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

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DOE OSTI2024

Improved deep learning prediction of antigen–antibody interactions

Identifying antibodies that neutralize specific antigens is crucial for developing effective immunotherapies, but this task remains challenging for many target antigens. The rise of deep learning–based computational approaches presents a promising avenue to address this challenge. Here, we assess the performance of a deep learning approach through two benchmark tests aimed at predicting antibodies for the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Three different strategies for constructing input sequence alignments are employed for predicting structural models of antigen–antibody complexes. In our initial testing set, which comprises known experimental structures, these strategies collectively yield a significant top-ranked prediction for 61% of cases and a success rate of 47%. Notably, one strategy that utilizes the sequences of known antigen binders outperforms the other two, achieving a precision of 90% in a subsequent test set of ~1,000 antibodies, balanced between true and control antibodies for the antigen, albeit with a lower recall of 25%. Our results underscore the potential of integrating deep learning methods with single B cell sequencing techniques to enhance the prediction accuracy of antigen–antibody interactions.

Science & Technology - Other Topics↗
DOE OSTI2022

A Conditional Autoencoder for Galaxy Photometric Parameter Estimation

Astronomical photometric surveys routinely image billions of galaxies, and traditionally infer the parameters of a parametric model for each galaxy. This approach has served us well, but the computational expense of deriving a full posterior probability distribution function is a challenge for increasingly ambitious surveys. In this paper, we use deep learning methods to characterize galaxy images, training a conditional autoencoder on mock data. The autoencoder can reconstruct and denoise galaxy images via a latent space engineered to include semantically meaningful parameters, such as brightness, location, size, and shape. Our model recovers galaxy fluxes and shapes on mock data with a lower variance than the Hyper Suprime-Cam photometry pipeline, and returns reasonable answers even for inputs outside the range of its training data. When applied to data in the training range, the regression errors on all extracted parameters are nearly unbiased with a variance near the Cramr-Rao bound.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Automatic Detection and Classification of Radio Galaxy Images by Deep Learning

Abstract Surveys conducted by radio astronomy observatories, such as SKA, MeerKAT, Very Large Array, and ASKAP, have generated massive astronomical images containing radio galaxies (RGs). This generation of massive RG images has imposed strict requirements on the detection and classification of RGs and makes manual classification and detection increasingly difficult, even impossible. Rapid classification and detection of images of different types of RGs help astronomers make full use of the observed astronomical image data for further processing and analysis. The classification of FRI and FRII is relatively easy, and there are more studies and literature on them at present, but FR0 and FRI are similar, so it is difficult to distinguish them. It poses a greater challenge to image processing. At present, deep learning has made breakthrough progress in the field of image analysis and processing and has preliminary applications in astronomical data processing. Compared with classification algorithms that can only classify galaxies, object detection algorithms that can locate and classify RGs simultaneously are preferred. In target detection algorithms, YOLOv5 has outstanding advantages in the classification and positioning of small targets. Therefore, we propose a deep-learning method based on an improved YOLOv5 object detection model that makes full use of multisource data, combining FIRST radio with SDSS optical image data, and realizes the automatic detection of FR0, FRI, and FRII RGs. The innovation of our work is that on the basis of the original YOLOv5 object detection model, we introduce the SE Net attention mechanism, increase the number of preset anchors, adjust the network structure of the feature pyramid, and modify the network structure, thereby allowing our model to demonstrate galaxy classification and position detection effects. Our improved model produces satisfactory results, as evidenced by experiments. Overall, the mean average precision (mAP@0.5) of our improved model on the test set reaches 89.4%, which can determine the position (R.A. and decl.) and automatically detect and classify FR0s, FRIs, and FRIIs. Our work contributes to astronomy because it allows astronomers to locate FR0, FRI, and FRII galaxies in a relatively short time and can be further combined with other astronomically generated data to study the properties of these galaxies. The target detection model can also help astronomers find FR0s, FRIs, and FRIIs in future surveys and build a large-scale star RG catalog. Moreover, our work is also useful for the detection of other types of galaxies.

