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DOE OSTI2022

A deep learning-enhanced framework for multiphysics joint inversion

Joint inversion has drawn considerable attention due to the availability of multiple geophysical data sets, ever-increasing computational resources, the development of advanced algorithms, and its ability to reduce inversion uncertainty. A key issue of joint inversion is to develop effective strategies to link different geophysical data in a unified mathematical framework, in which the information obtained from different models can complement each other. We have developed a deep learning-enhanced joint inversion framework to simultaneously reconstruct different physical models by fusing different types of geophysical data. Traditionally, structure similarity constraints are pursued by joint inversion algorithms using manually crafted formulations (e.g., cross gradient). The constraint is constructed by a deep neural network (DNN) during the learning process. The framework is designed to combine the DNN and a traditional independent inversion workflow and improve the joint inversion result iteratively. The network can be easily extended to incorporate multiphysics without structural changes. Numerical experiments on the joint inversion of 2D DC resistivity data and seismic traveltime are used to validate our method. In addition, this learning-based framework demonstrates excellent generalization abilities when tested on data sets using different geologic structures. It also can handle different sensing configurations and nonconforming discretization.

Geochemistry & Geophysics↗

DOE OSTI2024

Three-dimensional cooperative inversion of airborne magnetic and gravity gradient data using deep-learning techniques

Using multiple geophysical methods has become a prevailing approach in numerous geophysical applications to investigate subsurface structures and parameters. These multimethod-based exploration strategies have the potential to greatly diminish uncertainties and ambiguities encountered during geophysical data analysis and interpretation. One of the applications is the cooperative inversion of airborne magnetic and gravity gradient data for the interpretation of data obtained in mineral, oil and gas, and geothermal explorations. In this paper, a unified cooperative inversion framework is designed by combining the standard separate inversions with a deep neural network (DNN), which serves as the link between different types of data. A well-trained DNN takes the separately inverted susceptibility and density models as the inputs and provides improved models that will be used as the initial models of deterministic inversions. A two-round iteration strategy is adopted to guarantee the reasonability of the recovered models and overall efficiency of the inversion. In addition, this deep-learning (DL)-based framework demonstrates excellent generalization abilities when tested on models that are entirely distinct from the training data sets. The framework can easily incorporate multiphysics without necessitating any structural changes to the network. Synthetic experiments validate that our DL-based method outperforms conventional separate inversions and cross-gradient-based joint inversion in view of the accuracy of the recovered models and inversion efficiency. Successful application to field data further verifies the effectiveness of our DL-based method.

Geochemistry & Geophysics↗

DOE OSTI2017

Two-photon absorption measurements of deep UV transmissible materials at 213 nm

We report on two photon absorption measurements at 213nm of deep UV transmissible media including LiF, MgF 2 , CaF 2 , BaF 2 , Sapphire (Al 2 O 3 ) and high purity grades of fused-silica (SiO 2 ). A high stability 24ps Nd:YAG laser operating at the 5th harmonic (213nm) was used to generate a high intensity, long Rayleigh length Gaussian focus inside the samples. The measurements of the Fluoride crystals and Sapphire indicate two photon absorption coefficients between 0.004 and 0.82 cm/GW. We find that different grades of fused silica performed near identically for two photon absorption, however, there are differences in linear losses associated with purity. A low two photon absorption cross section is measured for MgF 2 making it an ideal material for the propagation of high intensity deep UV lasers.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Deep learning-based temporal deconvolution for photon time-of-flight distribution retrieval

The acquisition of the time of flight (ToF) of photons has found numerous applications in the biomedical field. Over the last decades, a few strategies have been proposed to deconvolve the temporal instrument response function (IRF) that distorts the experimental time-resolved data. However, these methods require burdensome computational strategies and regularization terms to mitigate noise contributions. Herein, we propose a deep learning model specifically to perform the deconvolution task in fluorescence lifetime imaging (FLI). The model is trained and validated with representative simulated FLI data with the goal of retrieving the true photon ToF distribution. Its performance and robustness are validated with well-controlled in vitro experiments using three time-resolved imaging modalities with markedly different temporal IRFs. The model aptitude is further established with in vivo preclinical investigation. Overall, these in vitro and in vivo validations demonstrate the flexibility and accuracy of deep learning model-based deconvolution in time-resolved FLI and diffuse optical imaging.

