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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Short Distance of Nuclei - Mining the Wealth of Existing Jefferson Lab Data - Final Report

Over the last fifteen years of operation, the Jefferson Lab CLAS Collaboration has performed many experiments using nuclear targets. Because the CLAS detector has a very large acceptance and because it used a very open (i.e., nonspecific) trigger, there is a vast amount of data on many different reaction channels yet to be analyzed. The goal of the Jefferson Lab Nuclear Data Mining grant was to (1) collect the data from nuclear target experiments using the CLAS detector, (2) collect the associated cuts and corrections used to analyze that data, (3) provide non-expert users with a software environment for easy analysis of the data, and (4) to search for interesting reaction signatures in the data. We formed the Jefferson Lab Nuclear Data Mining collaboration under the auspices of this grant. The collaboration successfully carried out all of our goals. Dr. Gavalian, the data mining scientist, created a remarkably user-friendly web-based interface to enable easy analysis of the nuclear-target data by non-experts. Data from many of the CLAS nuclear target experiments has been made available on servers at Old Dominion University. Many of the associated cuts and corrections have been incorporated into the data mining software. The data mining collaboration was extraordinarily successful in finding interesting reaction signatures in the data. Our paper Momentum sharing in imbalanced Fermi systems was published in Science. Several analyses of CLAS data are continuing and will result in papers after the end of the grant period. We have held several analysis workshops and have given many invited talks at international conferences and workshops related to the data mining initiative. Our initiative to maximize the impact of data collected with CLAS in the 6-GeV era was very successful. During the hiatus between the end of 6-GeV experiments and the beginning of 12-GeV experiments, our collaboration and the physics community at large benefited tremendously from the Jefferson Lab Nuclear Data Mining effort.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Network Anomaly Detection Using Federated Learning

The internet is turning out to be an integral part of every-one's lives as more and more devices are being connected to serve societal needs. Our work is motivated by two ma-jor observations. Firstly, one drawback of connecting to the network is the threat of network attacks that can compromise users' private information, leading to data loss and adversely affecting productivity. There are several traditional security mechanisms to defend against these attacks, such as firewalls, virtual private networks (VPNs), demilitarized zones (DMZs), and vulnerability scanners. One way to prevent these attacks is early detection and prevention. However, these kinds of architecture do not scale very well because of their centralized nature. Secondly, we observe from heuristics and data set distributions that the majority of the requests made to a server are innocuous. Therefore, almost all server request data sets are highly imbalanced, weighted highly towards the harmless requests.

Marfo, William↗
DOE OSTI2026

HydraGNN_Predictive_GFM_2026 - Ensemble of predictive graph foundation models for atomistic materials modeling