Astronomy & Astrophysics↗
DOE OSTI2025

MHD, disruptions and control physics: Chapter 4 of the special issue: on the path to tokamak burning plasma operation

In this chapter, we review the progress in MHD stability, disruptions and control in magnetic fusion research that has occurred over the past (more than) one and a half decades since the publication by Hender et al in 2007 on the same topic as part of the update of ITER Physics Basis. During this period, remarkable progress has been achieved in the understanding of the basic physics and overall control of MHD instabilities through a wide spectrum of dedicated experiments, theory and modeling. The sawtooth activities are probably today one of the best understood of MHD events and very robust control schemes have been developed for reliable operation of tokamaks through core heating. Similarly, significant improvements have been achieved in understanding and control of neoclassical tearing modes, resistive wall modes or locked modes and their control through ECCD or error field control. The field of disruption prediction through application of artificial intelligence, machine learning or deep learning methods, which had already started at the time of the 2007 review, has progressed significantly due to general progress in these fields and application of newer, more sophisticated algorithms. However, although remarkable progress has been achieved in the field of Disruptions, their understanding, prediction, possible avoidance and mitigation still remain probably the most active fields of R&D globally in this field. This is especially because reactor grade machines like ITER and DEMO will be much less tolerant in respect of disruptions and runaway currents, and their occurrences must be either avoided altogether or minimized to an acceptable value without causing any significant hindrance to robust machine operations. This review is intended to present a broad spectrum of the R&D that has occurred in this field in support of ITER, which will also be of immense significance for all future machines, especially reactors like DEMO.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

First application of a liquid argon time projection chamber for the search for intranuclear neutron-antineutron transitions and annihilation in 40 Ar using the MicroBooNE detector

We present a novel methodology to search for intranuclear neutron-antineutron transition (n→n̅) followed by n̅-nucleon annihilation within an 40 Ar nucleus, using the MicroBooNE liquid argon time projection chamber (LArTPC) detector. A discovery of n→n̅ transition or a new best limit on the lifetime of this process would either constitute physics beyond the Standard Model or greatly constrain theories of baryogenesis, respectively. The approach presented in this paper makes use of deep learning methods to select n→n̅ events based on their unique features and differentiate them from cosmogenic backgrounds. The achieved signal and background efficiencies are (70.22 ± 6.04)% and (0.0020 ± 0.0003)%, respectively. A demonstration of a search is performed with a data set corresponding to an exposure of 3.32 ×10 26 neutron-years, and where the background rate is constrained through direct measurement, assuming the presence of a negligible signal. With this approach, no excess of events over the background prediction is observed, setting a demonstrative lower bound on the n→n̅ lifetime in 40 Ar of τ m ≳ 1.1×10 26 years, and on the free n→n̅ transition time of τ n→n̅ ≳ 2.6×10 5 s, each at the 90% confidence level. This analysis represents a first-ever proof-of-principle demonstration of the ability to search for this rare process in LArTPCs with high efficiency and low background.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Transforming the bootstrap: using Transformers to compute scattering amplitudes in planar N = 4 Super Yang-Mills theory

Abstract We pursue the use of deep learning methods to improve state-of-the-art computations in theoretical high-energy physics. Planar N = 4 Super Yang-Mills theory is a close cousin to the theory that describes Higgs boson production at the Large Hadron Collider; its scattering amplitudes are large mathematical expressions containing integer coefficients. In this paper, we apply Transformers to predict these coefficients. The problem can be formulated in a language-like representation amenable to standard cross-entropy training objectives. We design two related experiments and show that the model achieves high accuracy (> 98%) on both tasks. Our work shows that Transformers can be applied successfully to problems in theoretical physics that require exact solutions.

