PaKman: A Scalable Algorithm for Generating Genomic Contigs on Distributed Memory Machines
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Results for “Graph algorithms”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Framework for Extensible, Asynchronous Task Scheduling (FEATS) in Fortran
Most parallel scientific programs contain compiler directives (pragmas) such as those from OpenMP, explicit calls to runtime library procedures such as those implementing the Message Passing Interface (MPI), or compiler-specific language extensions such as those provided by CUDA. By contrast, the recent Fortran standards empower developers to express parallel algorithms without directly referencing lower-level parallel programming models. Fortran’s parallel features place the language within the Partitioned Global Address Space (PGAS) class of programming models. When writing programs that exploit data-parallelism, application developers often find it straightforward to develop custom parallel algorithms. Problems involving complex, heterogeneous, staged calculations, however, pose much greater challenges. Such applications require careful coordination of tasks in a manner that respects dependencies prescribed by a directed acyclic graph. When rolling one’s own solution proves difficult, extending a customizable framework becomes attractive. The paper presents the design, implementation, and use of the Framework for Extensible Asynchronous Task Scheduling (FEATS), which we believe to be the first task-scheduling tool written in modern Fortran. We describe the benefits and compromises associated with choosing Fortran as the implementation language, and we propose ways in which future Fortran standards can best support the use case in this paper.
Richardson, Brad↗
Deep Learning Coordinate-Free Quantum Chemistry
Computing quantum chemical properties of small molecules and polymers can provide insights valuable to physicists, chemists and biologists when designing new materials, catalysts, biological probes and drugs. Deep learning can compute quantum chemical properties accurately in a fraction of the time required by commonly used methods such as density functional theory (DFT). However, many of these deep learning architectures require energy minimized molecular geometries as input, which is also computationally expensive, and decreasing the reproducibility and throughput of these methods. In this study, we demonstrate that accurate quantum chemical computations can be performed without optimized geometries by operating in the coordinate-free domain using deep learning on graph encodings. Furthermore, we also find that the choice of graph-encoding architecture substantially affects the performance of these methods. The Wave architecture outperforms graph convolution architectures, particularly on complex molecules. Furthermore, the structures of these graph encoding architectures provide an opportunity to probe an important, outstanding question in quantum mechanics: What types of quantum chemical properties can be represented by local-variable models? We find that Wave, a local-variable model, is more accurately calculates quantum chemical properties. Graph convolutional architectures require global variables, and are not as effective as as Wave. We anticipate that coordinate-free, deep-learning models of quantum chemistry will become valuable tools in chemistry and biology, enabling researchers to rapidly screen chemical databases or identify new molecules using automated, de-novo design algorithms.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Efficient and universal characterization of atomic structures through a topological graph order parameter
Abstract A graph-based order parameter, based on the topology of the graph itself, is introduced for the characterization of atomistic structures. The order parameter is universal to any material/chemical system and is transferable to all structural geometries. Four sets of data are used to validate both the generalizability and accuracy of the algorithm: (1) liquid lithium configurations spanning up to 300 GPa, (2) condensed phases of carbon along with nanotubes and buckyballs at ambient and high temperature, (3) a diverse set of aluminum configurations including surfaces, compressed and expanded lattices, point defects, grain boundaries, liquids, nanoparticles, all at nonzero temperatures, and (4) eleven niobium oxide crystal phases generated with ab initio molecular dynamics. We compare our proposed method to existing, state-of-the-art methods for the cases of aluminum and niobium oxide. Our order parameter uniquely classifies every configuration and outperforms all studied existing methods, opening the door for its use in a multitude of complex application spaces that can require fine structure-level characterization of atomistic graphs.