Pandey, Vikas (ORCID:0000000154771095)↗

DOE OSTI2023

FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi

mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models

Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and computer vision. By providing pre-trained models that can be fine-tuned for specific applications, they enable researchers to create accurate models with minimal effort and computational resources. Large scale genomics deep learning models come in two flavors: the first are large language models of DNA sequences trained in a self-supervised fashion, similar to the corresponding natural language models; the second are supervised learning models that leverage large scale genomics datasets from ENCODE and other sources. We argue that these models are the equivalent of foundation models in natural language processing in their utility, as they encode within them chromatin state in its different aspects, providing useful representations that allow quick deployment of accurate models of gene regulation. We demonstrate this premise by leveraging the recently created Sei model to develop simple, interpretable models of intron retention, and demonstrate their advantage over models based on the DNA language model DNABERT-2. Our work also demonstrates the impact of chromatin state on the regulation of intron retention. Using representations learned by Sei, our model is able to discover the involvement of transcription factors and chromatin marks in regulating intron retention, providing better accuracy than a recently published custom model developed for this purpose.

Biochemistry & Molecular Biology↗

DOE OSTI2015

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (GeneVec) for gene sequences, this representation can be widely used in applications of deep learning in proteomics and genomics. In the present paper, we focus on protein-vectors that can be utilized in a wide array of bioinformatics investigations such as family classification, protein visualization, structure prediction, disordered protein identification, and protein-protein interaction prediction. In this method, we adopt artificial neural network approaches and represent a protein sequence with a single dense n-dimensional vector. To evaluate this method, we apply it in classification of 324,018 protein sequences obtained from Swiss-Prot belonging to 7,027 protein families, where an average family classification accuracy of 93%±0.06% is obtained, outperforming existing family classification methods. In addition, we use ProtVec representation to predict disordered proteins from structured proteins. Two databases of disordered sequences are used: the DisProt database as well as a database featuring the disordered regions of nucleoporins rich with phenylalanine-glycine repeats (FG-Nups). Using support vector machine classifiers, FG-Nup sequences are distinguished from structured protein sequences found in Protein Data Bank (PDB) with a 99.8% accuracy, and unstructured DisProt sequences are differentiated from structured DisProt sequences with 100.0% accuracy. These results indicate that by only providing sequence data for various proteins into this model, accurate information about protein structure can be determined. Importantly, this model needs to be trained only once and can then be applied to extract a comprehensive set of information regarding proteins of interest. Moreover, this representation can be considered as pre-training for various applications of deep learning in bioinformatics.

Science & Technology - Other Topics↗

DOE OSTI2024

Substantial and overlooked greenhouse gas emissions from deep Arctic lake sediment - supporting data and code

This data package contains data, descriptions, and code-based analyses that were used to support conclusions drawn in “Substantial and overlooked greenhouse gas emissions from deep Arctic lake sediment”, by Freitas et al. (2025) (https://doi.org/10.1038/s41561-024-01614-y). The study evaluated greenhouse gas production along a deep sediment core (20 m) taken in 2018 from below Goldstream Lake, a field site approximately 15 km north of Fairbanks, Alaska.The file “ESSDive_NFreitas_2024_flmd.csv” includes an overview of all other csv files in this data package, namely: sediment descriptions (depth and type of sediment), sediment characterizations (bulk density, gravimetric water content, total carbon, etc.), calculated respiration and temperature sensitivity values associated with year-long incubations of the sediment core, and the R code used to process the dataset. Additional details regarding the content of these files and how the calculations were performed are described in the Methods section of this archive. The “data_dictionary_ESSDive_NFreitas_2024_dd.csv” is a data dictionary for all files included in the data package. Each row in the data dictionary represents a column name in a given file. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).Data package updates- August 2024: Title was updated, R code now includes a process for calculating potential production across the whole sediment column, the "sediment_column_production_potentials_ESSDive_NFreitas_2024.csv" is the associated data output file, and the file level metadata and data dictionaries were updated to reflect the contents of the additional csv file.- October 2024: Title was updated, and a statement was added to Step 2 of the Methods that describes that samples were collected (and exported) in a responsible manner and in accordance with relevant permits and local laws.- January 2025: Updated the associated manuscript details in the Abstract (manuscript title, publication date, DOI link) and in the Related References section (full citation).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Radiocarbon of deep fine roots across four in lowland seasonal tropical forests in Panama

