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DOE OSTI2024

Analysis of Superconducting Magnet Quench Antenna Data

Quenching poses a serious problem for superconducting magnets operating at high currents. It occurs when the material transitions from the superconducting to the normal state, which leads to heating and potential damage to the magnet. To understand and mitigate quenching, the Magnet Department at Fermilab is developing and testing superconducting magnet quench antenna arrays. This study delves into the anomalous events preceding the quench during magnet training by analyzing the collected data. With the moving average and Fast Fourier Transform techniques, we investigate the trends and frequency patterns of the data. Moreover, we introduce an unsupervised anomaly detection algorithm based on Principal Component Analysis and DBSCAN clustering. It can autonomously identify events within background noise, without relying on any predefined event features. Our analysis reveals that the spatio-temporal distribution of these anomalous events has little connection to the quench location, indicating that a majority of them bear no relation to the quenching process.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning

In 2007, an outbreak of African swine fever (ASF), a deadly disease of domestic swine and wild boar caused by the African swine fever virus (ASFV), occurred in Georgia and has since spread globally. Historically, ASFV was classified into 25 different genotypes. However, a newly proposed system recategorized all ASFV isolates into 6 genotypes exclusively using the predicted protein sequences of p72. However, ASFV has a large genome that encodes between 150–200 genes, and classifications using a single gene are insufficient and misleading, as strains encoding an identical p72 often have significant mutations in other areas of the genome. We present here a new classification of ASFV based on comparisons performed considering the entire encoded proteome. A curated database consisting of the protein sequences predicted to be encoded by 220 reannotated ASFV genomes was analyzed for similarity between homologous protein sequences. Weights were applied to the protein identity matrices and averaged to generate a genome-genome identity matrix that was then analyzed by an unsupervised machine learning algorithm, DBSCAN, to separate the genomes into distinct clusters. We conclude that all available ASFV genomes can be classified into 7 distinct biotypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Replacing non-biomedical concepts improves embedding of biomedical concepts

Embeddings are semantically meaningful representations of words in a vector space, commonly used to enhance downstream machine learning applications. Traditional biomedical embedding techniques often replace all synonymous words representing biological or medical concepts with a unique token, ensuring consistent representation and improving embedding quality. However, the potential impact of replacing non-biomedical concept synonyms has received less attention. Embedding approaches often employ concept replacement to replace concepts that span multiple words, such as non-small-cell lung carcinoma, with a single concept identifier (e.g., D002289). Also, all synonyms of each concept are merged into the same identifier. Here, we additionally leveraged WordNet to identify and replace sets of non-biomedical synonyms with their most common representatives. This combined approach aimed to reduce embedding noise from non-biomedical terms while preserving the integrity of biomedical concept representations. We applied this method to 1,055 biomedical concept sets representing molecular signatures or medical categories and assessed the mean pairwise distance of embeddings with and without non-biomedical synonym replacement. A smaller mean pairwise distance was interpreted as greater intra-cluster coherence and higher embedding quality. Embeddings were generated using the Word2Vec algorithm applied to a corpus of 10 million PubMed abstracts. Our results demonstrate that the addition of non-biomedical synonym replacement reduced the mean intra-cluster distance by an average of 8%, suggesting that this complementary approach enhances embedding quality. Future work will assess its applicability to other embedding techniques and downstream tasks. Python code implementing this method is provided under an open-source license.

