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At least 469 records · Page 26

All sources NASA NTRS DOE OSTI

DOE OSTI2023

GNATFinder

SAND2023-05510O GNATFinder is a software tool for extracting graphical neural activity threads (GNATs) from spiking neural networks. GNATFinder efficiently extracts GNATs from spiking neural network data. A GNAT is a graph that represents the causal relationships between individual spikes in a spiking network using a combination of the network connectivity structure and the timing of individual spikes. The software allows for identifying similar, repeating threads that often reappear in a dataset. Using quadtree data structures to recursively subdivide the time interval over which spikes were produced by the spiking network, GNATFinder allows for efficient pairwise comparisons of spike times to determine the degree of causal relatedness among all pairs of spikes in a dataset. 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.

SciDAC↗

DOE OSTI2024

sf-24-103

pyzag is a library for efficiently training generic models defined with a recursive nonlinear function. We developed it primarily to provide an efficient means to train NEML2 models it can be used to train other, more general types of models.

Messner, Mark [Argonne National Laboratory (ANL), ↗

DOE OSTI2025

Autonomous Anomaly Detection For Continuous Streams

The code implements the Isolation Forest (IFML) algorithm within the digital twin (DT) of the AGN-201 nuclear reactor. The DT captures real-time operational data including control rod positions, reactor power, and temperature. The IFML model isolates anomalies by detecting patterns that deviate from expected operational behavior. The algorithm recursively partitions the data and assigns anomaly scores based on the isolation of rare and different events. By tuning parameters specific to the reactor’s operational data, the IFML identifies deviations such as unauthorized material insertions or reactor reactivity shifts. The system streams data using LabView and integrates with the DeepLynx data warehouse for anomaly processing.

Trevino, Eduardo↗

DOE OSTI2025

LLaMP v0.1.0

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences, where reliability and reproducibility are crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. LLaMP is a multimodal retrieval-augmented generation (RAG) framework of hierarchical reasoning and acting (ReAct) agents that can dynamically and recursively interact with Materials Project to ground large language models on high-fidelity materials informatics.

Riebesell, Janosh [Lawrence Berkeley National Labo↗

DOE OSTI2026

Multithreaded copy ('cp')

This is a modification to 'cp' and 'mv' commands to make them multi-threaded. Simple benchmarks showed that multi-threading could reduce the time to copy a large Linux source directory by over 2x. The 'cp' and 'mv' utilities are part of the existing Coreutils (https://www.gnu.org/software/coreutils/) software package that get installed on all Linux distros. Changes: * Add '-j|--parallel ' flags to 'cp' and 'mv'. This allows the utilities to recursively copy regular files in directories in parallel. This does NOT parallelize multiple single file copies to a destination (like 'cp file2 file2 file3 dst/'). Along with this, add in new 'CP_NUM_THREADS' and 'MV_NUM_THREADS' environment variables to set the number of threads. This can be useful when you want to enable parallelism by default in /etc/profile. The maximum number of threads is internally capped to the number of CPUs. * Add a '-j' flag to 'sort' to complement its existing '--parallel' flag. This is only done for consistency with 'cp' and 'mv'. * Add test cases for the new flags. Also, run each 'cp' and 'mv' test both in single-threaded and multithreaded modes for extra coverage.

Hutter, AnthonyJ [Lawrence Livermore National Labo↗

DOE OSTI2024

Non-smooth Bayesian optimization in tuning scientific applications

Tuning algorithmic parameters to optimize the performance of large, complicated computational codes is an important problem involving finding the optima and identifying regimes defined by non-smooth boundaries in black-box functions. Within the Bayesian optimization framework, the Gaussian process surrogate model produces smooth mean functions, but functions in the tuning problem are often non-smooth, which is exacerbated by the fact that we usually have limited sequential samples from the black-box function. Here, motivated by these issues encountered in tuning, we propose a novel Gaussian process model called a clustered Gaussian process (cGP), where the components are dynamically updated by clustering. In our studies, the performance of cGP can be better than stationary GPs in nearly 90% of the experiments and better than non-stationary GPs in nearly 70% of the repeated experiments while requiring less computational cost. cGP provides a novel approach for dynamic GP, computes more efficiently than recursive partitioning, and discovers non-smoothness regimes. We provide extensive experiments including high-performance computing (HPC) and industrial simulation functions to show the effectiveness of our methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

