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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

HAPPA: A Modular Platform for HPC Application Resilience Analysis with LLMs Embedded

High-performance computing (HPC) systems are increasingly vulnerable to soft errors, which pose significant challenges in maintaining computational accuracy and reliability. Predicting the resilience of HPC applications to these errors is crucial for robust code protection and detailed resilience analysis. In this study, we present HAppA, a modular platform designed for HPC Application Resilience Analysis. Embedding Large Language Models (LLMs), HAppA addresses understanding the context information of long code sequences typical in HPC applications. HAppA implements a novel code representation module that chunks the code into fixed-size segments and aggregates the embeddings of these segments. Three aggregation methods have been explored: MeanPooling, MaxPooling, and LSTM-based techniques. We built a DAtaset for REsilience analysis using Fault Injection (FI), named DARE. Using our DARE dataset, HAppA is trained for regression prediction tasks. Our evaluation results demonstrate the predictive accuracy of HAppA compared to other models, particularly noting that the LSTM-based aggregation method -- HAppA-LSTM -- achieves a mean squared error (MSE) of 0.078 for SDC prediction, surpassing the existing state-of-the-art PARIS model, which recorded an MSE of 0.1172. Additionally, HAppA with the KeyBERT model extracts a list of keywords representing the source code. A comprehensive importance analysis of these keywords further elucidates the code patterns contributing to the error rate. These findings highlight the effectiveness of HAppA in analyzing the resilience of HPC applications and establish a new benchmark for predictive accuracy in resilience.

Jiang, Hailong [Kent State University]↗
DOE OSTI2022

Automatic information extraction from childhood cancer pathology reports

The International Classification of Childhood Cancer (ICCC) facilitates the effective classification of a heterogeneous group of cancers in the important pediatric population. However, there has been no development of machine learning models for the ICCC classification. We developed deep learning-based information extraction models from cancer pathology reports based on the ICD-O-3 coding standard. In this article, we describe extending the models to perform ICCC classification. We developed 2 models, ICD-O-3 classification and ICCC recoding (Model 1) and direct ICCC classification (Model 2), and 4 scenarios subject to the training sample size. We evaluated these models with a corpus consisting of 29206 reports with age at diagnosis between 0 and 19 from 6 state cancer registries. Our findings suggest that the direct ICCC classification (Model 2) is substantially better than reusing the ICD-O-3 classification model (Model 1). Applying the uncertainty quantification mechanism to assess the confidence of the algorithm in assigning a code demonstrated that the model achieved a micro-F1 score of 0.987 while abstaining (not sufficiently confident to assign a code) on only 14.8% of ambiguous pathology reports. Our experimental results suggest that the machine learning-based automatic information extraction from childhood cancer pathology reports in the ICCC is a reliable means of supplementing human annotators at state cancer registries by reading and abstracting the majority of the childhood cancer pathology reports accurately and reliably.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Examination of Global Midlatitude Atmospheric River Lifecycles Using an Object-Oriented Methodology

Tracking atmospheric rivers (ARs) across their lifecycles is a field of recent interest with a multitude of emerging methodologies. The CONNected-objECT (CONNECT) algorithm is adapted for the tracking of global midlatitude AR lifecycles and associated precipitation by implementing a seeded region growing segmentation algorithm, creating the AR-CONNECT algorithm. To facilitate the permissiveness of the methodology, AR-CONNECT is without hard-coded geometric criteria yet is still shown to extract synoptic-scale elongated objects >99.99% of the time. One of the consequences of the methodology is the ability to occasionally track atmospheric water vapor anomalies before evolving into AR geometries, effectively tracking AR genesis further back than other studies. With the aid of subdaily satellite-derived rain data, we investigate the climatology, trends, and patterns of AR lifecycles from 1983–2016 and compare with other AR tracking studies. We find that AR frequency, genesis, and terminus locations are in generally good agreement with other AR tracking methodologies, though with key differences, and that AR frequencies in each hemisphere are determined by the number of AR hotspots. Furthermore, we uncover evidence that certain AR characteristics, such as frequency, areal extent, and duration, show evidence of increasing trends. Midlatitude precipitation uncovered by AR-CONNECT shows contributions up to 50% over land and 65% over the ocean. Trend analysis of AR precipitation shows an increase in precipitation associated with ARs propagated by the Southern Jet Stream and ARs that traverse over the Sahara Desert, among others, but is determined not to be a driver of changes in global precipitation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The PAU Survey: Photometric redshifts using transfer learning from simulations

