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DOE OSTI2024

Grass Evolutionary Lineages Can Be Identified Using Hyperspectral Leaf Reflectance

Hyperspectral remote sensing has the potential to map numerous attributes of the Earth’s surface, including spatial patterns of biological diversity. Grasslands are one of the largest biomes on Earth. Accurate mapping of grassland biodiversity relies on spectral discrimination of endmembers of species or plant functional types. We focused on spectral separation of grass lineages that dominate global grassy biomes: Andropogoneae (C 4 ), Chloridoideae (C 4 ), and Pooideae (C 3 ). We examined leaf reflectance spectra (350–2,500 nm) from 43 grass species representing these grass lineages from four representative grassland sites in the Great Plains region of North America. Here, we assessed the utility of leaf reflectance data for classification of grass species into three major lineages and by collection site. Classifications had very high accuracy (94%) that were robust to site differences in species and environment. We also show an information loss using multispectral sensors, that is, classification accuracy of grass lineages using spectral bands provided by current multispectral satellites is much lower (accuracy of 85.2% and 61.3% using Sentinel 2 and Landsat 8 bands, respectively). Our results suggest that hyperspectral data have an exciting potential for mapping grass functional types as informed by phylogeny. Leaf-level hyperspectral separability of grass lineages is consistent with the potential increase in biodiversity and functional information content from the next generation of satellite-based spectrometers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Epidural anesthesia needle guidance by forward-view endoscopic optical coherence tomography and deep learning

Epidural anesthesia requires injection of anesthetic into the epidural space in the spine. Accurate placement of the epidural needle is a major challenge. To address this, we developed a forward-view endoscopic optical coherence tomography (OCT) system for real-time imaging of the tissue in front of the needle tip during the puncture. We tested this OCT system in porcine backbones and developed a set of deep learning models to automatically process the imaging data for needle localization. A series of binary classification models were developed to recognize the five layers of the backbone, including fat, interspinous ligament, ligamentum flavum, epidural space, and spinal cord. The classification models provided an average classification accuracy of 96.65%. During puncture, it is important to maintain a safe distance between the needle tip and the dura mater. Regression models were developed to estimate that distance based on the OCT imaging data. Based on the Inception architecture, our models achieved a mean absolute percentage error of 3.05% ± 0.55%. Overall, our results validated the technical feasibility of using this novel imaging strategy to automatically recognize different tissue structures and measure the distances ahead of the needle tip during the epidural needle placement.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Quantum machine learning with differential privacy

Abstract Quantum machine learning (QML) can complement the growing trend of using learned models for a myriad of classification tasks, from image recognition to natural speech processing. There exists the potential for a quantum advantage due to the intractability of quantum operations on a classical computer. Many datasets used in machine learning are crowd sourced or contain some private information, but to the best of our knowledge, no current QML models are equipped with privacy-preserving features. This raises concerns as it is paramount that models do not expose sensitive information. Thus, privacy-preserving algorithms need to be implemented with QML. One solution is to make the machine learning algorithm differentially private, meaning the effect of a single data point on the training dataset is minimized. Differentially private machine learning models have been investigated, but differential privacy has not been thoroughly studied in the context of QML. In this study, we develop a hybrid quantum-classical model that is trained to preserve privacy using differentially private optimization algorithm. This marks the first proof-of-principle demonstration of privacy-preserving QML. The experiments demonstrate that differentially private QML can protect user-sensitive information without signficiantly diminishing model accuracy. Although the quantum model is simulated and tested on a classical computer, it demonstrates potential to be efficiently implemented on near-term quantum devices [noisy intermediate-scale quantum (NISQ)]. The approach’s success is illustrated via the classification of spatially classed two-dimensional datasets and a binary MNIST classification. This implementation of privacy-preserving QML will ensure confidentiality and accurate learning on NISQ technology.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Quantum optical classifier with superexponential speedup

Abstract Classification is a central task in deep learning algorithms. Usually, images are first captured and then processed by a sequence of operations, of which the artificial neuron represents one of the fundamental units. This paradigm requires significant resources that scale (at least) linearly in the image resolution, both in terms of photons and computational operations. Here, we present a quantum optical pattern recognition method for binary classification tasks. It classifies objects without reconstructing their images, using the rate of two-photon coincidences at the output of a Hong-Ou-Mandel interferometer, where both the input and the classifier parameters are encoded into single-photon states. Our method exhibits the behaviour of a classical neuron of unit depth. Once trained, it shows a constant $${{\mathcal{O}}}(1)$$ O ( 1 ) complexity in the number of computational operations and photons required by a single classification. This is a superexponential advantage over a classical artificial neuron.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Quantifying patterns in optical micrographs of one- and two-dimensional ellipsoidal particle assemblies