algorithms↗
DOE OSTI2024

Buzzard to Cardinal: Improved Mock Catalogs for Large Galaxy Surveys

Abstract We present the Cardinal mock galaxy catalogs, a new version of the Buzzard simulation that has been updated to support ongoing and future cosmological surveys, including the Dark Energy Survey (DES), DESI, and LSST. These catalogs are based on a one-quarter sky simulation populated with galaxies out to a redshift of z = 2.35 to a depth of m r = 27. Compared to the Buzzard mocks, the Cardinal mocks include an updated subhalo abundance matching model that considers orphan galaxies and includes mass-dependent scatter between galaxy luminosity and halo properties. This model can simultaneously fit galaxy clustering and group–galaxy cross-correlations measured in three different luminosity threshold samples. The Cardinal mocks also feature a new color assignment model that can simultaneously fit color-dependent galaxy clustering in three different luminosity bins. We have developed an algorithm that uses photometric data to further improve the color assignment model and have also developed a novel method to improve small-scale lensing below the ray-tracing resolution. These improvements enable the Cardinal mocks to accurately reproduce the abundance of galaxy clusters and the properties of lens galaxies in the DES data. As such, these simulations will be a valuable tool for future cosmological analyses based on large sky surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Velocity dispersions of clusters in the Dark Energy Survey Y3 redMaPPer catalogue

ABSTRACT We measure the velocity dispersions of clusters of galaxies selected by the red-sequence Matched-filter Probabilistic Percolation (redMaPPer) algorithm in the first three years of data from the Dark Energy Survey (DES), allowing us to probe cluster selection and richness estimation, λ, in light of cluster dynamics. Our sample consists of 126 clusters with sufficient spectroscopy for individual velocity dispersion estimates. We examine the correlations between cluster velocity dispersion, richness, X-ray temperature, and luminosity, as well as central galaxy velocity offsets. The velocity dispersion–richness relation exhibits a bimodal distribution. The majority of clusters follow scaling relations between velocity dispersion, richness, and X-ray properties similar to those found for previous samples; however, there is a significant population of clusters with velocity dispersions that are high for their richness. These clusters account for roughly 22 per cent of the λ < 70 systems in our sample, but more than half (55 per cent) of λ < 70 clusters at z > 0.5. A couple of these systems are hot and X-ray bright as expected for massive clusters with richnesses that appear to have been underestimated, but most appear to have high velocity dispersions for their X-ray properties likely due to line-of-sight structure. These results suggest that projection effects contribute significantly to redMaPPer selection, particularly at higher redshifts and lower richnesses. The redMaPPer determined richnesses for the velocity dispersion outliers are consistent with their X-ray properties, but several are X-ray undetected and deeper data are needed to understand their nature.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The outer stellar mass of massive galaxies: a simple tracer of halo mass with scatter comparable to richness and reduced projection effects

ABSTRACT Using the weak gravitational lensing data from the Hyper Suprime-Cam Subaru Strategic Program (HSC survey), we study the potential of different stellar mass estimates in tracing halo mass. We consider galaxies with log10(M⋆/M⊙) > 11.5 at 0.2 < z < 0.5 with carefully measured light profiles, and clusters from the redMaPPer and CAMIRA richness-based algorithms. We devise a method (the ‘Top-N test’) to evaluate the scatter in the halo mass–observable relation for different tracers, and to inter-compare halo mass proxies in four number density bins using stacked galaxy–galaxy lensing profiles. This test reveals three key findings. Stellar masses based on CModel photometry and aperture luminosity within R <30 kpc are poor proxies of halo mass. In contrast, the stellar mass of the outer envelope is an excellent halo mass proxy. The stellar mass within R = [50, 100] kpc, M⋆, [50, 100], has performance comparable to the state-of-the-art richness-based cluster finders at log10Mvir ≳ 14.0 and could be a better halo mass tracer at lower halo masses. Finally, using N-body simulations, we find that the lensing profiles of massive haloes selected by M⋆, [50, 100] are consistent with the expectation for a sample without projection or mis-centring effects. Richness-selected clusters, on the other hand, display an excess at R ∼ 1 Mpc in their lensing profiles, which may suggest a more significant impact from selection biases. These results suggest that M⋆-based tracers have distinct advantages in identifying massive haloes, which could open up new avenues for cluster cosmology. The codes and data used in this work can be found here:

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Exploring the contamination of the DES-Y1 cluster sample with SPT-SZ selected clusters

