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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Metric DBSCAN

SAND2025-11725O Metric DBSCAN is an implementation of the popular DBSCAN clustering algorithm that works in general metric spaces. DBSCAN is a clustering algorithm, a fundamental building block in machine learning. It takes a set of objects and, given some notion of distance, identifies coherent groups of objects. With Metric DBSCAN, users can provide an arbitrary function to compute distance. Nearly all existing implementations of DBSCAN restrict distance to one of a few formulations. Metric DBScan accomplishes this cleanly and efficiently. The Python source code is on Github. 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.

Dalbey, Keith↗
DOE OSTI2021

Significant DBSCAN+: Statistically Robust Density-based Clustering

Cluster detection is important and widely used in a variety of applications, including public health, public safety, transportation, and so on. Given a collection of data points, we aim to detect density-connected spatial clusters with varying geometric shapes and densities, under the constraint that the clusters are statistically significant. The problem is challenging, because many societal applications and domain science studies have low tolerance for spurious results, and clusters may have arbitrary shapes and varying densities. As a classical topic in data mining and learning, a myriad of techniques have been developed to detect clusters with both varying shapes and densities (e.g., density-based, hierarchical, spectral, or deep clustering methods). However, the vast majority of these techniques do not consider statistical rigor and are susceptible to detecting spurious clusters formed as a result of natural randomness. On the other hand, scan statistic approaches explicitly control the rate of spurious results, but they typically assume a single “hotspot” of over-density and many rely on further assumptions such as a tessellated input space. To unite the strengths of both lines of work, we propose a statistically robust formulation of a multi-scale DBSCAN, namely Significant DBSCAN+, to identify significant clusters that are density connected. As we will show, incorporation of statistical rigor is a powerful mechanism that allows the new Significant DBSCAN+ to outperform state-of-the-art clustering techniques in various scenarios. We also propose computational enhancements to speed-up the proposed approach. Experiment results show that Significant DBSCAN+ can simultaneously improve the success rate of true cluster detection (e.g., 10–20% increases in absolute F1 scores) and substantially reduce the rate of spurious results (e.g., from thousands/hundreds of spurious detections to none or just a few across 100 datasets), and the acceleration methods can improve the efficiency for both clustered and non-clustered data.

Computer Science↗
DOE OSTI2023

Fast tree-based algorithms for DBSCAN for low-dimensional data on GPUs

DBSCAN is a well-known density-based clustering algorithm to discover arbitrary shape clusters. While conceptually simple in serial, the algorithm is challenging to efficiently parallelize on manycore GPU architectures. Common pitfalls, such as asynchronous range query calls, result in high thread execution divergence in many implementations. In this paper, we propose a new framework for GPU-accelerated DBSCAN, and describe two tree-based algorithms within that framework. Both algorithms fuse the search for neighbors with updating cluster information, but differ in their treatment of dense regions of the data. We show that the time taken to compute clusters is at most twice that of determination of the neighbors. We compare the proposed algorithms with existing CPU and GPU implementations, and demonstrate their competitiveness and performance using a fast traversal structure (bounding volume hierarchy) for low dimensional data. We also show that the memory usage can be reduced by processing object neighbors dynamically without storing them.

Prokopenko, Andrey↗
DOE OSTI2026

Geographic_Distribution_of_Populus_trichocarpa_Genotypes_by_DBSCAN_Cluster

Aninteractive mapshowingPopulus trichocarpaGWAS sub-population structure identified by DBSCAN clustering, which were derived from a UMAP projection of the top 8 PCs of LD-pruned pangenome SNP data. Geographic origins are searchable by genotype or river system using the search bar.

09 BIOMASS FUELS↗
DOE OSTI2022

Differentially Private DBSCAN

SAND2022-15185 O Differentially Private DBSCAN is a differential private clustering algorithm used for running experiments and conducting data analysis. 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.

