Logical activation functions for training arbitrary probabilistic Boolean operations
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96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
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Logical Activation Functions v.1.1
SAND2024-01501O Logical Activation Functions software is a PyTorch implementation from the paper, "Logical Activation Functions for Training Arbitrary Probabilistic Boolean Logic." The activation functions approximate logit-space marginalization of probabilistic truth tables from probabilistic interpretations of inputs. They also provide a general methodology to approximate logical relationships between abstract antecedents and consequents for machine learning architectures. They do not target any specific application or use-case. By training probabilistic truth tables, these activation functions can capture more expressive relationships in a neural network than typical elementwise activation functions. This code is only designed for a single compute node with a GPU and is limited to machine learning architectures than can fit within the memory of a single GPU. 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.
Duersch, Jed↗
Proceedings of the 2011 Monitoring Research Review: Ground-Based Nuclear Explosion Monitoring Technologies
These proceedings contain papers prepared for the Monitoring Research Review 2011: Ground-Based Nuclear Explosion Monitoring Technologies, held 13-15 September, 2011 in Tucson, Arizona. These papers represent the combined research related to ground-based nuclear explosion monitoring funded by the National Nuclear Security Administration (NNSA), Defense Threat Reduction Agency (DTRA), Air Force Research Laboratory (AFRL), US Army Space and Missile Defense Command, Comprehensive Nuclear-Test-Ban Treaty Organization (CTBTO), National Science Foundation (NSF), and other invited sponsors. The scientific objectives of the research are to improve the United States' capability to detect, locate, and identify nuclear explosions. The purpose of the meeting is to provide the sponsoring agencies, as well as potential users, an opportunity to review research accomplished during the preceding year and to discuss areas of investigation for the coming year. For the researchers, it provides a forum for the exchange of scientific information toward achieving program goals, and an opportunity to discuss results and future plans. Paper topics include: seismic regionalization and calibration; detection and location of sources; wave propagation from source to receiver; the nature of seismic sources, including mining practices; hydroacoustic, infrasound, and radionuclide methods; on-site inspection; and data processing.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
Extending Parsimonious Bayesian Inference
Parsimonious Bayesian inference is a theoretical framework for efficient data assimilation that seeks to balance increased consistency between predictions and training data against corresponding increases in model complexity. Within this framework, over-training is understood as optimization that encodes excessive information within model parameters while only achieving small improvements between predictions and training data. This project aims to develop practical methods of limiting excess model information during optimization. One key observation is that practical heuristics for parsimonious learning in high-dimensions must balance expressivity, i.e. the ability of the model to capture diverse predictions with only a few non-zero parameters, against discoverability, i.e. the ability to train the model with gradient-based optimization and drive parameters to low information states. As such, we developed logical activation functions that are able to adaptively approximate arbitrary truth tables that define Boolean logic operations within a probabilistic framework. These functions have demonstrated the ability to learn exclusive disjunction (XOR) and conditioned disjunction (if [condition] then [result_if_true] else [result_if_false]) within a single layer of a neural network. To efficiently exploit these activation functions to drive parsimonious learning required several other advances within the domain of variational inference. The most efficient form of complexity suppression is structured sparsification, driving most model parameters to zero while achieving the structural coherence among nonzeros needed for bandwidth reduction. Such models are not only far more efficient at suppressing information-theoretic complexity, they also reduce the other forms of complexity (computations, communication, storage, and the number of dependencies needed to evaluate predictions). Aiming to support enhanced sparsification, this project examined new approaches to high-dimensional variational inference that allow us to calibrate and control parameter uncertainty during optimization. By identifying which parameters can sustain sparsifying perturbations with little impact on prediction quality, we can develop better pruning strategies by framing them as approximate Bayesian inference. These advances also open paths to mitigate concerns with deploying advanced learning methods in resource-constrained environments, such as running models on power-limited or communication-limited devices.
97 MATHEMATICS AND COMPUTING↗
Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms
Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft 3 (1.27 m 3 ), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO 2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.