ABSTRACT We perform a cross validation of the cluster catalogue selected by the red-sequence Matched-filter Probabilistic Percolation algorithm (redMaPPer) in Dark Energy Survey year 1 (DES-Y1) data by matching it with the Sunyaev–Zel’dovich effect (SZE) selected cluster catalogue from the South Pole Telescope SPT-SZ survey. Of the 1005 redMaPPer selected clusters with measured richness $\hat{\lambda }\gt 40$ in the joint footprint, 207 are confirmed by SPT-SZ. Using the mass information from the SZE signal, we calibrate the richness–mass relation using a Bayesian cluster population model. We find a mass trend λ ∝ MB consistent with a linear relation (B ∼ 1), no significant redshift evolution and an intrinsic scatter in richness of σλ = 0.22 ± 0.06. By considering two error models, we explore the impact of projection effects on the richness–mass modelling, confirming that such effects are not detectable at the current level of systematic uncertainties. At low richness SPT-SZ confirms fewer redMaPPer clusters than expected. We interpret this richness dependent deficit in confirmed systems as due to the increased presence at low richness of low-mass objects not correctly accounted for by our richness-mass scatter model, which we call contaminants. At a richness $\hat{\lambda }=40$, this population makes up ${\gt}12{{\ \rm per\ cent}}$ (97.5 percentile) of the total population. Extrapolating this to a measured richness $\hat{\lambda }=20$ yields ${\gt}22{{\ \rm per\ cent}}$ (97.5 percentile). With these contamination fractions, the predicted redMaPPer number counts in different plausible cosmologies are compatible with the measured abundance. The presence of such a population is also a plausible explanation for the different mass trends (B ∼ 0.75) obtained from mass calibration using purely optically selected clusters. The mean mass from stacked weak lensing (WL) measurements suggests that these low-mass contaminants are galaxy groups with masses ∼3–5 × 1013 M⊙ which are beyond the sensitivity of current SZE and X-ray surveys but a natural target for SPT-3G and eROSITA.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

DFSynthesizer: Dataflow-based Synthesis of Spiking Neural Networks to Neuromorphic Hardware

Spiking Neural Networks (SNNs) are an emerging computation model that uses event-driven activation and bio-inspired learning algorithms. SNN-based machine learning programs are typically executed on tile-based neuromorphic hardware platforms, where each tile consists of a computation unit called a crossbar, which maps neurons and synapses of the program. However, synthesizing such programs on an off-the-shelf neuromorphic hardware is challenging. This is because of the inherent resource and latency limitations of the hardware, which impact both model performance, e.g., accuracy, and hardware performance, e.g., throughput. We propose DFSynthesizer, an end-to-end framework for synthesizing SNN-based machine learning programs to neuromorphic hardware. The proposed framework works in four steps. First, it analyzes a machine learning program and generates SNN workload using representative data. Second, it partitions the SNN workload and generates clusters that fit on crossbars of the target neuromorphic hardware. Third, it exploits the rich semantics of the Synchronous Dataflow Graph (SDFG) to represent a clustered SNN program, allowing for performance analysis in terms of key hardware constraints such as number of crossbars, dimension of each crossbar, buffer space on tiles, and tile communication bandwidth. Finally, it uses a novel scheduling algorithm to execute clusters on crossbars of the hardware, guaranteeing hardware performance. We evaluate DFSynthesizer with 10 commonly used machine learning programs. Our results demonstrate that DFSynthesizer provides a much tighter performance guarantee compared to current mapping approaches.

Computer Science↗
DOE OSTI2025

RANGE: A robust adaptive nature-inspired global explorer of potential energy surfaces

With the growing demand for realistic representations of chemical structures and the advent of exascale computing, the intelligent sampling of potential energy surfaces and efficient identification of global minima have become more essential but also more feasible. Building on prior studies demonstrating the efficiency of the Artificial Bee Colony (ABC) swarm intelligence algorithm, we report a hybrid metaheuristic framework that integrates the adaptive exploration capabilities of ABC coupled with the exploitation strengths of genetic algorithms (GA) in a scalable, Python-based implementation. The resulting tool, RANGE (Robust Adaptive Nature-inspired Global Explorer), provides seamless interfaces to multiple potential energy evaluators, either directly or via widely used Python libraries, and is designed for high-performance computing environments. We describe the implementation details of RANGE and evaluate its performance, relative to ABC- or GA-alone based algorithms, on a variety of chemical systems, including molecular clusters and heterogeneous surfaces. In conclusion, our results demonstrate RANGE’s efficiency, robustness, and broad applicability in addressing challenging global optimization problems in computational chemistry and materials science.

