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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A Generalized Transformer-Based Pulse Detection Algorithm

Pulse-like signals are ubiquitous in the field of single molecule analysis, e.g., electrical or optical pulses caused by analyte translocations in nanopores. The primary challenge in processing pulse-like signals is to capture the pulses in noisy backgrounds, but current methods are subjectively based on a user-defined threshold for pulse recognition. Here, we propose a generalized machine-learning based method, named pulse detection transformer (PETR), for pulse detection. PETR determines the start and end time points of individual pulses, thereby singling out pulse segments in a time-sequential trace. It is objective without needing to specify any threshold. It provides a generalized interface for downstream algorithms for specific application scenarios. PETR is validated using both simulated and experimental nanopore translocation data. It returns a competitive performance in detecting pulses through assessing them with several standard metrics. Finally, the generalization nature of the PETR output is demonstrated using two representative algorithms for feature extraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

PDF Entity Annotation Tool (PEAT)

While different text mining approaches – including the use of Artificial Intelligence (AI) and other machine based methods - continue to expand at a rapid pace, the tools used by researchers to create the labeled datasets required for training, modeling, and evaluation remain rudimentary. Labeled datasets contain the target attributes the machine is going to learn; for example, training an algorithm to delineate between images of a car or truck would generally require a set of images with a quantitative description of the underlying features of each vehicle type. Development of labeled textual data that can be used to build natural language machine learning models for scientific literature is not currently integrated into existing manual workflows used by domain experts. Published literature is rich with important information, such as different types of embedded text, plots, and tables that can all be used as inputs to train ML/natural language processing (NLP) models, when extracted and prepared in machine readable formats. Currently, both normalized data extraction of use to domain experts and extraction to support development of ML/NLP models are labor intensive and cumbersome manual processes. Automatic extraction of data and information from formats such as PDFs that are optimized for layout and human readability, not machine readability. The PDF (Portable Document Format) Entity Annotation Tool (PEAT) was developed with the goal of allowing users to annotate publications within their current print format, while also allowing those annotations to be captured in a machine-readable format. One of the main issues with traditional annotation tools is that they require transforming the PDF into plain text to facilitate the annotation process. While doing so lessens the technical challenges of annotating data, the user loses all structure and provenance that was inherent in the underlying PDF. Also, textual data extraction from PDFs can be an error prone process. Challenges include identifying sequential blocks of text and a multitude of document formats (multiple columns, font encodings, etc.). As a result of these challenges, using existing tools for development of NLP/ML models directly from PDFs is difficult because the generated outputs are not interoperable. We created a system that allows annotations to be completed on the original PDF document structure, with no plain text extraction. The result is an application that allows for easier and more accurate annotations. In addition, by including a feature that grants the user the ability to easily create a schema, we have developed a system that can be used to annotate text for different domain-centric schemas of relevance to subject matter experts. Different knowledge domains require distinct schemas and annotation tags to support machine learning.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Benchmarking Coordination Number Prediction Algorithms on Inorganic Crystal Structures

Coordination numbers and geometries form a theoretical framework for understanding and predicting materials properties. Algorithms to determine coordination numbers automatically are increasingly used for machine learning and automatic structural analysis. In this work, we introduce MaterialsCoord, a benchmark suite containing 56 experimentally-derived crystal structures (spanning elements, binaries, and ternary compounds) and their corresponding coordination environments as described in the research literature. We also describe CrystalNN, a novel algorithm for determining near neighbors. We compare CrystalNN against 7 existing near-neighbor algorithms on the MaterialsCoord benchmark, finding CrystalNN to perform similarly to several well-established algorithms. For each algorithm, we also assess computational demand and sensitivity towards small perturbations that mimic thermal motion. Finally, we investigate the similarity between bonding algorithms when applied to the Materials Project database. Finally, we expect that this work will aid the development of coordination prediction algorithms as well as improve structural descriptors for machine learning and other applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Quantum annealing-assisted lattice optimization

High Entropy Alloys (HEAs) have drawn great interest due to their exceptional properties compared to conventional materials. The configuration of HEA system is considered a key to their superior properties, but exhausting all possible configurations of atom coordinates and species to find the ground energy state is extremely challenging. In this work, we proposed a quantum annealing-assisted lattice optimization (QALO) algorithm, which is an active learning framework that integrates the Field-aware Factorization Machine (FFM) as the surrogate model for lattice energy prediction, Quantum Annealing (QA) as an optimizer and Machine Learning Potential (MLP) for ground truth energy calculation. By applying our algorithm to the NbMoTaW alloy, we reproduced the Nb depletion and W enrichment observed in bulk HEA. We found our optimized HEAs to have superior mechanical properties compared to the randomly generated alloy configurations. Our algorithm highlights the potential of quantum computing in materials design and discovery, laying a foundation for further exploring and optimizing structure-property relationships.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Entropy removal of medical diagnostics