Objectives:Fine roots are key to ecosystem-scale nutrient, carbon (C), and water cycling, but our understanding of fine root traits variation within and among tropical forests, one of Earth’s most C-rich ecosystems, is limited. In 2022 and 2023, we aimed to explore differences in deep root characteristics among four lowland tropical forests in Panama, which vary in fertility and mean annual precipitation. We measured radiocarbon content (fraction modern [FM] and Δ14C) and δ13C of live fine roots at depths greater than 80 cm, up to 120 cm. The goal was to understand how deep root characteristics differ across these sites.Datasets included:The datasets provided include .csv and .xlsx files for radiocarbon content (fraction modern [FM] and Δ14C) and δ13C of live fine roots at depths greater than 80 cm, up to 120 cm collected from late 2017 to 2018 across four different forests. Additionally, a .kml file is provided with coordinates for all 32 plots included in the study across four forests (n = 8 plots per site). This dataset serves as baseline data before a throughfall exclusion experiment, Panama Rainforest Changes with Experimental Drying (PARCHED), was implemented. No special software is needed to open these files.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Inverse Analysis with Variational Autoencoders: A Comparison of Shallow and Deep Networks

Inverse problems are applied to determine unknown properties by matching observational data with a physical model that often takes many parameters as input. To overcome the underconstrained nature of inverse problems and achieve good performance, an approach is presented involving regularization with a technique known as a variational autoencoder (VAE), which is trained to map a high-dimensional parameter space with a complex structure to a low-dimensional latent space with a simple structure. We apply this approach to unconditioned realizations of the parameters (heterogeneous hydraulic fields) for a hydrogeological inverse problem. Two types of hydraulic conductivity fields are used to evaluate the characterization for the different levels of heterogeneity complexity of the physical inputs. This approach keeps the computational cost of generating the training data low. The reason is unconditioned realizations neither rely on the observational data used to perform the inverse analysis nor require any groundwater flow model forward runs. In addition, this approach applies regularization on a low-dimensional latent space from the VAE and increases optimization efficiency through automatic differentiation. Furthermore, two different neural network (NN) structures are tested for their utility in using the VAE for inverse analysis. The performance of a deep, convolutional neural network strongly depends on the dimensionality of the latent space, which requires tuning. In contrast, a shallow, dense neural network provides consistently accurate characterization without tuning. Furthermore, our approach evaluates the advantages of the shallow, dense neural network over the deep, convolutional one and enables future application to a wide range of inverse problems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

DeepShake: Shaking Intensity Prediction Using Deep Spatiotemporal RNNs for Earthquake Early Warning

Abstract We propose a deep spatiotemporal recurrent neural network, DeepShake, to project future shaking intensity directly from current ground-motion observations. DeepShake is a network-based forecasting model, able to predict future shaking intensity at all stations within a network given previously measured ground shaking. The model is not given any a priori knowledge of station locations; instead, it learns wave propagation amplitudes and delays solely from training data. We developed DeepShake with the 35,679 earthquakes from the 2019 Ridgecrest sequence. Tasked with alerting for modified Mercalli intensity (MMI) IV+ shaking on 3568 validation earthquakes at least 5 s in advance, DeepShake achieves an equal error rate of 11.4%. For the Mw 7.1 earthquake that hit Ridgecrest on 5 July 2019, DeepShake was able to provide targeted alerts to all stations inside the network 5 s prior to the arrival of MMI IV+ waveforms. DeepShake demonstrates that deep spatiotemporal neural networks can effectively provide one-step earthquake early warning with reasonable accuracy and latency.

