics processing units (GPUs) or Intel Xeon Phi processors. We describe the mapping of the algorithms to accelerated processors, techniques used for eliminating redundant calculations due to symmetries, and strategies for efficient mapping of the calculations to many-node parallel systems. Results are presented demonstrating high per-node performance and near-ideal parallel scalability with rates of more than nine quadrillion (9 × 10 15 ) elementwise comparisons achieved per second with the latest optimized code on the ORNL Titan system, this being orders of magnitude faster than rates achieved using other codes and platforms as reported in the literature. Also it is estimated that as many as 90 quadrillion (90 × 10 15 ) comparisons per second may be achievable on the upcoming ORNL Summit system, an additional 10X performance increase. Finally, in a companion paper we describe corresponding techniques applied to calculations of the Proportional Similarity metric for comparative genomics applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Parallel accelerated vector similarity calculations for genomics applications

The surge in availability of genomic data holds promise for enabling determination of genetic causes of observed individual traits, with applications to problems such as discovery of the genetic roots of phenotypes, be they molecular phenotypes such as gene expression or metabolite concentrations, or complex phenotypes such as diseases. However, the growing sizes of these datasets and the quadratic, cubic or higher scaling characteristics of the relevant algorithms pose a serious computational challenge necessitating use of leadership scale computing. In this study we describe a new approach to performing vector similarity metrics calculations, suitable for parallel systems equipped with graphics processing units (GPUs) or Intel Xeon Phi processors. Our primary focus is the Proportional Similarity metric applied to Genome Wide Association Studies (GWAS) and Phenome Wide Association Studies (PheWAS). We describe the implementation of the algorithms on accelerated processors, methods used for eliminating redundant calculations due to symmetries, and techniques for efficient mapping of the calculations to many-node parallel systems. Finally, results are presented demonstrating high per-node performance and parallel scalability with rates of more than five quadrillion (5 × 10 15 ) elementwise comparisons achieved per second on the ORNL Titan system. In a companion paper we describe corresponding techniques applied to calculations of the Custom Correlation Coefficient for comparative genomics applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Attacking the Opioid Epidemic: Determining the Epistatic and Pleiotropic Genetic Architectures for Chronic Pain and Opioid Addiction

We describe the CoMet application for large-scale epistatic Genome-Wide Association Studies (eGWAS) and pleiotropy studies. High performance is attained by transforming the underlying vector comparison methods into highly performant generalized distributed dense linear algebra operations. The 2-way and 3-way Proportional Similarity metric and Custom Correlation Coefficient are implemented using native or adapted GEMM kernels optimized for GPU architectures. By aggressive overlapping of communications, transfers and computations, high efficiency with respect to single GPU kernel performance is maintained up to the full Titan and Summit systems. Nearly 300 quadrillion element comparisons per second and over 2.3 mixed precision ExaOps are reached on Summit by use of Tensor Core hardware on the Nvidia Volta GPUs. Performance is four to five orders of magnitude beyond comparable state of the art. CoMet is currently being used in projects ranging from bioenergy to clinical genomics, including for the genetics of chronic pain and opioid addiction.

Joubert, Wayne↗
DOE OSTI2019

CoMet

CoMet is an application for finding epistatic and pleiotropic relationships from large quantities of genomic data. It solves these large combinatorial problems on GPU-accelerated systems with thousands of compute nodes. Its methods include the 2-way Proportional Similarity method, the Custom Correlation Coefficient and the DUO method. CoMet was developed at the Oak Ridge Leadership Computing Facility in collaboration with the Computational Biology and Bioinformatics Group at Oak Ridge National Laboratory.