ROBOT: A Tool for Automating Ontology Workflows

BACKGROUND:Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool. RESULTS:ROBOT (a recursive acronym for "ROBOT is an OBO Tool") is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems. CONCLUSIONS:ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2019

Risk of Distant Metastasis in Parathyroid Carcinoma and Its Effect on Survival: A Retrospective Review from a High-Volume Center

Background: Development of distant metastases (DM) is associated with markedly decreased survival in parathyroid carcinoma (PC). We sought to identify factors associated with development of DM and to quantify the effect that development of DM had on overall survival (OS). Methods: Patients with surgically resected local/regional PC treated or surveilled at a tertiary-referral cancer hospital from 1980 to 2017 were included. We assessed the association between biochemical and clinicopathologic factors (preoperative parathyroid hormone (PTH) levels, sex, race, age, preoperative serum calcium levels, serum calcium levels at 6 months postop, tumor size, and extent of resection) with the development of DM. We also assessed the effect of development of DM on OS. Results: Seventy-five patients with PC were assessed; 17 (22.7%) developed DM at a median follow-up of 77 months. The cumulative incidence of DM in the cohort was 20, 30, and 38% at 5, 10, and 20 years respectively. Tumor size > 3.2 cm based on recursive partitioning analysis was the only significant predictor for development of DM (hazard ratio (HR) = 3.51; 95% confidence interval [CI] 1.04–11.91; p = 0.04). Median OS for the entire cohort was 17 years compared with 40 months for the cohort who developed DM. The HR for death after distant metastasis was 9.6 (95% CI 4.2–22.3; p < 0.0001). Conclusions: Development of distant metastasis during surveillance is associated with decreased OS, including late recurrences. Primary tumor size should be considered in future interval surveillance and development of treatment algorithms.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2019

A Novel N Staging System for Predicting Survival in Patients with Medullary Thyroid Cancer

Introduction: Despite the crucially prognostic value of lymph node metastasis (LNM) in patients with medullary thyroid cancer (MTC), only the LNM compartment alone was reflected in the 8th edition of the American Joint Committee on Cancer (AJCC) system. Objective: This study aimed to incorporate the metastatic lymph node number and metastatic lymph node ratio to generate a more accurate and appropriate N staging system for patients with MTC based on recursive partitioning analysis. Design, Setting, and Patients: Two cohorts were included in the analysis, including 1374 MTC patients from the Surveillance, Epidemiology, and End Results database as the derivation cohort, and 164 patients from Fudan University Shanghai Cancer Center as the validation cohort. The predictive performance of the alternative proposed N staging system was compared with that of the 8th AJCC system by using the Harrell concordance index (C-index) and the area under the receiver operating characteristic curve (AUC). Results: In the derivation cohort, the C-index and the AUC at 10 years were 0.778 and 0.789, respectively, for the novel N staging system, and 0.749 and 0.741, respectively, for the 8th AJCC N staging system. Similar trends were also observed in the validation cohort. The proposed N staging system had a better prognostic performance. Conclusion: With some improvements, the novel N staging system for MTC suggested from this research may be assessed for potential adoption in the next edition of the AJCC N staging system.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2025

Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture

The Cellular-Potts model is a powerful and ubiquitous framework for developing computational models for simulating complex multicellular biological systems. Cellular-Potts models (CPMs) are often computationally expensive due to the explicit modeling of interactions among large numbers of individual model agents and diffusive fields described by partial differential equations (PDEs). In this work, we develop a convolutional neural network (CNN) surrogate model using a U-Net architecture that accounts for periodic boundary conditions. We use this model to accelerate the evaluation of a mechanistic CPM previously used to investigate in vitro vasculogenesis. The surrogate model was trained to predict 100 computational steps ahead (Monte-Carlo steps, MCS), accelerating simulation evaluations by a factor of 562 times compared to single-core CPM code execution on CPU. Over short timescales of up to 3 recursive evaluations, or 300 MCS, our model captures the emergent behaviors demonstrated by the original Cellular-Potts model such as vessel sprouting, extension and anastomosis, and contraction of vascular lacunae. This approach demonstrates the potential for deep learning to serve as a step toward efficient surrogate models for CPM simulations, enabling faster evaluation of computationally expensive CPM simulations of biological processes.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Machine learning of factors for improving oyster hatchery production