This release contains data and parameters of HydraGNN-based graph foundation models trained as a result of the work published in the pre-print "Exascale Multi-Task Graph Foundation Models for Imbalanced, Multi-Fidelity Atomistic Data" by M. Lupo Pasini et al. (https://arxiv.org/abs/2604.15380). We jointly train on 16 open first-principles datasets (544+ million structures covering 85+ elements) using a multi-task architecture with per-dataset heads and a scalable ADIOS2/DDStore data pipeline. On Frontier, we execute six large-scale DeepHyper hyperparameter optimization campaigns in FP64 and promote the top-performing message-passing models to sustained 2,048-node training, yielding a PaiNN-based lead model. The version of HydraGNN used to generate the outputs provided in this release is HydraGNN v5.0 (https://github.com/ORNL/HydraGNN/releases/tag/v5.0) The list of datasets used for the training of the graph foundation model is the following: 1) Alexandria [1] 2) ANI1x [2] 3) MPTrj [3] 4) Open Catalyst 2020 (OC20) [4] 5) Open Catalyst 2022 (OC22) [5] 6) Open Catalyst 2025 (OC25) [6] 7) Open Direct ir Capture 2023 (ODAC23) [7] 8) Open Materials 2024 (OMat24) [8] 9) Open Molecules 2025 (OMol25) [9] 10) OMol25-neutral (subset of OMol25 that contains only molecules with zero total charge) 11) OMol25-non-neutral (subset of OMol25 that contains only molecules with non-zero total charge) 12) Open Polymers 2026 (OPoly2026) [10] 13) Nabla2DFT [11] 14) QCML [12] 15) QM7X [reference 13] 16) transition1x [14] Dataset references: [1] J. Schmidt et al., “A dataset of 175k stable and metastable materials calculated with the PBEsol and SCAN functionals,” Scientific Data, vol. 9, p. 64, 2022. [2] J. S. Smith et al., “The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules,” Scientific Data, vol. 7, p. 134, 2020. [Online]. Available: https: //www.nature.com/articles/s41597-020-0473-z [3] A. Jain et al., “Commentary: The Materials Project: A materials genome approach to accelerating materials innovation,” APL Materials, vol. 1, no. 1, p. 011002, 07 2013. [Online]. Available: https://doi.org/10.1063/1.4812323 [4] L. Chanussot et al., “Open catalyst 2020 (oc20) dataset and community challenges,” ACS Catalysis, vol. 11, no. 10, pp. 6059–6072, 2021. [Online]. Available: https://doi.org/10.1021/acscatal.0c04525 [5] K. Tran et al., “Open catalyst 2022 (oc22) dataset and challenges for oxidation electrocatalysts,” ACS Catalysis, vol. 13, no. 5, pp. 3066–3084, 2023. [Online]. Available: https://doi.org/10.1021/acscatal.2c05426 [6] S. J. Sahoo et al., “The open catalyst 2025 (oc25) dataset and models for solid-liquid interfaces,” arXiv preprint arXiv:2509.17862, 2025. [Online]. Available: https://arxiv.org/abs/2509.17862 [7] A. Sriram et al., “The open DAC 2023 dataset and challenges for sorbent discovery in direct air capture,” ACS Central Science, vol. 10, no. 5, pp. 923–941, 2024. [8] L. Barroso-Luque et al., “Open materials 2024 (omat24) inorganic materials dataset and models,” 2024. [Online]. Available: https://arxiv.org/abs/2410.12771 [9] D. S. Levine et al., “The open molecules 2025 (OMol25) dataset, evaluations, and models,” 2025. [Online]. Available: https://arxiv.org/abs/2505.08762 [10] D. S. Levine et al., The open polymers 2026 (OPoly26) dataset and evaluations,” arXiv preprint arXiv:2512.23117, 2025. [Online]. Available: https://arxiv.org/abs/2512.23117 [11] K. Khrabrov et al., “Nabla2dft: A universal quantum chemistry dataset of drug-like molecules and a benchmark for neural network potentials,” in NeurIPS 2024 Datasets and Benchmarks Track, 2024. [Online]. Available: https://openreview.net/forum?id=ElUrNM9U8c [12] S. Ganscha et al., “The QCML dataset, quantum chemistry reference data from 33.5M DFT and 14.7B semi-empirical calculations,” Scientific Data, vol. 12, p. 406, 2025. [13] J. Hoja et al., “QM7-X, a comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules,” Scientific Data, vol. 8, p. 43, 2021. [Online]. Available: https://www.nature.com/articles/s41597-021-00812-2 [14] M. Schreiner et al., “Transition1x - a dataset for building generalizable reactive machine learning potentials,” Scientific Data, vol. 9, p. 779, 2022. The folder "datasets_ADIOS2_format" contains the set of pre-processed datasets in Adaptable I/O System (ADIOS) format (https://www.exascaleproject.org/research-project/adios/) that have been used for the development and training of GFMs in this work. The "datasets_ADIOS2_format" directory contains 2 sub-directories, one for the version "v1" of the datasets and one for the version "v2" of the datasets. The version "v1" of the datasets provides values of the total energy as they are extracted from the original data as it was released by the respective institutions. The version "v2" of the datasets provides values of the energy that have been realigned. The realignment was performed by training a linear regression model that predicts the total energy as a function of the chemical composition of the atomistic structure, and then subtract such prediction from the original value of the total energy. Both folders "v1" and "v2" contain 16 sub-directories, each corresponding to an ADIOS2-formatted dataset The folder "DeepHyper-results" contains the configurational files and model's parameters for all the 186 HPO trials that were successfully completed by the scalable hyperparameter optimization (HPO) runs on Frontier. The content of the folder "DeepHyper-results" I structured as follows: 1) task-list.txt: list of mpnn name, jobid, and deephyper task id 2) gfm_${MPNN}_${JOBID}_0.${TASKID}: run directory with checkpoint files 3) gfm_${MPNN}: deephyper summary directory (*.csv) for each specific MPNN type 4) deephyper-experiment-${JOBID}: output and error logs for each job The file "deephyper-sorted.csv" contains the details of each HydraGNN model built and tested by HPO, obtained by merging the (*.csv) filed from each HPO run executed. Out of all the HPO trials, we selected 10 to continue the training of the respective HydraGNN models. Due to limited computational budget available in the LRN070 allocation we could not complete the training till convergence for all these 10 selected models. The folder "models" contains multiple sub-folders, one per each HydraGNN model trained. Each model sub-folder contains the parameters of each HydraGNN model, with multiple checkpoint-restarts. The list of sub-folders are as follows: 1) multidataset_hpo-BEST1-fp64 2) multidataset_hpo-BEST2-fp64 3) multidataset_hpo-BEST3-fp64 4) multidataset_hpo-BEST4-fp64 5) multidataset_hpo-BEST5-fp64 6) multidataset_hpo-BEST6-fp64 7) multidataset_hpo-BEST7-fp64 8) multidataset_hpo-BEST8-fp64 9) multidataset_hpo-BEST9-fp64 10) multidataset_hpo-BEST10-fp64 Within each one of these folders, additional auxiliary log files are provided with descriptions about how the training proceeded. The lead PaiNN-model is contained inside "multidataset_hpo-BEST6-fp64". The file "mlp_branch_weights" contains the parameters of the multi-layer perceptron (MLP) used to reconcile the predictions of the 16 output decoding heads of the HydragNN architectures. The MLP takes in input the chemical composition of the atomistic structure and predicts averaging weights to linearly mix the predictions of each output decoding head toward consolidating them into a single one. The folder "1.1billion-structure-inference" contains 1.1 billion atomistic structures randomly generated. Each structures is associated with energy and forces predicted with the lead-PaiNN model combined with the MLP model for reconciliation of the multi-branch predictions generated by the 16 output decoding heads. The folder "1.1billion-structure-inference" contains 9,300 (*.tar.gz) subdirectories, one per Frontier compute node used to execute the inference at exascale. Once uncompressed, each (*.tar.gz) subdirectory contains an ADIOS2 (*.bp) file container, where each atomistic structure is stored as a PyTorch-Geometric Data object. The file "export_dataset_environment_variables.sh" contains the environment variables that need to be set before running the HydraGNN code to reproduce the results provided in this dataset release. The code that can be used to load the ADIOS2 files, load HydraGNN models, and run inference is available at: https://github.com/ORNL/HydraGNN/releases/tag/v5.0

