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At least 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC–ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mitigating Catastrophic Forgetting in Deep Learning in a Streaming Setting Using Historical Summary

Recent advancements in scientific equipment and the adaptation of electronics and the Internet of Things (IoT) in our everyday lives resulted in large and complex data production at a high rate. Making meaningful and timely knowledge discovery at a modest cost from this big data is difficult for computing power and storage limitations. Training deep learning models incrementally in a streaming setting can help us with overcoming these limitations. However, in a well-known phenomenon named catastrophic forgetting, incrementally trained models increasingly perform poorly on the past data. To mitigate catastrophic forgetting in training in a streaming setting, we propose constructing a historical summary over time and use the summary with newly arrived data during incremental training. We propose various data summarization techniques such as random sampling, micro clustering, coreset computation, and Auto Encoders to counteract catastrophic forgetting. We built a pipeline for incremental training with a historical summary for training deep learning models for streaming data. We demonstrate the effectiveness of historical summary in mitigating catastrophic forgetting using three case studies involving three different deep learning applications: an Artificial Neural Network (ANN) for classification task on MNIST dataset, a language model (RNN-LM) on the WikiText2 dataset, and a Convolutional Neural Network (CNN), ResNet50 to classify the ImageNet dataset. Through the training of the models, we observe that catastrophic forgetting is evident in ANN and CNN but not in an RNN. For the first task, our method recovers up to 47.9% lost accuracy due to catastrophic forgetting. For the third task, the historical summary recovers classification accuracy by up to 25%. For the second task, though there is not proof of catastrophic forgetting, the training performance (PPL) improves by up to 26% with historical summary.

Dash, Sajal↗
DOE OSTI2025

Deep Reinforcement Learning-Based Control of Energy Storage for Interarea Oscillation Damping

With the increasing electricity consumption and lack of transmission investment, today's power systems are operated much closer to their limits, raising concerns of inter-area oscillations that deteriorate the system stability. Here, this article presents a novel energy storage placement and control approach for enhanced damping of interarea oscillations. Combining the residual analysis and dominant mode analysis, we are able to identify the advantageous locations for placing energy storage that achieve improved damping performance. To overcome the challenges, such as fixed control parameters and insufficient damping, we propose to use a deep reinforcement learning-based approach for energy storage control. A state-of-the-art guided surrogate-gradient-based evolutionary strategy is used to train a learning agent in a robust, efficient, and reproducible manner. Parallel computing is also adopted to speed up the training process. The proposed strategy has been tested on both medium and large-scale systems. The proposed methods have demonstrated their effectiveness in mitigating various interarea oscillations within a timeframe of 20 s, thereby averting system collapse and enhancing power grid stability effectively.

25 ENERGY STORAGE↗
DOE OSTI2022

Physics-assisted generative adversarial network for X-ray tomography

X-ray tomography is capable of imaging the interior of objects in three dimensions non-invasively, with applications in biomedical imaging, materials science, electronic inspection, and other fields. The reconstruction process can be an ill-conditioned inverse problem, requiring regularization to obtain satisfactory results. Recently, deep learning has been adopted for tomographic reconstruction. Unlike iterative algorithms which require a distribution that is known a priori , deep reconstruction networks can learn a prior distribution through sampling the training distributions. In this work, we develop a Physics-assisted Generative Adversarial Network (PGAN), a two-step algorithm for tomographic reconstruction. In contrast to previous efforts, our PGAN utilizes maximum-likelihood estimates derived from the measurements to regularize the reconstruction with both known physics and the learned prior. Compared with methods with less physics assisting in training, PGAN can reduce the photon requirement with limited projection angles to achieve a given error rate. The advantages of using a physics-assisted learned prior in X-ray tomography may further enable low-photon nanoscale imaging.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Learning crystal field parameters using convolutional neural networks

We present a deep machine learning algorithm to extract crystal field (CF) Stevens parameters from thermodynamic data of rare-earth magnetic materials. The algorithm employs a two-dimensional convolutional neural network (CNN) that is trained on magnetization, magnetic susceptibility and specific heat data that is calculated theoretically within the single-ion approximation and further processed using a standard wavelet transformation. We apply the method to crystal fields of cubic, hexagonal and tetragonal symmetry and for both integer and half-integer total angular momentum values J J of the ground state multiplet. We evaluate its performance on both theoretically generated synthetic and previously published experimental data on CeAgSb _2 2 , PrAgSb _2 2 and PrMg _2 2 Cu _9 9 , and find that it can reliably and accurately extract the CF parameters for all site symmetries and values of J J considered. This demonstrates that CNNs provide an unbiased approach to extracting CF parameters that avoids tedious multi-parameter fitting procedures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Uncertainties in Density and Simulation Parameters for Radiographic Reconstructions Using Machine Learning