Smith, MichaelReed↗
DOE OSTI2026

Machine Learning–Based Condition Monitoring of a Circulating Water System of a Canadian Nuclear Plant

With the need to maintain long-term reliable energy using nuclear power plants, there is an underlying demand to ensure that the maintenance of plant components and systems is also done in an efficient and cost-effective manner. One way to achieve this is by moving from time-based maintenance to condition-based maintenance. The research presented in this paper focuses on applying statistical and machine-learning-based methods to capture anomalies within data for fault detection to further develop into condition monitoring. This paper focuses on system data for a circulating water system (CWS) of a pressurized heavy-water reactor for detecting anomalies. The different methodologies used for detecting and capturing anomalies in the CWS data are matrix profile, density-based spatial clustering of applications with noise (DBSCAN), and support vector machines (SVMs). Matrix profile and DBSCAN are used to distinguish between normal data and anomalous data. This paper presents a hybrid method using DBSCAN and SVM when a portion of the data is used for DBSCAN to generate clusters. This portion of data is then used to train the SVM along with the clusters generated by DBSCAN as output. SVM is then tested on unseen data as a predictive tool, which can work in real time to categorize data points as either normal or anomalous. This paper presents results that show the high accuracies of DBSCAN and SVM in capturing anomalies within the data for a CWS for fault detection. Thus, the maintenance plan would be focused on component condition rather than a time-based schedule by switching to an automated system to identify and predict faults within a CWS.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2024

Advances in ArborX to support exascale applications

ArborX is a performance portable geometric search library developed as part of the Exascale Computing Project (ECP). In this paper, we explore a collaboration between ArborX and a cosmological simulation code HACC. Large cosmological simulations on exascale platforms encounter a bottleneck due to the in-situ analysis requirements of halo finding, a problem of identifying dense clusters of dark matter (halos). This problem is solved by using a density-based DBSCAN clustering algorithm. With each MPI rank handling hundreds of millions of particles, it is imperative for the DBSCAN implementation to be efficient. In addition, the requirement to support exascale supercomputers from different vendors necessitates performance portability of the algorithm. We describe how this challenge problem guided ArborX development, and enhanced the performance and the scope of the library. We explore the improvements in the basic algorithms for the underlying search index to improve the performance, and describe several implementations of DBSCAN in ArborX. Further, we report the history of the changes in ArborX and their effect on the time to solve a representative benchmark problem, as well as demonstrate the real world impact on production end-to-end cosmology simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Automated Identification of Characteristic Droplet Size Distributions in Stratocumulus Clouds Utilizing a Data Clustering Algorithm

Abstract Droplet-level interactions in clouds are often parameterized by a modified gamma fitted to a “global” droplet size distribution. Do “local” droplet size distributions of relevance to microphysical processes look like these average distributions? This paper describes an algorithm to search and classify characteristic size distributions within a cloud. The approach combines hypothesis testing, specifically, the Kolmogorov–Smirnov (KS) test, and a widely used class of machine learning algorithms for identifying clusters of samples with similar properties: density-based spatial clustering of applications with noise (DBSCAN) is used as the specific example for illustration. The two-sample KS test does not presume any specific distribution, is parameter free, and avoids biases from binning. Importantly, the number of clusters is not an input parameter of the DBSCAN-type algorithms but is independently determined in an unsupervised fashion. As implemented, it works on an abstract space from the KS test results, and hence spatial correlation is not required for a cluster. The method is explored using data obtained from the Holographic Detector for Clouds (HOLODEC) deployed during the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) field campaign. The algorithm identifies evidence of the existence of clusters of nearly identical local size distributions. It is found that cloud segments have as few as one and as many as seven characteristic size distributions. To validate the algorithm’s robustness, it is tested on a synthetic dataset and successfully identifies the predefined distributions at plausible noise levels. The algorithm is general and is expected to be useful in other applications, such as remote sensing of cloud and rain properties. Significance Statement A typical cloud can have billions of drops spread over tens or hundreds of kilometers in space. Keeping track of the sizes, positions, and interactions of all of these droplets is impractical, and, as such, information about the relative abundance of large and small drops is typically quantified with a “size distribution.” Droplets in a cloud interact locally, however, so this work is motivated by the question of whether the cloud droplet size distribution is different in different parts of a cloud. A new method, based on hypothesis testing and machine learning, determines how many different size distributions are contained in a given cloud. This is important because the size distribution describes processes such as cloud droplet growth and light transmission through clouds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Machine Learning-Driven Quantification of CO2 Plume Dynamics at Illinois Basin Decatur Project Sites Using Microseismic Data