Current developments in colloidal science include the assembly of anisotropic colloids with broad geometric diversity. As the complexity of particle assemblies increases, the need for ubiquitous algorithms that quantitatively analyze images of the assemblies to deliver key information such as quantification of crystal structures becomes more urgent. This contribution describes algorithms capable of image analysis for classifying colloidal structures based on abstracted interparticle relationship information and quantitatively analyzing the abundance of each structure in mixed pattern assemblies. The algorithm parameters can be adjusted, allowing for the algorithms to be adapted for different image analyses. Three different ellipsoidal particle assembly images are presented to demonstrate the effectiveness of the algorithms: a one-dimensional (1D) particle chain assembly and two two-dimensional (2D) polymorphic crystals each consisting of assemblies of two distinct plane symmetry groups. Angle relationships between neighbouring particles are calculated and neighbour counts of each particle are determined. Combining these two parameters as rules for classification criteria allows for the labeling and quantification of each particle into a defined symmetry class within an assembly. The algorithms provide a labelled image comprising classification results and particle counts of each defined class. For multiple images or individual frames from a video, the script can be looped to achieve automatic processing. The yielded classification data allow for more in-depth image analysis of mixed pattern particle assemblies. Finally, we envision that these algorithms will have utility in quantitative analysis of images comprising ellipsoidal colloidal materials, nanoparticles, or biological matter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Creating ground truth for nanocrystal morphology: a fully automated pipeline for unbiased transmission electron microscopy analysis

Control over colloidal nanocrystal morphology (size, size distribution, and shape) is important for tailoring the functionality of individual nanocrystals and their ensemble behavior. Despite this, traditional methods to quantify nanocrystal morphology are laborious. New developments in automated morphology classification will accelerate these analyses but the assessment of machine learning models is limited by human accuracy for ground truth, causing even unsupervised machine learning models to have inherent bias. Herein, we introduce synthetic image rendering to solve the ground truth problem of nanocrystal morphology classification. By simulating 2D images of nanocrystal shapes via a function of high-dimensional parameter space, we trained a convolutional neural network to link unique morphologies to their simulated parameters, defining nanocrystal morphology quantitatively rather than qualitatively. An automated pipeline then processes, quantitatively defines, and classifies nanocrystal morphology from experimental transmission electron microscopy (TEM) images. Using improved computer vision techniques, 42,650 nanocrystals were identified, assessed, and labeled with quantitative parameters, offering a 600-fold improvement in efficiency over best-practice manual measurements. Further, a classification algorithm was trained with a prediction accuracy of 99.5%, which can successfully analyze a range of concave, convex, and irregular nanocrystal shapes. The resulting pipeline was applied to differentiating two syntheses of nominally cuboidal CsPbBr 3 nanocrystals and uniquely classifying binary nickel sulfide nanocrystal phase based on morphology. This pipeline provides a simple, efficient, and unbiased method to quantify nanocrystal morphology and represents a practical route to construct large datasets with an absolute ground truth for training unbiased morphology-based machine learning algorithms.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2026

Random forest models accurately classify synthetic opioids using high-dimensionality mass spectrometry datasets

Detection of novel threat agents presents several challenges, a principle one being the development of untargeted methods to screen an increasing number of threat chemicals whose exact structures are unknown. With the use of Machine Learning (ML) tools, we can guide the development of analytical methods for broad-spectrum detection of unbounded threat chemical families in complex mixtures. Toward this goal, we used nominal mass and high-resolution mass spectrometry data for hundreds of synthetic opioids and non-opioid compounds. We tested two ML techniques, logistic regression and random forest, to develop models towards a practical, implementable method for opioid detection. We found that of these tested ML methods, random forest models resulted in the highest validation accuracy (95+%) for both nominal mass and high-resolution classification of opioids versus non-opioids, with low false positive and false negative rates. The RF models were then used to successfully predict the classification of 10 compounds—five opioids and five non-opioids not part of the training and validation analysis. This application of ML is a critical step towards the development of field-deployable nominal mass spectrometers with ML-driven analyses for classification of emergent threats.

