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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel

Abstract Estimates of plant traits derived from hyperspectral reflectance data have the potential to efficiently substitute for traits, which are time or labor intensive to manually score. Typical workflows for estimating plant traits from hyperspectral reflectance data employ supervised classification models that can require substantial ground truth datasets for training. We explore the potential of an unsupervised approach, autoencoders, to extract meaningful traits from plant hyperspectral reflectance data using measurements of the reflectance of 2151 individual wavelengths of light from the leaves of maize ( Zea mays ) plants harvested from 1658 field plots in a replicated field trial. A subset of autoencoder‐derived variables exhibited significant repeatability, indicating that a substantial proportion of the total variance in these variables was explained by difference between maize genotypes, while other autoencoder variables appear to capture variation resulting from changes in leaf reflectance between different batches of data collection. Several of the repeatable latent variables were significantly correlated with other traits scored from the same maize field experiment, including one autoencoder‐derived latent variable (LV8) that predicted plant chlorophyll content modestly better than a supervised model trained on the same data. In at least one case, genome‐wide association study hits for variation in autoencoder‐derived variables were proximal to genes with known or plausible links to leaf phenotypes expected to alter hyperspectral reflectance. In aggregate, these results suggest that an unsupervised, autoencoder‐based approach can identify meaningful and genetically controlled variation in high‐dimensional, high‐throughput phenotyping data and link identified variables back to known plant traits of interest.

Tross, Michael C.↗
DOE OSTI2022

A comparison of neural network architectures for data-driven reduced-order modeling

The popularity of deep convolutional autoencoders (CAEs) has engendered new and effective reduced-order models (ROMs) for the simulation of large-scale dynamical systems. Despite this, it is still unknown whether deep CAEs provide superior performance over established linear techniques or other network-based methods in all modeling scenarios. To elucidate this, the effect of autoencoder architecture on its associated ROM is studied through the comparison of deep CAEs against two alternatives: a simple fully connected autoencoder, and a novel graph convolutional autoencoder. Through benchmark experiments, it is shown that the superior autoencoder architecture for a given ROM application is highly dependent on the size of the latent space and the structure of the snapshot data, with the proposed architecture demonstrating benefits on data with irregular connectivity when the latent space is sufficiently large.

42 ENGINEERING↗
DOE OSTI2022

Challenges for unsupervised anomaly detection in particle physics

Anomaly detection relies on designing a score to determine whether a particular event is uncharacteristic of a given background distribution. One way to define a score is to use autoencoders, which rely on the ability to reconstruct certain types of data (background) but not others (signals). In this paper, we study some challenges associated with variational autoencoders, such as the dependence on hyperparameters and the metric used, in the context of anomalous signal (top and W) jets in a QCD background. We find that the hyperparameter choices strongly affect the network performance and that the optimal parameters for one signal are non-optimal for another. In exploring the networks, we uncover a connection between the latent space of a variational autoencoder trained using mean-squared-error and the optimal transport distances within the dataset. We then show that optimal transport distances to representative events in the background dataset can be used directly for anomaly detection, with performance comparable to the autoencoders. Whether using autoencoders or optimal transport distances for anomaly detection, we find that the choices that best represent the background are not necessarily best for signal identification. These challenges with unsupervised anomaly detection bolster the case for additional exploration of semi-supervised or alternative approaches.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Transfer Learning using Denoising Auto-Encoders for Cellular-Level Annotation of Tumor in Pathology Slides

Adversarial examples can produce altered classifications using only seemingly innocuous, imperceptible perturbations to the original image. The imperceptibility of adversarial perturbations suggests that the corresponding classifiers use decision criteria different than those of a human. In a medical setting, inexplicable decision criteria confound a pathologist’s willingness to trust machine-generated annotations. Here, we analyze denoising tumor detection models to see if they are robust to imperceptible adversarial perturbations. Moreover, to be more fully trusted by pathologists, we require tumor detectors that generate interpretable annotations which segment pathology slides into tumorous and normal regions at the cellular level. We therefore compare transfer learning based on two different autoencoder architectures, one derived from a deep denoising bottleneck autoencoder and one from an over-complete sparse autoencoder. Both autoencoders were first trained in an unsupervised manner on a set of pathology slides drawn from the Camelyon16 dataset. The latent representations produced by each autoencoder were then passed to separate neural networks that were trained in a supervised manner on binary tumor-normal masks generated by pathologists at cellular resolution. Both tumor detectors supported better than 90% AUC PR as measured by the area under the precision/recall curve on a held-out pathology slide. To assess the underlying decision criteria used by both tumor detectors, we constructed imperceptible adversarial examples which reduced the AUC PR of both models to less than 70%. Random noise of the same amplitude had almost no effect on the AUC PR of either model. Additionally, each tumor detector was resistant to adversarial “transfer” attacks targeting the other. The adversarial perturbations showed strong characteristic differences: the deep denoising models perturbations were a very diffuse, seemingly unrecognizable pattern while the sparse coding models perturbations showed traces of tissue cells.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Deep learning for in situ data compression of large turbulent flow simulations