59 BASIC BIOLOGICAL SCIENCES↗
The potential of positron emission tomography for intratreatment dynamic lung tumor tracking: A phantom study
Purpose: This study aims to evaluate the potential and feasibility of positron emission tomography for dynamic lung tumor tracking during radiation treatment. The authors propose a center of mass (CoM) tumor tracking algorithm using gated-PET images combined with a respiratory monitor and investigate the geometric accuracy of the proposed algorithm. Methods: The proposed PET dynamic lung tumor tracking algorithm estimated the target position information through the CoM of the segmented target volume on gated PET images reconstructed from accumulated coincidence events. The information was continuously updated throughout a scan based on the assumption that real-time processing was supported (actual processing time at each frame ≈10 s). External respiratory motion and list-mode PET data were acquired from a phantom programmed to move with measured respiratory traces (external respiratory motion and internal target motion) from human subjects, for which the ground truth target position was known as a function of time. The phantom was cylindrical with six hollow sphere targets (10, 13, 17, 22, 28, and 37 mm in diameter). The measured respiratory traces consisted of two sets: (1) 1D-measured motion from ten healthy volunteers and (2) 3D-measured motion from four lung cancer patients. The authors evaluated the geometric accuracy of the proposed algorithm by quantifying estimation errors (Euclidean distance) between the actual motion of targets (1D-motion and 3D-motion traces) and CoM trajectories estimated by the proposed algorithm as a function of time. Results: The time-averaged error of 1D-motion traces over all trajectories of all targets was 1.6 mm. The error trajectories decreased with time as coincidence events were accumulated. The overall error trajectory of 1D-motion traces converged to within 2 mm in approximately 90 s. As expected, more accurate results were obtained for larger targets. For example, for the 37 mm target, the average error over all 1D-motion traces was 1.1 mm; and for the 10 mm target, the average error over all 1D-motion traces was 2.8 mm. The overall time-averaged error of 3D-motion traces was 1.6 mm, which was comparable to that of the 1D-motion traces. There were small variations in the errors between the 3D-motion traces, although the motion trajectories were very different. The accuracy of the estimates was consistent for all targets except for the smallest. Conclusions: The authors developed an algorithm for dynamic lung tumor tracking using list-mode PET data and a respiratory motion signal, and demonstrated proof-of-principle for PET-guided lung tumor tracking. The overall tracking error in phantom studies is less than 2 mm.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Neural conditional reweighting
There is a growing use of neural network classifiers as unbinned, high-dimensional (and variable-dimensional) reweighting functions. To date, the focus has been on marginal reweighting, where a subset of features are used for reweighting while all other features are integrated over. There are some situations, though, where it is preferable to condition on auxiliary features instead of marginalizing over them. Here, we introduce neural conditional reweighting, which extends neural marginal reweighting to the conditional case. This approach is particularly relevant in high-energy physics experiments for reweighting detector effects conditioned on particle-level truth information. Furthermore we leverage a custom loss function that not only allows us to achieve neural conditional reweighting through a single training procedure, but also yields sensible interpolation even in the presence of phase space holes. As a specific example, we apply neural conditional reweighting to the energy response of high-energy jets, which could be used to improve the modeling of physics objects in parametrized fast simulation packages.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Dynamic calibration of differential equations using machine learning, with application to turbulence models
We present a methodology for calibration of parametric ordinary and partial differential equation models, using off-the-shelf software for back-propagation in Neural Networks (NN). As a prototypical example, we consider calibration of a Reynolds-averaged Navier-Stokes (RANS) turbulence closure model, against ground truth data from direct numerical simulations (DNS) of two different turbulent flows. Numerical time integration is represented as a custom NN, where only the RANS model parameters are trainable. A loss function is defined to quantify the mismatch between the NN prediction and the ground truth over a predefined, finite time integration window. This loss function is then minimized using a gradient descent method utilizing the back-propagation algorithm. Furthermore, this dynamic approach to training is to be contrasted with a static approach, wherein a least square regression estimate for parameters is obtained in the limit of an infinitesimal time integration window. In a first test of static and dynamic approaches against ground truth data generated by the model, the former proves to be significantly faster and more accurate than the latter at recovering the parameters. When both calibration approaches are tested against DNS data, for which it is known that the model cannot achieve a perfect fit, the static approach yields a good prediction only for short times, while the dynamic approach results in physical and stable predictions over the entire integration window. After optimization of the dynamic approach for time step, spatial resolution, stability, and physics-based constraints, we obtain a 50% improvement of outcomes over those obtained from the existing, manually calibrated set of parameters, demonstrating the merits of this systematic and automated procedure.