Joubert, WayneD↗
DOE OSTI2021

Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples

The accurate identification of SARS-CoV-2 (SC2) variants and estimation of their abundance in mixed population samples (e.g., air or wastewater) is imperative for successful surveillance of community level trends. Assessing the performance of SC2 variant composition estimators (VCEs) should improve our confidence in public health decision making. Here, we introduce a linear regression based VCE and compare its performance to four other VCEs: two re-purposed DNA sequence read classifiers (Kallisto and Kraken2), a maximum-likelihood based method (Lineage deComposition for Sars-Cov-2 pooled samples (LCS)), and a regression based method (Freyja). We simulated DNA sequence datasets of known variant composition from both Illumina and Oxford Nanopore Technologies (ONT) platforms and assessed the performance of each VCE. We also evaluated VCEs performance using publicly available empirical wastewater samples collected for SC2 surveillance efforts. Bioinformatic analyses were performed with a custom NextFlow workflow (C-WAP, CFSAN Wastewater Analysis Pipeline). Relative root mean squared error (RRMSE) was used as a measure of performance with respect to the known abundance and concordance correlation coefficient (CCC) was used to measure agreement between pairs of estimators. Based on our results from simulated data, Kallisto was the most accurate estimator as it had the lowest RRMSE, followed by Freyja. Kallisto and Freyja had the most similar predictions, reflected by the highest CCC metrics. We also found that accuracy was platform and amplicon panel dependent. For example, the accuracy of Freyja was significantly higher with Illumina data compared to ONT data; performance of Kallisto was best with ARTICv4. However, when analyzing empirical data there was poor agreement among methods and variations in the number of variants detected (e.g., Freyja ARTICv4 had a mean of 2.2 variants while Kallisto ARTICv4 had a mean of 10.1 variants). This work provides an understanding of the differences in performance of a number of VCEs and how accurate they are in capturing the relative abundance of SC2 variants within a mixed sample (e.g., wastewater). Such information should help officials gauge the confidence they can have in such data for informing public health decisions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

In situ investigation of high-pressure hydrogen-induced swelling in elastomers and its correlation with material properties

The resistance of elastomeric materials to high-pressure hydrogen-induced damage is essential for ensuring the reliability of hydrogen infrastructure. Here, in this study, we systematically investigated the swelling behavior and hydrogen transport properties of four elastomer types – EPDM, NBR, FKM, and HNBR – using a custom in-situ view cell system capable of real-time monitoring during decompression from pressures up to 96.5 MPa. Each elastomer was formulated with and without fillers and plasticizers to assess the effects of formulation on swelling response. Thermal desorption analysis (TDA) was employed to determine equilibrium hydrogen content and diffusion coefficients, providing insight into gas uptake and mobility within each material. Correlation analyses using Pearson and Spearman coefficients revealed that the diffusion coefficient showed a stronger relationship with swelling behavior than hydrogen content, highlighting the dominant role of hydrogen mobility. Filled elastomers, particularly those with carbon black, consistently showed reduced swelling due to enhanced stiffness and reduced diffusivity. These results deepen our understanding of diffuso-mechanical interactions in elastomers and support the rational design of sealing materials for high-pressure hydrogen systems.

EPDM↗
DOE OSTI2018

Improving Spectral Image Classification through a Custom Data Sparsing and Pixel Clustering Algorithm

The Underground Nuclear Explosion Signatures Experiment (UNESE) seeks to characterize non-prompt observables from underground nuclear explosions (UNE). As part of this effort, we evaluated the ability of Digital Globe’s World View-3 (WV3) to detect and map UNE signatures. WV3 has proven capabilities in the detection of large-scale, anomalous, man-made features; however, it has relatively limited spectral and spatial resolution as compared to airborne hyperspectral imaging. These limitations impede standard image classifiers from identifying UNE signatures that are spatially small and lack distinct spectral features. In order to improve image classification results, we developed a custom algorithm that increases the true positive rate, while decreasing the false positive rate. Our algorithm’s flexible front-end allows the user to choose the method used to sparse the data. These methods include band-ratio optimization, correlation coefficient threshold, or Adaptive Coherence Estimator (ACE) threshold. The resulting sparsed pixels are clustered into like-objects. A novel weighted-sum of ACE and correlation coefficient scores is used to classify each object based on the average spectrum of its constituent pixels. WV3 and AVIRIS data of Cuprite, Nevada were used as a verification data set. This algorithm improves overall pixel classification accuracy over standard classifiers by up to 14%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

A Digitally Interfaced Analog Correlation Filter System for Object Tracking Applications

This study reports a 24×57 correlation filter system for object tracking applications. While digital interfacing of the input and output data enabled a standard and flexible way of communication with pre- and post-processing digital blocks, the multiply-accumulate (MAC) operations were performed in the analog domain to save power and area. The proposed system utilizes non-volatile floating-gate memories to store filter coefficients. The chip was fabricated in a 0.13- μm CMOS process and occupies 3.23 mm 2 of silicon area. The system dissipates 388.4 μW of power at a throughput of 11.3 kVec/s, achieving an energy efficiency of 25.2 pJ/MAC. Finally, experimental results for a custom filter designed to detect vehicles are presented.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Multiplanar Stiffness of Commercial Carbon Composite Ankle-Foot Orthoses

