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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Advancing Cyber-Attack Detection in Power Systems: A Comparative Study of Machine Learning and Graph Neural Network Approaches

This paper explores the detection and localization of cyber-attacks on power systems, focusing on comparing conventional machine learning (ML) and deep learning methods, and graph neural network (GNN)-based techniques. We assess the detection accuracy of these approaches and their potential to pinpoint the locations of specific buses under attack. Given the demonstrated success of GNNs in other time series anomaly detection applications, we aim to evaluate their performance within the context of power systems cyber-attack. Utilizing the IEEE 68-bus system, we simulated four types of attacks to test the selected approaches. Our results indicate that GNN-based methods outperform conventional machine learning and deep learning models in detection. Additionally, GNNs show promise in accurately localizing attacks for simple scenarios, although they still face challenges in more complex cases.

artificial intelligence↗
DOE OSTI2023

CholecTriplet2021: A benchmark challenge for surgical action triplet recognition

Context-aware decision support in the operating room can foster surgical safety and efficiency by leveraging real-time feedback from surgical workflow analysis. Most existing works recognize surgical activities at a coarse-grained level, such as phases, steps or events, leaving out fine-grained interaction details about the surgical activity; yet those are needed for more helpful AI assistance in the operating room. Recognizing surgical actions as triplets of ‹ instrument, verb, target › combination delivers more comprehensive details about the activities taking place in surgical videos. This paper presents CholecTriplet2021: an endoscopic vision challenge organized at MICCAI 2021 for the recognition of surgical action triplets in laparoscopic videos. Here, the challenge granted private access to the large-scale CholecT50 dataset, which is annotated with action triplet information. In this paper, we present the challenge setup and the assessment of the state-of-the-art deep learning methods proposed by the participants during the challenge. Here, a total of 4 baseline methods from the challenge organizers and 19 new deep learning algorithms from the competing teams are presented to recognize surgical action triplets directly from surgical videos, achieving mean average precision (mAP) ranging from 4.2% to 38.1%. This study also analyzes the significance of the results obtained by the presented approaches, performs a thorough methodological comparison between them, in-depth result analysis, and proposes a novel ensemble method for enhanced recognition. Our analysis shows that surgical workflow analysis is not yet solved, and also highlights interesting directions for future research on fine-grained surgical activity recognition which is of utmost importance for the development of AI in surgery.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Towards deep computer vision for in-line defect detection in polymer electrolyte membrane fuel cell materials

Polymer Electrolyte Membrane (PEM) fuel cells are a promising source of alternative energy. However, their production is limited by a lack of well-established methods for quality control of their constituent materials like the membrane-electrode assembly during roll-to-roll manufacturing. One potential solution is the implementation of deep learning methods to detect unwanted defects through their detection in scanned images. Here we explore the detection of defects like scratches, pinholes, and scuffs in a sample dataset of PEM optical images using two deep learning algorithms: Patch Distribution Modeling (PaDiM) for unsupervised anomaly detection and Faster-RCNN for supervised object detection. Both methods achieve scores on performance metrics (ROC-AUC and PRO-AUC for PaDiM and AP for Faster-RCNN) that are comparable to their scores on benchmark datasets. These methods also have the potential to detect a wider range of defects compared to IR thermography and previous optical inspection methods. Overall, deep learning shows promise at detecting relevant defects of interest and has the potential to achieve real-time defect detection.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2023

Domain Adaptation for Measurements of Strong Gravitational Lenses

Upcoming surveys are predicted to discover galaxy-scale strong lenses on the order of 10\textsuperscript{5}, making deep learning methods necessary in lensing data analysis. Currently, there is insufficient real lensing data to train deep learning algorithms, but the alternative of training only on simulated data results in poor performance on real data. Domain Adaptation may be able to bridge the gap between simulated and real datasets. We utilize domain adaptation for the estimation of Einstein radius ($\Theta_E$) in simulated galaxy-scale gravitational lensing images with different levels of observational realism. We evaluate two domain adaptation techniques - Domain Adversarial Neural Networks (DANN) and Maximum Mean Discrepancy (MMD). We train on a source domain of simulated lenses and apply it to a target domain of lenses simulated to emulate noise conditions in the Dark Energy Survey (DES). We show that both domain adaptation techniques can significantly improve the model performance on the more complex target domain dataset. This work is the first application of domain adaptation for a regression task in strong lensing imaging analysis. Our results show the potential of using domain adaptation to perform analysis of future survey data with a deep neural network trained on simulated data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Domain Adaptation for Measurements of Strong Gravitational Lenses

