SEARCH · Engineering Papers
Results for “Deep learning”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Statistical characterization of experimental magnetized liner inertial fusion stagnation images using deep-learning-based fuel–background segmentation
Significant variety is observed in spherical crystal x-ray imager (SCXI) data for the stagnated fuel–liner system created in Magnetized Liner Inertial Fusion (MagLIF) experiments conducted at the Sandia National Laboratories Z-facility. As a result, image analysis tasks involving, e.g., region-of-interest selection (i.e. segmentation), background subtraction and image registration have generally required tedious manual treatment leading to increased risk of irreproducibility, lack of uncertainty quantification and smaller-scale studies using only a fraction of available data. We present a convolutional neural network (CNN)-based pipeline to automate much of the image processing workflow. This tool enabled batch preprocessing of an ensemble of N scans = 139 SCXI images across N exp = 67 different experiments for subsequent study. The pipeline begins by segmenting images into the stagnated fuel and background using a CNN trained on synthetic images generated from a geometric model of a physical three-dimensional plasma. The resulting segmentation allows for a rules-based registration. Our approach flexibly handles rarely occurring artifacts through minimal user input and avoids the need for extensive hand labelling and augmentation of our experimental dataset that would be needed to train an end-to-end pipeline. Here we also fit background pixels using low-degree polynomials, and perform a statistical assessment of the background and noise properties over the entire image database. Our results provide a guide for choices made in statistical inference models using stagnation image data and can be applied in the generation of synthetic datasets with realistic choices of noise statistics and background models used for machine learning tasks in MagLIF data analysis. We anticipate that the method may be readily extended to automate other MagLIF stagnation imaging applications.
Predicting Prostate Cancer Directly from Tissue Images using Deep Learning on Mass Spectrometry Imaging and Whole Slide Imaging Data
Explore the source record for details and available documents.
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.
Artificial Intelligence Driving Materials Discovery? Perspective on the Article: Scaling Deep Learning for Materials Discovery
Not Available
A Deep Learning Based Framework to Identify Undocumented Orphaned Oil and Gas Wells from Historical Maps: A Case Study for California and Oklahoma
Undocumented Orphaned Wells (UOWs) are wells without an operator that have limited or no documentation with regulatory authorities. An estimated 310,000 to 800,000 UOWs exist in the United States (US), whose locations are largely unknown. These wells can potentially leak methane and other volatile organic compounds to the atmosphere, and contaminate groundwater. In this study, we developed a novel framework utilizing a state-of-the-art computer vision neural network model to identify the precise locations of potential UOWs. The U-Net model is trained to detect oil and gas well symbols in georeferenced historical topographic maps, and potential UOWs are identified as symbols that are further than 100 m from any documented well. A custom tool was developed to rapidly validate the potential UOW locations. We applied this framework to four counties in California and Oklahoma, leading to the discovery of 1301 potential UOWs across >40,000 km 2 . We confirmed the presence of 29 UOWs from satellite images and 15 UOWs from magnetic surveys in the field with a spatial accuracy on the order of 10 m. This framework can be scaled to identify potential UOWs across the US since the historical maps are available for the entire nation.
Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning
Accurately predicting small molecule partitioning and hydrophobicity is critical in the drug discovery process. There are many heterogeneous chemical environments within a cell and entire human body. For example, drugs must be able to cross the hydrophobic cellular membrane to reach their intracellular targets, and hydrophobicity is an important driving force for drug–protein binding. Atomistic molecular dynamics (MD) simulations are routinely used to calculate free energies of small molecules binding to proteins, crossing lipid membranes, and solvation but are computationally expensive. Machine learning (ML) and empirical methods are also used throughout drug discovery but rely on experimental data, limiting the domain of applicability. We present atomistic MD simulations calculating 15,000 small molecule free energies of transfer from water to cyclohexane. This large data set is used to train ML models that predict the free energies of transfer. We show that a spatial graph neural network model achieves the highest accuracy, followed closely by a 3D-convolutional neural network, and shallow learning based on the chemical fingerprint is significantly less accurate. A mean absolute error of ~4 kJ/mol compared to the MD calculations was achieved for our best ML model. We also show that including data from the MD simulation improves the predictions, tests the transferability of each model to a diverse set of molecules, and show multitask learning improves the predictions. This work provides insight into the hydrophobicity of small molecules and ML cheminformatics modeling, and our data set will be useful for designing and testing future ML cheminformatics methods.
Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning
Not Available
Single-Point Extrapolation to the Complete Basis Set Limit through Deep Learning
Machine learning (ML) offers an attractive method for making predictions about molecular systems while circumventing the need to run expensive electronic structure calculations. Once trained on ab initio data, the promise of ML is to deliver accurate predictions of molecular properties that were previously computationally infeasible. In this work, we develop and train a graph neural network model to correct the basis set incompleteness error (BSIE) between a small and large basis set at the RHF and B3LYP levels of theory. Our results show that, when compared to fitting to the total potential, an ML model fitted to correct the BSIE is better at generalizing to systems not seen during training. We test this ability by training on single molecules while evaluating on molecular complexes. We also show that ensemble models yield better behaved potentials in situations where the training data is insufficient. However, even when only fitting to the BSIE, acceptable performance is only achieved when the training data sufficiently resemble the systems one wants to make predictions on. As a result, the test error of the final model trained to predict the difference between the cc-pVDZ and cc-pV5Z potential is 0.184 kcal/mol for the B3LYP density functional, and the ensemble model accurately reproduces the large basis set interaction energy curves on the S66x8 dataset.
Generating Protein Structures for Pathway Discovery Using Deep Learning
Resolving the intricate details of biological phenomena at the molecular level is fundamentally limited by both length- and time scales that can be probed experimentally. Molecular dynamics (MD) simulations at various scales are powerful tools frequently employed to offer valuable biological insights beyond experimental resolution. However, while it is relatively simple to observe long-lived, stable configurations of, for example, proteins, at the required spatial resolution, simulating the more interesting rare transitions between such states often takes orders of magnitude longer than what is feasible even on the largest supercomputers available today. One common aspect of this challenge is pathway discovery, where the start and end states of a scientific phenomenon are known or can be approximated, but the mechanistic details in between are unknown. Here, we propose a representation-learning-based solution that uses interpolation and extrapolation in an abstract representation space to synthesize potential transition states, which are automatically validated using MD simulations. The new simulations of the synthesized transition states are subsequently incorporated into the representation learning, leading to an iterative framework for targeted path sampling. Our approach is demonstrated by recovering the transition of a RAS-RAF protein domain (CRD) from membrane-free to interacting with the membrane using coarse-grain MD simulations.
Quantitative Imaging of Cobalt Phthalocyanine Distribution on Carbon Nanotubes: A Deep Learning Approach to Catalyst Characterization
Electrochemical reduction of carbon dioxide (CO 2 ) offers a pathway to valuable products, with catalysts playing a crucial role. This study investigates the distribution of cobalt tetraaminophthalocyanine (CoPc-NH 2 ) immobilized on carbon nanotubes (CNTs), utilizing high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) to characterize CoPc-NH 2 distribution. A challenge in the quantitative HAADF-STEM analysis is the introduction of bias from manual Co atom identification. To address this, we developed and trained a convolutional neural network (CNN) using a data set generated from images of CoPc-NH 2 /CNT samples with varying Co loadings. The CNN, implemented in TensorFlow and Keras, facilitated Co atom detections. Analysis of the CNN-generated data confirmed a correlation between Co loading and surface density, consistent with findings from UV–vis spectroscopy. Furthermore, the application of Ripley’s L(d) function highlighted the presence of slight Co atom clustering. Furthermore, this work demonstrates the utility of the combined HAADF-STEM and CNN approach for providing spatially resolved information about catalyst distribution on nonplanar supports, revealing structural details that are typically lost through other characterization methods.
Locating Hydrides in Ligand-Protected Copper Nanoclusters by Deep Learning
Not provided.
Thermodynamic and Transport Properties of LiF and FLiBe Molten Salts with Deep Learning Potentials
Not provided.
Deep-Learning Interatomic Potential Connects Molecular Structural Ordering to the Macroscale Properties of Polyacrylonitrile
Polyacrylonitrile (PAN) is an important commercial polymer, bearing atactic stereochemistry resulting from nonselective radical polymerization. As such, an accurate, fundamental understanding of governing interactions among PAN molecular units is indispensable for advancing the design principles of final products at reduced processability costs. While ab initio molecular dynamics (AIMD) simulations can provide the necessary accuracy for treating key interactions in polar polymers, such as dipole–dipole interactions and hydrogen bonding, and analyzing their influence on the molecular orientation, their implementation is limited to small molecules only. Herein, we show that the neural network interatomic potentials (NNIPs) that are trained on the small-scale AIMD data (acquired for oligomers) can be efficiently employed to examine the structures and properties at large scales (polymers). NNIP provides critical insight into intra- and interchain hydrogen-bonding and dipolar correlations and accurately predicts the amorphous bulk PAN structure validated by modeling the experimental X-ray structure factor. Furthermore, the NNIP-predicted PAN properties, such as density and elastic modulus, are in good agreement with their experimental values. Overall, the trend in the elastic modulus is found to correlate strongly with the PAN structural orientations encoded in the Hermans orientation factor. In conclusion, this study enables the ability to predict the structure–property relations for PAN and analogues with sustainable ab initio accuracy across scales.