The mechanical properties of an ankle-foot orthosis (AFO) can impact how a user's movement is either restricted or augmented by the device. However, standardized methods for assessing stiffness properties of AFOs are lacking, posing a challenge for comparing between devices and across vendors. Therefore, the purpose of this study was to quantify the rotational stiffness of thirteen commercial, nonarticulated, carbon composite ankle-foot orthoses. A custom, instrumented test fixture, for evaluating mechanical properties in rotating exoskeletons (EMPIRE), deflected an AFO through 20 deg of plantar/dorsiflexion motion about a specified, but adjustable, ankle axis. Sagittal, frontal, and transverse plane rotational stiffness were calculated, and reliability was assessed between cycles, sessions, and testers. The EMPIRE demonstrated good-to-excellent reliability between testers, sessions, and cycles (intraclass correlation coefficients all ≥0.95 for sagittal plane stiffness measures). Sagittal plane AFO stiffness ranged from 0.58 N·m/deg to 3.66 N·m/deg. AFOs with a lateral strut demonstrated frontal plane stiffnesses up to 0.71 N·m/deg of eversion while those with a medial strut demonstrated frontal plane stiffnesses up to 0.53 N·m/deg of inversion. Transverse plane stiffnesses were less than 0.30 N·m/deg of internal or external rotation. These results directly compare AFOs of different models and from different manufacturers using consistent methodology and are intended as a resource for clinicians in identifying a device with stiffness properties for individual patients.

Biophysics↗
DOE OSTI2018

Localization and Quantification of Trace-gas Fugitive Emissions Using a Portable Optical Spectrometer

We present a portable optical spectrometer for fugitive emissions monitoring of methane (CH4). The sensor operation is based on tunable diode laser absorption spectroscopy (TDLAS), using a 5 cm open path design, and targets the 2ν3 R(4) CH4 transition at 6057.1 cm-1 (1651 nm) to avoid cross-talk with common interfering atmospheric constituents. Sensitivity analysis indicates a normalized precision of 2.0 ppmv∙Hz-1/2, corresponding to a noise-equivalent absorption (NEA) of 4.4×10-6 Hz-1/2 and minimum detectible absorption (MDA) coefficient of αmin = 8.8×10-7 cm-1∙Hz-1/2. Our TDLAS sensor is deployed at the Methane Emissions Technology Evaluation Center (METEC) at Colorado State University (CSU) for initial demonstration of single-sensor based source localization and quantification of CH4 fugitive emissions. The TDLAS sensor is concurrently deployed with a customized chemi-resistive metal-oxide (MOX) sensor for accuracy benchmarking, demonstrating good visual correlation of the concentration time-series. Initial angle-of-arrival (AOA) results will be shown, and development towards source magnitude estimation will be described.

03 NATURAL GAS↗
DOE OSTI2021

Discriminating Quantum States with Quantum Machine Learning

Quantum machine learning (QML) algorithms have obtained great relevance in the machine learning (ML) field due to the promise of quantum speedups when performing basic linear algebra subroutines (BLAS), a fundamental element in most ML algorithms. By making use of BLAS operations, we propose, implement and analyze a quantum k-means (qk-means) algorithm with a low time complexity of O(NKlog(D)I/C) to apply it to the fundamental problem of discriminating quantum states at readout. Discriminating quantum states allows the identification of quantum states |0⟩ and |1⟩ from low-level in-phase and quadrature signal (IQ) data, and can be done using custom ML models. In order to reduce dependency on a classical computer, we use the qk-means to perform state discrimination on the IBMQ Bogota device and managed to find assignment fidelities of up to 98.7% that were only marginally lower than that of the k-means algorithm. We also performed a cross-talk benchmark on the quantum device by applying both algorithms to perform state discrimination on a combination of quantum states and using Pearson Correlation coefficients and assignment fidelities of discrimination results to conclude on the presence of cross-talk on qubits. Evidence shows cross-talk in the (1, 2) and (2, 3) neighboring qubit couples for the analyzed device.