Chemistry↗

DOE OSTI2024

Recovered supernova Ia rate from simulated LSST images

Aims.TheVera C. RubinObservatory’s Legacy Survey of Space and Time (LSST) will revolutionize time-domain astronomy by detecting millions of different transients. In particular, it is expected to increase the number of known type Ia supernovae (SN Ia) by a factor of 100 compared to existing samples up to redshift ∼1.2. Such a high number of events will dramatically reduce statistical uncertainties in the analysis of the properties and rates of these objects. However, the impact of all other sources of uncertainty on the measurement of the SN Ia rate must still be evaluated. The comprehension and reduction of such uncertainties will be fundamental both for cosmology and stellar evolution studies, as measuring the SN Ia rate can put constraints on the evolutionary scenarios of different SN Ia progenitors. Methods.We used simulated data from the Dark Energy Science Collaboration (DESC) Data Challenge 2 (DC2) and LSST Data Preview 0 to measure the SN Ia rate on a 15 deg 2 region of the “wide-fast-deep” area. We selected a sample of SN candidates detected in difference images, associated them to the host galaxy with a specially developed algorithm, and retrieved their photometric redshifts. We then tested different light-curve classification methods, with and without redshift priors (albeit ignoring contamination from other transients, as DC2 contains only SN Ia). We discuss how the distribution in redshift measured for the SN candidates changes according to the selected host galaxy and redshift estimate. Results.We measured the SN Ia rate, analyzing the impact of uncertainties due to photometric redshift, host-galaxy association and classification on the distribution in redshift of the starting sample. We find that we are missing 17% of the SN Ia, on average, with respect to the simulated sample. As 10% of the mismatch is due to the uncertainty on the photometric redshift alone (which also affects classification when used as a prior), we conclude that this parameter is the major source of uncertainty. We discuss possible reduction of the errors in the measurement of the SN Ia rate, including synergies with other surveys, which may help us to use the rate to discriminate different progenitor models.

Astronomy & Astrophysics↗

DOE OSTI2024

ATAT: Astronomical Transformer for time series and Tabular data

Context. The advent of next-generation survey instruments, such as theVera C. RubinObservatory and its Legacy Survey of Space and Time (LSST), is opening a window for new research in time-domain astronomy. The Extended LSST Astronomical Time-Series Classification Challenge (ELAsTiCC) was created to test the capacity of brokers to deal with a simulated LSST stream. Aims. Our aim is to develop a next-generation model for the classification of variable astronomical objects. We describe ATAT, the Astronomical Transformer for time series And Tabular data, a classification model conceived by the ALeRCE alert broker to classify light curves from next-generation alert streams. ATAT was tested in production during the first round of the ELAsTiCC campaigns. Methods. ATAT consists of two transformer models that encode light curves and features using novel time modulation and quantile feature tokenizer mechanisms, respectively. ATAT was trained on different combinations of light curves, metadata, and features calculated over the light curves. We compare ATAT against the current ALeRCE classifier, a balanced hierarchical random forest (BHRF) trained on human-engineered features derived from light curves and metadata. Results. When trained on light curves and metadata, ATAT achieves a macro F1 score of 82.9 ± 0.4 in 20 classes, outperforming the BHRF model trained on 429 features, which achieves a macro F1 score of 79.4 ± 0.1. Conclusions. The use of transformer multimodal architectures, combining light curves and tabular data, opens new possibilities for classifying alerts from a new generation of large etendue telescopes, such as theVera C. RubinObservatory, in real-world brokering scenarios.

Astronomy & Astrophysics↗

DOE OSTI2024

FEW questions, many answers: using machine learning to assess how students connect food–energy–water (FEW) concepts