In this paper, we introduce the DEEPZ deep learning photometric redshift (photo-z) code. As a test case, we apply the code to the PAU survey (PAUS) data in the COSMOS field. DEEPZ reduces the σ68 scatter statistic by 50 percent at iAB = 22.5 compared to existing algorithms. This improvement is achieved through various methods, including transfer learning from simulations where the training set consists of simulations as well as observations, which reduces the need for training data. The redshift probability distribution is estimated with a mixture density network (MDN), which produces accurate redshift distributions. Our code includes an autoencoder to reduce noise and extract features from the galaxy SEDs. It also benefits from combining multiple networks, which lowers the photo-z scatter by 10 percent. Furthermore, training with randomly constructed coadded fluxes adds information about individual exposures, reducing the impact of photometric outliers. In addition to opening up the route for higher redshift precision with narrow bands, these machine learning techniques can also be valuable for broad-band surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Spectroscopic quadrupole moments in 124 $\mathrm{Xe}$

The Xe isotopic chain with four valence protons above the Z=50 shell closure is an ideal laboratory for the study of the evolution of nuclear deformation. At the N=82 shell closure, 136 Xe presents all characteristics of a doubly closed shell nucleus with a spherical shape. In the very neutron-deficient isotopes close to N=50, the α-decay chain of Xe was investigated to probe the radioactive decay properties near the drip-line and the magicity of 100 Sn. Additionally, the Xe isotopes present higher order symmetries in the nuclear deformation such as the octupole degree of freedom near N=60 and N=90 or O(6) symmetry in stable isotopes. The relevance of the O(6) symmetry has been investigated by measuring the spectroscopic quadrupole moment of the first excited states in 124 Xe. In the O(6) symmetry limit, the spectroscopic quadrupole moment of collective states is expected to be null. A stable 124 Xe beam with energies of 4.03A MeV and 4.11 A MeV was used to bombard a nat W target at the GANIL facility. Excited states were populated via the safe Coulomb excitation reaction. The collision of the heavy ions with a large Z at low energy make this reaction sensitive to the diagonal E2 matrix element of the excited states. The recoils were detected in the VAMOS++ magnetic spectrometer and the γ rays in the AGATA tracking array. The least squares fitting code gosia was used for the analysis to extract both E2 and M1 transitional and E2 diagonal matrix elements. The rotational ground state band was populated up to the 8$^{+}_{1}$ state as well as the 2$^{+}_{2}$ and 4$^{+}_{2}$ states. Using high precision spectroscopic data to constrain the gosia fit, the spectroscopic quadrupole moments of the 2$^{+}_{1}$, 4$^{+}_{1}$, and 6$^{+}_{1}$ states were determined for the first time. The spectroscopic quadrupole moments were found to be negative, large, and constant in the ground state band underlining the prolate axially deformed ground state band of 124 Xe. Here, the present experimental data confirm that the O(6) symmetry is substantially broken in 124 Xe .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

All-Atom Simulation of 3D Hot Spot Formation in Shocked TATB Explosive

TATB is an insensitive high explosive (IHE) critical to the stockpile that is challenging to model at the continuum scale. Advanced detonation models in the Cheetah high explosive chemistry code require validation though subscale simulations. High explosive initiation is determined by micron-scale physics of hot spots formed a shock-collapsed pores. Pore sizes between 100 nm and 1 μm are believed to be the most important for determining the shock sensitivity of TATB. This range of pore sizes is difficult to access at the atomic scale through allatom molecular dynamics (MD) simulations, even with Sierra-class computers. Quasi-2D simulations are widely used and allow much larger pore sizes (up to 400 nm) to be studied, but the applicability of 2D simulations to the actual 3D pore response is not understood. Resolving these uncertainties through “full physics” MD modeling is key for generalizing, parameterizing, and validating the kinds of continuum models used to inform design, safety, and performance. This work was a continuation of FY20 efforts pushing simulations to full 3D with the largest-ever all-atom simulations of an explosive. These were the first all-atom full-3D simulations of large hot spots thought to govern explosive detonation and required over a billion atoms. Simulations were performed using LAMMPS, an open SNL science code. MD explosive models present unique challenges, even for established codes such as LAMMPS. Their model forms are more complex than typical models for metals, while simulating high temperature-pressure conditions is demanding and increases computational cost. Scaling problems in GPU-enabled MD algorithms initially limited simulations to <100 million atoms but were resolved through collaboration with SNL. An overall 24x speedup was obtained relative to CPU machines. Specialized analysis of these simulations required a bottom-up refactoring and algorithm parallelization of in-house codes and application of computer vision algorithms to extract meaningful information.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structure of Low-spin States in \(^{45}\)Sc Studied via Coulomb Excitation