36 MATERIALS SCIENCE↗
DOE OSTI2018

Wildfire Mapping in Interior Alaska Using Deep Neural Networks on Imbalanced Datasets

Wildfires are the dominant disturbance impacting many regions in Alaska and is expected to intensify due to climate change. Accurate tracking and quantification of wildfires are important for climate modeling and ecological studies in this region. Remote sensing platforms (e.g., MODIS, Landsat) are an important tool for mapping wildfires in Alaska at varying spatial and temporal scales. Deep neural networks (DNN) have shown superior performance in many classification problems such as high-dimensional remote sensing data. Detection of wildfires is an imbalanced classification problem where one class contains a much smaller or larger sample size and DNNs performance can decline. We take a known weight-selection strategy during DNN training and apply them to MODIS variables (e.g., NDVI, surface reflectance) for a binary classification (i.e., wildfire or no-wildfire) across Alaska during the 2004 wildfire year, which is one of the largest on record. The method splits the input training data into sets, one for training the DNN to update weights and the other that splits into a validation set that is equally balanced between the wildfire and no-wildfire class. The performance is monitored on the validation set to select the weights based on the best validation-loss score. This approach was applied to two sampled datasets, such as where the no-wildfire class can significantly outweigh the wildfire class. The normal DNN training strategy was unable to map wildfires for the highly imbalanced dataset, however, the weight-selection strategy was able to map wildfires very accurately (0.96 recall score for 78,702 wildfire pixels (500×500 m)).

Langford, Zach↗
DOE OSTI2022

Training a Quantum Annealing Based Restricted Boltzmann Machine on Cybersecurity Data