Algorithms and data structure↗
DOE OSTI2022

Distribution Cutoff for Clusters near the Gel Point

The mechanical and dynamic properties of developing networks near the gel point are susceptible to the distribution of clusters coexisting with percolating networks. The distribution of cluster numbers follows a broad power law, wrapped by a cutoff function that rapidly decays at a characteristic size. The form of the cutoff function has been speculated based on known results from lattice percolation and, in certain cases, solved. We obtained this cutoff function from simulated dynamic clusters of polymeric precursor chains using a hybrid Monte Carlo algorithm. The results obtained from three different precursor chain lengths are consistent with each other and are consistent with the expectation from lattice percolation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Deducing subnanometer cluster size and shape distributions of heterogeneous supported catalysts

Abstract Infrared (IR) spectra of adsorbate vibrational modes are sensitive to adsorbate/metal interactions, accurate, and easily obtainable in-situ or operando. While they are the gold standards for characterizing single-crystals and large nanoparticles, analogous spectra for highly dispersed heterogeneous catalysts consisting of single-atoms and ultra-small clusters are lacking. Here, we combine data-based approaches with physics-driven surrogate models to generate synthetic IR spectra from first-principles. We bypass the vast combinatorial space of clusters by determining viable, low-energy structures using machine-learned Hamiltonians, genetic algorithm optimization, and grand canonical Monte Carlo calculations. We obtain first-principles vibrations on this tractable ensemble and generate single-cluster primary spectra analogous to pure component gas-phase IR spectra. With such spectra as standards, we predict cluster size distributions from computational and experimental data, demonstrated in the case of CO adsorption on Pd/CeO 2 (111) catalysts, and quantify uncertainty using Bayesian Inference. We discuss extensions for characterizing complex materials towards closing the materials gap.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Practical jet flavour through NNLO

Abstract An infrared and collinear (IRC) safe definition of the partonic flavour of a jet is vital for precision predictions of quantum chromodynamics at colliders. Jet flavour definitions have been presented in the literature, but they are typically defined through modification of the jet algorithm to be sensitive to partonic flavour at every stage of the clustering. While this does ensure that the sum of flavours in a jet is IRC safe, a flavour-sensitive clustering procedure is difficult to apply to realistic data. We introduce a distinct and novel approach to jet flavour that can be applied to a collection of partons defined by any algorithm. Our definition of jet flavour is the sum of flavours of all partons that remain after Soft Drop grooming, reclustered with the "Image missing" <#comment/> algorithm. We prove that this prescription is IRC safe through next-to-next-to-leading order (NNLO), and so can interface with the most precise fixed-order calculations for jets available at present. We validate the IRC safety of this definition with numeric fixed-order codes and further show that jet flavour with Soft Drop reclustered with a generalised $$k_T$$ k T algorithm fails to be IRC safe at NNLO.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Constraints on the normal branch of DGP gravity from SPT galaxy clusters with DES and HST weak-lensing mass calibration and from P l a n c k PR4 CMB anisotropies