Upcoming surveys are predicted to discover galaxy-scale strong lenses on the order of $10^5$, making deep learning methods necessary in lensing data analysis. Currently, there is insufficient real lensing data to train deep learning algorithms, but the alternative of training only on simulated data results in poor performance on real data. Domain Adaptation may be able to bridge the gap between simulated and real datasets. We utilize domain adaptation for the estimation of Einstein radius ($\Theta_E$) in simulated galaxy-scale gravitational lensing images with different levels of observational realism. We evaluate two domain adaptation techniques - Domain Adversarial Neural Networks (DANN) and Maximum Mean Discrepancy (MMD). We train on a source domain of simulated lenses and apply it to a target domain of lenses simulated to emulate noise conditions in the Dark Energy Survey (DES). We show that both domain adaptation techniques can significantly improve the model performance on the more complex target domain dataset. This work is the first application of domain adaptation for a regression task in strong lensing imaging analysis. Our results show the potential of using domain adaptation to perform analysis of future survey data with a deep neural network trained on simulated data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Domain Adaptation for Measurements of Strong Gravitational Lenses

Upcoming surveys are predicted to discover galaxy-scale strong lenses on the magnitude of 105, making deep learning methods necessary in lensing data analysis. Currently, there is insufficient real lensing data to train deep learning algorithms, but training only on simulated data results in poor performance on real data. Domain adaptation can bridge the gap between simulated and real datasets. We adopt domain adaptation on the estimation of Einstein radius in simulated galaxy-scale gravitational lensing images. We evaluate two domain adaptation techniques - domain adversarial neural networks (DANN) and maximum mean discrepancy (MMD). We train on a source domain of simulated lenses and apply it to a target domain with emulation of DES survey conditions. We show that both domain adaptation techniques can significantly improve the model performance on the more complex target domain datasets. Our results show the potential of using domain adaptation to perform analysis on future survey data with a deep neural network trained on simulated data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction

Abstract Deep learning has emerged as a revolutionary technology for protein residue‐residue contact prediction since the 2012 CASP10 competition. Considerable advancements in the predictive power of the deep learning‐based contact predictions have been achieved since then. However, little effort has been put into interpreting the black‐box deep learning methods. Algorithms that can interpret the relationship between predicted contact maps and the internal mechanism of the deep learning architectures are needed to explore the essential components of contact inference and improve their explainability. In this study, we present an attention‐based convolutional neural network for protein contact prediction, which consists of two attention mechanism‐based modules: sequence attention and regional attention. Our benchmark results on the CASP13 free‐modeling targets demonstrate that the two attention modules added on top of existing typical deep learning models exhibit a complementary effect that contributes to prediction improvements. More importantly, the inclusion of the attention mechanism provides interpretable patterns that contain useful insights into the key fold‐determining residues in proteins. We expect the attention‐based model can provide a reliable and practically interpretable technique that helps break the current bottlenecks in explaining deep neural networks for contact prediction. The source code of our method is available at https://github.com/jianlin-cheng/InterpretContactMap .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Identifying Genomic Islands with Deep Neural Networks

Background Horizontal gene transfer is the main source of adaptability for bacteria, through which genes are obtained from different sources including bacteria, archaea, viruses, and eukaryotes. This process promotes the rapid spread of genetic information across lineages, typically in the form of clusters of genes referred to as genomic islands (GIs). Different types of GIs exist, and are often classified by the content of their cargo genes or their means of integration and mobility. While various computational methods have been devised to detect different types of GIs, no single method is capable of detecting all types. Results We propose a method, which we call Shutter Island, that uses a deep learning model (Inception V3, widely used in computer vision) to detect genomic islands. The intrinsic value of deep learning methods lies in their ability to generalize. Via a technique called transfer learning, the model is pre-trained on a large generic dataset and then re-trained on images that we generate to represent genomic fragments. We demonstrate that this image-based approach generalizes better than the existing tools. Conclusions We used a deep neural network and an image-based approach to detect the most out of the correct GI predictions made by other tools, in addition to making novel GI predictions. The fact that the deep neural network was re-trained on only a limited number of GI datasets and then successfully generalized indicates that this approach could be applied to other problems in the field where data is still lacking or hard to curate.