A restricted Boltzmann machine (RBM) is a generative model that could be used in effectively balancing a cybersecurity dataset because the synthetic data a RBM generates follows the probability distribution of the training data. RBM training can be performed using contrastive divergence (CD) and quantum annealing (QA). QA-based RBM training is fundamentally different from CD and requires samples from a quantum computer. We present a real-world application that uses a quantum computer. Specifically, we train a RBM using QA for cybersecurity applications. The D-Wave 2000Q has been used to implement QA. RBMs are trained on the ISCX data, which is a benchmark dataset for cybersecurity. For comparison, RBMs are also trained using CD. CD is a commonly used method for RBM training. Our analysis of the ISCX data shows that the dataset is imbalanced. We present two different schemes to balance the training dataset before feeding it to a classifier. The first scheme is based on the undersampling of benign instances. The imbalanced training dataset is divided into five sub-datasets that are trained separately. A majority voting is then performed to get the result. Our results show the majority vote increases the classification accuracy up from 90.24% to 95.68%, in the case of CD. For the case of QA, the classification accuracy increases from 74.14% to 80.04%. In the second scheme, a RBM is used to generate synthetic data to balance the training dataset. We show that both QA and CD-trained RBM can be used to generate useful synthetic data. Balanced training data is used to evaluate several classifiers. Among the classifiers investigated, K-Nearest Neighbor (KNN) and Neural Network (NN) perform better than other classifiers. They both show an accuracy of 93%. Our results show a proof-of-concept that a QA-based RBM can be trained on a 64-bit binary dataset. The illustrative example suggests the possibility to migrate many practical classification problems to QA-based techniques. Further, we show that synthetic data generated from a RBM can be used to balance the original dataset.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Tree, Shrub, and Grass Classification Using Only RGB Images

In this work, a semantic segmentation-based deep learning method, DeepLabV3+, is applied to classify three vegetation land covers, which are tree, shrub, and grass using only three band color (RGB) images. DeepLabV3+’s detection performance has been studied on low and high resolution datasets that both contain tree, shrub, and grass and some other land cover types. The two datasets are heavily imbalanced where shrub pixels are much fewer than tree and grass pixels. A simple weighting strategy known as median frequency weighting was incorporated into DeepLabV3+ to mitigate the data imbalance issue, which originally used uniform weights. The tree, shrub, grass classification performances are compared when all land cover types are included in the classification and also when classification is limited to the three vegetation classes with both uniform and median frequency weights. Among the three vegetation types, shrub is found to be the most challenging one to classify correctly whereas correct classification accuracy was highest for tree. It is observed that even though the median frequency weighting did not improve the overall accuracy, it resulted in better classification accuracy for the underrepresented classes such as shrub in our case and it also significantly increased the average class accuracy. The classification performance and computation time comparison of DeepLabV3+ with two other pixel-based classification methods on sampled pixels of the three vegetation classes showed that DeepLabV3+ achieves significantly higher accuracy than these methods with a trade-off for longer model training time.

58 GEOSCIENCES↗
DOE OSTI2025

Design Choices in Anomaly Detection for Industrial Control Systems: Insights from Gas Pipeline Data

Industrial control systems (ICS) remain vulnerable to increasingly sophisticated cyberattacks, yet evaluating anomaly detection models in these environments is challenging due to temporal dependencies, missing-not-at-random patterns, and extremely imbalanced datasets. These factors make common practices—especially random data splits and naïve imputation—prone to severe temporal leakage, which can inflate reported performance and obscure real-world limitations. In this work, we systematically examine classical machine learning models, temporal deep learning architecture, and tensor-decomposition–based methods on a gas-pipeline dataset using a fully temporally separated evaluation pipeline designed to mimic realistic deployment conditions. Our findings show that proper temporal handling and MNAR-aware preprocessing significantly alter the relative performance of popular anomaly-detection methods, providing practical guidance for designing reliable, leakage-resistant ICS intrusion-detection systems.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2017

Zoledronate Prevents Simulated Weightlessness-Induced Bone Loss in the Cancellous Compartment While Blunting the Efficacy of a Mechanical Loading Countermeasure

