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DOE OSTI2022

FINETUNA: fine-tuning accelerated molecular simulations

Abstract Progress towards the energy breakthroughs needed to combat climate change can be significantly accelerated through the efficient simulation of atomistic systems. However, simulation techniques based on first principles, such as density functional theory (DFT), are limited in their practical use due to their high computational expense. Machine learning approaches have the potential to approximate DFT in a computationally efficient manner, which could dramatically increase the impact of computational simulations on real-world problems. However, they are limited by their accuracy and the cost of generating labeled data. Here, we present an online active learning framework for accelerating the simulation of atomic systems efficiently and accurately by incorporating prior physical information learned by large-scale pre-trained graph neural network models from the Open Catalyst Project. Accelerating these simulations enables useful data to be generated more cheaply, allowing better models to be trained and more atomistic systems to be screened. We also present a method of comparing local optimization techniques on the basis of both their speed and accuracy. Experiments on 30 benchmark adsorbate-catalyst systems show that our method of transfer learning to incorporate prior information from pre-trained models accelerates simulations by reducing the number of DFT calculations by 91%, while meeting an accuracy threshold of 0.02 eV 93% of the time. Finally, we demonstrate a technique for leveraging the interactive functionality built in to Vienna ab initio Simulation Package (VASP) to efficiently compute single point calculations within our online active learning framework without the significant startup costs. This allows VASP to work in tandem with our framework while requiring 75% fewer self-consistent cycles than conventional single point calculations. The online active learning implementation, and examples using the VASP interactive code, are available in the open source FINETUNA package on Github.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Network analysis of earthquake ground motion spatial correlation: a case study with the San Jacinto seismic nodal array

SUMMARY The spatial correlation of earthquake ground motion intensity can be measured from strong motion data; however, the data used in past studies is sparsely sampled in space, and only the interstation distance was considered as a correlation variable. These limitations mean that we have only weak constraints on the true correlation structure of ground motion and that potentially important aspects of spatial correlation are unconstrained. In this study, we combine a large-N seismic array and graph analytics to explore this issue at a local scale using small local and regional earthquakes. Our result suggests site conditions, and how they interact with the incident seismic wavefield, strongly condition the spatial correlation of ground motion. Future progress in characterizing ground motion spatial variability will require dense wavefield measurements, either through nodal deployments, or perhaps distributed acoustic sensing measurements, of seismic wavefields. Aftershock sequences of major earthquakes would provide particularly data-rich targets of opportunity.

58 GEOSCIENCES↗

DOE OSTI2026

Dark Energy Survey Year 3 results: Simulation-based 𝑤CDM inference from weak lensing and galaxy clustering maps with deep learning: Analysis design

Data-driven approaches using deep learning are emerging as powerful techniques to extract non-Gaussian information from cosmological large-scale structure. Here, this work presents the first simulation-based inference (SBI) pipeline that combines weak lensing and galaxy clustering maps in a realistic Dark Energy Survey Year 3 (DES Y3) configuration and serves as preparation for a forthcoming analysis of the survey data. We develop a scalable forward model based on the CosmoGridV1 suite of N-body simulations to generate over one million self-consistent mock realizations of DES Y3 at the map level. Leveraging this large dataset, we train deep graph convolutional neural networks on the full survey footprint in spherical geometry to learn low-dimensional features that approximately maximize mutual information with target parameters. These learned compressions enable neural density estimation of the implicit likelihood via normalizing flows in a ten-dimensional parameter space spanning cosmological 𝑤CDM, intrinsic alignment, and linear galaxy bias parameters, while marginalizing over baryonic, photometric redshift, and shear bias nuisances. To ensure robustness, we extensively validate our inference pipeline using synthetic observations derived from both systematic contaminations in our forward model and independent Buzzard galaxy catalogs. Our forecasts yield significant improvements in cosmological parameter constraints, achieving 2−3× higher figures of merit in the 𝛺 𝑚 − 𝑆 8 plane relative to our implementation of baseline two-point statistics and effectively breaking parameter degeneracies through probe combination. These results demonstrate the potential of SBI analyses powered by deep learning for upcoming Stage-IV wide-field imaging surveys.