Shannon entropy is a core concept in machine learning and information theory, particularly in decision tree modeling. To date, no studies have extensively and quantitatively applied Shannon entropy in a systematic way to quantify the entropy of clinical situations using diagnostic variables (true and false positives and negatives, respectively). Decision tree representations of medical decision-making tools can be generated using diagnostic variables found in literature and entropy removal can be calculated for these tools. This concept of clinical entropy removal has significant potential for further use to bring forth healthcare innovation, such as quantifying the impact of clinical guidelines and value of care and applications to Emergency Medicine scenarios where diagnostic accuracy in a limited time window is paramount. This analysis was done for 623 diagnostic tools and provided unique insights into their utility. For studies that provided detailed data on medical decision-making algorithms, bootstrapped datasets were generated from source data to perform comprehensive machine learning analysis on these algorithms and their constituent steps, which revealed a novel and thorough evaluation of medical diagnostic algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Quantum anomaly detection for collider physics

We explore the use of Quantum Machine Learning (QML) for anomaly detection at the Large Hadron Collider (LHC). In particular, we explore a semi-supervised approach in the four-lepton final state where simulations are reliable enough for a direct background prediction. This is a representative task where classification needs to be performed using small training datasets - a regime that has been suggested for a quantum advantage. We find that Classical Machine Learning (CML) benchmarks outperform standard QML algorithms and are able to automatically identify the presence of anomalous events injected into otherwise background-only datasets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Fiber optic computing using distributed feedback

Abstract The widespread adoption of machine learning and other matrix intensive computing algorithms has renewed interest in analog optical computing, which has the potential to perform large-scale matrix multiplications with superior energy scaling and lower latency than digital electronics. However, most optical techniques rely on spatial multiplexing, requiring a large number of modulators and detectors, and are typically restricted to performing a single kernel convolution operation per layer. Here, we introduce a fiber-optic computing architecture based on temporal multiplexing and distributed feedback that performs multiple convolutions on the input data in a single layer. Using Rayleigh backscattering in standard single mode fiber, we show that this technique can efficiently apply a series of random nonlinear projections to the input data, facilitating a variety of computing tasks. The approach enables efficient energy scaling with orders of magnitude lower power consumption than GPUs, while maintaining low latency and high data-throughput.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Adaptive 3D convolutional neural network-based reconstruction method for 3D coherent diffraction imaging

We present a novel adaptive machine-learning based approach for reconstructing three-dimensional (3D) crystals from coherent diffraction imaging. We represent the crystals using spherical harmonics (SH) and generate the corresponding synthetic diffraction patterns. We utilize 3D convolutional neural networks (CNNs) to learn a mapping between 3D diffraction volumes and the SH, which describe the boundary of the physical volumes from which they were generated. We use the 3D CNN-predicted SH coefficients as the initial guesses, which are then fine-tuned using adaptive model-independent feedback for improved accuracy. We also adaptively tune the locations, intensities, and decay rates of collections of radial basis functions in order to reproduce the non-uniform internal structure of 3D objects and demonstrate the method for a synthetic volume that has an internal void and a density ramp.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Barren Plateaus Preclude Learning Scramblers

Scrambling processes, which rapidly spread entanglement through many-body quantum systems, are difficult to investigate using standard techniques, but are relevant to quantum chaos and thermalization. In this Letter, we ask if quantum machine learning (QML) could be used to investigate such processes. In this study we prove a no-go theorem for learning an unknown scrambling process with QML, showing that it is highly probable for any variational Ansatz to have a barren plateau landscape, i.e., cost gradients that vanish exponentially in the system size. This implies that the required resources scale exponentially even when strategies to avoid such scaling (e.g., from Ansatz -based barren plateaus or no-free-lunch theorems) are employed. Furthermore, we numerically and analytically extend our results to approximate scramblers. Hence, our work places generic limits on the learnability of unitaries when lacking prior information.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Analytic Theory for the Dynamics of Wide Quantum Neural Networks

Here, parametrized quantum circuits can be used as quantum neural networks and have the potential to outperform their classical counterparts when trained for addressing learning problems. To date, much of the results on their performance on practical problems are heuristic in nature. In particular, the convergence rate for the training of quantum neural networks is not fully understood. Here, we analyze the dynamics of gradient descent for the training error of a class of variational quantum machine learning models. We define wide quantum neural networks as parametrized quantum circuits in the limit of a large number of qubits and variational parameters. Then, we find a simple analytic formula that captures the average behavior of their loss function and discuss the consequences of our findings. For example, for random quantum circuits, we predict and characterize an exponential decay of the residual training error as a function of the parameters of the system. Finally, we validate our analytic results with numerical experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Representation Learning via Quantum Neural Tangent Kernels