The electromagnetic structure of 45 Sc at low excitation energy was investigated via low-energy Coulomb excitation at the Heavy Ion Laboratory (HIL) of the University of Warsaw and at the Inter-University Accelerator Centre (IUAC) in New Delhi. A set of reduced E2, E3, and M1 matrix elements was extracted from the collected data using the GOSIA code. The reduced transition probability B(E2; 11/2 – → 7/2 – ) has been determined, allowing us to deduce the lifetime of the 11/2 – state at 1237 keV. In addition, the upper limit on the reduced transition probability B(E3; 7/2 – → 5/2 + ) has been determined for the first time. Finally, new large-scale shellmodel and beyond-mean-field calculations were performed to interpret the structure of this nucleus.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Single-shot quantum error correction in intertwined toric codes

We construct a subsystem code in three dimensions that exhibits single-shot error correction in a user-friendly and transparent way. As this code is a subsystem version of coupled toric codes, we call it the intertwined toric code (ITC). Although previous codes share the property of single-shot error correction, the ITC is distinguished by its physically motivated origin, geometrically straightforward logical operators and errors, and a simple phase diagram. The code arises from three-dimensional (3D) stabilizer toric codes in a way that emphasizes the physical origin of the single-shot property. In particular, starting with two copies of the 3D toric code, we add check operators that provide for the confinement of pointlike excitations without condensing the loop excitations. Geometrically, the bare and dressed logical operators in the ITC derive from logical operators in the underlying toric codes, creating a clear relationship between errors and measurement outcomes. The syndromes of the ITC resemble the syndromes of the single-shot code by Kubica and Vasmer, allowing us to use their decoding schemes. We also extract the phase diagram corresponding to ITC and show that it contains the phases found in the Kubica-Vasmer code. Lastly, we suggest various connections to Walker-Wang models and measurement-based quantum computation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

The CXSFIT spectral fitting code: Past, present and future

Magnetically confined plasma experiments generate a wealth of spectroscopic data. The first step toward extracting physical parameters is to fit a spectral model to the often complex spectra. The CXSFIT (Charge eXchange Spectroscopy FITting) spectral fitting code was originally developed for fitting charge exchange spectra on JET from the late 1980s onward and has been further developed over decades to keep up with the needs of the users. The primary use is to efficiently fit a large number of spectra with many constrained Gaussian spectral lines of which the physical parameters can be coupled in a user-friendly manner. More recent additions to the code include time-dependent couplings between parameters, flexible background subtraction, and a non-linear coupling scheme between fit parameters. The latter was a pre-requisite for implementing Zeeman and motional Stark effect multiplets in the library of spectral features. The ability to save and replay “fit recipes,” even when multiple iterations are required, has ensured the traceability of the results and is one of the keys to the longevity and success of the code. The code is also in use on other tokamaks (AUG, ST-40) and to fit data from other spectroscopic diagnostics on JET. In this paper, we document the current capabilities and philosophy behind the structure of the code, including some of the algorithms used to calculate spectral features numerically efficiently. We also provide an outline of how CXSFIT could be transferred into a framework that would be able to meet the spectral fitting requirements of future devices, such as ITER.

Delabie, Ephrem G.↗
DOE OSTI2025

Hierarchical memories: Simulating quantum LDPC codes with local gates

Constant-rate low-density parity-check (LDPC) codes are promising candidates for constructing efficient fault-tolerant quantum memories. However, if physical gates are subject to geometric-locality constraints, it becomes challenging to realize these codes. In this paper, we construct a new family of [[N,K,D]] codes, referred to as hierarchical codes, that encode a number of logical qubits K=Ω(N/log(N) 2 ). The N th element of this code family is obtained by concatenating a constant-rate quantum LDPC code with a surface code; nearest-neighbor gates in two dimensions are sufficient to implement the corresponding syndrome-extraction circuit and achieve a threshold. Below threshold the logical failure rate vanishes superpolynomially as a function of the distance D(N). We present a bilayer architecture for implementing the syndrome-extraction circuit, and estimate the logical failure rate for this architecture. Under conservative assumptions, we find that the hierarchical code outperforms the basic encoding where all logical qubits are encoded in the surface code.