Thomsen, A. [Zurich, ETH] (ORCID:0000000203099021)↗

DOE OSTI2024

A Novel Framework to Quantify Power Grid Resilience

The quantification of an operating power grid’s resilience is highly significant today, given its criticality as an enabler of other infrastructures, complexity, and the threat it faces due to a wide range of detrimental events, from extreme climate to cyber attacks. Currently, there exist no standardized definitions and metrics for measuring the resilience of an operating grid. In this paper, we introduce a novel resilience quantification framework and demonstrate a method to measure the flexibility towards topological/structural changes due to potential failures in the power grid to assess operational resilience. We start with the state estimation data from a large utility and use the graph analysis methods and power flow simulation tools to compute the identified resilience parameters.

Yoginath, Srikanth↗

DOE OSTI2021

Sparse Approximate Multifrontal Factorization with Butterfly Compression for High-Frequency Wave Equations

In this work, we present a fast and approximate multifrontal solver for large-scale sparse linear systems arising from finite-difference, finite-volume or finite-element discretization of high-frequency wave equations. The proposed solver leverages the butterfly algorithm and its hierarchical matrix extension for compressing and factorizing large frontal matrices via graph-distance guided entry evaluation or randomized matrix-vector multiplication-based schemes. Complexity analysis and numerical experiments demonstrate $\mathcal{O}(N\log^2 N)$ computation and $\mathcal{O}(N)$ memory complexity when applied to an $N\times N$ sparse system arising from 3D high-frequency Helmholtz and Maxwell problems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

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↗

DOE OSTI2020

Towards real-time forecasting of natural gas production by harnessing graph theory for stochastic discrete fracture networks

In this work, we compare hydrocarbon production curves obtained from a graph-based reduced-order model with the high-fidelity Discrete Fracture Network (DFN) predictions for a fracture network created using data from a real shale site. We observe that the bounds for the high fidelity DFN model lie within the bounds for the reduced order model, implying that the reduced-order model provides a conservative estimate. Moreover, we found that except for first-passage times and late arriving mass, the production curves from the reduced-order model predict transport accurately. However, it is to be noted that the results are inspite of trading a three-dimensional geometry for a reduced system in the form of a graph, one that is 500–1000 times faster in terms of computational efficiency (for this particular application). In addition, we also compare the production curves for large drawdown and small drawdown using our graph approach. The reduced-order model is successful in showing that the long term productivity is higher in case of small drawdown although the initial productivity is higher for large drawdown. Thus, this reduced-order model offers great potential in uncertainty quantification for production, as well as in providing operators with information to make real-time decisions for optimal production.

03 NATURAL GAS↗

DOE OSTI2023

Graph Sparsification by Approximate matrix Multiplication

Graphs arising in statistical problems, signal processing, large networks, combinatorial optimization, and data analysis are often dense, which causes both computational and storage bottlenecks. One way of sparsifying a weighted graph, while sharing the same vertices as the original graph but reducing the number of edges, is through spectral sparsification. We study this problem through the perspective of RandNLA. Specifically, we utilize randomized matrix multiplication to give a clean and simple analysis of how sampling according to edge weights gives a spectral approximation to graph Laplacians, without requiring spectral information. Through the CR–MM algorithm, we attain a simple and computationally efficient sparsifier whose resulting Laplacian estimate is unbiased and of minimum variance. Here, we define a new notion of additive spectral sparsifiers, which has not been considered in the literature.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Network-Level Traffic Signal Cooperation: A Higher-Order Conflict Graph Approach