97 MATHEMATICS AND COMPUTING↗
The image quality of ion computed tomography at clinical imaging dose levels
Purpose: Accurately predicting the range of radiotherapy ions in vivo is important for the precise delivery of dose in particle therapy. Range uncertainty is currently the single largest contribution to the dose margins used in planning and leads to a higher dose to normal tissue. The use of ion CT has been proposed as a method to improve the range uncertainty and thereby reduce dose to normal tissue of the patient. A wide variety of ions have been proposed and studied for this purpose, but no studies evaluate the image quality obtained with different ions in a consistent manner. However, imaging doses ion CT is a concern which may limit the obtainable image quality. In addition, the imaging doses reported have not been directly comparable with x-ray CT doses due to the different biological impacts of ion radiation. The purpose of this work is to develop a robust methodology for comparing the image quality of ion CT with respect to particle therapy, taking into account different reconstruction methods and ion species. Methods: A comparison of different ions and energies was made. Ion CT projections were simulated for five different scenarios: Protons at 230 and 330 MeV, helium ions at 230 MeV/u, and carbon ions at 430 MeV/u. Maps of the water equivalent stopping power were reconstructed using a weighted least squares method. The dose was evaluated via a quality factor weighted CT dose index called the CT dose equivalent index (CTDEI). Spatial resolution was measured by the modulation transfer function. This was done by a noise-robust fit to the edge spread function. Second, the image quality as a function of the number of scanning angles was evaluated for protons at 230 MeV. In the resolution study, the CTDEI was fixed to 10 mSv, similar to a typical x-ray CT scan. Finally, scans at a range of CTDEI’s were done, to evaluate dose influence on reconstruction error. Results: All ions yielded accurate stopping power estimates, none of which were statistically different from the ground truth image. Resolution (as defined by the modulation transfer function = 10% point) was the best for the helium ions (18.21 line pairs/cm) and worst for the lower energy protons (9.37 line pairs/cm). The weighted quality factor for the different ions ranged from 1.23 for helium to 2.35 for carbon ions. For the angle study, a sharp increase in absolute error was observed below 45 distinct angles, giving the impression of a threshold, rather than smooth, limit to the number of angles. Conclusions: The method presented for comparing various ion CT modalities is feasible for practical use. While all studied ions would improve upon x-ray CT for particle range estimation, helium appears to give the best results and deserves further study for imaging.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
A divergence-free constrained magnetic field interpolation method for scattered data
An interpolation method to evaluate magnetic fields, given its unstructured and scattered magnetic data, is presented. The method is based on the reconstruction of the global magnetic field using a superposition of orthogonal functions. The coefficients of the expansion are obtained by minimizing a cost function defined as the L2 norm of the difference between the ground truth and the reconstructed magnetic field evaluated on the training data. The divergence-free condition is incorporated as a constraint in the cost function, allowing the method to achieve arbitrarily small errors in the magnetic field divergence. An exponential decay of the approximation error is observed and compared with the less favorable algebraic decay of local splines. Compared to local methods involving computationally expensive search algorithms, the proposed method exhibits a significant reduction of the computational complexity of the field evaluation, while maintaining a small error in the divergence even in the presence of magnetic islands and stochasticity. Finally, applications to the computation of Poincaré sections using data obtained from numerical solutions of the magnetohydrodynamic equations in toroidal geometry are presented and compared with local methods currently in use.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
2012 Monitoring Research Review: Ground-Based Nuclear Explosion Monitoring Technologies
No abstract prepared.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
Extracting Grain Orientations from EBSD Patterns of Polycrystalline Materials Using Convolutional Neural Networks
Abstract We present a deep learning approach to the indexing of electron backscatter diffraction (EBSD) patterns. We design and implement a deep convolutional neural network architecture to predict crystal orientation from the EBSD patterns. We design a differentiable approximation to the disorientation function between the predicted crystal orientation and the ground truth; the deep learning model optimizes for the mean disorientation error between the predicted crystal orientation and the ground truth using stochastic gradient descent. The deep learning model is trained using 374,852 EBSD patterns of polycrystalline nickel from simulation and evaluated using 1,000 experimental EBSD patterns of polycrystalline nickel. The deep learning model results in a mean disorientation error of 0.548° compared to 0.652° using dictionary based indexing.
Materials Science↗
Energy landscapes from cryo-EM snapshots: a benchmarking study
Abstract Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.