We present constraints on the normal branch of the Dvali-Gabadadze-Porrati (nDGP) braneworld gravity model from the abundance of massive galaxy clusters. On scales below the nDGP crossover scale r c , the nDGP model features an effective gravitylike fifth force that alters the growth of structure, leading to an enhancement of the halo mass function (HMF) on cluster scales. The enhanced cluster abundance allows for constraints on the nDGP model using cluster samples. We employ the South Pole Telescope (SPT) cluster sample, selected through the thermal Sunyaev-Zel’dovich effect with the SPT and with mass calibration using weak-lensing data from the Dark Energy Survey (DES) and the Hubble Space Telescope (HST). The cluster sample contains 1,005 clusters with redshifts 0.25 < z < 1.78 , which are confirmed with the multicomponent matched filter algorithm using optical and near-infrared data. Weak-lensing data from DES and HST enable a robust mass measurement of the cluster sample. We use DES Year 3 data for 688 clusters with redshifts z < 0.95 , and HST data for 39 clusters with redshifts 0.6 < z < 1.7 . We account for the enhancement in the HMF through a semi-analytic correction factor to the standard cosmology HMF derived from the spherical collapse model in the nDGP model. We then further calibrate this model using N -body simulations. In addition, for the first time, we analyze the primary CMB temperature and polarization anisotropy measurements from Planck PR4 within the nDGP model. We obtain a competitive constraint from the joint analysis of the SPT cluster abundance with the Planck PR4 data, and report an upper bound of 1 / H 0 r c < 1.41 at 95% when assuming a cosmology with massive neutrinos.

Vogt, S. M.L. [Munich U. Observ.; LMU Munich (main↗
DOE OSTI2023

Prepare Ground States of Highly Frustrated Magnetic Clusters on Quantum Computers

Solving challenging problems in physical, chemical, and materials sciences is one of the most promising applications of quantum utility that can be realized on current noisy hardware, considering (i) the direct map (encoding) from the quantum particles and their interactions to the qubits and their entangling gates and (ii) the rapidly improved quantum hardware and advanced error-mitigation techniques. Understanding quantum spin liquid in frustrated magnetic materials is a longstanding challenge in condensed matter physics and the nature of the ground-state phases is highly debated among researchers. Using IBM quantum computers with superconducting qubits, we implemented a variational quantum eigensolver (VQE) algorithm to prepare the ground states of two 12-site cluster approximations of these highly frustrated magnetic materials. The interaction graphs of the two corresponding Hamiltonians are (a) the six-pointed star graph (a unit cell of the kagome lattice) and (b) the cuboctahedral graph (the kagome on a sphere). These are also two instances of Quantum Max Cut problem. With the VQE based on the Hamiltonian variational ansatz acting on a valence bond solid initial trial state, we prepared the ground states and obtained the exact ground energy on simulator and high accuracy on noisy hardware. The deep ansatz necessary to reach the ground state of the cuboctahedral graph indicates that it is a hard instance of Quantum Max Cut.

Wang, Yan↗
DOE OSTI2024

Emulating ab initio computations of infinite nucleonic matter

We construct efficient emulators for the computation of the infinite nuclear matter equation of state. These emulators are based on the subspace-projected coupled-cluster method for which we here develop a new algorithm called small-batch voting to eliminate spurious states that might appear when emulating quantum many-body methods based on a non-Hermitian Hamiltonian. The efficiency and accuracy of these emulators facilitate a rigorous statistical analysis within which we explore nuclear matter predictions for > 10 6 different parametrizations of a chiral interaction model with explicit Δ -isobars at next-to-next-to leading order. Constrained by nucleon-nucleon scattering phase shifts and bound-state observables of light nuclei up to He 4 , we use history matching to identify nonimplausible domains for the low-energy coupling constants of the chiral interaction. Within these domains we perform a Bayesian analysis using sampling and importance resampling with different likelihood calibrations and study correlations between interaction parameters, calibration observables in light nuclei, and nuclear matter saturation properties. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Distributed-Memory Parallel Symmetric Nonnegative Matrix Factorization

We develop the first distributed-memory parallel implementation of Symmetric Nonnegative Matrix Factorization (SymNMF), a key data analytics kernel for clustering and dimensionality reduction. Our implementation includes two different algorithms for SymNMF, which give comparable results in terms of time and accuracy. The first algorithm is a parallelization of an existing sequential approach that uses solvers for non symmetric NMF. The second algorithm is a novel approach based on the Gauss-Newton method. It exploits second-order information without incurring large computational and memory costs. We evaluate the scalability of our algorithms on the Summit system at Oak Ridge National Laboratory, scaling up to 128 nodes (4,096 cores) with 70% efficiency. Additionally, we demonstrate our software on an image segmentation task.

Eswar, Srinivas↗