We will develop new and improved methods that will enable a fuller and more extensive use of experimental data, such as from radiographic imaging, towards better characterizing and reducing uncertainties in predictive modeling of weapons performance. We will achieve this by leveraging recent developments in the areas of computational imaging, statistical and machine learning, and reduced order modeling. Key new aspects of our approach include (a) a coupling of deep learning based density reconstruction with fast hydrodynamics simulators that will permit the development of certain guarantees on extrapolatability and bounds on certain other hydrodynamics-related para- metric uncertainties and (b) a dual approach towards better characterizing uncertainties in density reconstruction using deep learning based surrogates to accelerate Bayesian reconstructions on the one hand and using variational inference and Bayesian machine learning on the other hand.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2021

Analytic continuation of noisy data using Adams Bashforth residual neural network

We propose a data-driven learning framework for the analytic continuation problem in numerical quantum many-body physics. Designing an accurate and efficient framework for the analytic continuation of imaginary time using computational data is a grand challenge that has hindered meaningful links with experimental data. The standard Maximum Entropy (MaxEnt)-based method is limited by the quality of the computational data and the availability of prior information. Also, the MaxEnt is not able to solve the inversion problem under high level of noise in the data. Here we introduce a novel learning model for the analytic continuation problem using a Adams-Bashforth residual neural network (AB-ResNet). Additionally, the advantage of this deep learning network is that it is model independent and, therefore, does not require prior information concerning the quantity of interest given by the spectral function. More importantly, the ResNet-based model achieves higher accuracy than MaxEnt for data with higher level of noise. Finally, numerical examples show that the developed AB-ResNet is able to recover the spectral function with accuracy comparable to MaxEnt where the noise level is relatively small.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Prediction of DIII-D Pedestal Structure from Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. An experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (ne) and electron temperature (Te) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (Ip), toroidal magnetic field (Bφ), neutral beam heating power (PNBI) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Multisource Mobile Transfer Learning Algorithm Based on Dynamic Model Compression

With the development of the Internet of Things, the application of computer vision on mobile phones is becoming more and more extensive and people have higher and higher requirements for the timeliness of the recognition results returned and the processing capabilities of the mobile phone for image recognition. However, the processing capability and storage capability of the user terminal equipment cannot meet the needs of identifying and storing a large number of pictures, and the data transmission process will cause high energy consumption of the terminal equipment. At the same time, multisource deep transfer learning has outstanding performance in computer vision and image classification. However, due to the huge amount of calculation of the deep network model, it is impossible to use the existing excellent network model to realize image recognition and classification on the mobile terminal. In order to solve the abovementioned problems, we propose a multisource mobile transfer learning algorithm based on dynamic model compression, this algorithm considers the realization of multisource transfer learning computing in the case of multiple mobile device computing source domains, and the method also guarantees data privacy and security for each device (origin domain). Meanwhile, extensive experiments show that our method can achieve remarkable results in popular image classification datasets.

Gao, Peng↗
DOE OSTI2021

Preprocessing for Unintended Conducted Emissions Classification with ResNet

Characterization of Unintended Conducted Emissions (UCE) from electronic devices is important when diagnosing electromagnetic interference, performing nonintrusive load monitoring (NILM) of power systems, and monitoring electronic device health, among other applications. Prior work has demonstrated that UCE analysis can serve as a diagnostic tool for energy efficiency investigations and detailed load analysis. While explaining the feature selection of deep networks with certainty is often not fully comprehensive, or in other applications, quite lacking, additional tools/methods for further corroboration and confirmation can help further the understanding of the researcher. This is true especially in the subject application of the study in this paper. Often the focus of such efforts is the selected features themselves, and there is not as much understanding gained about the noise in the collected data. If selected feature and noise characteristics are known, it can be used to further shape the design of the deep network or associated preprocessing. This is additionally difficult when the available data are limited, as in the case which the authors investigated in this study. Here, the authors present a novel work (which is a proposed complementary portion of the overall solution to the deep network classification explainability problem for this application) by applying a systematic progression of preprocessing and a deep neural network (ResNet architecture) to classify UCE data obtained via current transformers. By using a methodical application of preprocessing techniques prior to a deep classifier, hypotheses can be produced concerning what features the deep network deems important relative to what it perceives as noise. For instance, it is hypothesized in this particular study as a result of execution of the proposed method and periodic inspection of the classifier output that the UCE spectral features are relatively close to each other or to the interferers, as systematically reducing the beta parameter of the Kaiser window produced progressively better classification performance, but only to a point, as going below the Beta of eight produced decreased classifier performance, as well as the hypothesis that further spectral feature resolution was not as important to the classifier as rejection of the leakage from a spectrally distant interference. This can be very important in unpredictable low-FNR applications, where knowing the difference between features and noise is difficult. As a side-benefit, much was learned regarding the best preprocessing to use with the selected deep network for the UCE collected from these low power consumer devices obtained via current transformers. Baseline rectangular windowed FFT preprocessing provided a 62% classification increase versus using raw samples. After performing a more optimal preprocessing, more than 90% classification accuracy was achieved across 18 low-power consumer devices for scenarios in which the in-band features-to-noise ratio (FNR) was very poor.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Autotuning PolyBench benchmarks with LLVM Clang/Polly loop optimization pragmas using Bayesian optimization

