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DOE OSTI2021

Distance-Weighted Graph Neural Networks on FPGAs for Real-Time Particle Reconstruction in High Energy Physics

Graph neural networks have been shown to achieve excellent performance for several crucial tasks in particle physics, such as charged particle tracking, jet tagging, and clustering. An important domain for the application of these networks is the FGPA-based first layer of real-time data filtering at the CERN Large Hadron Collider, which has strict latency and resource constraints. We discuss how to design distance-weighted graph networks that can be executed with a latency of less than one μs on an FPGA. To do so, we consider a representative task associated to particle reconstruction and identification in a next-generation calorimeter operating at a particle collider. We use a graph network architecture developed for such purposes, and apply additional simplifications to match the computing constraints of Level-1 trigger systems, including weight quantization. Using the hls4ml library, we convert the compressed models into firmware to be implemented on an FPGA. Performance of the synthesized models is presented both in terms of inference accuracy and resource usage.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2012

A Multithreaded Algorithm for Network Alignment Via Approximate Matching

Network alignment is an optimization problem to find the best one-to-one map between the vertices of a pair of graphs that overlaps in as many edges as possible. It is a relaxation of the graph isomorphism problem and is closely related to the subgraph isomorphism problem. The best current approaches are entirely heuristic, and are iterative in nature. They generate real-valued heuristic approximations that must be rounded to find integer solutions. This rounding requires solving a bipartite maximum weight matching problem at each step in order to avoid missing high quality solutions. We investigate substituting a parallel, half-approximation for maximum weight matching instead of an exact computation. Our experiments show that the resulting difference in solution quality is negligible. We demonstrate almost a 20-fold speedup using 40 threads on an 8 processor Intel Xeon E7-8870 system (from 10 minutes to 36 seconds).

network alignment, matching, multicore↗

DOE OSTI2023

Short-Depth QAOA circuits and Quantum Annealing on Higher-Order Ising Models (Rev.2)

The Quantum Alternating Operator Ansatz (QAOA) and Quantum Annealing (QA) are quantum algorithms that are both based on the adiabatic theorem and both have the goal of sampling the optimal solution(s) of combinatorial optimization problems. Quantum annealing has been physically instantiated on D-Wave devices using superconducting flux qubits, and QAOA can be programmed on digital gate-model quantum computers such as the programmable superconducting transmon qubits devices of the IBMQ series, for instance ibm washington. QAOA and QA address the same types of problems, but it is unclear how they will scale to large problem sizes and to larger and higher-fidelity quantum computers. In this article, we present a direct comparison between QAOA, one and two rounds, run on all 127 qubits of ibm washington and QA run on D-Wave Advantage system4.1 and Advantage system6.1. The problems which allow for this comparison are random Ising model problems whose connectivity matches the heavy hexagonal lattice topology of ibm washington and the Pegasus graph connectivity of the two D-Wave devices. We create two classes of problem instances for this comparison: one with higher order terms (ZZZ variable interactions), linear terms, and quadratic terms, and a separate problem type with only linear and quadratic terms. Our QAOA circuits are novel and extremely short depth, with a CNOT depth of 6 per round, which allows whole chip usage of ibm washington’s heavy hexagonal lattice and can be applied to future heavy-hex chips. We also test the effectiveness of the error suppression technique digital dynamical decoupling on the QAOA circuits. The QAOA circuits compiled to ibm washington are composed of several thousand circuit instructions, approximately 3, 000 depending on the details of the circuit, making these some the largest quantum circuits ever executed on a digital quantum processor. QAOA and QA are compared against the classical heuristic algorithm of simulated annealing and all problem instances are exactly solved using CPLEX in order to evaluate which samplers, if any, correctly found the ground state solution(s) of the problem instances. We find that (i) QA outperforms QAOA on all problem instances, (ii) QAOA samples the problems better than random sampling, and (iii) QAOA angle computation exhibits clear parameter concentration across the ensemble of Ising models.