As the size of turbulent flow simulations continues to grow, in situ data compression is becoming increasingly important for visualization, analysis, and restart checkpointing. For these applications, single-pass compression techniques with low computational and communication overhead are crucial. In this paper we present a deep-learning approach to in situ compression using an autoencoder architecture that is customized for three-dimensional turbulent flows and is well suited for contemporary heterogeneous computing resources. The autoencoder is compared against a recently introduced randomized single-pass singular value decomposition (SVD) for three different canonical turbulent flows: decaying homogeneous isotropic turbulence, a Taylor-Green vortex, and turbulent channel flow. Our proposed fully convolutional autoencoder architecture compresses turbulent flow snapshots by a factor of 64 with a single pass, allows for arbitrarily sized input fields, is cheaper to compute than the randomized single-pass SVD for typical simulation sizes, performs well on unseen flow configurations, and has been made publicly available. The results reported here show that the autoencoder dramatically outperforms a randomized single-pass SVD with similar compression ratio and yields comparable performance to a higher-rank decomposition with an order of magnitude less compression in regard to preserving a number of important statistical quantities such as turbulent kinetic energy, enstrophy, and Reynolds stresses.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2019

Feature Learning for Multispectral Satellite Imagery Classification Using Neural Architecture Search

Automated classification of remote sensing data is an integral tool for earth scientists, and deep learning has proven very successful at solving such problems. However, building deep learning models to process the data requires expert knowledge of machine learning. We introduce DELTA, a software toolkit to bridge this technical gap and make deep learning easily accessible to earth scientists. Visual feature engineering is a critical part of the machine learning lifecycle, and hence is a key area that will be automated by DELTA. Hand-engineered features can perform well, but require a cross functional team with expertise in both machine learning and the specific problem domain, which is costly in both researcher time and labor. The problem is more acute with multispectral satellite imagery, which requires considerable computational resources to process. In order to automate the feature learning process, a neural architecture search samples the space of asymmetric and symmetric autoencoders using evolutionary algorithms. Since denoising autoencoders have been shown to perform well for feature learning, the autoencoders are trained on various levels of noise and the features generated by the best performing autoencoders evaluated according to their performance on image classification tasks. The resulting features are demonstrated to be effective for Landsat-8 flood mapping, as well as benchmark datasets CIFAR10 and SVHN.

Robert Campbell↗
DOE OSTI2022

Finding Hidden Patterns in High Resolution Wind Flow Model Simulations

Wind flow data is critical in terms of investment decisions and policy making. High resolution data from wind flow model simulations serve as a supplement to the limited resource of original wind flow data collection. Given the large size of data, finding hidden patterns in wind flow model simulations are critical for reducing the dimensionality of the analysis. In this work, we first perform dimension reduction with two autoencoder models: the CNN-based autoencoder (CNN-AE) [1], and hierarchical autoencoder (HIER-AE) [2], and compare their performance with the Principal Component Analysis (PCA). We then investigate the super-resolution of the wind flow data. By training a Generative Adversarial Network (GAN) with 300 epochs, we obtained a trained model with 2× resolution enhancement. We compare the results of GAN with Convolutional Neural Network (CNN), and GAN results show finer structure as expected in the data field images. Also, the kinetic energy spectra comparisons show that GAN outperforms CNN in terms of reproducing the physical properties for high wavenumbers and is critical for analysis where high-wavenumber kinetics play an important role.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

tLaSDI: Thermodynamics-informed latent space dynamics identification

Here we propose a latent space dynamics identification method, namely tLaSDI, that embeds the first and second principles of thermodynamics. The latent variables are learned through an autoencoder as a nonlinear dimension reduction model. The latent dynamics are constructed by a neural network-based model that precisely preserves certain structures for the thermodynamic laws through the GENERIC formalism. An abstract error estimate is established, which provides a new loss formulation involving the Jacobian computation of autoencoder. The autoencoder and the latent dynamics are simultaneously trained to minimize the new loss. Computational examples demonstrate the effectiveness of tLaSDI, which exhibits robust generalization ability, even in extrapolation. In addition, an intriguing correlation is empirically observed between a quantity from tLaSDI in the latent space and the behaviors of the full-state solution.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Cy-Phy ADS: Cyber Physical Anomaly Detection Framework for EV Charging Systems