Pattison, Christopher A. [California Institute of ↗
DOE OSTI2024

Tracking the topology of neural manifolds across populations

Neural manifolds summarize the intrinsic structure of the information encoded by a population of neurons. Advances in experimental techniques have made simultaneous recordings from multiple brain regions increasingly commonplace, raising the possibility of studying how these manifolds relate across populations. However, when the manifolds are nonlinear and possibly code for multiple unknown variables, it is challenging to extract robust and falsifiable information about their relationships. We introduce a framework, called the method of analogous cycles, for matching topological features of neural manifolds using only observed dissimilarity matrices within and between neural populations. We demonstrate via analysis of simulations and in vivo experimental data that this method can be used to correctly identify multiple shared circular coordinate systems across both stimuli and inferred neural manifolds. Conversely, the method rejects matching features that are not intrinsic to one of the systems. Further, as this method is deterministic and does not rely on dimensionality reduction or optimization methods, it is amenable to direct mathematical investigation and interpretation in terms of the underlying neural activity. We thus propose the method of analogous cycles as a suitable foundation for a theory of cross-population analysis via neural manifolds.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Understanding extraction limits of plasma cathodes with experiment and simulation

The project is focused on computations for enhanced ionization near the exit orifice of a plasma cathode and how the cathode extraction electrode geometry and stray magnetic field structure influence available extractable current. The computational effort will take place at the Princeton Collaborative Research Laboratory (PCRF). The specific modeling platform to be utilized from PCRF is the electrostatic direct implicit particle in cell (EDIPIC) code. EDIPIC will be used to study ionization processes in the electron extraction region of the cathode. The control of electron energy is a key aspect to minimizing power losses in the plasma. Exiting electrons ionize gas leaving the orifice and in the process produce the dense plasma from which large amounts of current can be extracted. Project activities include studying processes that determine the energy distribution of the exiting electrons thus providing insight into how to optimize the source. The model will be validated and developed using experimental measurements as warranted. The familiarity and expertise of the team at PPPL with this type of plasma and the challenges posed greatly enhances the likelihood of gaining insight into the extraction sheath under the duration of the proposed activity. The effort is expected to shed a great deal of insight into electron extraction processes and pathways for optimization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Resilience of the surface code to error bursts

Quantum error correction works effectively only if the error rate of gate operations is sufficiently low. However, some rare physical mechanisms can cause a temporary increase in the error rate that affects many qubits; examples include ionizing radiation in superconducting hardware and large deviations in the global control of atomic systems. We refer to such rare transient spikes in the gate error rate as error bursts. In this work, we investigate the resilience of the rotated surface code to generic error bursts. We assume that, after appropriate mitigation strategies, the spike in the error rate lasts for only a single syndrome-extraction cycle; we also assume that the enhanced error rate is uniform across the code block. Under these assumptions, and for a circuit-level depolarizing noise model, we perform Monte Carlo simulations to determine the regime in burst error rate and background error rate for which the memory time becomes arbitrarily long as the code block size grows. Our results indicate that suitable hardware mitigation methods combined with standard decoding methods may suffice to protect against transient error bursts in the rotated surface code.

Quantum error correction↗
DOE OSTI2023

Few-shot leaf segmentation

In this work, we use few-shot learning to segment the body and vein architecture of Populus trichocarpa leaves from high-resolution scans obtained in the UC Davis common garden. Leaf and vein segmentation are formulated as separate tasks, in which convolutional neural networks (CNNs) are used to iteratively expand partial segmentations until reaching stopping criteria. Our leaf and vein segmentation approaches use just 50 and 8 manually traced images for training, respectively, and are applied to a set of 2,634 top and bottom leaf scans. We show that both methods achieve high segmentation accuracy, in some cases exceeding even human-level segmentation. The leaf and vein segmentations are subsequently used to extract 68 morphological traits using traditional open-source image processing tools, which are validated using real-world physical measurements. For a biological perspective, we perform a genome-wide association study using the "vein density" trait to discover novel genetic architectures associated with multiple physiological processes relating to leaf development and function. In addition to sharing all of the few-shot learning code, we are releasing all images, manual segmentations, model predictions, 68 extracted leaf phenotypes, and a new set of SNPs called against the v4 P. trichocarpa genome for 1,419 genotypes.

Lagergren, John [Oak Ridge National Lab. (ORNL), O↗
DOE OSTI2024

Verification of RESRAD-OFFSITE Code (V.4)