Computer Vision↗
DOE OSTI2024

Deep Learning for Fish Identification from Sonar Data (CRADA 481 Final Report)

In eastern regions of the United States, the American eel is a species of management and regulatory concern because of significant population declines, despite the species’ previous abundance in all tributaries of rivers flowing into the Atlantic Ocean. The American eel is also a candidate for listing under the U.S. Endangered Species Act. While hydropower construction and operation are only one of several factors contributing to this population decline, such a listing could impose additional regulatory challenges for a large number of hydropower projects. In this CRADA project, we improved technologies for identifying migrating eels with the goal of reducing the cost and time required for future American eel hydropower impact assessment and mitigation studies, while maintaining accuracy. We built on results from a previous FOA project (FOA# DE-FOA-0001662), led by the Electric Power Research Institute (EPRI), which developed a highly accurate, deep-learning method for identifying migrating eels from imaging sonar data. The current study aimed to further optimize this deep-learning model, originally designed for image classification, and to develop an object detection software capable of identifying fish from sonar videos in real time, enabling the detection of events like fish migrations and specific species, such as the American eel, at hydropower dams. The data conversion algorithms were packaged as software with a graphical user interface, and the software is evaluated by external collaborators. We focused on the American eel in this project and explored the transferability of the developed deep learning models to the sea lamprey, given the similar body shape and swimming behavior between the two species.

13 HYDRO ENERGY↗
DOE OSTI2021

TEMImageNet training library and AtomSegNet deep-learning models for high-precision atom segmentation, localization, denoising, and deblurring of atomic-resolution images

Abstract Atom segmentation and localization, noise reduction and deblurring of atomic-resolution scanning transmission electron microscopy (STEM) images with high precision and robustness is a challenging task. Although several conventional algorithms, such has thresholding, edge detection and clustering, can achieve reasonable performance in some predefined sceneries, they tend to fail when interferences from the background are strong and unpredictable. Particularly, for atomic-resolution STEM images, so far there is no well-established algorithm that is robust enough to segment or detect all atomic columns when there is large thickness variation in a recorded image. Herein, we report the development of a training library and a deep learning method that can perform robust and precise atom segmentation, localization, denoising, and super-resolution processing of experimental images. Despite using simulated images as training datasets, the deep-learning model can self-adapt to experimental STEM images and shows outstanding performance in atom detection and localization in challenging contrast conditions and the precision consistently outperforms the state-of-the-art two-dimensional Gaussian fit method. Taking a step further, we have deployed our deep-learning models to a desktop app with a graphical user interface and the app is free and open-source. We have also built a TEM ImageNet project website for easy browsing and downloading of the training data.

25 ENERGY STORAGE↗
DOE OSTI2023

Physics-informed neural network with transfer learning (TL-PINN) based on domain similarity measure for prediction of nuclear reactor transients

Nuclear reactor safety and efficiency can be enhanced through the development of accurate and fast methods for prediction of reactor transient (RT) states. Physics informed neural networks (PINNs) leverage deep learning methods to provide an alternative approach to RT modeling. Applications of PINNs in monitoring of RTs for operator support requires near real-time model performance. However, as with all machine learning models, development of a PINN involves time-consuming model training. Here, we show that a transfer learning (TL-PINN) approach achieves significant performance gain, as measured by reduction of the number of iterations for model training. Using point kinetic equations (PKEs) model with six neutron precursor groups, constructed with experimental parameters of the Purdue University Reactor One (PUR-1) research reactor, we generated different RTs with experimentally relevant range of variables. The RTs were characterized using Hausdorff and Fréchet distance. We have demonstrated that pre-training TL-PINN on one RT results in up to two orders of magnitude acceleration in prediction of a different RT. The mean error for conventional PINN and TL-PINN models prediction of neutron densities is smaller than 1%. We have developed a correlation between TL-PINN performance acceleration and similarity measure of RTs, which can be used as a guide for application of TL-PINNs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Scaling deep learning for material imaging with a pseudo 3D model for domain transfer