Quiroga, David↗
DOE OSTI2019

Opportunistic bone density screening for the abdominal radiologist using colored CT images: a pilot retrospective study

Purpose: The purpose of the study was to develop an accurate and reproducible method for detecting low spinal bone density on abdominal CT images. Methods: For this IRB-approved HIPAA-compliant single-center retrospective study, nonenhanced CT images of the lower abdomen were obtained in 631 African-American participants. Mean attenuation of L3/L4 was associated with quantitative CT bone density (QCT) in a randomly selected training cohort (N = 511), and receiver operating characteristics analysis was used to identify the optimal mean attenuation threshold for differentiating normal from low bone density. Custom image processing software was used to generate grayscale and colored CT images of the midline spine, with green for normal and red for low bone density. Five radiologists independently assessed bone density at L3/L4 in a validation cohort (N = 120) using various methods: QCT, visual assessment of sagittal grayscale images (Grayscale), quantitative measurement of mean attenuation on a midline sagittal image (Attenuation), and visual assessment of a midline sagittal colored image (Color). Accuracy was calculated using the average QCT bone density as a reference standard. Inter-observer agreement was assessed using intraclass correlation coefficient (ICC). Results: The optimal mean attenuation threshold for differentiating normal from low bone density at L3/L4 was 145 Hounsfield Units. The average accuracy of Grayscale, Attenuation, and Color methods was 58, 87, and 91% (p < 0.001), respectively. Inter-observer agreement was poor for Grayscale (ICC: 0.20; 95% CI 0.12, 0.28) and excellent for both Attenuation (ICC: 0.85; 95% CI 0.73, 0.91) and Color methods (ICC: 0.87; 95% CI 0.83, 0.90). Conclusion: Detection of low spinal bone density using colored abdominal CT images was highly accurate and reproducible.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2020

CONTROLLED END GAS AUTO IGNITION WITH EXHAUST GAS RECIRCULATION ON A STOICHIOMETRIC, SPARK IGNITED, NATURAL GAS ENGINE

The goal of this study is to address fundamental limitations to achieving diesel-like efficiencies in heavy duty on-highway natural gas (NG) engines. Engine knock and misfire are barriers to pathways leading to higher efficiency engines. This study explores enabling technologies for development of high efficiency stoichiometric, spark ignited, natural gas engines. These include design strategies for fast and stable combustion and higher dilution tolerance. Additionally, advanced control methodologies are implemented to maintain stable operation between knock and misfire limits. To implement controlled end- gas autoignition (C-EGAI) strategies a Combustion Intensity Metric (CIM) is used for ignition control with the use of a Woodward large engine control module (LECM). Tests were conducted using a single cylinder, variable compression ratio, cooperative fuel research (CFR) engine with baseline conditions of 900 RPM, engine load of 800 kPa indicated mean effective pressure (IMEP), and stoichiometric air/fuel ratio. Exhaust gas recirculation (EGR) tests were performed using a custom EGR system that simulates a high pressure EGR loop and can provide a range of EGR rates from 0 to 40%. The experimental measurements included the variance of EGR rate, compression ratio, engine speed, IMEP, and CIM. These five variables were optimized through a Modified Box- Benken design Surface Response Method (RSM), with brake efficiency as the merit function. A positive linear correlation between CIM and f-EGAI was identified. Consequently, CIM was used as the feedback control parameter for C-EGAI. As such, implementation of C-EGAI effectively allowed for the utilization of high EGR rates and CRs, controlling combustion between a narrower gap between knock and lean limits. The change from fixed to parametric ignition timing with CIM targeted select values of f-EGAI with an average coefficient of variance (COV) of peak pressure of 5.4. The RSM efficiency optimization concluded with operational conditions of 1080 RPM, 1150 kPa IMEP, 10.55:1 compression ratio, and 17.8% EGR rate with a brake efficiency of 21.3%. At this optimized point of peak performance, a f-EGAI for C-EGAI was observed at 34.1% heat release due to auto ignition, a knock onset crank angle value of 10.3° aTDC and ignition timing of - 24.7° aTDC. This work has demonstrated that combustion at a fixed f-EGAI can be maintained through advanced ignition control of CIM without experiencing heavy knocking events.

Cooperative Fuel Research Engine, Auto Ignition, E↗