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At least 307 records · Page 17

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DOE OSTI2024

Using spatio-temporal graph neural networks to estimate fleet-wide photovoltaic performance degradation patterns

Accurate estimation of photovoltaic (PV) system performance is crucial for determining its feasibility as a power generation technology and financial asset. PV-based energy solutions offer a viable alternative to traditional energy resources due to their superior Levelized Cost of Energy (LCOE). A significant challenge in assessing the LCOE of PV systems lies in understanding the Performance Loss Rate (PLR) for large fleets of PV systems. Estimating the PLR of PV systems becomes increasingly important in the rapidly growing PV industry. Precise PLR estimation benefits PV users by providing real-time monitoring of PV module performance, while explainable PLR estimation assists PV manufacturers in studying and enhancing the performance of their products. However, traditional PLR estimation methods based on statistical models have notable drawbacks. Firstly, they require user knowledge and decision-making. Secondly, they fail to leverage spatial coherence for fleet-level analysis. Additionally, these methods inherently assume the linearity of degradation, which is not representative of real world degradation. To overcome these challenges, we propose a novel graph deep learning-based decomposition method called the Spatio-Temporal Graph Neural Network for fleet-level PLR estimation (PV-stGNN-PLR). PV-stGNN-PLR decomposes the power timeseries data into aging and fluctuation components, utilizing the aging component to estimate PLR. PV-stGNN-PLR exploits spatial and temporal coherence to derive PLR estimation for all systems in a fleet and imposes flatness and smoothness regularization in loss function to ensure the successful disentanglement between aging and fluctuation. We have evaluated PV-stGNN-PLR on three simulated PV datasets consisting of 100 inverters from 5 sites. Experimental results show that PV-stGNN-PLR obtains a reduction of 33.9% and 35.1% on average in Mean Absolute Percent Error (MAPE) and Euclidean Distance (ED) in PLR degradation pattern estimation compared to the state-of-the-art PLR estimation methods.

14 SOLAR ENERGY↗

DOE OSTI2026

Data Summarization and Inference at Scale

This is the final report for the DOE ASCR grant SC-0022260, Data Summarization and Inference at Scale, PI: Alex Pothen, Purdue University. The goal of the project was to solve data-intensive and compute-intensive problems in the physical sciences, engineering, information science, data science, etc. by designing and implementing new algorithms that could work with a subset of the data. The four subgoals were: (a) The solution of problems where the data is too large to be stored in the memory of a computer. In this streaming model of computation, the data arrives as a stream of elements to the computer, each element is processed as it arrives, and a decision is made to discard the data or to store it; only a small subset of the data proportional to the size of the output solution is stored, and when all the data has been streamed, a solution to the problem is computed from the stored subset. (b) The use of machine learning methods to compute solutions to data-intensive problems. The use of GPUs is critical to obtain high performance on machine learning tasks, but their memory sizes are smaller relative to that of CPUs. For large-scale problems, the data is sampled many times, and small samples are used with repetition, for robustness, to compute solutions to inference tasks. This sampling reduces the memory required to solve the problem, but attention is needed to avoid slow convergence to the solutions, and reduced accuracy of inference. We propose submodular optimization, Large Language Models, and physics-informed neural networks to enable GPU computations here. (c) Modeling and visualization of high-dimensional data using interpretable features. Clinical proteomic data sets from immunology for the detection of cancer and other diseases are temporal and high-dimensional, and algorithms for visualizing these data sets using clinically interpretable features are lacking. We propose methods that compute distances based on the optimal transportation problem and graph edit distances to address this problem. We also propose the use of optimal transport-based distances, spatial statistics, and network structure to classify image data sets, We apply these algorithms to electron micrographs of the peripheral nervous system in the digestive tract. (d) The design of data-intensive algorithms on emerging architectures, specifically, noisy, intermediate-scale quantum (NISQ) devices. Quantum computers offer the possibility of exploring large solution spaces due to the principle of superposition, but current quantum computers are limited by few qubits, short coherence times due to noise, poor interconections among the qubits, etc. We propose the use of the divide and conquer paradigm to solve large-scale problems, wherein collections of small subproblems are solved on the quantum devices, and the solutions to the subproblems are integrated into a solution for the original problem on a classical computer.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Causal discovery from data assisted by large language models