Oyster aquaculture and restoration in the Chesapeake Bay are vital, yet hatcheries frequently struggle with inconsistent larval growth and sudden mass mortality events. Unpredictable disruptions in larval production cause large economic losses, represent a perceived risk to growers, and impede industry expansion. To better understand associations between production yield and its potential predictors, we applied machine learning (random forest, and neural network) and statistical (generalized additive model) models to a comprehensive dataset of environmental, water quality, and operational parameters from a Maryland oyster hatchery, aiming to identify key yield predictors and develop a robust forecasting tool. We used recursive Boruta algorithm for variable selection, pinpointing critical predictors, and employed cross-validation to fine-tune model settings. Shapley value analysis offered crucial insights into model interpretations, highlighting week number, Normalized Difference Vegetation Index, salinity, turbidity, and fecundity as primary drivers of yield variability. For low-yield cases, salinity-related variables were particularly important. Our findings provide an early warning system for potential production downturns, empowering hatchery operators to make data-driven decisions for optimizing water conditions, feeding schedules, and broodstock management. By boosting predictability and efficiency, this research directly supports economic stability of the oyster industry and ecological health of the Chesapeake Bay.

Vishwakarma, Srishti [Oak Ridge National Laborator↗

DOE OSTI2020

Traversing large graphs on GPUs with unified memory

Due to the limited capacity of GPU memory, the majority of prior work on graph applications on GPUs has been restricted to graphs of modest sizes that fit in memory. Recent hardware and software advances make it possible to address much larger host memory transparently as a part of a feature known as unified virtual memory. While accessing host memory over an interconnect is understandably slower, the problem space has not been sufficiently explored in the context of a challenging workload with low computational intensity and an irregular data access pattern such as graph traversal. We analyse the performance of breadth first search (BFS) for several large graphs in the context of unified memory and identify the key factors that contribute to slowdowns. Next, we propose a lightweight offline graph reordering algorithm, HALO (Harmonic Locality Ordering), that can be used as a pre-processing step for static graphs. HALO yields speedups of 1.5x-1.9x over baseline in subsequent traversals. Our method specifically aims to cover large directed real world graphs in addition to undirected graphs whereas prior methods only account for the latter. Additionally, we demonstrate ties between the locality ordering problem and graph compression and show that prior methods from graph compression such as recursive graph bisection can be suitably adapted to this problem.

Gera, Prasun↗

DOE OSTI2019

Cumulative Spatial Impact Layers™

Cumulative Spatial Impact Layers™ (CSIL) is a GIS-based tool that summarizes spatio-temporal datasets based on overlapping features and attributes. Applying a recursive quadtree method and multiple additive frameworks, the CSIL tool allows users to analyze raster and vector datasets simultaneously by calculating data, record, or attribute density. The CSIL tool was designed based on the original approach (Bauer et al. 2015) and more information on the tool overall along with applications can be found in Romeo et al. 2019). Providing an efficient summary of disparate geospatial data, CSIL bridges the gap between understanding data and analysis. Bauer, J. R., Nelson, J., Romeo, L., Eynard, J., Sim, L., Halama, J., Rose, K., & Graham, J. (2015). A spatio-temporal approach to analyze broad risks and potential impacts associated with uncontrolled hydrocarbon release events in the offshore Gulf of Mexico (NETL-TRS-2-2015 EPAct Technical Report Series). U.S. Department of Energy, National Energy Technology Laboratory: Morgantown, WV; p 60. Romeo, L., Nelson, J., Wingo, P., Bauer, J., Justman, D., & Rose, K. (2019). Cumulative spatial impact layers: A novel multivariate spatio-temporal analytical summarization tool. Transactions in GIS.