36 MATERIALS SCIENCE↗
Learning Optimal Multigrid Smoothers via Neural Networks
Multigrid methods are one of the most efficient techniques for solving large sparse linear systems arising from partial differential equations (PDEs) and graph Laplacians from machine learning applications. One of the key components of multigrid is smoothing, which aims at reducing high-frequency errors on each grid level. However, finding optimal smoothing algorithms is problem-dependent and can impose challenges for many problems. In this paper, we propose an efficient adaptive framework for learning optimized smoothers from operator stencils in the form of convolutional neural networks (CNNs). Here, the CNNs are trained on small-scale problems from a given type of PDEs based on a supervised loss function derived from multigrid convergence theories and can be applied to large-scale problems of the same class of PDEs. Numerical results on anisotropic rotated Laplacian problems and variable coefficient diffusion problems demonstrate improved convergence rates and solution time compared with classical hand-crafted relaxation methods.
97 MATHEMATICS AND COMPUTING↗
Enhancing ACPF Analysis: Integrating Newton-Raphson Method with Gradient Descent and Computational Graphs
This paper presents a new method for enhancing Alternating Current Power Flow (ACPF) analysis. The method integrates the Newton-Raphson (NR) method with Enhanced-Gradient Descent (GD) and computational graphs. The integration of renewable energy sources in power systems introduces variability and unpredictability, and this method addresses these challenges. It leverages the robustness of NR for accurate approximations and the flexibility of GD for handling variable conditions, all without requiring Jacobian matrix inversion. Furthermore, computational graphs provide a structured and visual framework that simplifies and systematizes the application of these methods. The goal of this fusion is to overcome the limitations of traditional ACPF methods and improve the resilience, adaptability, and efficiency of modern power grid analyses. We validate the effectiveness of our advanced algorithm through comprehensive testing on established IEEE benchmark systems. Furthermore, our findings demonstrate that our approach not only speeds up the convergence process but also ensures consistent performance across diverse system states, representing a significant advancement in power flow computation.
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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↗
Optimizing power system restoration with damaged communications
Utility procedures for power system blackstart and restoration typically assume that energization decisions can be reliably communicated across the grid. In reality, the communications and control network would likely also be affected in power outages, such as those caused by extreme weather events or cyber-attacks. This paper studies the effect of damage to the power system communications and control infrastructure on restoration operations following a blackout. We model the communications infrastructure as a graph, overlaying the power grid, and imposing the requirement that every energized element in the power grid be observable from a control center. We expand on a specialized branch-and-bound algorithm from the literature to optimize the restoration process and devise an initialization heuristic and a rounding heuristic to improve solution speed. We perform numerical experiments on synthetic systems for Illinois and Texas with outages based on a solar flare or hurricane. We compare the results of our specialized branch-and-bound algorithm to the results from (i) the initialization heuristic alone, (ii) a variation of this heuristic that we use as a baseline, and (iii) the restoration optimization for the power system without communications constraints. Here, we find that damage to the communications infrastructure significantly increases the time required to re-energize the grid. Moreover, by simultaneously optimizing communications repairs and grid energization decisions, we are able to re-energize the grid significantly faster than if communications repairs and energization decisions were made independently or with partial coordination, motivating improvements to current industry practice.
97 MATHEMATICS AND COMPUTING↗
Semi-Automated, Object-Based Tomography of Dislocation Structures
The characterization of the three-dimensional arrangement of dislocations is important for many analyses in materials science. Dislocation tomography in transmission electron microscopy is conventionally accomplished through intensity-based reconstruction algorithms. Although such methods work successfully, a disadvantage is that they require many images to be collected over a large tilt range. Here, we present an alternative, semi-automated object-based approach that reduces the data collection requirements by drawing on the prior knowledge that dislocations are line objects. Our approach consists of three steps: (1) initial extraction of dislocation line objects from the individual frames, (2) alignment and matching of these objects across the frames in the tilt series, and (3) tomographic reconstruction to determine the full three-dimensional configuration of the dislocations. Drawing on innovations in graph theory, we employ a node-line segment representation for the dislocation lines and a novel arc-length mapping scheme to relate the dislocations to each other across the images in the tilt series. We demonstrate the method for a dataset collected from a dislocation network imaged by diffraction-contrast scanning transmission electron microscopy. Based on these results and a detailed uncertainty analysis for the algorithm, we discuss opportunities for optimizing data collection and further automating the method.