Astronauts using high-force resistance training while weightless show a high-turnover remodeling state within the skeletal system, with resorption and formation biomarkers being elevated. One countermeasure for the skeletal health of astronauts includes an antiresorptive of the bisphosphonate (BP) drug class. We asked, does the combination of an anti-resorptive and high-force exercise during weightlessness have negative effects on bone remodeling and strength? In this study, we developed an integrated model to mimic the mechanical strain of exercise via cyclical loading (CL) in mice treated with the BP Zoledronate (ZOL) combined with hind limb unloading (HU) to simulate weightlessness. We hypothesized that ZOL prevents structural degradation from simulated weightlessness and that CL and ZOL interact to render CL less effective. Thirty-two C57BL/6 mice (male, 16 weeks old, n=8/group) were exposed to 3 weeks of either HU or normal ambulation (NA). Cohorts of mice received one subcutaneous injection of ZOL (45μg/kg), or saline vehicle (VEH), prior to the start of HU. The right tibia was axially compressed in vivo 60x/day to 9N (+1200μstrain on the periosteal surface) and repeated 3x/week during HU. Left tibiae served as a within subject, non-compressed control. Ex vivo μCT was performed on all subjects to determine cancellous and cortical architectural parameters. Static and dynamic histomorphometry were carried out for the left and right tibiae to determine osteoclast- and osteoblast relevant surfaces. Further, micro damage was assessed in select groups by basic-fuchsin staining to test whether CL had an effect. For all assays, a multivariate (2x2x2) ANCOVA model was used to account for body weight changes. Additionally, for the tibiae, we incorporated a random effect for the subject (hence, a mixed model) to account for observations of both left and right tibiae within each subject. P < 0.05 was considered significant. In the cancellous compartment of the proximal tibial metaphysis, we observed a main effect from each independent variable, as determined by structural and histomorphometric assays. Specifically, as expected, ZOL showed an increase in the cancellous bone volume to total volume fraction (BV/TV, +32%) and trabecular number (+18%) compared to the VEH. As expected, ZOL decreased osteoclast surface (OC/BS) by -45% compared to VEH. Surprisingly, ZOL reduced mineralizing surface (MS/BS) and bone formation rate (BFR), indicators of osteoblast activity, by -40% and -54%, respectively, compared to VEH. Altogether, ZOL-treated mice displayed a low turnover state of remodeling in the metaphysis. In the context of skeletal aging, we speculate that ZOL prevented age-related cancellous strut loss during the experiment. As a main effect, as expected, HU decreased BV/TV by - 31% via reductions in both trabecular thickness (-11%) and number (-22%) compared to NA controls. Additionally, HU decreased MS/BS by -38% and bone formation rate (BFR) by -50% compared to NA controls. Altogether, these data are consistent with structural degradation resulting from imbalanced remodeling that favors resorption. As a main effect, CL increased BV/TV by +15% via increased trabecular thickness (+12%) compared to the noncompressed limb. As expected, CL increased MS/BS (+20%) and BFR (+24%), indicating osteoblast mineralization contributed to bone gains. These data show that CL provided an anabolic stimulus to the cancellous tissue. We observed unique interactions in ZOL*CL and HU*CL. First, ZOL prevented CL-induced increases in BV/TV and trabecular number, as compared to VEH. In the context of skeletal aging, these data suggest no added benefit from CL in the ZOL-treated mice. Interestingly, no microdamage was observed in mice that were unloaded and treated with ZOL (independent of CL). Secondly, HU prevented CL-induced increases in BFR, as compared to NA controls. These data suggest that either exercise is less effective or the kinetics of formation are slower during simulated weightlessness. Osteoclast surface was unchanged by either treatment. Thus, in contrast to exercising astronauts, these data do not suggest a high-turnover state in the metaphysis. To assess mechanical properties as a function of HU or ZOL, we tested the left femur in three-point bending ex vivo. As expected, HU decreased stiffness (-30%) compared to NA, and ZOL increased stiffness compared to VEH (+28%). Interestingly, HU increased the post-yield displacement, related to collagenous tensile loading, compared to NA (+20%). ZOL increased yield force (+11%) and ultimate force (+17%), which seems to explain the significant effect of ZOL increasing total energy (work-to-fracture, +15%), while not affecting the post yield displacement. Taken together, ZOL did not have detrimental affect on mechanical properties. Our integrated model simulates the combination of weightlessness, exercise-induced mechanical strain, and anti-resorptive treatment that astronauts experience during space missions. We conclude that Zoledronate was an effective countermeasure against weightlessness-induced bone loss, though zoledronate, as well as weightlessness, rendered exercise-related mechanical loading less effective.

bone↗
DOE OSTI2025

HydraGNN v4.0

The new version of HydraGNN v4.0 provides additional core capabilities, such as: Inclusion of multi-body atomistic cluster expansion MACE, polarizable atom interaction neural network PAINN, and equivariant principal neighborhood aggregation (PNAEq) among the message passing layers supported -Inclusion of graph transformers to directly model long-range interactions between nodes that are distant in the graph topology Integration of graph transformers with message passing layers by combining the graph embedding generated by the two mechanisms, which allows for an improved expressivity of the HydraGNN architecture Improved re-implementation of multi-task learning (MTL) to allow its use for stabilized training across imbalanced, multi-source, multi-fidelity data Introduction of multi-task parallelism, a newly proposed type of model parallelism specifically for MTL architectures, which allows to dispatch different output decoding heads to different GPU devices Integration of multi-task parallelism with pre-existing distributed data parallelism to enable a 2D parallelization for distributed training Improved portability of the distributed training across Intel GPUs, which has been testes on ALCF exascale supercomputer Aurora Inclusion of 2-level fine-grained energy profilers portable across NVIDIA, AMD, and Intel GPUs to monitor the power and energy consumption associated with different functions executed by the HydraGNN code during data pre-load and training Restructuring of previous examples and inclusion of new sets of examples to illustrate the download, preprocess, and training of HydraGNN models on new large-scale open-source datasets for atomistic materials modeling (e.g., Alexandria, Transition1x, OMat24, OMol25)