Traffic signal control and cooperation are extremely important to alleviate traffic congestion in a large traffic network. This study develops a higher-order conflict graph approach for network-wide traffic signal control and cooperation. A conflict graph is applied to model the traffic signal configurations, which identifies the conflict and unconflicted movements for each intersection. In conflict graph, the node represents each movement. The weight of each node can be defined as traffic volume, queue length, fuel consumption, or any weighted combinations of these measurements. The calculation of the optimal green light duration and green light sequence (for different movements) is equivalent to sequentially finding the maximum weight independent set (MWIS) in the conflict graph. The conflict graph also provides a uniform and efficient way to connect traffic signal operations among nearby intersections spatially. Then, we introduced the concept of the k -th order neighborhood to model the degree of connectivity between each movement to the movements at upstream or downstream intersections. The weight of each node in the higher-order conflict graph not only represents its own congestion level, but also relates to the traffic conditions of nearby intersections. Through this approach, the cooperation of multiple intersections can be realized by incorporating their spatial connectivity into conflict graph and solving the MWIS problem. A simulation network is built in SUMO to test the effectiveness of the proposed method. Results suggested that the proposed model outperformed other state-of-the-art signal control methods. Also, the scheme maintains good performance under varying traffic demands.

42 ENGINEERING↗

DOE OSTI2024

AGS-GNN: Attribute-guided Sampling for Graph Neural Networks

We propose AGS-GNN, a novel attribute-guided sampling algorithm for Graph Neural Networks (GNNs) that exploits node features and connectivity structure of a graph while simultaneously adapting for both homophily and heterophily in graphs. (In homophilic graphs vertices of the same class are more likely to be connected, and vertices of different classes tend to be linked in heterophilic graphs.) While GNNs have been successfully applied to homophilic graphs, their application to heterophilic graphs remains challenging. The best-performing GNNs for heterophilic graphs do not fit the sampling paradigm, suffer high computational costs, and are not inductive. We employ samplers based on feature-similarity and feature-diversity to select subsets of neighbors for a node, and adaptively capture information from homophilic and heterophilic neighborhoods using dual channels. Currently, AGS-GNN is the only algorithm that we know of that explicitly controls homophily in the sampled subgraph through similar and diverse neighborhood samples. For diverse neighborhood sampling, we employ submodularity, which was not used in this context prior to our work. The sampling distribution is pre-computed and highly parallel, achieving the desired scalability. Using an extensive dataset consisting of 35 small (<=100K nodes) and large (>100K nodes) homophilic and heterophilic graphs, we demonstrate the superiority of AGS-GNN compare to the current approaches in the literature. AGS-GNN achieves comparable test accuracy to the best-performing heterophilic GNNs, even outperforming methods using the entire graph for node classification. AGS-GNN also converges faster compared to methods that sample neighborhoods randomly, and can be incorporated into existing GNN models that employ node or graph sampling.

artificial intelligence↗

DOE OSTI2024

Data-driven modeling of dislocation mobility from atomistics using physics-informed machine learning

Dislocation mobility, which dictates the response of dislocations to an applied stress, is a fundamental property of crystalline materials that governs the evolution of plastic deformation. Traditional approaches for deriving mobility laws rely on phenomenological models of the underlying physics, whose free parameters are in turn fitted to a small number of intuition-driven atomic scale simulations under varying conditions of temperature and stress. This tedious and time-consuming approach becomes particularly cumbersome for materials with complex dependencies on stress, temperature, and local environment, such as body-centered cubic crystals (BCC) metals and alloys. In this paper, we present a novel, uncertainty quantification-driven active learning paradigm for learning dislocation mobility laws from automated high-throughput large-scale molecular dynamics simulations, using Graph Neural Networks (GNN) with a physics-informed architecture. We demonstrate that this Physics-informed Graph Neural Network (PI-GNN) framework captures the underlying physics more accurately compared to existing phenomenological mobility laws in BCC metals.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Hypergraph Analytics of Domain Name System Relationships