Cai, Tianji (ORCID:0000000232359486)↗
DOE OSTI2025

CryoTEN: efficiently enhancing cryo-EM density maps using transformers

Abstract Motivation Cryogenic electron microscopy (cryo-EM) is a core experimental technique used to determine the structure of macromolecules such as proteins. However, the effectiveness of cryo-EM is often hindered by the noise and missing density values in cryo-EM density maps caused by experimental conditions such as low contrast and conformational heterogeneity. Although various global and local map-sharpening techniques are widely employed to improve cryo-EM density maps, it is still challenging to efficiently improve their quality for building better protein structures from them. Results In this study, we introduce CryoTEN—a 3D UNETR++ style transformer to improve cryo-EM maps effectively. CryoTEN is trained using a diverse set of 1295 cryo-EM maps as inputs and their corresponding simulated maps generated from known protein structures as targets. An independent test set containing 150 maps is used to evaluate CryoTEN, and the results demonstrate that it can robustly enhance the quality of cryo-EM density maps. In addition, automatic de novo protein structure modeling shows that protein structures built from the density maps processed by CryoTEN have substantially better quality than those built from the original maps. Compared to the existing state-of-the-art deep learning methods for enhancing cryo-EM density maps, CryoTEN ranks second in improving the quality of density maps, while running >10 times faster and requiring much less GPU memory than them. Availability and implementation The source code and data are freely available at https://github.com/jianlin-cheng/cryoten.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Galaxy Zoo DECaLS: Detailed visual morphology measurements from volunteers and deep learning for 314,000 galaxies

We present Galaxy Zoo DECaLS: detailed visual morphological classifications for Dark Energy Camera Legacy Survey images of galaxies within the SDSS DR8 footprint. Deeper DECaLS images (r = 23.6 versus r = 22.2 from SDSS) reveal spiral arms, weak bars, and tidal features not previously visible in SDSS imaging. To best exploit the greater depth of DECaLS images, volunteers select from a new set of answers designed to improve our sensitivity to mergers and bars. Galaxy Zoo volunteers provide 7.5 million individual classifications over 314 000 galaxies. 140 000 galaxies receive at least 30 classifications, sufficient to accurately measure detailed morphology like bars, and the remainder receive approximately 5. All classifications are used to train an ensemble of Bayesian convolutional neural networks (a state-of-the-art deep learning method) to predict posteriors for the detailed morphology of all 314 000 galaxies. We use active learning to focus our volunteer effort on the galaxies which, if labelled, would be most informative for training our ensemble. When measured against confident volunteer classifications, the trained networks are approximately 99 per cent accurate on every question. Morphology is a fundamental feature of every galaxy; our human and machine classifications are an accurate and detailed resource for understanding how galaxies evolve.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Fast and efficient identification of anomalous galaxy spectra with neural density estimation

ABSTRACT Current large-scale astrophysical experiments produce unprecedented amounts of rich and diverse data. This creates a growing need for fast and flexible automated data inspection methods. Deep learning algorithms can capture and pick up subtle variations in rich data sets and are fast to apply once trained. Here, we study the applicability of an unsupervised and probabilistic deep learning framework, the probabilistic auto-encoder, to the detection of peculiar objects in galaxy spectra from the SDSS survey. Different to supervised algorithms, this algorithm is not trained to detect a specific feature or type of anomaly, instead it learns the complex and diverse distribution of galaxy spectra from training data and identifies outliers with respect to the learned distribution. We find that the algorithm assigns consistently lower probabilities (higher anomaly score) to spectra that exhibit unusual features. For example, the majority of outliers among quiescent galaxies are E+A galaxies, whose spectra combine features from old and young stellar population. Other identified outliers include LINERs, supernovae, and overlapping objects. Conditional modelling further allows us to incorporate additional information. Namely, we evaluate the probability of an object being anomalous given a certain spectral class, but other information such as metrics of data quality or estimated redshift could be incorporated as well. We make our code publicly available.