Here, we develop a ytopt autotuning framework that leverages Bayesian optimization to explore the parameter space search and compare four different supervised learning methods within Bayesian optimization and evaluate their effectiveness. We select six of the most complex PolyBench benchmarks and apply the newly developed LLVM Clang/Polly loop optimization pragmas to the benchmarks to optimize them. We then use the autotuning framework to optimize the pragma parameters to improve their performance. The experimental results show that our autotuning approach outperforms the other compiling methods to provide the smallest execution time for the benchmarks syr2k, 3mm, heat-3d, lu, and covariance with two large datasets in 200 code evaluations for effectively searching the parameter spaces with up to 170,368 different configurations. We find that the Floyd-Warshall benchmark did not benefit from autotuning. To cope with this issue, we provide some compiler option solutions to improve the performance. Then we present loop autotuning without a user's knowledge using a simple mctree autotuning framework to further improve the performance of the Floyd-Warshall benchmark. We also extend the ytopt autotuning framework to tune a deep learning application.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Machine learning-based real-time kinetic profile reconstruction in DIII-D

Abstract Kinetic equilibrium reconstruction plays a vital role in the physical analysis of plasma stability and control in fusion tokamaks. However, the traditional approach is subjective and prone to human biases. To address this, the consistent automatic kinetic equilibrium reconstruction (CAKE) method was introduced, providing objective results. Nonetheless, its offline nature limits its application in real-time plasma control systems (PCSs). To address this limitation, we present RTCAKENN, a machine learning model that approximates 7 CAKE-level output profiles, namely pressure, inverse q , toroidal current density, electron temperature and density, carbon ion impurity temperature and rotation profiles, using real-time available inputs. The deep neural network consists of an encoder layer, where the scalars and interdependent inputs such as plasma boundary coordinates and motional Stark effect data are encoded using multi-layer perceptrons (MLPs), while profile inputs are encoded by 1D convolutional layers. The encoded data is passed through a MLP for latent feature extraction, before being decoded in the decoding layers, which consist of upsampling and convolutional layers. RTCAKENN has been implemented in the DIII-D PCS and our model achieves accuracy comparable to CAKE and surpasses existing real-time alternatives. Through clever dropout training, RTCAKENN exhibits robustness and can operate even in the absence of Thomson scattering data or charge exchange recombination data. It executes in under 8 ms in the real-time environment, enabling future application in real-time control and analysis.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Integrating Overhead Camera Imagery with Reinforcement Learning to Improve Fuel Economy Through Adaptive Traffic Control

Overhead cameras have been deployed for some time as a sensor for traffic control, with many advantages over conventional inductive loop sensors in terms of robustness, ease of installation, and simplicity with respect to maintenance. We explore the utility of such imagery (in particular, fisheye lens cameras) for intelligent traffic control in real-time using reinforcement learning, with a goal of improving fuel economy for the overall intersection and grid of intersections. We summarize our initial work in data collection and approach to ascertain the ability to visually sense vehicular fuel consumption using real-world data. We then describe our deep reinforcement learning topology to test adaptive control informed by the camera capabilities. Next, we tested the proof-of-concept through a variety of simulation scenarios using the Simulation of Urban Mobility (SUMO) traffic simulator, which included different estimates on vehicle classifications, different traffic distributions, and different traffic densities. Six different control policies were tested ranging from simple timing, to heuristic visual-based methods, to actual policies learned via the reinforcement learning approach. Our results demonstrate the feasibility of the approach for controlling traffic lights for better fuel efficiency based on visual vehicle estimates from commercial, fisheye lens cameras.

Karnowski, Thomas↗
DOE OSTI2020

Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples

Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.