We report on the use of novel mathematical methods in hypergraph analytice over a large quantity of DNS data. Hypergraphs generalize graphs, as used in network science, to better model complex multiway relations in cyber data. Specifically, casting DNS data from Georgia Tech's ActiveDNS repository as hypergraphs allows us to fully represent the interactions between {\em collections} of domains and IP addresses. To facilitate large-scale analytics, we fielded an analytical pipeline of two capabilities. HyperNetX (HNX) is a Python package for the exploration and visualization of hypergraphs, acting as a frontend. For the backend, the Chapel HyperGraph Library (CHGL) is a library for high performance hypergraph analytics written in the exascale programming language Chapel. CHGL was used to process gigascale DNS data, performing compute-intensive calculations for data reduction and segmentation. Identified portions are then sent to HNX for both exploratory analysis and knowledge discovery targeting known tactics, techniques, and procedures.

Joslyn, Cliff A.↗

DOE OSTI2022

Coherent manipulation of graph states composed of finite-energy Gottesman-Kitaev-Preskill-encoded qubits

Graph states are a central resource in measurement-based quantum information processing. In the photonic qubit architecture based on Gottesman-Kitaev-Preskill (GKP) encoding, the generation of high-fidelity graph states composed of realistic, finite-energy approximate GKP-encoded qubits thus constitutes a key task. We consider the finite-energy approximation of GKP-qubit states given by a coherent superposition of shifted finite-squeezed vacuum states, where the displacements are Gaussian distributed. We present an exact description of graph states composed of such approximate GKP qubits as a coherent superposition of a Gaussian ensemble of randomly displaced ideal GKP-qubit graph states. Using standard Gaussian dynamics, we track the transformation of the covariance matrix and the mean-displacement vector elements of the Gaussian distribution of the ensemble under tools such as GKP-Steane error-correction and fusion operations that can be used to grow large high-fidelity GKP-qubit graph states. The covariance matrix elements capture the noise in the graph state due to the finite-energy approximation of GKP qubits, while the mean displacements relate to the possible absolute shift errors on the individual qubits arising conditionally from the homodyne measurements that are a part of these tools. Our work thus pins down an exact coherent error model for graph states generated from truly finite-energy GKP qubits, which can shed light on their error-correction properties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Accelerating amorphous polymer electrolyte screening by learning to reduce errors in molecular dynamics simulated properties

Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous systems: the amorphous structure of polymers requires multiple, repeated sampling to reduce noise and the slow relaxation requires long simulation time for convergence. Here, we accelerate the screening with a multi-task graph neural network that learns from a large amount of noisy, unconverged, short MD data and a small number of converged, long MD data. We achieve accurate predictions of 4 different converged properties and screen a space of 6247 polymers that is orders of magnitude larger than previous computational studies. Further, we extract several design principles for polymer electrolytes and provide an open dataset for the community. Our approach could be applicable to a broad class of material discovery problems that involve the simulation of complex, amorphous materials.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Many-body expansion based machine learning models for octahedral transition metal complexes

Abstract Graph-based machine learning (ML) models for material properties show great potential to accelerate virtual high-throughput screening of large chemical spaces. However, in their simplest forms, graph-based models do not include any 3D information and are unable to distinguish stereoisomers such as those arising from different orderings of ligands around a metal center in coordination complexes. In this work we present a modification to revised autocorrelation descriptors, a molecular graph featurization method, for predicting spin state dependent properties of octahedral transition metal complexes (TMCs). Inspired by analytical semi-empirical models for TMCs, the new modeling strategy is based on the many-body expansion (MBE) and allows one to tune the captured stereoisomer information by changing the truncation order of the MBE. We present the necessary modifications to include this approach in two commonly used ML methods, kernel ridge regression and feed-forward neural networks. On a test set composed of all possible isomers of binary TMCs, the best MBE models achieve mean absolute errors (MAEs) of 2.75 kcal mol −1 on spin-splitting energies and 0.26 eV on frontier orbital energy gaps, a 30%–40% reduction in error compared to models based on our previous approach. We also observe improved generalization to previously unseen ligands where the best-performing models exhibit MAEs of 4.00 kcal mol −1 (i.e. a 0.73 kcal mol −1 reduction) on the spin-splitting energies and 0.53 eV (i.e. a 0.10 eV reduction) on the frontier orbital energy gaps. Because the new approach incorporates insights from electronic structure theory, such as ligand additivity relationships, these models exhibit systematic generalization from homoleptic to heteroleptic complexes, allowing for efficient screening of TMC search spaces.