Today’s large-scale Electric Vehicle (EV) infrastructures are heavily dependent on information communication technologies to maintain their operation and to support communication within sub-system components as well as the outside world. These technologies are vulnerable to various cyber and physical threats. Timely identification and mitigation of these threats are critical for improving human safety, avoiding economic losses, and preventing catastrophic system failures. By addressing this, our work presents a ResNet Autoencoder (AE) based Cyber-Physical Anomaly Detection System (Cy-Phy ADS) for detecting anomalies in EV Controller Area Network (CAN) protocol communication. It consists of four main components: Cyber-Physical Feature Extractor, ResNet AE-based Anomaly Detection Framework, Cyber-Physical Health Metric (CPHM), and Visualization Dashboard. The presented framework was trained and tested using CAN data collected from the EV charging system testbed at the Idaho National Laboratory. The presented Cy-Phy ADS compared against six widely used unsupervised anomaly detection algorithms: One Class Support Vector Machine (OCSVM), Variational Autoencoder (VAE), LSTM Autoencoder (LSTM AE), Isolation Forest (IForest), Principle Component Analysis (PCA) and Local Outlier Factor (LOF). Here the presented approach showed the highest accuracy among the compared methods. Further, the proposed approach showed comparable performance in terms of precision, F1, and False positive rate. It also showed the lowest training and inference time compared to the neural network-based baseline algorithms compared against with. Additionally, the Cy-Phy ADS has advantages such as unsupervised training, the ability to provide a holistic metric for system health characterization, and non-linear feature extraction.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2022

Harnessing structural stochasticity in the computational discovery and design of microstructures

This paper presents a deep generative model-based design methodology for tailoring the structural stochasticity of microstructures. Although numerous methods have been established for designing deterministic (periodic) or stochastic microstructures, a systematic design approach that allows the unified treatment of both deterministic and stochastic microstructure design domains has yet to be created. The proposed methodology resolves this issue by learning a unified feature space that embodies diverse structural patterns with continuously varying stochasticity levels. A highly diverse microstructure database is established to incorporate various types of deterministic and stochastic microstructure patterns. A property-aware deep generative model is proposed to learn a unified feature space of the structural characteristics, as well as the relationship between structure features and properties of interest. Autoencoder (AE), Variational Autoencoder (VAE), and Adversarial Autoencoder (AAE) are compared to understand their relative merits in the property-aware learning of the unified feature space. Microstructural designs with tailorable stochasticity and properties are obtained by searching the unified feature space. Multiple design cases are presented to demonstrate the capability of designing microstructures for structural stochasticity and properties. Furthermore, the proposed method is employed to create stochastically graded structures, which manipulate the mechanical behaviors by varying the local stochasticity of the structure.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Understanding latent timescales in neural ordinary differential equation models of advection-dominated dynamical systems

The neural ordinary differential equation (ODE) framework has shown considerable promise in recent years in developing highly accelerated surrogate models for complex physical systems characterized by partial differential equations (PDEs). For PDE-based systems, state-of-the-art neural ODE strategies leverage a two-step procedure to achieve this acceleration: a nonlinear dimensionality reduction step provided by an autoencoder, and a time integration step provided by a neural-network based model for the resultant latent space dynamics (the neural ODE). This work explores the applicability of such autoencoder-based neural ODE strategies for PDEs in which advection terms play a critical role. More specifically, alongside predictive demonstrations, physical insight into the sources of model acceleration (i.e., how the neural ODE achieves its acceleration) is the scope of the current study. Such investigations are performed by quantifying the effects of both autoencoder and neural ODE components on latent system time-scales using eigenvalue analysis of dynamical system Jacobians. To this end, the sensitivity of various critical training parameters – de-coupled versus end-to-end training, latent space dimensionality, and the role of training trajectory length, for example – to both model accuracy and the discovered latent system timescales is quantified. Furthermore, this work specifically uncovers the key role played by the training trajectory length (the number of rollout steps in the loss function during training) on the latent system timescales: larger trajectory lengths correlate with an increase in limiting neural ODE time-scales, and optimal neural ODEs are found to recover the largest time-scales of the full-order (ground-truth) system. Demonstrations are performed across fundamentally different unsteady fluid dynamics configurations influenced by advection: (1) the Kuramoto–Sivashinsky equations (2) Hydrogen-Air channel detonations (the compressible reacting Navier–Stokes equations with detailed chemistry), and (3) 2D Atmospheric flow.

Advection-dominated dynamical systems↗