47 OTHER INSTRUMENTATION↗
tapir: A tool for topologies, amplitudes, partial fraction decomposition and input for reductions
The demand for precision predictions in the field of high energy physics has dramatically increased over recent years. Experiments conducted at the LHC, as well as precision measurements at the intensity frontier such as Belle II require equally precise theoretical predictions to make full use of the acquired data. To match the experimental precision, second-, third- and, for certain quantities, even higher-order calculations in perturbative quantum field theory are required. To facilitate such calculations, computer software automating as many steps as possible is required. Yet, each calculation poses different challenges and thus, a high level of configurability is required. In this context we present tapir: a tool for identification, manipulation and minimization of Feynman integral families. It is designed to integrate in toolchains based on the computer algebra system FORM, the use of which is common practice in the field. tapir can be used to reduce the complexity of multi-loop problems with cut-filters, topology mapping, partial fraction decomposition and alike. Program Title:tapir CPC Library link to program files:https://doi.org/10.17632/ptc9t46xyn.1 Developer's repository link:https://gitlab.com/tapir-devs/tapir Licensing provisions: GPLv3 Programming language:python 3, C++ Nature of problem: Multi-loop computations require the automatization of a large number of different tasks related to Feynman integral topologies. Among them are the identification and minimization of integral topologies, partial fraction decomposition of topologies in the case of linearly dependent propagators as well as mapping scalar products of loop momenta to scalar functions. Solution method: The minimization of topologies is performed by comparison of their respective Nickel indices [1], even further minimization utilizes Pak's algorithm [2]. To efficiently map scalar products of loop momenta to scalar functions FORM [3] code is generated. Additional comments including restrictions and unusual features: Minimization based on Pak's algorithm slows down for many lines and scales. A coarser minimization using the Nickel indices, however, is still possible. [1]B. Nickel, D. Meiron, G.A.J. Baker, Compilation of 2-pt and 4-pt graphs for continuous spin model, Report, University of Guelph, 1977.[2]A. Pak, J. Phys. Conf. Ser. 368 (2012) 012049, https://doi.org/10.1088/1742-6596/368/1/012049, arXiv:1111.0868.[3]B. Ruijl, T. Ueda, J. Vermaseren, FORM version 4.2, arXiv:1707.06453, 7 2017.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
SA-GAT-SR: self-adaptable graph attention networks with symbolic regression for high-fidelity material property prediction
Recent advances in machine learning have demonstrated an enormous utility of deep learning approaches, particularly Graph Neural Networks (GNNs) for materials science. These methods have emerged as powerful tools for high-throughput prediction of material properties, offering a compelling enhancement and alternative to traditional first-principles calculations. While the community has predominantly focused on developing increasingly complex and universal models to enhance predictive accuracy, such approaches often lack physical interpretability and insights into materials behavior. Here, we introduce a novel computational paradigm—Self-Adaptable Graph Attention Networks integrated with Symbolic Regression (SA-GAT-SR)—that synergistically combines the predictive capability of GNNs with the interpretative power of symbolic regression. Our framework employs a self-adaptable encoding algorithm that automatically identifies and adjust attention weights so as to screen critical features from an expansive 180-dimensional feature space while maintaining O(n) computational scaling. The integrated SR module subsequently distills these features into compact analytical expressions that explicitly reveal quantum-mechanically meaningful relationships, achieving 23 × acceleration compared to conventional SR implementations that heavily rely on first-principle calculations-derived features as input. This work suggests a new framework in computational materials science, bridging the gap between predictive accuracy and physical interpretability, offering valuable physical insights into material behavior.
36 MATERIALS SCIENCE↗
GSAS Tools
SAND2023-06684O GSAS Tools is a web application that manages user access to modeling and simulation tools and promotional material. This software, which is a spiking neural network (SNN) simulator, represents an SNN as a graph of stochastic differential equations and simulates the time-evolution of these equations. It has the capability of reading inputs from file and writing outputs to file, and generally supports experimentation, analysis, and algorithm development using SNNs. 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.