The recent introduction of deep learning methods for image processing has greatly advanced the characterization of materials using three-dimensional (3D) X-ray imaging techniques. However, deep learning models often have difficulty performing consistently across images owing to unavoidable variations in imaging conditions, which create inconsistencies even for the same material. As a result, networks must frequently be retrained for new datasets, limiting their applicability and generalization. Thus, it is critical to reduce the variations between images to enable a single model to process multiple datasets. Herein, we introduce P3T-Net, a pseudo-3D domain transfer network that transfers diverse 3D images into a uniform domain before processing using deep learning models. Remarkably, P3T-Net enables the reuse of previously trained networks for processing new images and considerably reduces the computational cost of transferring 3D images across domains. These unique capabilities were demonstrated in the following scenarios: (i) image enhancement of fast scans for geological rock and hydrogen fuel cells, (ii) enhancement of images to match the quality of multi-source imaging for lithium-ion batteries, (iii) accurate segmentation of images captured under different conditions, and (iv) tera-scale 3D transfer (10 11 voxels) on a single GPU. Overall, the proposed approach addresses cross-domain inconsistencies across various materials and conditions, thereby enabling more robust and generalizable deep learning solutions for a wide range of material imaging tasks.

25 ENERGY STORAGE↗
DOE OSTI2022

DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network

Abstract Background Estimation of the accuracy (quality) of protein structural models is important for both prediction and use of protein structural models. Deep learning methods have been used to integrate protein structure features to predict the quality of protein models. Inter-residue distances are key information for predicting protein’s tertiary structures and therefore have good potentials to predict the quality of protein structural models. However, few methods have been developed to fully take advantage of predicted inter-residue distance maps to estimate the accuracy of a single protein structural model. Result We developed an attentive 2D convolutional neural network (CNN) with channel-wise attention to take only a raw difference map between the inter-residue distance map calculated from a single protein model and the distance map predicted from the protein sequence as input to predict the quality of the model. The network comprises multiple convolutional layers, batch normalization layers, dense layers, and Squeeze-and-Excitation blocks with attention to automatically extract features relevant to protein model quality from the raw input without using any expert-curated features. We evaluated DISTEMA’s capability of selecting the best models for CASP13 targets in terms of ranking loss of GDT-TS score. The ranking loss of DISTEMA is 0.079, lower than several state-of-the-art single-model quality assessment methods. Conclusion This work demonstrates that using raw inter-residue distance information with deep learning can predict the quality of protein structural models reasonably well. DISTEMA is freely at https://github.com/jianlin-cheng/DISTEMA

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ASK: Adversarial Soft k-Nearest Neighbor Attack and Defense

K-Nearest Neighbor (kNN)-based deep learning methods have been applied to many applications due to their simplicity and geometric interpretability. However, the robustness of kNN-based deep classification models has not been thoroughly explored and kNN attack strategies are underdeveloped. In this paper, we first propose an Adversarial Soft kNN (ASK) loss for developing more effective kNN-based deep neural network attack strategies and designing better defense methods against them. Our ASK loss provides a differentiable surrogate of the expected kNN classification error. It is also interpretable as it preserves the mutual information between the perturbed input and the in-class-reference data. We use the ASK loss to design a novel attack method called the ASK-Attack (ASK-Atk), which shows superior attack efficiency and accuracy degradation relative to previous kNN attacks on hidden layers. We then derive an ASK-Defense (ASK-Def) method that optimizes the worst-case ASK training loss. Experiments on CIFAR-10 (ImageNet) show that (i) ASK-Atk achieves ≥13% (≥ 13% ) improvement in attack success rate over previous kNN attacks, and (ii) ASK-Def outperforms the conventional adversarial training method by ≥ 6.9% (≥ 3.5% ) in terms of robustness improvement. Relevant codes are available at https://github.com/wangren09/ASK .

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

ASDFL: An adaptive super‐pixel discriminative feature‐selective learning for vehicle matching

Abstract There are a large number of cameras in modern transportation system that capture numerous vehicle images continuously. Therefore, automatic analysis of these vehicle images is helpful for traffic flow management, criminal investigations and vehicle inspections. Vehicle matching, which aims to determine whether two input images depict an identical vehicle, is one of the core tasks in vehicle analysis. Recent relevant studies have focused on local feature extraction instead of global extraction, since local details can provide crucial cues to distinguish between cars. However, these methods do not select local features; that is, they do not assign weights to local features. Therefore, in this research, we systematically study the vehicle matching task, and present a novel annotation‐free local‐based deep learning method called Adaptive super‐pixel discriminative feature‐selective learning (ASDFL) to address this issue. In ASDFL, vehicle images are segmented into clusters of super‐pixels of similar size by considering the location and colour similarities of pixels without using any component‐level annotation. These super‐pixels are deemed to be the virtual components of vehicles. Moreover, a convolutional neural network is used to extract the deep features of these virtual components. Thereafter, an instance‐specific mask generation module driven by the extracted global features is enhanced to produce a mask to select the most distinctive virtual components of each vehicle image pair in the feature space. Finally, the vehicle matching task is accomplished by classifying the selected virtual component features of each imaged vehicle pair. Extensive experiments on two popular vehicle identification benchmarks demonstrate that our method is 1.57% and 0.8% more accurate than the previous baselines in a vehicle matching task on the VeRi and VehicleID datasets, respectively, which demonstrates the effectiveness of our method.