Geochemistry & Geophysics↗

DOE OSTI2025

Improving the Transportability of a Deep Learning Denoising Model Using Transfer Learning Techniques

The adoption of machine learning techniques in the seismology community has led to great performance improvements in several areas, including signal processing. Specifically, the development of deep learning–based seismic waveform denoising models has the potential to yield improvements in signal detection capabilities for networks operating in particularly noisy environments. Recent advancements in the design of these deep learning denoising models have included the incorporation of continuous and discrete wavelet transform functions into the network architecture to improve the learning capabilities and efficiency of said models. These wavelet transform–based seismic denoising models have shown improved denoising capabilities in regions where there is good agreement between the data features present in the training and evaluation datasets. However, questions remain about the overall transportability of these models to other monitoring regions. Here, in this study, we will determine the baseline transportability of a newly developed multilevel wavelet‐transform convolutional neural network (MWCNN) seismic denoising model. We accomplish this by taking a version of the MWCNN denoising model trained on data collected from the Utah region and evaluating its denoising performance on datasets collected from the neighboring Nevada region, which differ with regard to monitoring sensor types and event histories. We find that there is a notable variability in denoising performance related to the degree of similarity between the initial and new target datasets. The most notable difference in denoising performance is the ability of the denoising model to preserve accurate amplitude information associated with the signal energy present in the waveform data. Finally, we evaluate the ability of transfer learning techniques to improve the transportability of the MWCNN denoising model. We find that although there is still a performance gap present in the denoising results of the MWCNN model, transfer learning did yield improved results.

Quinones, Louis [Sandia National Laboratories (SNL↗

DOE OSTI2024

Datasets and U-Net Model for "A Deep Learning Based Framework to Identify Undocumented Orphaned Oil and Gas Wells from Historical Maps: a Case Study for California and Oklahoma"

This dataset has results and the model associated with the publication Ciulla et al., (2024). It contains a U-Net semantic segmentation model (unet_model.h5) and associated code implemented in tensorflow 2.0 for the model training and identification of oil and gas well symbols in USGS historical topographic maps (HTMC). Given a quadrangle map (7.5 minutes), downloadable at this url: https://ngmdb.usgs.gov/topoview/, and a list of coordinates of the documented wells present in the area, the model returns the coordinates of oil and gas symbols in the HTMC maps. For reproducibility of our workflow, we provide a sample map in California and the documented well locations for the entire State of California (CalGEM_AllWells_20231128.csv) downloaded from https://www.conservation.ca.gov/calgem/maps/Pages/GISMapping2.aspx. Additionally, the locations of 1,301 potential undocumented orphaned wells identified using our deep learning framework or the counties of Los Angeles and Kern in California, and Osage and Oklahoma in Oklahoma are provided in the file found_potential_UOWs.zip. The results of the visual inspection of satellite imagery in Osage County is in the file visible_potential_UOWs.zip. The dataset also includes a custom tool to validate the detected symbols in the HTMC maps (vetting_tool.py). More details about the methodology can be found in the associated paper: Ciulla, F., Santos, A., Jordan, P., Kneafsey, T., Biraud, S.C., and Varadharajan, C. (2024) A Deep Learning Based Framework to Identify Undocumented Orphaned Oil and Gas Wells from Historical Maps: a Case Study for California and Oklahoma. Accepted for publication in Environmental Science and Technology. The geographical coordinates provided correspond to the locations of potential undocumented orphaned oil and gas wells (UOWs) extracted from historical maps. The actual presence of wells need to be confirmed with on-the-ground investigations. For your safety, do not attempt to visit or investigate these sites without appropriate safety training, proper equipment, and authorization from local authorities. Approaching these well sites without proper personal protective equipment (PPE) may pose significant health and safety risks. Oil and gas wells can emit hazardous gasses including methane, which is flammable, odorless and colorless, as well as hydrogen sulfide, which can be fatal even at low concentrations. Additionally, there may be unstable ground near the wellhead that may collapse around the wellbore. This dataset was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor the Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or the Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or the Regents of the University of California.

Artificial Intelligence↗

DOE OSTI2024

SRF CAVITY FAULT PREDICTION USING DEEP LEARNING AT JEFFERSON LAB

In this study, we present a deep learning-based pipeline for predicting superconducting radio-frequency (SRF) cavity faults in the Continuous Electron Beam Accelera-tor Facility (CEBAF) at Jefferson Lab. We leverage pre-fault RF signals from C100-type cavities and employ deep learning to predict faults in advance of their onset. We train a binary classifier model to distinguish between stable and impending fault signals. Test results show accuracies exceeding 99% for distinguishing between normal signals and pre-fault signals from a class of more slowly developing fault types, such as microphonics. We describe results from a proof-of-principle demonstration on a realistic, imbalanced data set and report performance metrics. Encouraging results suggest that future SRF systems could leverage this framework and implement measures to mitigate the onset in more slowly developing fault types.