127 Qubits↗

DOE OSTI2016

SU-F-J-97: A Joint Registration and Segmentation Approach for Large Bladder Deformations in Adaptive Radiotherapy

Purpose: To improve results of deformable image registration (DIR) in adaptive radiotherapy for large bladder deformations in CT/CBCT pelvis imaging. Methods: A variational multi-modal DIR algorithm is incorporated in a joint iterative scheme, alternating between segmentation based bladder matching and registration. Using an initial DIR to propagate the bladder contour to the CBCT, in a segmentation step the contour is improved by discrete image gradient sampling along all surface normals and adapting the delineation to match the location of each maximum (with a search range of +−5/2mm at the superior/inferior bladder side and step size of 0.5mm). An additional graph-cut based constraint limits the maximum difference between neighboring points. This improved contour is utilized in a subsequent DIR with a surface matching constraint. By calculating an euclidean distance map of the improved contour surface, the new constraint enforces the DIR to map each point of the original contour onto the improved contour. The resulting deformation is then used as a starting guess to compute a deformation update, which can again be used for the next segmentation step. The result is a dense deformation, able to capture much larger bladder deformations. The new method is evaluated on ten CT/CBCT male pelvis datasets, calculating Dice similarity coefficients (DSC) between the final propagated bladder contour and a manually delineated gold standard on the CBCT image. Results: Over all ten cases, an average DSC of 0.93±0.03 is achieved on the bladder. Compared with the initial DIR (0.88±0.05), the DSC is equal (2 cases) or improved (8 cases). Additionally, DSC accuracy of femoral bones (0.94±0.02) was not affected. Conclusion: The new approach shows that using the presented alternating segmentation/registration approach, the results of bladder DIR in the pelvis region can be greatly improved, especially for cases with large variations in bladder volume. Fraunhofer MEVIS received funding from a research grant by Varian Medical Systems.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Modeling Complex Relationships in Large-Scale Data using Hypergraphs (LDRD Final Report)

This SAND report documents the findings of the LDRD project, "Modeling Complex Relationships in Large-Scale Data using Hypergraphs". The project ran from October 2017 through September 2019. The focus of the project was the development and application of hypergraph data analytics to Sandia relational data applications. In this project, we attempted to apply a hypergraph data analysis method—specifically, hypergraph eigenvector centrality—to Sandia mission problems to identify influential entities (people, location, times, etc.) in the data. Unfortunately, the application data led to graph and hypergraph representations containing disconnected components. To date, there are no well-established techniques for applying eigenvector centrality to such graphs and hypergraphs. In this report, we present several heuristics for computing eigenvector centrality for disconnected graphs. We believe this is an important start to understanding how to approach the similar problem for hypergraphs, but this project concluded before we made progress on that problem. The ideas, methods, and suggestions presented here can be used for further research into this challenging problem. We also present our ideas for generating graphs with known degree and centrality distributions. The goal in presenting this work is to identify a procedure for analyzing such graphs once the problem of addressing disconnected components has been addressed. When working with a single data set, this generator can be used to create many instances of graphs that can be used to analyze the robustness of the centrality computations for the original data set. Although the results did not match perfectly in the case of the Facebook Ego dataset used in the experiments presented here, this again represents a good start in the direction of a graph generator for such problems. We note that there are potential trade-offs between how the degree and centrality distributions are fit to the original data and suggested several possible avenues for follow-on research efforts.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1990

Partitioning sparse matrices with eigenvectors of graphs

The problem of computing a small vertex separator in a graph arises in the context of computing a good ordering for the parallel factorization of sparse, symmetric matrices. An algebraic approach for computing vertex separators is considered in this paper. It is shown that lower bounds on separator sizes can be obtained in terms of the eigenvalues of the Laplacian matrix associated with a graph. The Laplacian eigenvectors of grid graphs can be computed from Kronecker products involving the eigenvectors of path graphs, and these eigenvectors can be used to compute good separators in grid graphs. A heuristic algorithm is designed to compute a vertex separator in a general graph by first computing an edge separator in the graph from an eigenvector of the Laplacian matrix, and then using a maximum matching in a subgraph to compute the vertex separator. Results on the quality of the separators computed by the spectral algorithm are presented, and these are compared with separators obtained from other algorithms for computing separators. Finally, the time required to compute the Laplacian eigenvector is reported, and the accuracy with which the eigenvector must be computed to obtain good separators is considered. The spectral algorithm has the advantage that it can be implemented on a medium-size multiprocessor in a straightforward manner.