Qin, Rong↗
DOE OSTI2021

Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

Abstract The inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (EMA) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). To further leverage the improved inter-residue distance predictions to enhance EMA, during the 2020 CASP14 experiment, we integrated several new inter-residue distance features with the existing model quality assessment features in several deep learning methods to predict the quality of protein structural models. According to the evaluation of performance in selecting the best model from the models of CASP14 targets, our three multi-model predictors of estimating model accuracy (MULTICOM-CONSTRUCT, MULTICOM-AI, and MULTICOM-CLUSTER) achieve the averaged loss of 0.073, 0.079, and 0.081, respectively, in terms of the global distance test score (GDT-TS). The three methods are ranked first, second, and third out of all 68 CASP14 predictors. MULTICOM-DEEP, the single-model predictor of estimating model accuracy (EMA), is ranked within top 10 among all the single-model EMA methods according to GDT-TS score loss. The results demonstrate that inter-residue distance features are valuable inputs for deep learning to predict the quality of protein structural models. However, larger training datasets and better ways of leveraging inter-residue distance information are needed to fully explore its potentials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

MultiTaskDeltaNet: change detection-based image segmentation for operando ETEM with application to carbon gasification kinetics

Transforming in situ transmission electron microscopy (TEM) imaging into a tool for spatially-resolved operando characterization of solid-state reactions requires automated, high-precision semantic segmentation of dynamically evolving features. However, traditional deep learning methods for semantic segmentation often face limitations due to the scarcity of labeled data, visually ambiguous features of interest, and scenarios involving small objects. To tackle these challenges, we introduce MultiTaskDeltaNet (MTDN), a novel deep learning architecture that creatively reconceptualizes the segmentation task as a change detection problem. By implementing a unique Siamese network with a U-Net backbone and using paired images to capture feature changes, MTDN effectively leverages minimal data to produce high-quality segmentations. Furthermore, MTDN utilizes a multi-task learning strategy to exploit correlations between physical features of interest. In an evaluation using data from in situ environmental TEM (ETEM) videos of filamentous carbon gasification, MTDN demonstrated a significant advantage over conventional segmentation models, particularly in accurately delineating fine structural features. Notably, MTDN achieved a 10.22% performance improvement over conventional segmentation models in predicting small and visually ambiguous physical features. This work bridges key gaps between deep learning and practical TEM image analysis, advancing automated characterization of nanomaterials in complex experimental settings.

08 HYDROGEN↗
DOE OSTI2022

Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps

Abstract The information about the domain architecture of proteins is useful for studying protein structure and function. However, accurate prediction of protein domain boundaries (i.e., sequence regions separating two domains) from sequence remains a significant challenge. In this work, we develop a deep learning method based on multi-head U-Nets (called DistDom) to predict protein domain boundaries utilizing 1D sequence features and predicted 2D inter-residue distance map as input. The 1D features contain the evolutionary and physicochemical information of protein sequences, whereas the 2D distance map includes the structural information of proteins that was rarely used in domain boundary prediction before. The 1D and 2D features are processed by the 1D and 2D U-Nets respectively to generate hidden features. The hidden features are then used by the multi-head attention to predict the probability of each residue of a protein being in a domain boundary, leveraging both local and global information in the features. The residue-level domain boundary predictions can be used to classify proteins as single-domain or multi-domain proteins. It classifies the CASP14 single-domain and multi-domain targets at the accuracy of 75.9%, 13.28% more accurate than the state-of-the-art method. Tested on the CASP14 multi-domain protein targets with expert annotated domain boundaries, the average per-target F1 measure score of the domain boundary prediction by DistDom is 0.263, 29.56% higher than the state-of-the-art method.

59 BASIC BIOLOGICAL SCIENCES↗