This report documents the verification of RESRAD-OFFSITE Version 4.0 and describes, where necessary, the verification of the following: • The data comprising the standard dose and risk coefficient libraries in the RESRAD database files Master_dcf_ICRP07.mdb and Master_dcf_2k.mdb. • The extraction and transfer of the data from the selected database file to the computational code by the RESRAD-OFFSITE 4.0 interface, ResOWin.exe. • The different processes that are modeled by the main computational code in RESRAD OFFSITE 4.0, ResOMain.exe. • The data displayed in the graphical and text reports. Many verifications were performed as part of the quality assurance quality control program associated with the development and release of RESRAD-OFFSITE 4.0, namely: • developer testing, • internal independent testing, and • release testing. Some were also performed in response to questions from users regarding the performance of the code. The main text of the report focuses on summarizing a subset of those tests, both independent and developer tests that verified the computations performed by the code. The verifications included in this report served as the basis for the development of the release tests of the computational executables and provided the quantitative results to be compared with the code output. The input and output interfaces and the data transfers between the various executables of the code were tested while performing the verification testing. They were tested intentionally during release testing. This report also provides some basic information to help in understanding the activities that were verified. The report: • outlines the components of RESRAD-OFFSITE 4.0 and the interconnections between these components, • outlines the processes modeled by the computational code, • provides summary figures and tables to offer confirmation of the verification of the computational components of the code, • reproduces the verifiers’ reports, if available, in individual appendices, • refers to the previous verification report (Yu et al. 2011) for more details about some of the verifications, and • reproduces the test cases and the testers’ reports from the release testing in individual appendices, when possible.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Data and Code for: Observation-constrained agroecosystem model inversion reveals continental-scale variation of winter wheat traits

This repository contains the simulation outputs and processing scripts associated with the study of winter wheat traits across the United States, utilizing the Ecosys agroecosystem model. The dataset includes model results for both rainfed and irrigated winter wheat systems, supporting the findings presented in the manuscript titled "Observation-constrained agroecosystem model inversion reveals continental-scale variation of winter wheat traits." Data includes the original Ecosys simulation outputs (archived in .db format within the compressed .zip files) and extracted analysis data (stored in .pkl files for efficient processing). Python code for data processing and figure generation is provided in a Jupyter notebook. External Observational Datasets should refer to the following official repositories for the input and validation data used in this study. The eddy covariance data from the AmeriFlux network (https://ameriflux.lbl.gov/). Climate-forcing data of NLDAS-2 from NASA LDAS (https://ldas.gsfc.nasa.gov/nldas/nldas-2-forcing-data). Soil data from the Gridded Soil Survey Geographic Database (gSSURGO), available at (https://www.nrcs.usda.gov/resources/data-and-reports/gridded-soil-survey-geographic-gssurgo-database). Crop yields, planting and harvest dates from the USDA public databases (https://quickstats.nass.usda.gov/; https://webapp.rma.usda.gov/apps/actuarialinformationbrowser/CropCriteria.aspx). Satellite-derived SLOPE GPP data from ORNL DAAC (https://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=1786). Land use and crop progress information from the USDA Crop Data Layer and Crop Progress and Condition Gridded Layers (https://www.nass.usda.gov/Research_and_Science/). The Ecosys model code is available online at https://github.com/jinyun1tang/ECOSYS.

Wheat↗
DOE OSTI2025

Extracting symplectic maps for space-charge dominated beams

Symplecticity of transfer maps is important for reliable evaluation of space-charge dominated beams in accelerators. Unfortunately, most simulation codes that include collective effects, such as space charge, do not use canonical phase-space variables and therefore are not symplectic in the presence of electromagnetic fields. In this paper, we present a numerical method to extract local linear symplectic transfer maps using particle tracking simulation code for space-charge dominated beams. We demonstrate this method for the photoinjector (113 MHz SRF gun) section of the Coherent electron Cooling (CeC) Proof of Principle (POP) experiment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Clinical knowledge extraction via sparse embedding regression (KESER) with multi-center large scale electronic health record data

The increasing availability of electronic health record (EHR) systems has created enormous potential for translational research. However, it is difficult to know all the relevant codes related to a phenotype due to the large number of codes available. Traditional data mining approaches often require the use of patient-level data, which hinders the ability to share data across institutions. In this project, we demonstrate that multi-center large-scale code embeddings can be used to efficiently identify relevant features related to a disease of interest. We constructed large-scale code embeddings for a wide range of codified concepts from EHRs from two large medical centers. We developed knowledge extraction via sparse embedding regression (KESER) for feature selection and integrative network analysis. We evaluated the quality of the code embeddings and assessed the performance of KESER in feature selection for eight diseases. Besides, we developed an integrated clinical knowledge map combining embedding data from both institutions. The features selected by KESER were comprehensive compared to lists of codified data generated by domain experts. Features identified via KESER resulted in comparable performance to those built upon features selected manually or with patient-level data. The knowledge map created using an integrative analysis identified disease-disease and disease-drug pairs more accurately compared to those identified using single institution data. Analysis of code embeddings via KESER can effectively reveal clinical knowledge and infer relatedness among codified concepts. KESER bypasses the need for patient-level data in individual analyses providing a significant advance in enabling multi-center studies using EHR data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