Böhm, Vanessa↗
DOE OSTI2023

Reconstructing the neutron star equation of state from observational data via automatic differentiation

Neutron star observables like masses, radii, and tidal deformability are direct probes to the dense matter equation of state (EoS). Here, a novel deep learning method that optimizes an EoS in the automatic differentiation framework of solving inverse problems is presented. The trained neural network EoS yields narrow bands for the relationship between the pressure and speed of sound as a function of the mass density. The results are consistent with those obtained from conventional approaches and the observational bound on the tidal deformability inferred from the gravitational wave event, GW170817.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Distilling Knowledge from Ensembles of Cluster-Constrained-Attention Multiple-Instance Learners for Whole Slide Image Classification

The peculiar nature of whole slide imaging (WSI), digitizing conventional glass slides to obtain multiple high resolution images which capture microscopic details of a patient’s histopathological features, has garnered increased interest from the computer vision research community over the last two decades. Given the unique computational space and time complexity inherent to gigapixel-size whole slide image data, researchers have proposed novel machine learning algorithms to aid in the performance of diagnostic tasks in clinical pathology. One effective algorithm represents a Whole slide image as a bag of smaller image patches, which can be represented as low-dimension image patch embeddings. Weakly supervised deep-learning methods, such as cluster-constrained-attention multiple instance learning (CLAM), have shown promising results when combined with image patch embeddings. While traditional ensemble classifiers yield improved task performance, such methods come with a steep cost in model complexity. Through knowledge distillation, it is possible to retain some performance improvements from an ensemble, while minimizing costs to model complexity. In this work, we implement a weakly supervised ensemble using clustering-constrained-attention multiple-instance learners (CLAM), which uses attention and instance-level clustering to identify task salient regions and feature extraction in whole slides. By applying logit-based and attention-based knowledge distillation, we show it is possible to retain some performance improvements resulting from the ensemble at zero cost to model complexity.

Alamudun, Folami↗
DOE OSTI2022

Driver Distraction Behavior Detection using a Vision Transformer Model based on Transfer Learning Strategy

Driver distraction behavior is one of the critical factors in traffic accidents. Thus, advanced driver state detection system has become the focus in the field of intelligent vehicle. However, in practical applications, insufficient samples of driving distraction behaviors bring great challenges to training a personalized behavior distraction detection model for a specific driver. To this end, a novel transformer model based on a transfer learning strategy is proposed in this paper to accurately recognize driver distraction behavior. Inspired by the effect of the transformer network in visual recognition, we firstly present a transformer behavior distraction detection system to identify the behavior categories that cause driver distraction. Then, for the specific driving dataset in practical application scenarios, the transfer learning strategy is introduced into the driver distraction detection model to further train the general transformer network. The effectiveness of the transformer based on the transfer learning strategy is validated compared with other traditional deep learning methods. The results show that the proposed detection method has better generalization ability and higher accuracy.

Fang, Zhenwu↗
DOE OSTI2024

Entropy-Infused Deep Learning Loss Function for Capturing Extreme Values in Wind Power Forecasting

Extreme scenarios in wind power generation occur with higher frequency and larger magnitude in the recent years due to the ever-increasing extreme meteorological factors. Accurate forecasting of the occurrence of extreme values in wind power generation is of great concern to ensure reliable power system operation. Recently, deep learning models have surged in popularity for wind power forecasting, with the mean squared error (MSE) loss function being commonly used. However, the MSE loss function, being sensitive to extreme values, disproportionately penalizes larger errors, cannot adequately capture the extreme values present in wind energy data, and novel loss functions have seldom been tailored for wind power forecasting. To this end, in this paper, we introduce a novel loss function specifically crafted to capture extreme values in wind power forecasting. The experimental results with four fundamental deep learning methods on open source wind power dataset validate that the new loss function is efficient and superior in all cases compared to MSE in capturing extreme values while maintaining forecasting performance.