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗
DOE OSTI2023

FPGA Acceleration of GCN in Light of the Symmetry of Graph Adjacency Matrix

Graph Convolutional Neural Networks (GCNs) are widely used to process large-scale graph data. Different from deep neural networks (DNNs), GCNs are sparse, irregular, and unstructured, posing unique challenges to hardware acceleration with regular processing elements (PEs). In particular, the adjacency matrix of a GCN is extremely sparse, leading to frequent but irregular memory access, low spatial/temporal data locality and poor data reuse. Furthermore, a realistic graph usually consists of unstructured data (e.g., unbalanced distributions), creating significantly different processing times and imbalanced workload for each node in GCN acceleration. To overcome these challenges, we propose an end-to-end hardware-software co-design to accelerate GCNs on resource-constrained FPGAs with the features including: (1) A custom dataflow that leverages symmetry along the diagonal of the adjacency matrix to accelerate feature aggregation for undirected graphs. We utilize either the upper or the lower triangular matrix of the adjacency matrix to perform aggregation in GCN to improve data reuse. (2) Unified compute cores for both aggregation and transform phases, with full support to the symmetry-based dataflow. These cores can be dynamically reconfigured to the systolic mode for transformation or as individual accumulators for aggregation in GCN processing. (3) Preprocessing of the graph in software to rearrange the edges and features to match the custom dataflow. This step improves the regularity in memory access and data reuse in the aggregation phase. Moreover, we quantize the GCN precision from FP32 to INT8 to reduce the memory footprint without losing the inference accuracy. We implement our accelerator design in Intel Stratix10 MX FPGA board with HBM2, and demonstrate 1.3x-110.5x improvement in end-to-end GCN latency as compared to the state-of the-art FPGA implementations, on the graph datasets of Cora, Pubmed, Citeseer and Reddit.

Nair, Gopikrishnan R.↗
DOE OSTI2026

The Impact of Time-Aware Design Choices in ICS Anomaly Detection

Industrial control systems (ICS) remain vulnerable to increasingly sophisticated cyberattacks, yet evaluating anomaly detection models in these environments is challenging due to temporal dependencies, missing-not-at-random patterns, and extremely imbalanced datasets. These factors make common practices—especially random data splits and na¨ıve imputation— prone to severe temporal leakage, which can inflate reported performance and obscure real-world limitations. In this work, we systematically examine classical machine learning models, temporal deep learning architecture, and tensordecomposition– based methods on a gas-pipeline dataset using a fully temporally separated evaluation pipeline designed to mimic realistic deployment conditions. Our findings show that proper temporal handling and MNAR-aware preprocessing significantly alter the relative performance of popular anomaly-detection methods, providing practical guidance for designing reliable, leakage-resistant ICS intrusion-detection systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Results of the Photometric LSST Astronomical Time-series Classification Challenge (PLAsTiCC)

Abstract Next-generation surveys like the Legacy Survey of Space and Time (LSST) on the Vera C. Rubin Observatory (Rubin) will generate orders of magnitude more discoveries of transients and variable stars than previous surveys. To prepare for this data deluge, we developed the Photometric LSST Astronomical Time-series Classification Challenge (PLAsTiCC), a competition that aimed to catalyze the development of robust classifiers under LSST-like conditions of a nonrepresentative training set for a large photometric test set of imbalanced classes. Over 1000 teams participated in PLAsTiCC, which was hosted in the Kaggle data science competition platform between 2018 September 28 and 2018 December 17, ultimately identifying three winners in 2019 February. Participants produced classifiers employing a diverse set of machine-learning techniques including hybrid combinations and ensemble averages of a range of approaches, among them boosted decision trees, neural networks, and multilayer perceptrons. The strong performance of the top three classifiers on Type Ia supernovae and kilonovae represent a major improvement over the current state of the art within astronomy. This paper summarizes the most promising methods and evaluates their results in detail, highlighting future directions both for classifier development and simulation needs for a next-generation PLAsTiCC data set.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Predictive Big Data Analytics: A Study of Parkinson’s Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations

Background A unique archive of Big Data on Parkinson’s Disease is collected, managed and disseminated by the Parkinson’s Progression Markers Initiative (PPMI). The integration of such complex and heterogeneous Big Data from multiple sources offers unparalleled opportunities to study the early stages of prevalent neurodegenerative processes, track their progression and quickly identify the efficacies of alternative treatments. Many previous human and animal studies have examined the relationship of Parkinson’s disease (PD) risk to trauma, genetics, environment, co-morbidities, or life style. The defining characteristics of Big Data–large size, incongruency, incompleteness, complexity, multiplicity of scales, and heterogeneity of information-generating sources–all pose challenges to the classical techniques for data management, processing, visualization and interpretation. We propose, implement, test and validate complementary model-based and model-free approaches for PD classification and prediction. To explore PD risk using Big Data methodology, we jointly processed complex PPMI imaging, genetics, clinical and demographic data. Methods and Findings Collective representation of the multi-source data facilitates the aggregation and harmonization of complex data elements. This enables joint modeling of the complete data, leading to the development of Big Data analytics, predictive synthesis, and statistical validation. Using heterogeneous PPMI data, we developed a comprehensive protocol for end-to-end data characterization, manipulation, processing, cleaning, analysis and validation. Specifically, we (i) introduce methods for rebalancing imbalanced cohorts, (ii) utilize a wide spectrum of classification methods to generate consistent and powerful phenotypic predictions, and (iii) generate reproducible machine-learning based classification that enables the reporting of model parameters and diagnostic forecasting based on new data. We evaluated several complementary model-based predictive approaches, which failed to generate accurate and reliable diagnostic predictions. However, the results of several machine-learning based classification methods indicated significant power to predict Parkinson’s disease in the PPMI subjects (consistent accuracy, sensitivity, and specificity exceeding 96%, confirmed using statistical n-fold cross-validation). Clinical (e.g., Unified Parkinson's Disease Rating Scale (UPDRS) scores), demographic (e.g., age), genetics (e.g., rs34637584, chr12), and derived neuroimaging biomarker (e.g., cerebellum shape index) data all contributed to the predictive analytics and diagnostic forecasting. Conclusions Model-free Big Data machine learning-based classification methods (e.g., adaptive boosting, support vector machines) can outperform model-based techniques in terms of predictive precision and reliability (e.g., forecasting patient diagnosis). We observed that statistical rebalancing of cohort sizes yields better discrimination of group differences, specifically for predictive analytics based on heterogeneous and incomplete PPMI data. UPDRS scores play a critical role in predicting diagnosis, which is expected based on the clinical definition of Parkinson’s disease. Even without longitudinal UPDRS data, however, the accuracy of model-free machine learning based classification is over 80%. The methods, software and protocols developed here are openly shared and can be employed to study other neurodegenerative disorders (e.g., Alzheimer’s, Huntington’s, amyotrophic lateral sclerosis), as well as for other predictive Big Data analytics applications.

Science & Technology - Other Topics↗
DOE OSTI2020

Structure–activity relationship-based chemical classification of highly imbalanced Tox21 datasets

Abstract The specificity of toxicant-target biomolecule interactions lends to the very imbalanced nature of many toxicity datasets, causing poor performance in Structure–Activity Relationship (SAR)-based chemical classification. Undersampling and oversampling are representative techniques for handling such an imbalance challenge. However, removing inactive chemical compound instances from the majority class using an undersampling technique can result in information loss, whereas increasing active toxicant instances in the minority class by interpolation tends to introduce artificial minority instances that often cross into the majority class space, giving rise to class overlapping and a higher false prediction rate. In this study, in order to improve the prediction accuracy of imbalanced learning, we employed SMOTEENN, a combination of Synthetic Minority Over-sampling Technique (SMOTE) and Edited Nearest Neighbor (ENN) algorithms, to oversample the minority class by creating synthetic samples, followed by cleaning the mislabeled instances. We chose the highly imbalanced Tox21 dataset, which consisted of 12 in vitro bioassays for > 10,000 chemicals that were distributed unevenly between binary classes. With Random Forest (RF) as the base classifier and bagging as the ensemble strategy, we applied four hybrid learning methods, i.e., RF without imbalance handling (RF), RF with Random Undersampling (RUS), RF with SMOTE (SMO), and RF with SMOTEENN (SMN). The performance of the four learning methods was compared using nine evaluation metrics, among which F 1 score, Matthews correlation coefficient and Brier score provided a more consistent assessment of the overall performance across the 12 datasets. The Friedman’s aligned ranks test and the subsequent Bergmann-Hommel post hoc test showed that SMN significantly outperformed the other three methods. We also found that a strong negative correlation existed between the prediction accuracy and the imbalance ratio (IR), which is defined as the number of inactive compounds divided by the number of active compounds. SMN became less effective when IR exceeded a certain threshold (e.g., > 28). The ability to separate the few active compounds from the vast amounts of inactive ones is of great importance in computational toxicology. This work demonstrates that the performance of SAR-based, imbalanced chemical toxicity classification can be significantly improved through the use of data rebalancing.