Knowledge-driven discovery of novel materials necessitates the development of causal models for property emergence. While in the classical physical paradigm, the causal relationships are deduced based on physical principles or via experiment, the rapid accumulation of observational data necessitates learning causal relationships between dissimilar aspects of material structure and functionalities based on observations. For this, it is essential to integrate experimental data with prior domain knowledge. Here, we demonstrate this approach by combining high-resolution scanning transmission electron microscopy data with insights derived from large language models (LLMs). By applying ChatGPT to domain-specific literature, such as arXiv papers on ferroelectrics, and combining the obtained information with data-driven causal discovery, we construct adjacency matrices for directed acyclic graphs that map the causal relationships between structural, chemical, and polarization degrees of freedom in Sm-doped BiFeO 3 . This approach enables us to hypothesize how synthesis conditions influence material properties and guides experimental validation. Furthermore, the ultimate objective of this work is to develop a unified framework that integrates LLM-driven literature analysis with data-driven discovery, facilitating the precise engineering of ferroelectric materials by establishing clear connections between synthesis conditions and their resulting material properties.

Causal inference↗

DOE OSTI2021

Mechanical coupling in the nitrogenase complex

The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Graph Contractions for Calculating Correlation Functions in Lattice QCD

Computing correlation functions for many-particle systems in Lattice QCD is vital to extract nuclear physics observables like the energy spectrum of hadrons such as protons. However, this type of calculation has long been considered to be very challenging and computing-resource intensive because of the complex nature of a hadron composed of quarks with many degrees of freedom. In particular, a correlation function can be calculated through a sum of all possible pairs of quark contractions, each of which is a batched tensor contraction, dictated by Wick's theorem. Because the number of terms of this sum can be very large for any hadronic system of interest, fast evaluation of the sum faces several challenges: an extremely large number of contractions, a huge memory footprint at runtime, and the speed of tensor contractions. In this paper, we present a Lattice QCD analysis software suite, Redstar, which addresses these challenges by utilizing novel algorithmic and software engineering methods targeting modern computing platforms such as many-core CPUs and GPUs. In particular, Redstar represents every term in the sum of a correlation function by a graph, applies efficient graph algorithms to reduce the number of contractions to lower the cost of computations, and minimizes the total memory footprint. Moreover, Redstar carries out the contractions on either CPUs or GPUs utilizing an internal and highly efficient Hadron contraction library. Specifically, we illustrate some important algorithmic optimizations of Redstar, show various key design features of Hadron library, and present the speedup values due to the optimizations along with performance figures for calculating six correlations functions on four computing platforms.

Chen, Jie↗

DOE OSTI2023

Graph Contractions for Calculating Correlation Functions in Lattice QCD

Chen, Jie↗

DOE OSTI2024

How the Galaxy–Halo Connection Depends on Large-scale Environment

We investigate the connection between galaxies, dark matter halos, and their large-scale environments at z = 0 with Illustris TNG300 hydrodynamic simulation data. We predict stellar masses from subhalo properties to test two types of machine learning (ML) models: explainable boosting machines (EBMs) with simple galaxy environment features and E(3)-invariant graph neural networks (GNNs). The best-performing EBM models leverage spherically averaged overdensity features on 3 Mpc scales. Interpretations via SHapley Additive exPlanations also suggest that in the context of the TNG300 galaxy–halo connection, simple spherical overdensity on ∼3 Mpc scales is more important than cosmic web distance features measured using the DisPerSE algorithm. Meanwhile, a GNN with connectivity defined by a fixed linking length, L, outperforms the EBM models by a significant margin. As we increase the linking length scale, GNNs learn important environmental contributions up to the largest scales we probe (L = 10 Mpc). We conclude that 3 Mpc distance scales are most critical for describing the TNG galaxy–halo connection using the spherical overdensity parameterization, but that information on larger scales, which is not captured by simple environmental parameters or cosmic web features, can further augment these models. Our study highlights the benefits of using interpretable ML algorithms to explain models of astrophysical phenomena, and the power of using GNNs to flexibly learn complex relationships directly from data while imposing constraints from physical symmetries.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