There is growing support and interest in postsecondary interdisciplinary environmental education which integrate concepts and disciplines in addition to providing varied perspectives. There is a need to assess student learning in these programs as well as rigorous evaluation of educational practices, especially of complex synthesis concepts. This work tests a text classification machine learning model as a tool to assess student systems thinking capabilities using two questions anchored by the Food-Energy-Water (FEW) Nexus phenomena by answering two questions (1) Can machine learning models be used to identify instructor-determined important concepts in student responses? (2) What do college students know about the interconnections between food, energy and water, and how have students assimilated systems thinking into their constructed responses about FEW? Reported here are a broad range of model performances across 26 text classification models associated with two different assessment items, with model accuracy ranging from 0.755 to 0.992. Expert-like responses were infrequent in our dataset compared to responses providing simpler, incomplete explanations of the systems presented in the question. For those students moving from describing individual effects to multiple effects, their reasoning about the mechanism behind the system indicates advanced systems thinking ability. Specifically, students exhibit higher expertise for explaining changing water usage than discussing tradeoffs for such changing usage. This research represents one of the first attempts to assess the links between foundational, discipline-specific concepts and systems thinking ability. These text classification approaches to scoring student FEW Nexus Constructed Responses (CR) indicate how these approaches can be used, in addition to several future research priorities for interdisciplinary, practice-based education research. Development of further complex question items using machine learning would allow evaluation of the relationship between foundational concept understanding and integration of those concepts as well as more nuanced understanding of student comprehension of complex interdisciplinary concepts.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2023

Machine learning methods for fission product identification from Bragg curves

A fission time projection chamber (fission-TPC) was developed to provide precise neutron-induced fission measurements for several major actinides. As fission fragments lose energy in one of the gas volumes of the fission-TPC, energy loss information is captured and may be used to determine fission product yields as the stopping power of an ion is dependent on the atomic number. The work presented here demonstrates the ability to apply machine learning techniques for Bragg curve classification. A set of one million energy loss curves for 24 different fission-fragment elements was generated using common stopping power software. A ResNet architecture optimized for 1D data was used to train, test, and validate a model for light and heavy fission fragments using the simulated data. The resultant classification accuracy for the light and heavy fragments indicates that this could be a viable method for elemental classification of data from the fission-TPC.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Probabilistic locked mode predictor in the presence of a resistive wall and finite island saturation in tokamaks

We present a framework for estimating the probability of locking to an error field in a rotating tokamak plasma. This leverages machine learning methods trained on data from a mode-locking model, including an error field, resistive magnetohydrodynamics modeling of the plasma, a resistive wall, and an external vacuum region, leading to a fifth-order ordinary differential equation (ODE) system. It is an extension of the model without a resistive wall introduced by Akçay et al. [Phys. Plasmas 28, 082106 (2021)]. Tearing mode saturation by a finite island width is also modeled. We vary three pairs of control parameters in our studies: the momentum source plus either the error field, the tearing stability index, or the island saturation term. The order parameters are the time-asymptotic values of the five ODE variables. Normalization of them reduces the system to 2D and facilitates the classification into locked (L) or unlocked (U) states, as illustrated by Akçay et al., [Phys. Plasmas 28, 082106 (2021)]. This classification splits the control space into three regions: L̂, with only L states; Û, with only U states; and a hysteresis (hysteretic) region Ĥ, with both L and U states. In regions L̂ and Û, the cubic equation of torque balance yields one real root. Region Ĥ has three roots, allowing bifurcations between the L and U states. The classification of the ODE solutions into L/U is used to estimate the locking probability, conditional on the pair of the control parameters, using a neural network. We also explore estimating the locking probability for a sparse dataset, using a transfer learning method based on a dense model dataset.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Sparse-Data Deep Learning Strategies for Radiographic Non-Destructive Testing

Radiography is an imaging technique used in a variety of applications, such as medical diagnosis, airport security, and nondestructive testing. We present a deep learning system for extracting information from radiographic images. We perform various prediction tasks using our system, including material classification and regression on the dimensions of a given object that is being radiographed. Our system is designed to address the sparse-data issue for radiographic nondestructive testing applications. It uses a radiographic simulation tool for synthetic data augmentation, and it uses transfer learning with a pre-trained convolutional neural network model. Using this system, our preliminary results indicate that the object geometry regression task saw an improvement of 70% in the R-squared value when using a multi-regime model. In addition, we increase the performance of the object material classification tasks by utilizing data from different imaging systems. In particular, using neutron imaging improved the material classification accuracy by 20% when compared to x-ray imaging.

convolutional neural networks↗

DOE OSTI2023

Automated characterization of spatial and dynamical heterogeneity in supercooled liquids via implementation of machine learning