Meyer, Ralf (ORCID:0000000322360261)↗

DOE OSTI2022

MICCO: An Enhanced Multi-GPU Scheduling Framework for Many-Body Correlation Functions

Calculation of many-body correlation functions is one of the critical kernels utilized in many scientific computing areas, especially in Lattice Quantum Chromodynamics (Lattice QCD). It is formalized as a sum of a large number of contraction terms each of which can be represented by a graph consisting of vertices describing quarks inside a hadron node and edges designating quark propagations at specific time intervals. Due to its computation- and memory-intensive nature, real-world physics systems (e.g., multi-meson or multi-baryon systems) explored by Lattice QCD prefer to leverage multi-GPUs. Different from general graph processing, many-body correlation function calculations show two specific features: a large number of computation-/data-intensive kernels and frequently repeated appearances of original and intermediate data. The former results in expensive memory operations such as tensor movements and evictions. The latter offers data reuse opportunities to mitigate the data-intensive nature of many-body correlation function calculations. However, existing graph-based multi-GPU schedulers cannot capture these data-centric features, thus resulting in a sub-optimal performance for many-body correlation function calculations. To address this issue, this paper presents a multi-GPU scheduling framework, MICCO, to accelerate contractions for correlation functions particularly by taking the data dimension (e.g., data reuse and data eviction) into account. This work first performs a comprehensive study on the interplay of data reuse and load balance, and designs two new concepts: local reuse pattern and reuse bound to study the opportunity of achieving the optimal trade-off between them. Based on this study, MICCO proposes a heuristic scheduling algorithm and a machine-learning-based regression model to generate the optimal setting of reuse bounds. Specifically, MICCO is integrated into a real-world Lattice QCD system, Redstar, for the first time running on multiple GPUs. The evaluation demonstrates MICCO outperforms other state-of-art works, achieving up to 2.25× speedup in synthesized datasets, and 1.49× speedup in real-world correlation functions.

Wang, Qihan↗

DOE OSTI2021

Searching for metastable particles using graph computing

The reconstruction of charged particle trajectories at the Large Hadron Collider and future colliders relies on energy depositions in sensors placed at distances ranging from a centimeter to a meter from the colliding beams. We propose a method of detecting charged particles that decay invisibly after traversing a short distance of about 25 cm inside the experimental apparatus. One of the decay products may constitute the dark matter known to be 84% of all matter at galactic and cosmological distance scales. Our method uses graph computing to cluster spacepoints recorded by two-dimensional silicon pixel sensors into mathematically-defined patterns. The algorithm may be implemented on silicon-based integrated circuits using field-programmable gate array technology to augment or replace traditional computing platforms.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Exaflops Biomedical Knowledge Graph Analytics

We are motivated by newly proposed methods for mining large-scale corpora of scholarly publications (e.g., full biomedical literature), which consists of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover relationships among concepts. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as an all-pairs shortest paths (APSP) and validate connective paths against curated biomedical knowledge graphs (e.g., Spoke). In this context, we present Coast (Exascale Communication-Optimized All-Pairs Shortest Path) and demonstrate 1.004 EF/s on 9,200 Frontier nodes (73,600 GCDs). We develop hyperbolic performance models (HYPERMOD), which guide optimizations and parametric tuning. The proposed Coast algorithm achieved the memory constant parallel efficiency of 99% in the single-precision tropical semiring. Looking forward, Coast will enable the integration of scholarly corpora like PubMed into the Spoke biomedical knowledge graph.

Kannan, Ramakrishnan {ramki}↗