Pothen, Alex↗

NASA NTRS1997

Wavelet Methods Developed to Detect and Control Compressor Stall

A "wavelet" is, by definition, an amplitude-varying, short waveform with a finite bandwidth (e.g., that shown in the first two graphs). Naturally, wavelets are more effective than the sinusoids of Fourier analysis for matching and reconstructing signal features. In wavelet transformation and inversion, all transient or periodic data features (as in compressor-inlet pressures) can be detected and reconstructed by stretching or contracting a single wavelet to generate the matching building blocks. Consequently, wavelet analysis provides many flexible and effective ways to reduce noise and extract signals which surpass classical techniques - making it very attractive for data analysis, modeling, and active control of stall and surge in high-speed turbojet compressors. Therefore, fast and practical wavelet methods are being developed in-house at the NASA Lewis Research Center to assist in these tasks. This includes establishing user-friendly links between some fundamental wavelet analysis ideas and the classical theories (or practices) of system identification, data analysis, and processing.

Le, Dzu K.↗

DOE OSTI2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

Abstract Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI’s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Visualizing Comparisons of Bill of Materials

Protecting critical infrastructure from cyber attacks, natural disasters, and other disruptions is a priority of the U.S. Government. Critical infrastructure includes providing electricity to homes and businesses, supplying natural gas for heating, and producing renewable energy sources. A loss of these services, as seen in the Solarwinds supply chain attack in 2020 , Texas snowstorm of 2021, the Colonial Pipeline cyber incident of 2021, and the Washington power substation attacks in 2022 result in high costs to consumers, disruption of everyday life, and even death. To protect the infrastructure, we first have to know what equipment we are protecting. The complexity of distributed manufacturing and development coupled with the increasing prevalence of cyber and supply chain attacks necessitates a greater understanding of the hardware and software components that comprise equipment in critical infrastructure. When a vulnerability in a single software library can have disastrous consequences, it is vital to understand critical equipment and systems at a granular level. This need has led to increased energy around the development and incorporation of bill-of-materials (BOM) into existing asset management practices to aid in mitigating, and responding to future attacks \cite{noauthor_software_nodate}. While much of the current research is devoted to creating BOMs, it is equally important to develop methodologies for leveraging BOMs to answer questions, such as: How has my software changed? Are two pieces of equipment equivalent? Does this piece of equipment that just arrived match my historical information? In this work, we demonstrate how BOMs can be represented by graph structures. We then describe how these structures can be fed into a graph comparison algorithm to produce a novel interactive visualization that allows us to not only identify differences in BOMs, but show exactly where they are in the product.

Jones, Rebecca D.↗

NASA NTRS1989

Diffraction of impulsive sounds by a curved obstruction - A time-domain study

The diffraction of spark-discharge-produced sound waves produced by a half circular cylinder covered with absorbing material is investigated theoretically and experimentally. The test bench setup and the measurement instrumentation and procedure are described; the derivation of an analytical model on the basis of the matched asymptotic expansion theory of Pierce (1981) is outlined; and the results are compared in graphs. Good general agreement is obtained, except in the deep shadow of the obstacle, where the theory underpredicts the magnitude of the received pulse. This discrepancy is tentatively attributed to the creeping-wave mechanism described by Pierce.