Variational quantum circuits are used in quantum machine learning and variational quantum simulation tasks. Designing good variational circuits or predicting how well they perform for given learning or optimization tasks is still unclear. Here we discuss these problems, analyzing variational quantum circuits using the theory of neural tangent kernels. We define quantum neural tangent kernels, and derive dynamical equations for their associated loss function in optimization and learning tasks. We analytically solve the dynamics in the frozen limit, or lazy training regime, where variational angles change slowly and a linear perturbation is good enough. We extend the analysis to a dynamical setting, including quadratic corrections in the variational angles. We then consider a hybrid quantum classical architecture and define a large-width limit for hybrid kernels, showing that a hybrid quantum classical neural network can be approximately Gaussian. The results presented here show limits for which analytical understandings of the training dynamics for variational quantum circuits, used for quantum machine learning and optimization problems, are possible. These analytical results are supported by numerical simulations of quantum machine-learning experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Different CT slice thickness and contrast‐enhancement phase in radiomics models on the differential performance of lung adenocarcinoma

Abstract Background To investigate the effects of computed tomography (CT) reconstruction slice thickness and contrast‐enhancement phase on the differential diagnosis performance of radiomic signature in lung adenocarcinoma. Methods A total of 187 patients who had been pathologically confirmed with lung adenocarcinoma and nonadenocarcinoma were divided into a training cohort ( n = 149) and validation cohort ( n = 38). All the patients underwent contrast‐enhanced CT and the images were reconstructed with different slice thickness. The radiomic features were extracted from different slice thickness and scan phase. The logistic regression (LR) algorithm was used to build a machine learning model for each group. The area under the curve (AUC) obtained from the receiver operating characteristic (ROC) curve and DeLong test was used to evaluate its discriminating performance. Results Finally, 34 image features and five semantic features were selected to establish a radiomics model. Based on the three contrast‐enhanced CT phases and four reconstruction slice thickness, 12 groups of radiomics models showed good discrimination ability with the AUCs range from 0.9287 to 0.9631, sensitivity range from 0.8349 to 0.9083, specificity range from 0.825 to 0.925 in the training group. Similar results were observed in the validation group. However, there was no statistical significance between the different CT scan phase groups and different slice thickness ( p > 0.05). Conclusions The radiomic analysis of contrast‐enhanced CT can be used for the differential diagnosis of lung adenocarcinoma. Moreover, different slice thickness and contrast‐enhanced scan phase did not affect the discriminating ability in the radiomics models.

Wang, Yang↗
DOE OSTI2023

Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing

Modern quantum chemistry algorithms are increasingly able to accurately predict molecular properties that are useful for chemists in research and education. Despite this progress, performing such calculations is currently unattainable to the wider chemistry community, as they often require domain expertise, computer programming skills, and powerful computer hardware. In this review, we outline methods to eliminate these barriers using cutting-edge technologies. We discuss the ingredients needed to create accessible platforms that can compute quantum chemistry properties in real time, including graphical processing units–accelerated quantum chemistry in the cloud, artificial intelligence–driven natural molecule input methods, and extended reality visualization. We end by highlighting a series of exciting applications that assemble these components to create uniquely interactive platforms for computing and visualizing spectra, 3D structures, molecular orbitals, and many other chemical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Metric DBSCAN

SAND2025-11725O Metric DBSCAN is an implementation of the popular DBSCAN clustering algorithm that works in general metric spaces. DBSCAN is a clustering algorithm, a fundamental building block in machine learning. It takes a set of objects and, given some notion of distance, identifies coherent groups of objects. With Metric DBSCAN, users can provide an arbitrary function to compute distance. Nearly all existing implementations of DBSCAN restrict distance to one of a few formulations. Metric DBScan accomplishes this cleanly and efficiently. The Python source code is on Github. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Dalbey, Keith↗
DOE OSTI2021

Deep learning techniques to disentangle water use efficiency, climate change, and carbon sequestration across ecosystem scales

Focal Areas: We plan to use machine learning (ML) to disentangle the impact of climate change on plant water use efficiency (WUE) across the leaf level, structured canopy, and community ecosystem scales. Due to the complex behavior of modeling plant WUE’s connection to carbon storage (and hidden co-varying interactions) we suggest that physics-based deep learning must be utilized. The second topic we propose is, based on a better understanding of WUE response to climate change, there is a need to predict how WUE will limit or enhance the recycling of water from transpiration by vegetation back to the land surface worldwide, and thus impact water storage capacity (i.e., natural and reservoirs), using machine learning optimization techniques such as genetic algorithms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Homomorphic Encryption for Machine Learning and Artificial Intelligence Applications

Third-party and expert analysis is a cost-effective solution for solving specialized problems or processing large datasets related to reactor structural health monitoring and nondestructive evaluation. However, when handling proprietary information, third-party and expert analysts pose a privacy risk. To address this challenge, Homomorphic Encryption (HE) permits arithmetic operations on encrypted data without exposing the underlying data. Implementations of Machine Learning (ML) and Artificial Intelligence (AI) algorithms using HE greatly enhances the capabilities of third-party analysts while maintaining a low security risk. This paper details current success in applying Principal Component Analysis (PCA) and Fully Connected Neural Networks (NN) using the Microsoft SEAL implementation of the popular CKKS Fully Homomorphic Encryption (FHE) algorithm. The MNIST Handwritten Dataset is analyzed as a proof-of-concept demonstration of the implementations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