Noel, Todd↗
Model-based Hierarchical Reinforcement Learning for Improved Physical Security Design: A Prototype
Prior work in FY24 developed an adversarial AI agent aid in path analysis of physical protection systems. This agent, trained using a model-based reinforcement learning algorithm, was able to successfully learn the most vulnerable path in facilities. It was able to extend the current state of practice for physical protection design by exhibiting dynamic behavior based on current environmental conditions. Whereas PathTrace largely performs a static, graph-based analysis, the AI agent was able to make decisions based on relative position in the facility, current conditions (was the adversarial agnet discovered?), and proximity to secondary targets. The agent demonstrated some novel capabilities, but had limitations that need to be resolved before it can be used for production purposes. For example, the adversarial agent generalizes poorly and takes a relatively long time to train. Nonetheless, there is still considerable promise for developing the adversarial agent further in order to explore even richer, more dynamic behaviors (e.g., adversary motivations, environmental debris, and more). This work considers a complementary idea; development of a planning agent. The planning agent is envisioned as an auto-complete-like tool that can help accelerate security system design by human experts. The agent would respect existing barriers and sensors placed by a human expert while offering cost-effective suggestions (i.e., implicitly balancing effectiveness with cost) to improve the design. The goal is for this agent to be part of an expert’s toolbox, not to totally upend the current state-of-practice, or to displace human experts. The ultimate goal would be concurrent training of both the adversarial and planning agent together, to learn entirely through self-play. This would represent an entirely new way of performing system deign. We selected a hierarchical, model-based reinforcement learning algorithm to serve as the planning agent. This is an extension of concepts used in the prior FY24 adversarial agent work. There, we had a single agent acting an environment. Here, we have two different sub-agents (policies), working together, to form a complete agent. There is a manager policy, which can select abstract goals on slower time scales, and a worker, which performs primitive actions to reach goals selected by the manager. It is worth noting that this class of algorithm is challenging to work with. From our understanding, our work is one of the first successful uses of model-based reinforcement learning (MBRL) in nuclear energy1 , and likely the first hierarchical model-based reinforcement learning application in nuclear energy. Further, this work is one of the first known attempts to apply AI to perform a design tasks in nuclear energy. Consequently, there were significant implementation challenges and the bulk of the work was focused on successful implementation and algorithm design. The results presented here are very low technology readiness level as a consequence of the lack of related literature, but still represent a significant step forward in the pursuit of applied AI for design.
42 ENGINEERING↗
Leveraging graph clustering techniques for cyber‐physical system analysis to enhance disturbance characterisation
Abstract Cyber‐physical systems have behaviour that crosses domain boundaries during events such as planned operational changes and malicious disturbances. Traditionally, the cyber and physical systems are monitored separately and use very different toolsets and analysis paradigms. The security and privacy of these cyber‐physical systems requires improved understanding of the combined cyber‐physical system behaviour and methods for holistic analysis. Therefore, the authors propose leveraging clustering techniques on cyber‐physical data from smart grid systems to analyse differences and similarities in behaviour during cyber‐, physical‐, and cyber‐physical disturbances. Since clustering methods are commonly used in data science to examine statistical similarities in order to sort large datasets, these algorithms can assist in identifying useful relationships in cyber‐physical systems. Through this analysis, deeper insights can be shared with decision‐makers on what cyber and physical components are strongly or weakly linked, what cyber‐physical pathways are most traversed, and the criticality of certain cyber‐physical nodes or edges. This paper presents several types of clustering methods for cyber‐physical graphs of smart grid systems and their application in assessing different types of disturbances for informing cyber‐physical situational awareness. The collection of these clustering techniques provide a foundational basis for cyber‐physical graph interdependency analysis.