Rahman, M.↗

DOE OSTI2022

Real-Time Cavity Fault Prediction in CEBAF Using Deep Learning

Data-driven prediction of future faults is a major research area for many industrial applications. In this work, we present a new procedure of real-time fault prediction for superconducting radio-frequency (SRF) cavities at the Continuous Electron Beam Accelerator Facility (CEBAF) using deep learning. CEBAF has been afflicted by frequent downtime caused by SRF cavity faults. We perform fault prediction using pre-fault RF signals from C100-type cryomodules. Using the pre-fault signal information, the new algorithm predicts the type of cavity fault before the actual onset. The early prediction may enable potential mitigation strategies to prevent the fault. In our work, we apply a two-stage fault prediction pipeline. In the first stage, a model distinguishes between faulty and normal signals using a U-Net deep learning architecture. In the second stage of the network, signals flagged as faulty by the first model are classified into one of seven fault types based on learned signatures in the data. Initial results show that our model can successfully predict most fault types 200 ms before onset. We will discuss reasons for poor model performance on specific fault types.

Rahman, M.↗

DOE OSTI2022

HP-PdF2-type FeCl2 as a potential Cl-carrier in the deep Earth

Here, we report for the first time the formation of a HP-PdF 2 -type FeCl 2 phase (space group Pa$\bar{3}$), through high pressure-temperature (P-T) reactions in the hydrous systems (Mg 0.6 Fe 0.4 )SiO 3 –H 2 O–NaCl and FeO2H–NaCl in a laser-heated diamond-anvil cell up to 108 GPa and 2000 K. Applying single-crystal X-ray diffraction (XRD) analysis to individual submicrometer-sized grains, we have successfully determined the crystal structure of the as-synthesized FeCl 2 phase, in agreement with our theoretical structure search results. In situ high P-T XRD data revealed the substitution of Cl for OH(O) in such a cubic Pa$\bar{3}$ structure, demonstrating that this topology is a potential host for both H and Cl in the deep Earth. The chemical analysis of the recovered sample showed that the post-perovskite phase contains considerable amounts of Na 2 O and Fe 2 O 3 . The coexistence of the cubic FeCl 2 phase and post-perovskite suggests that the lowermost mantle could be a potential reservoir of Cl. The possible presence of volatiles such as H and Cl in the deep lower mantle would impact the composition and iron valence state of the post-perovskite phase.

58 GEOSCIENCES↗

DOE OSTI2020

A guide for deploying Deep Learning in LHC searches: How to achieve optimality and account for uncertainty

Deep learning tools can incorporate all of the available information into a search for new particles, thus making the best use of the available data. This paper reviews how to optimally integrate information with deep learning and explicitly describes the corresponding sources of uncertainty. Simple illustrative examples show how these concepts can be applied in practice.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2013

Transportation Energy Futures: Combining Strategies for Deep Reductions in Energy Consumption and GHG Emissions [Brochure]

This fact sheet summarizes actions in the areas of light-duty vehicle, non-light-duty vehicle, fuel, and transportation demand that show promise for deep reductions in energy use. Energy efficient transportation strategies have the potential to simultaneously reduce oil consumption and greenhouse gas (GHG) emissions. The Transportation Energy Futures (TEF) project examined how the combination of multiple strategies could achieve deep reductions in GHG emissions and petroleum use on the order of 80%. Led by NREL, in collaboration with Argonne National Laboratory, the project's primary goal was to help inform domestic decisions about transportation energy strategies, priorities, and investments, with an emphasis on underexplored opportunities. TEF findings reveal three strategies with the potential to displace most transportation-related petroleum use and GHG emissions: 1) Stabilizing energy use in the transportation sector through efficiency and demand-side approaches. 2) Using additional advanced biofuels. 3) Expanding electric drivetrain technologies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