Idakwo, Gabriel↗
DOE OSTI2022

TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks

Background: With cancer as one of the leading causes of death worldwide, accurate primary tumor type prediction is critical in identifying genetic factors that can inhibit or slow tumor progression. There have been efforts to categorize primary tumor types with gene expression data using machine learning, and more recently with deep learning, in the last several years. Methods In this paper, we developed four 1-dimensional (1D) Convolutional Neural Network (CNN) models to classify RNA-seq count data as one of 17 highly represented primary tumor types or 32 primary tumor types regardless of imbalanced representation. Additionally, we adapted the models to take as input either all Ensembl genes (60,483) or protein coding genes only (19,758). Unlike previous work, we avoided selection bias by not filtering genes based on expression values. RNA-seq count data expressed as FPKM-UQ of 9,025 and 10,940 samples from The Cancer Genome Atlas (TCGA) were downloaded from the Genomic Data Commons (GDC) corresponding to 17 and 32 primary tumor types respectively for training and validating the models. Results: All 4 1D-CNN models had an overall accuracy of 94.7% to 97.6% on the test dataset. Further evaluation indicates that the models with protein coding genes only as features performed with better accuracy compared to the models with all Ensembl genes for both 17 and 32 primary tumor types. For all models, the accuracy by primary tumor type was above 80% for most primary tumor types. Conclusions: We packaged all 4 models as a Python-based deep learning classification tool called TULIP (TUmor CLassIfication Predictor) for performing quality control on primary tumor samples and characterizing cancer samples of unknown tumor type. Further optimization of the models is needed to improve the accuracy of certain primary tumor types.

Jones, Sara↗
DOE OSTI2018

Filter pruning of Convolutional Neural Networks for text classification: A case study of cancer pathology report comprehension

Convolutional Neural Networks (CNN) have recently demonstrated effective performance in many Natural Language Processing tasks. In this study, we explore a novel approach for pruning a CNN's convolution filters using our new data-driven utility score. We have applied this technique to an information extraction task of classifying a dataset of cancer pathology reports by cancer type, a highly imbalanced dataset. Compared to standard CNN training, our new algorithm resulted in a nearly .07 increase in the micro-averaged F1-score and a strong .22 increase in the macro-averaged F1-score using a model with nearly a third fewer network weights. We show how directly utilizing a network's interpretation of data can result in strong performance gains, particularly with severely imbalanced datasets.

Yoon, Hong-Jun↗
DOE OSTI2022

EE-SMOTE: An oversampling method in conjunction with information entropy for imbalanced learning

Imbalanced learning attracts great attention in various research fields. Existing literature-reported methodologies in imbalanced learning have shown drawbacks including over-generation or noisy/wrong samples generations. This paper presents EE-SMOTE, an oversampling technique based on information entropy, to support the imbalance classifications. Specifically, we propose a metric, Eigen-Entropy (EE), to identify homogenous samples from minority classes for oversampling technique, specifically, SMOTE to reach data balances for classification. Experiments on public dataset and real-world datasets demonstrate the efficacy and effectiveness of the proposed EE-SMOTE in imbalanced learning.

Huang, Jiajing↗
DOE OSTI2021

Asynchronous and Load-Balanced Union-Find for Distributed and Parallel Scientific Data Visualization and Analysis

We present a novel distributed union-find algorithm that features asynchronous parallelism and k-d tree based load balancing for scalable visualization and analysis of scientific data. Applications of union-find include level set extraction and critical point tracking, but distributed union-find can suffer from high synchronization costs and imbalanced workloads across parallel processes. In this study, we prove that global synchronizations in existing distributed union-find can be eliminated without changing final results, allowing overlapped communications and computations for scalable processing. We also use a k-d tree decomposition to redistribute inputs, in order to improve workload balancing. We benchmark the scalability of our algorithm with up to 1,024 processes using both synthetic and application data. Here, we demonstrate the use of our algorithm in critical point tracking and super-level set extraction with high-speed imaging experiments and fusion plasma simulations, respectively.

97 MATHEMATICS AND COMPUTING↗