Abstract A computational approach by an implementation of the principle component analysis (PCA) with K -means and Gaussian mixture (GM) clustering methods from machine learning algorithms to identify structural and dynamical heterogeneities of supercooled liquids is developed. In this method, a collection of the average weighted coordination numbers ( W C N s ‾ ) of particles calculated from particles’ positions are used as an order parameter to build a low-dimensional representation of feature (structural) space for K -means clustering to sort the particles in the system into few meso-states using PCA. Nano-domains or aggregated clusters are also formed in configurational (real) space from a direct mapping using associated meso-states’ particle identities with some misclassified interfacial particles. These classification uncertainties can be improved by a co-learning strategy which utilizes the probabilistic GM clustering and the information transfer between the structural space and configurational space iteratively until convergence. A final classification of meso-states in structural space and domains in configurational space are stable over long times and measured to have dynamical heterogeneities. Armed with such a classification protocol, various studies over the thermodynamic and dynamical properties of these domains indicate that the observed heterogeneity is the result of liquid–liquid phase separation after quenching to a supercooled state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Using active learning to improve quasar identification for the DESI spectra processing pipeline

The Dark Energy Spectroscopic Instrument (DESI) survey uses an automatic spectral classification pipeline to classify spectra. QuasarNET is a convolutional neural network used as part of this pipeline originally trained using data from the Baryon Oscillation Spectroscopic Survey (BOSS). In this paper we implement an active learning algorithm to optimally select spectra to use for training a new version of the QuasarNET weights file using only DESI data, with the goal of improving classification accuracy. This active learning algorithm includes a novel outlier rejection step using a Self-Organizing Map to ensure we label spectra representative of the larger quasar sample observed in DESI. We perform two iterations of the active learning pipeline, assembling a final dataset of 5600 labeled spectra, a small subset of the approximately 1.3 million quasar targets in DESI's Data Release 1. When splitting the spectra into training and validation subsets we achieve similar performance to the previously trained weights file in completeness and purity calculated on the validation dataset but do so with less than one tenth of the amount of training data. The new weights also more consistently classify objects in the same way when used on unlabeled data compared to the old weights file. In the process of improving QuasarNET's classification accuracy we discovered a systemic error in QuasarNET's redshift estimation and used our findings to improve our understanding of QuasarNET's redshifts.

Machine learning↗

DOE OSTI2023

Graph Neural Network for Object Reconstruction in Liquid Argon Time Projection Chambers

The Exa.TrkX project presents a graph neural network (GNN) technique for low-level reconstruction of neutrino interactions in a Liquid Argon Time Projection Chamber (LArTPC). GNNs are still a relatively novel technique, and have shown great promise for similar reconstruction tasks in the Large Hadron Collider (LHC). Graphs describing particle interactions are formed by treating each detector hit as a node, with edges describing the relationships between hits. We utilise a multi-head attention message passing network which performs graph convolutions in order to label each node with a particle type.We present an updated variant of our GNN architecture, with several improvements. After testing the model on more realistic simulation with regions of unresponsive wires, the target was modified from edge classification to node classification in order to increase robustness. Removing edges as a classification target opens up a broader possibility space for edge-forming techniques; we explore the model’s performance across a variety of approaches, such as Delaunay triangulation, kNN, and radius-based methods. We also extend this model to the 3D context, sharing information between detector views. By using reconstructed 3D spacepoints to map detector hits from each wire plane, the model naively constructs 2D representations that are independent yet fully consistent.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Coarse-grain cluster analysis of tensors with application to climate biome identification

A tensor provides a concise way to codify the interdependence of complex data. Treating a tensor as a d-way array, each entry records the interaction between the different indices. Clustering provides a way to parse the complexity of the data into more readily understandable information. Clustering methods are heavily dependent on the algorithm of choice, as well as the chosen hyperparameters of the algorithm. However, their sensitivity to data scales is largely unknown. In this work, we apply the discrete wavelet transform to analyze the effects of coarse-graining on clustering tensor data. We are particularly interested in understanding how scale affects clustering of the Earth's climate system. The discrete wavelet transform allows classification of the Earth's climate across a multitude of spatial-temporal scales. The discrete wavelet transform is used to produce an ensemble of classification estimates, as opposed to a single classification. Each element of the ensemble is a clustering at a different spatial-temporal scale. Information theoretic approaches are used to identify important scale lengths in clustering the L15 Climate Datset. We also discover a sub-collection of the ensemble that spans the majority of the variance observed, allowing for efficient consensus clustering techniques that can be used to identify climate biomes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.

59 BASIC BIOLOGICAL SCIENCES↗