97 MATHEMATICS AND COMPUTING↗
Graph theory and nighttime imagery based microgrid design
Reducing the duration and frequency of blackouts in remote communities poses an engineering challenge for grid operators. Outage effects can also be mitigated locally through microgrids. This paper develops a systematic procedure to account for these challenges by creating microgrids prioritizing high value assets within vulnerable communities. Nighttime satellite imagery is used to identify vulnerable communities. Using an asset classification and rating system, multi-asset clusters within these communities are prioritized. Infrastructure data, geographic information systems, satellite imagery, and spectral clustering are used to form and rank microgrid candidates. A microgrid sizing algorithm is included to guide through the microgrid design process. Finally, an application of the methodology is presented using real event, location, and asset data.
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Programming Strategies for Irregular Algorithms on the Emu Chick
The Emu Chick prototype implements migratory memory-side processing in a novel hardware system. Rather than transferring large amounts of data across the system interconnect, the Emu Chick moves lightweight thread contexts to near-memory cores before the beginning of each remote memory read. Previous work has characterized the performance of the Chick prototype in terms of memory bandwidth and programming differences from more typical, non-migratory platforms, but there has not yet been an analysis of algorithms on this system. This work evaluates irregular algorithms that could benefit from the lightweight, memory-side processing of the Chick and demonstrates techniques and optimization strategies for achieving performance in sparse matrix-vector multiply operation (SpMV), breadth-first search (BFS), and graph alignment across up to eight distributed nodes encompassing 64 nodelets in the Chick system. We also define and justify relative metrics to compare prototype FPGA-based hardware with established ASIC architectures. The Chick currently supports up to 68x scaling for graph alignment, 80 MTEPS for BFS on balanced graphs, and 50% of measured STREAM bandwidth for SpMV.
Hein, Eric↗
Empirical performance bounds for quantum approximate optimization
The quantum approximate optimization algorithm (QAOA) has been put forth as a method for near-term quantum computers to solve optimization problems. However, assessments of QAOA performance have mostly focused on small structured problem instances while performance on more general instances is less clear. Here, we numerically simulate QAOA pure state dynamics for every instance of MaxCut on non-isomorphic unweighted graphs with nine or fewer vertices with depth parameters p ≤ 3. We find the approximation ratios and optimized circuit parameters concentrate across graphs of a given size and empirically show increases in concentration as graph size increases. The parameter concentration leads to two median-angle heuristics that overcome difficulties in QAOA parameter optimization and obtain mean approximation ratios within 3% and 0.2% of the optimal. We also analyze the probability to measure an optimal solution and find increasing variations between graphs as depth increases, in stark contrast to the approximation ratios which concentrate as depth increases. Furthermore, the resulting benchmark data set gives empirical bounds for on-going experimental realizations and lays groundwork for theoretical extensions to greater problem sizes and depths where QAOA may prove important for practically relevant problems.
79 ASTRONOMY AND ASTROPHYSICS↗
Certifiably Correct Range-Aided SLAM
We present the first algorithm capable of efficiently computing certifiably optimal solutions to range-aided simultaneous localization and mapping (RA-SLAM) problems. Robotic navigation systems are increasingly incorporating point-to-point ranging sensors, leading state estimation which takes the form of RA-SLAM. However, the RA-SLAM problem is more difficult to solve than traditional pose-graph SLAM; ranging sensor models introduce additional non-convexity, unlike pose-pose or pose-landmark measurements, a single range measurement does not uniquely determine the relative transform between the involved sensors, and RA-SLAM inference is highly sensitive to initial estimates. Our approach relaxes the RA-SLAM problem to a semidefinite program (SDP), which we show how to solve efficiently using the Riemannian staircase methodology. The solution of this SDP provides a high-quality initialization for our original RA-SLAM problem, which is subsequently refined via local optimization, as well as a lower-bound on the RA-SLAM problem's optimal value. Our algorithm, named certifiably correct RA-SLAM (CORA), applies to problems comprised of arbitrary pose-pose, pose-landmark, and ranging measurements. Evaluation on simulated and real-world marine examples shows that our algorithm frequently produces certifiably optimal RA-SLAM solutions; moreover, even suboptimal estimates are typically within 1-2\% of the optimal value.
Papalia, Alan↗