Colby, Sean M.↗
DOE OSTI2025

Estimating the Impacts of Increasing Temperatures and the Efficacy of Climate Adaptation Strategies in Urban Microclimates with Deep Learning

As urbanization and climate change progress, understanding and addressing urban heat becomes a priority for climate adaptation efforts. High temperatures concentrated in the urban core can drive increased risk of heat-related death and illness as well as increased energy demand for cooling. However, modeling the urban microclimate is an ongoing field of research typically burdened by an imprecise description of the built environment, incomplete observational records, significant computational cost, and a lack of high-resolution estimates of the impacts of increasing temperatures. Here, we present computationally efficient machine learning methods that can improve the accuracy of urban temperature estimates when compared to historical reanalysis data. These models are applied to a neighborhood in Los Angeles, and we compare the energy benefits of heat mitigation strategies to the impacts of climate change. We find that cooling demand is likely to increase substantially through midcentury, but engineered high-albedo surfaces could lessen this increase by more than 50 %. The corresponding increase in winter gas heating offsets the summer cooling benefit in the current climate, but total annual energy use from combined heating and cooling with electric heat pumps benefits from the engineered heat mitigation strategies under both current and future climates.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Phase Identification in Synchrotron X-ray Diffraction Patterns of Ti–6Al–4V Using Computer Vision and Deep Learning

X-ray diffraction patterns contain information about the atomistic structure and microstructure (defect population) of materials, extracting detailed information from diffraction patterns is complex, demanding and relies on prior knowledge. Here, we hypothesize that deep-learning techniques can help to perform an effective and accurate analysis with high throughput rates. To demonstrate this concept, we applied a novel deep learning framework to determine the evolution of the β-phase volume fraction in a Ti–6Al–4V alloy during heat-treatment from video sequences of 2D diffraction patterns recorded in transmission and with highly monochromatic radiation in a synchrotron beamline. In particular, we studied the impact of network design on prediction reliability and computational performance. Networks of different architectures were trained using 3008 experimental 2D patterns. A well-tuned model was found to reproduce the phase fractions of another experimental data set, consisting of 1100 diffraction patterns, with a mean-square error as small as 2.6 x 10 -4 . The average prediction error of β-phase volume fraction was within 1.6 x 10 -2 (in each diffraction pattern) of the values obtained by conventional methods. Our work demonstrates that convolutional neural networks can evaluate high energy X-ray diffraction patterns with a remarkable level of reliability. Furthermore, it demonstrates the significance of network design on the reliability of predictions and computational performance. The most complex models do not necessarily result in highest accuracy and may even fail to learn from the data.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Making Invisible Visible: Data-Driven Seismic Inversion With Spatio-Temporally Constrained Data Augmentation

Deep learning and data-driven approaches have shown great potential in scientific domains. The promise of data-driven techniques relies on the availability of a large volume of high-quality training datasets. Due to the high cost of obtaining data through expensive physical experiments, instruments, and simulations, data augmentation techniques for scientific applications have emerged as a new direction for obtaining scientific data recently. However, existing data augmentation techniques originating from computer vision yield physically unacceptable data samples that are not helpful for the domain problems that we are interested in. In this article, we develop new data augmentation techniques based on convolutional neural networks. Specifically, our generative models leverage different physics knowledge (such as governing equations, observable perception, and physics phenomena) to improve the quality of the synthetic data. To validate the effectiveness of our data augmentation techniques, we apply them to solve a subsurface seismic full-waveform inversion using simulated CO 2 leakage data. Our interest is to invert for subsurface velocity models associated with very small CO 2 leakage. We validate the performance of our methods using comprehensive numerical tests. Here via comparison and analysis, we show that data-driven seismic imaging can be significantly enhanced by using our data augmentation techniques. Particularly, the imaging quality has been improved by 15% in test scenarios of general-sized leakage and 17% in small-sized leakage when using an augmented training set obtained with our techniques.

58 GEOSCIENCES↗
DOE OSTI2021

Advances in the electron diffraction characterization of atomic clusters and nanoparticles

Nanoparticles and metallic clusters continue to make a remarkable impact on novel and emerging technologies. In recent years, there have been impressive advances in the controlled synthesis of clusters and their advanced characterization. One of the most common ways to determine the structures of nanoparticles and clusters is by means of X-ray diffraction methods. However, this requires the clusters to crystallize in a similar way to those used in protein studies, which is not possible in many cases. Novel methods based on electron diffraction have been used to efficiently study individual nanoparticles and clusters and these can overcome the obstacles commonly encountered during X-ray diffraction methods without the need for large crystals. These novel methodologies have improved with advances in electron microscopy instrumentation and electron detection. Here, we review advanced methodologies for characterizing metallic nanoparticles and clusters using a variety of electron diffraction procedures. These include selected area electron diffraction, nanobeam diffraction, coherent electron diffraction, precession electron diffraction, scanning transmission electron microcopy diffraction, and high throughput data analytics, which leverage deep learning to reduce the propensity for data errors and translate nanometer and atomic scale measurements into material data.

77 NANOSCIENCE AND NANOTECHNOLOGY↗