59 BASIC BIOLOGICAL SCIENCES↗
Dynamic Learning of Correlation Potentials for a Time-Dependent Kohn-Sham System
We develop methods to learn the correlation potential for a time-dependent Kohn-Sham (TDKS) system in one spatial dimension. We start from a low-dimensional two-electron system for which we can numerically solve the time-dependent Schr¨odinger equation; this yields electron densities suitable for training models of the correlation potential. We frame the learning problem as one of optimizing a least-squares objective subject to the constraint that the dynamics obey the TDKS equation. Applying adjoints, we develop efficient methods to compute gradients and thereby learn models of the correlation potential. Our results show that it is possible to learn values of the correlation potential such that the resulting electron densities match ground truth densities. We also show how to learn correlation potential functionals with memory, demonstrating one such model that yields reasonable results for trajectories outside the training set.
97 MATHEMATICS AND COMPUTING↗
A deep learning approach for semantic segmentation of unbalanced data in electron tomography of catalytic materials
In computed TEM tomography, image segmentation represents one of the most basic tasks with implications not only for 3D volume visualization, but more importantly for quantitative 3D analysis. In case of large and complex 3D data sets, segmentation can be an extremely difficult and laborious task, and thus has been one of the biggest hurdles for comprehensive 3D analysis. Heterogeneous catalysts have complex surface and bulk structures, and often sparse distribution of catalytic particles with relatively poor intrinsic contrast, which possess a unique challenge for image segmentation, including the current state-of-the-art deep learning methods. To tackle this problem, we apply a deep learning-based approach for the multi-class semantic segmentation of a γ-Alumina/Pt catalytic material in a class imbalance situation. Specifically, we used the weighted focal loss as a loss function and attached it to the U-Net’s fully convolutional network architecture. We assessed the accuracy of our results using Dice similarity coefficient (DSC), recall, precision, and Hausdorff distance (HD) metrics on the overlap between the ground-truth and predicted segmentations. Our adopted U-Net model with the weighted focal loss function achieved an average DSC score of 0.96 ± 0.003 in the γ-Alumina support material and 0.84 ± 0.03 in the Pt NPs segmentation tasks. We report an average boundary-overlap error of less than 2 nm at the 90th percentile of HD for γ-Alumina and Pt NPs segmentations. The complex surface morphology of γ-Alumina and its relation to the Pt NPs were visualized in 3D by the deep learning-assisted automatic segmentation of a large data set of high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) tomography reconstructions.
36 MATERIALS SCIENCE↗
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↗
Automated detector simulation and reconstruction parametrization using machine learning
Rapidly applying the effects of detector response to physics objects (e.g. electrons, muons, showers of particles) is essential in high energy physics. Presently available tools for the transformation from truth-level physics objects to reconstructed detector-level physics objects involve manually defining resolution functions. These resolution functions are typically derived in bins of variables that are correlated with the resolution (e.g. pseudorapidity and transverse momentum). This process is time consuming, requires manual updates when detector conditions change, and can miss important correlations. Machine learning offers a way to automate the process of building these truth-to-reconstructed object transformations and can capture complex correlation for any given set of input variables. Such machine learning algorithms, with sufficient optimization, could have a wide range of applications: improving phenomenological studies by using a better detector representation, allowing for more efficient production of Geant4 simulation by only simulating events within an interesting part of phase space, and studies on future experimental sensitivity to new physics.
47 OTHER INSTRUMENTATION↗
Downfolding from ab initio to interacting model Hamiltonians: comprehensive analysis and benchmarking of the DFT+cRPA approach
Abstract Model Hamiltonians are regularly derived from first principles to describe correlated matter. However, the standard methods for this contain a number of largely unexplored approximations. For a strongly correlated impurity model system, here we carefully compare a standard downfolding technique with the best possible ground-truth estimates for charge-neutral excited-state energies and wave functions using state-of-the-art first-principles many-body wave function approaches. To this end, we use the vanadocene molecule and analyze all downfolding aspects, including the Hamiltonian form, target basis, double-counting correction, and Coulomb interaction screening models. We find that the choice of target-space basis functions emerges as a key factor for the quality of the downfolded results, while orbital-dependent double-counting corrections diminish the quality. Background screening of the Coulomb interaction matrix elements primarily affects crystal-field excitations. Our benchmark uncovers the relative importance of each downfolding step and offers insights into the potential accuracy of minimal downfolded model Hamiltonians.
Chemistry↗