This study utilizes machine learning to quantify CO2 plume extents by analyzing microseismic data from the Illinois Basin Decatur Project (IBDP). Leveraging a unique dataset of well logs, microseismic records, and CO2 injection metrics, this work aims to predict the temporal evolution of subsurface CO2 saturation plumes. The findings illustrate that machine learning can predict plume dynamics, revealing vertical clustering of microseismic events over distinct time periods within certain proximities to the injection well, consistent with an invasion percolation model. The buoyant CO2 plume partially trapped within sandstone intervals periodically breaches localized barriers or baffles, which act as leaky seals and impede vertical migration until buoyancy overcomes gravity and capillary forces, leading to breakthroughs along vertical zones of weakness. Between different unsupervised clustering techniques, K-Means and DBSCAN were applied and analyzed in detail, where K-means outperformed DBSCAN in this specific study by indicating the combination of the highest Silhouette Score and the lowest Davies–Bouldin Index. The predictive capability of machine learning models in quantifying CO2 saturation plume extension is significant for real-time monitoring and management of CO2 sequestration sites. The models exhibit high accuracy, validated against physical models and injection data from the IBDP, reinforcing the viability of CO2 geological sequestration as a climate change mitigation strategy and enhancing advanced tools for safe management of these operations.

Iyegbekedo, Ikponmwosa↗
DOE OSTI2022

Machine-learning-based automatic small-angle measurement between planar surfaces in interferometer images: A 2D multilayer Laue lenses case

Here, we report a new machine-learning-based approach to automatically measure the small angle between multiple planar surfaces characterized by white light interferometers. By applying an unsupervised clustering algorithm, DBSCAN (Density-Based Spatial Clustering of Applications with Noise), the multiple surfaces in an interferometer image are automatically identified as distinct surfaces. The angles between every two surfaces are then calculated through the surface fitting. This method can be applied to multiple surfaces regardless of their shapes and locations and significantly simplifies the angle measurement procedure. Using the developed method, we have demonstrated a quick and precise angle measurement for the alignment of 2D Multilayer Laue Lenses (MLLs) for the development of high-resolution x-ray microscopy. This automatic, accurate, and robust small-angle measurement method is compatible with widely used white light interferometers and can be further applied to other metrology applications of interferometer results.

36 MATERIALS SCIENCE↗
DOE OSTI2022

High-energy γ -ray detection of supernova remnants in the Large Magellanic Cloud

ABSTRACT We present the results of a cluster search in the γ-ray sky images of the Large Magellanic Cloud (LMC) region by means of the Minimum Spanning Tree (MST) and DBSCAN algorithms, at energies higher than 6 and 10 GeV, using 12 yr of Fermi-LAT data. Several significant clusters were found, the majority of which associated with previously known γ-ray sources. We confirm our previous detection of the supernova remnants N 49B and N 63A and found new significant clusters associated with the SNRs N 49, N 186D, and N 44. These sources are among the brightest X-ray remnants in the LMC and corresponds to core-collapse supernovae interacting with dense H ii regions, indicating that a hadronic origin of high-energy photons is the most likely process.

Campana, R. (ORCID:0000000247945453)↗
DOE OSTI2025

Explainable AI for Multivariate Time Series Pattern Exploration: Latent Space Visual Analytics With Temporal Fusion Transformer and Variational Autoencoders in Power Grid Event Diagnosis

Detecting and analyzing complex patterns in multivariate time-series data is crucial for decision-making in urban and environmental system operations. However, challenges arise from the high dimensionality, intricate complexity, and interconnected nature of complex patterns, which hinder the understanding of their underlying physical processes. Existing AI methods often face limitations in interpretability, computational efficiency, and scalability, reducing their applicability in real-world scenarios. This paper proposes a novel visual analytics framework that integrates two generative AI models, Temporal Fusion Transformer (TFT) and Variational Autoencoders (VAEs), to reduce complex patterns into lower-dimensional latent spaces and visualize them in 2D using dimensionality reduction techniques such as PCA, t-SNE, and UMAP with DBSCAN. These visualizations, presented through coordinated and interactive views and tailored glyphs, enable intuitive exploration of complex multivariate temporal patterns, identifying patterns’ similarities and uncover their potential correlations for a better interpretability of the AI outputs. The framework is demonstrated through a case study on power grid signal data, where it identifies multi-label grid event signatures, including faults and anomalies with diverse root causes. Additionally, novel metrics and visualizations are introduced to validate the models and assess the performance, efficiency, and consistency of latent maps generated by VAE, which have been utilized in prior studies for latent space cartography and used as a benchmark in this study, and the emerging TFT architecture under various configurations. These analyses provide actionable insights for model parameter tuning and reliability improvements. Comparative results highlight that TFT achieves shorter run times and superior scalability to diverse time-series data shapes compared to VAE. This work advances fault diagnosis in multivariate time series, fostering explainable AI to support critical system operations.