Multivariate Visualization↗

DOE OSTI2021

Gravity loop integrands from the ultraviolet

We demonstrate that loop integrands of (super-)gravity scattering amplitudes possess surprising properties in the ultraviolet (UV) region. In particular, we study the scaling of multi-particle unitarity cuts for asymptotically large momenta and expose an improved UV behavior of four-dimensional cuts through seven loops as compared to standard expectations. For N=8 supergravity, we show that the improved large momentum scaling combined with the behavior of the integrand under BCFW deformations of external kinematics uniquely fixes the loop integrands in a number of non-trivial cases. In the integrand construction, all scaling conditions are homogeneous. Therefore, the only required information about the amplitude is its vanishing at particular points in momentum space. This homogeneous construction gives indirect evidence for a new geometric picture for graviton amplitudes similar to the one found for planar N=4 super Yang-Mills theory. We also show how the behavior at infinity is related to the scaling of tree-level amplitudes under certain multi-line chiral shifts which can be used to construct new recursion relations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Many-gluon tree amplitudes on modern GPUs: A case study for novel event generators

The compute efficiency of Monte-Carlo event generators for the Large Hadron Collider is expected to become a major bottleneck for simulations in the high-luminosity phase. Aiming at the development of a full-fledged generator for modern GPUs, we study the performance of various recursive strategies to compute multi-gluon tree-level amplitudes. We investigate the scaling of the algorithms on both CPU and GPU hardware. Finally, we provide practical recommendations as well as baseline implementations for the development of future simulation programs. The GPU implementations can be found at: https://www.gitlab.com/ebothmann/blockgen-archive.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Codebase release 1.0 for BlockGen

Bothmann, Enrico↗

DOE OSTI2023

A simple coin for a 2d entangled walk

We analyze the effect of a simple coin operator, built out of Bell pairs, in a 2d Discrete Quantum Random Walk (DQRW) problem. The specific form of the coin enables us to find analytical and closed form solutions to the recursion relations of the DQRW. The coin induces entanglement between the spin and position degrees of freedom, which oscillates with time and reaches a constant value asymptotically. We probe the entangling properties of the coin operator further, by two different measures. First, by integrating over the space of initial tensor product states, we determine the Entangling Power of the coin operator. Secondly, we compute the Generalized Relative Rényi Entropy between the corresponding density matrices for the entangled state and the initial pure unentangled state. Both the Entangling Power and Generalized Relative Rényi Entropy behaves similar to the entanglement with time. Finally, in the continuum limit, the specific coin operator reduces the 2d DQRW into two 1d massive fermions coupled to synthetic gauge fields, where both the mass term and the gauge fields are built out of the coin parameters.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Predicting initial trans-membrane pressure across cycles in the ultrafiltration process using random forest

With growing freshwater scarcity, direct potable reuse (DPR) systems that reclaim wastewater for drinking are becoming increasingly important for sustainable water supply. Reliable operation requires minimizing downtime in ultrafiltration (UF) units, where membrane fouling leads to elevated trans-membrane pressure (TMP). This study develops data-driven regression models based on random forest (RF) and autoregressive (AR) approaches to forecast the initial TMP at the start of each UF filtration cycle in a pilot-scale DPR system. The RF model consistently outperforms baseline methods, including historical mean, last observation carried forward, and AR models, across multiple forecast horizons, achieving the lowest root mean square error. To evaluate how different classes of process variables contribute to TMP dynamics over time, we examine the feature importance of independent input variables across multiple forecast horizons. This analysis provides insight into the temporal relevance of operational and sensor-derived features, guiding control and monitoring strategies. Additionally, the impact of hyperparameter tuning on TMP prediction performance is assessed for both direct and recursive RF modelling approaches. The proposed RF framework establishes a robust foundation for predictive monitoring and real-time optimization of UF operations, supporting sustainable and reliable water reuse.

direct potable reuse↗