17 WIND ENERGY↗
DOE OSTI2025

DeepAndes: A Self-Supervised Vision Foundation Model for Multispectral Remote Sensing Imagery of the Andes

By mapping sites at large scales usingremotely sensed data, archaeologists can generate unique insights into long-term demographic trends, interregional social networks, and human adaptations in the past. Remote sensing surveys complement field-based approaches, and their reach can be especially great when combined with deep learning and computer vision techniques. However, conventional supervised deep learning methods face challenges in annotating fine-grained archaeological features at scale. In addition, while recent vision foundation models have shown remarkable success in learning large-scale remote sensing data with minimal annotations, most off-the-shelf solutions are designed for RGB images rather than multispectral satellite imagery, such as the eight-band data used in our study. In this article, we introduce DeepAndes, a transformer-based vision foundation model trained on three million multispectral satellite images, specifically tailored for Andean archaeology. DeepAndes incorporates a customized DINOv2 self-supervised learning algorithm optimized for eight-band multispectral imagery, marking the first foundation model designed explicitly for the Andes region. We evaluate its image understanding performance through imbalanced image classification, image instance retrieval, and pixel-level semantic segmentation tasks. Our experiments show that DeepAndes achieves superior F1 scores, mean average precision, and Dice scores in few-shot learning scenarios, significantly outperforming models trained from scratch or pretrained on smaller datasets. This underscores the effectiveness of large-scale self-supervised pretraining in archaeological remote sensing.

Guo, Junlin [Vanderbilt Univ., Nashville, TN (Unit↗
DOE OSTI2023

ML for microbiomes

The software provides machine learning analysis and visualization to detect patterns in microbiome data, including topic modeling, probabilistic graphical modeling, conventional machine learning methods, and deep learning. The software is written in python and R, it uses some python and R libraries as well as big open-source libraries like sklearn, networkX, pytorch (python), pgmpy (python), and bnlearn (R). It also has a script to use for MALLET and DTM (open-source packages for topic modeling, written in Java).

Kim, Anastasiia↗
DOE OSTI2021

pnnl/neuromancer

Dynamics-based deep learning methods to modernize current scientific computing methods. Neuromancer is currently capable of solving inverse problems for a system of ordinary differential equations. The functionality includes system identification and constrained optimal control of unknown or partially known ODEs.

Skomski, Elliott↗
DOE OSTI2024

Modeling Spatial Asymmetries in Teleconnected Extreme Temperatures

Abstract Combining strengths from deep learning and extreme value theory can help describe complex relationships between variables where extreme events have significant impacts (e.g., environmental or financial applications). Neural networks learn complicated nonlinear relationships from large datasets under limited parametric assumptions. By definition, the number of occurrences of extreme events is small, which limits the ability of the data-hungry, nonparametric neural network to describe rare events. Inspired by recent extreme cold winter weather events in North America caused by atmospheric blocking, we examine several probabilistic generative models for the entire multivariate probability distribution of daily boreal winter surface air temperature. We propose metrics to measure spatial asymmetries, such as long-range anticorrelated patterns that commonly appear in temperature fields during blocking events. Compared to vine copulas, the statistical standard for multivariate copula modeling, deep learning methods show improved ability to reproduce complicated asymmetries in the spatial distribution of ERA5 temperature reanalysis, including the spatial extent of in-sample extreme events.

Krock, Mitchell L.↗
DOE OSTI2023

Machine learning and deep learning for brain tumor MRI image segmentation

Brain tumors are often fatal. Therefore, accurate brain tumor image segmentation is critical for the diagnosis, treatment, and monitoring of patients with these tumors. Magnetic resonance imaging (MRI) is a commonly used imaging technique for capturing brain images. Both machine learning and deep learning techniques are popular in analyzing MRI images. This article reviews some commonly used machine learning and deep learning techniques for brain tumor MRI image segmentation. The limitations and advantages of the reviewed machine learning and deep learning methods are discussed. Even though each of these methods has a well-established status in their individual domains, the combination of two or more techniques is currently an emerging trend.

Research & Experimental Medicine↗