Berthelot, Yves H.↗

DOE OSTI2021

Theoretically and practically efficient parallel nucleus decomposition

This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves a work complexity matching the best sequential algorithm while also having low depth (parallel running time), which significantly improves upon the only existing parallel nucleus decomposition algorithm (Sariyüce et al. , PVLDB 2018). The key to the theoretical efficiency of our algorithm is a new lemma that bounds the amount of work done when peeling cliques from the graph, combined with the use of a theoretically-efficient parallel algorithms for clique listing and bucketing. We introduce several new practical optimizations, including a new multi-level hash table structure to store information on cliques space-efficiently and a technique for traversing this structure cache-efficiently. On a 30-core machine with two-way hyper-threading on real-world graphs, we achieve up to a 55x speedup over the state-of-the-art parallel nucleus decomposition algorithm by Sariyüce et al. , and up to a 40x self-relative parallel speedup. We are able to efficiently compute larger nucleus decompositions than prior work on several million-scale graphs for the first time.

Computer Science↗

DOE OSTI2018

TimeChart

TimeChart is a Python Qt-based graphing application for control systems. It is intended to be the modern, feature-by-feature matching alternative to the Motif EPICS Strip Tool application. Comparing with Strip Tool, TimeChart possesses the inherent cross-platform, responsive, and regularly maintained and supported advantages offered by Python Display Manager (PyDM). As a Python Qt-based framework, PyDM is also created and maintained by SLAC. Its charting capability is built upon pyqtgraph, and the PyDM's TimePlot is the central widget in TimeChart.

Bui, Hai↗

DOE OSTI2020

Computer processing through distance-based quality score method in geospatial-temporal semantic graphs

A computer-implemented method of improving processing of overhead image data by a processor using a distance-based quality score in a geospatial-temporal semantic graph. An allowable range for each attribute in the subgraph search template is defined. For each match in a comparison, attribute values of each match element are compared against the preferred range and the allowable range to compute a corresponding distance of each match attribute from the subgraph search template. A corresponding overall match quality score is determined for each match from the subgraph search template, wherein determining the corresponding overall match qualities is performed using a corresponding required quality score and a corresponding optional quality score. All corresponding overall match quality scores are sorted into an ordered list and then displayed.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1977

Synchronization of the ERDA-NASA 100 kW wind turbine generator with large utility networks

The synchronizing of a wind turbine generator against an infinite bus under random conditions is studied for the first time. With a digital computer, complete solutions for rotor speed, generator power angle, electromagnetic torque, wind turbine torque, wind turbine blade pitch angle, and armature current are obtained and presented by graphs. Experiments have been recently performed on the ERDA-NASA 100 kW wind turbine. Experimental results matched computer study results very closely and confirmed that the synchronization can be accomplished by means of the existing speed control system and an automatic synchronizer.

Hwang, H. H.↗

DOE OSTI2015

Control strategy optimization of HVAC plants

In this paper we present a methodology to optimize the operating conditions of heating, ventilation and air conditioning (HVAC) plants to achieve a higher energy efficiency in use. Semi-empiric numerical models of the plant components are used to predict their performances as a function of their set-point and the environmental and occupied space conditions. The optimization is performed through a graph-based algorithm that finds the set-points of the system components that minimize energy consumption and/or energy costs, while matching the user energy demands. The resulting model can be used with systems of almost any complexity, featuring both HVAC components and energy systems, and is sufficiently fast to make it applicable to real-time setting.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

GraphAide: Advanced Graph-Assisted Query and Reasoning System

Curating knowledge from multiple siloed sources that contain both structured and unstructured data is a major challenge in many real-world applications. Pattern matching and querying represent fundamental tasks in modern data analytics that leverage this curated knowledge. The development of such applications necessitates overcoming several research challenges, including data extraction, named entity recognition, data modeling, and designing query interfaces. Moreover, the explainability of these functionalities is critical for their broader adoption. The emergence of Large Language Models (LLMs) has accelerated the development lifecycle of new capabilities. Nonetheless, there is an ongoing need for domain-specific tools tailored to user activities. The creation of digital assistants has gained considerable traction in recent years, with LLMs offering a promising avenue to develop such assistants utilizing domain-specific knowledge and assumptions. In this context, we introduce an advanced query and reasoning system, GraphAide, which constructs a knowledge graph (KG) from diverse sources and allows to query and reason over the resulting KG. GraphAide harnesses both the KG and LLMs to rapidly develop domain-specific digital assistants. It integrates design patterns from retrieval augmented generation (RAG) and the semantic web to create an agentic LLM application. GraphAide underscores the potential for streamlined and efficient development of specialized digital assistants, thereby enhancing their applicability across various domains.