Explainable AI↗
DOE OSTI2025

ArborX 2.0

ArborX library tackles a problem of efficiently finding geometric objects that are close in space. Variations of this problem, such as finding the nearest neighbors of a point, or finding all objects within a certain distance, are inherent components of applications in many fields. The data may be large so that solving the problem efficiently may require significant computational resources, such as multiple processors or accelerators such as general purpose GPUs. ArborX' main advantage in its ability to solve large problems efficiently utilizing a combination of distributed and on-node parallelism. ArborX can be run efficiently on a wide variety of hardware, including GPUs from different vendors, which distinguishes it from other available libraries which typically choose only few of these. The other advantage is that it supports both types of user problems: spatial problems (useful for intersections and finding objects within certain distance), and nearest neighbor problems. ArborX also supports flexible interface in its interaction with a user. Particularly, it allows a user to call user's own function on a positive match, a functionality not rarely available in other libraries. ArborX implements construction and traversal algorithms using efficient tree structures, such as bounding volume hierarchy (BVH). At its core, ArborX uses linear BVH for its low construction cost and sufficient quality. ArborX implements both spatial and nearest-neighbor traversal algorithms. ArborX also provides several clustering algorithms (minimum spanning tree, DBSCAN, HDBSCAN*), interpolation using minimum least squares and ray tracing. ArborX is written using C++, and is parallelized using the message passing interface (MPI) for the distributed communication, and the Kokkos library for on-node parallelism. This approach allows ArborX to be run on a wide variety of hardware, from common laptops and desktops to supercomputers while using the same codebase.

Prokopenko, Andrey [Oak Ridge National Laboratory ↗
DOE OSTI2024

Frosted Tracks

SAND2025-01893O Frosted Tracks is a software tool to group trajectories according to sequences of their behavior. The goal is to start with a very large number of trajectories and identify groups that exhibit similar behavior patterns. The application combines TICC and Metric DBSCAN clustering algorithms for behavioral segmentation and labeling of air/sea trajectory data. 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.

Dalbey, Keith↗
DOE OSTI2024

Poplar

SAND2025-00683O Poplar is a software tool that generates a phylogenetic tree from input gene and genome sequences. It integrates established tools to identify genes within genomes, group sequences, construct gene trees, and infer a species tree. Poplar processes nucleotide sequences, identifies similar sequences using Nucleotide BLAST, groups them with DBSCAN, aligns sequences with MAFFT, constructs gene trees with RAxML-NG, and infers a species tree using ASTRAL-Pro3. This pipeline provides a structured approach to phylogenetic analysis, facilitating the study of evolutionary relationships among species. 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.

Krishnakumar, Raga↗
DOE OSTI2025

SCULPT (Supervised Clustering and Uncovering Latent Patterns with Training) v1

SCULPT (Supervised Clustering and Uncovering Latent Patterns with Training) is a comprehensive data visualization and analysis application focused on working with COLTRIMS (COLd Target Recoil Ion Momentum Spectroscopy) data, which is used in atomic and molecular physics experiments. The application offers several powerful features: - Data uploading and processing capabilities for COLTRIMS files - Multiple visualization methods using UMAP (Uniform Manifold Approximation and Projection) for dimensionality reduction - Interactive selection of data points across multiple views - Feature engineering through various methods: - Manual feature selection from calculated physics parameters - Deep autoencoder for dimension reduction - Genetic programming for discovering meaningful features - Mutual information-based feature selection - Multiple clustering approaches (DBSCAN, KMeans, Agglomerative) - Quality metrics for evaluating clustering results - Export capabilities for selections and generated features

Daoud, Hazem [Lawrence Berkeley National Laborator↗