Purohit, Sumit [BATTELLE (PACIFIC NW LAB)] (ORCID:↗

DOE OSTI2026

Intelligent Experiments Through Real-time AI: Fast Data Processing and Autonomous Detector Control for sPHENIX and Future EIC Detectors (Final Report)

The overall vision of this project was to integrate real-time artificial intelligence (AI) directly into the data acquisition and detector-control systems of nuclear physics experiments, including both fast online event selection and an autonomous detector-control feedback loop. The work carried out under the award focused on the fast online event-selection half of that vision: the efficient recording of low-momentum heavy-flavor (HF) hadron decays in proton-proton collisions at the sPHENIX experiment at the Relativistic Heavy Ion Collider (RHIC)—an observable that requires fast tracking and topological trigger selection not previously demonstrated at RHIC, and that is essential for QCD studies at future facilities such as the Electron-Ion Collider (EIC). The autonomous detector-control (GPU-based feedback) component named in the project title remained a design concept and was not implemented under this award. The Massachusetts Institute of Technology (MIT) group led the offline simulation and data processing needed to train the machine-learning (ML) models, the translation of trained models to Field-Programmable Gate Array (FPGA) firmware using the hls4ml framework, and the physics validation of heavy-flavor reconstruction. Over the award period, the team developed and hardware-tested the principal components of an AI-based heavy-flavor trigger on simulated and recorded sPHENIX tracker data: a software Bipartite Graph Attention Network (BiGAT) trigger model reaching > 95% signal efficiency at 99% background rejection; an FPGA-native hit clusterizer matching the offline clustering; smaller networks synthesized to FPGA within the required sub-10 µs latency; and an assembled decoder–clusterizer–inference firmware chain exercised on the FELIX readout board. A complete, fully integrated hardware demonstrator was not finished within the award period. This report documents the project goals, the MIT group’s contributions, the technical accomplishments, and the outlook toward applications at the future EIC ePIC detector.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2019

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes

Shotgun metagenomics has greatly advanced our understanding of microbial communities over the last decade. Metagenomic analyses often include assembly and genome binning, computationally daunting tasks especially for big data from complex environments such as soil and sediments. In many studies, however, only a subset of genes and pathways involved in specific functions are of interest; thus, it is not necessary to attempt global assembly. In addition, methods that target genes can be computationally more efficient and produce more accurate assembly by leveraging rich databases, especially for those genes that are of broad interest such as those involved in biogeochemical cycles, biodegradation, and antibiotic resistance or used as phylogenetic markers. Here, we review six gene-targeted assemblers with unique algorithms for extracting and/or assembling targeted genes: Xander, MegaGTA, SAT-Assembler, HMM-GRASPx, GenSeed-HMM, and MEGAN. We tested these tools using two datasets with known genomes, a synthetic community of artificial reads derived from the genomes of 17 bacteria, shotgun sequence data from a mock community with 48 bacteria and 16 archaea genomes, and a large soil shotgun metagenomic dataset. We compared assemblies of a universal single copy gene (rplB) and two N cycle genes (nifH and nirK). We measured their computational efficiency, sensitivity, specificity, and chimera rate and found Xander and MegaGTA, which both use a probabilistic graph structure to model the genes, have the best overall performance with all three datasets, although MEGAN, a reference matching assembler, had better sensitivity with synthetic and mock community members chosen from its reference collection. Also, Xander and MegaGTA are the only tools that include post-assembly scripts tuned for common molecular ecology and diversity analyses. Additionally, we provide a mathematical model for estimating the probability of assembling targeted genes in a metagenome for estimating required sequencing depth.

59 BASIC BIOLOGICAL SCIENCES↗