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↗

DOE OSTI2023

AMORE-Isoprene v1.0: a new reduced mechanism for gas-phase isoprene oxidation

Abstract. Gas-phase oxidation of isoprene by ozone (O3) and the hydroxyl (OH) and nitrate (NO3) radicals significantly impacts tropospheric oxidant levels and secondary organic aerosol formation. The most comprehensive and up-to-date chemical mechanism for isoprene oxidation consists of several hundred species and over 800 reactions. Therefore, the computational expense of including the entire mechanism in large-scale atmospheric chemical transport models is usually prohibitive, and most models employ reduced isoprene mechanisms ranging in size from ∼ 10 to ∼ 200 species. We have developed a new reduced isoprene oxidation mechanism using a directed-graph path-based automated model reduction approach, with minimal manual adjustment of the output mechanism. The approach takes as inputs a full isoprene oxidation mechanism, the environmental parameter space, and a list of priority species which are protected from elimination during the reduction process. Our reduced mechanism, AMORE-Isoprene (where AMORE stands for Automated Model Reduction), consists of 12 species which are unique to the isoprene mechanism as well as 22 reactions. We demonstrate its performance in a box model in comparison with experimental data from the literature and other current isoprene oxidation mechanisms. AMORE-Isoprene's performance with respect to predicting the time evolution of isoprene oxidation products, including isoprene epoxydiols (IEPOX) and formaldehyde, is favorable compared with other similarly sized mechanisms. When AMORE-Isoprene is included in the Community Regional Atmospheric Chemistry Multiphase Mechanism 1.0 (CRACMM1AMORE) in the Community Multiscale Air Quality Model (CMAQ, v5.3.3), O3 and formaldehyde agreement with Environmental Protection Agency (EPA) Air Quality System observations is improved. O3 bias is reduced by 3.4 ppb under daytime conditions for O3 concentrations over 50 ppb. Formaldehyde bias is reduced by 0.26 ppb on average for all formaldehyde measurements compared with the base CRACMM1. There was no significant change in computation time between CRACMM1AMORE and the base CRACMM. AMORE-Isoprene shows a 35 % improvement in agreement between simulated IEPOX concentrations and chamber data over the base CRACMM1 mechanism when compared in the Framework for 0-D Atmospheric Modeling (F0AM) box model framework. This work demonstrates a new highly reduced isoprene mechanism and shows the potential value of automated model reduction for complex reaction systems.

58 GEOSCIENCES↗

DOE OSTI2026

Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials

Accurate molecular property predictions require 3D geometries, which are typically obtained using expensive methods such as density functional theory (DFT). Here, we attempt to obtain molecular geometries by relying solely on machine learning interatomic potential (MLIP) models. To this end, we first curate a large-scale molecular relaxation dataset comprising 3.5 million molecules and 300 million snapshots. Then MLIP pre-trained models are trained with supervised learning to predict energy and forces given 3D molecular structures. Once trained, we show that the pre-trained models can be used in different ways to obtain geometries either explicitly or implicitly. First, it can be used to obtain approximate low-energy 3D geometries via geometry optimization. While these geometries do not consistently reach DFT-level chemical accuracy or convergence, they can still improve downstream performance compared to non-relaxed structures. To mitigate potential biases and enhance downstream predictions, we introduce geometry fine-tuning based on the relaxed 3D geometries. Second, the pre-trained models can be directly fine-tuned for property prediction when ground truth 3D geometries are available. Our results demonstrate that MLIP pre-trained models trained on relaxation data can learn transferable molecular representations to improve downstream molecular property prediction and can provide practically valuable but approximate molecular geometries that benefit property predictions. Our code is publicly available at: https://github.com/divelab/AIRS/.

Fu, Cong [Texas A & M Univ., College Station, TX (↗

DOE OSTI2022

Automated exploitation of the big configuration space of large adsorbates on transition metals reveals chemistry feasibility

Mechanistic understanding of large molecule conversion and the discovery of suitable heterogeneous catalysts have been lagging due to the combinatorial inventory of intermediates and the inability of humans to enumerate all structures. Here, we introduce an automated framework to predict stable configurations on transition metal surfaces and demonstrate its validity for adsorbates with up to 6 carbon and oxygen atoms on 11 metals, enabling the exploration of ~10 8 potential configurations. It combines a graph enumeration platform, force field, multi-fidelity DFT calculations, and first-principles trained machine learning. Clusters in the data reveal groups of catalysts stabilizing different structures and expose selective catalysts for showcase transformations, such as the ethylene epoxidation on Ag and Cu and the lack of C-C scission chemistry on Au. Deviations from the commonly assumed atom valency rule of small adsorbates are also manifested. This library can be leveraged to identify catalysts for converting large molecules computationally.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Sampling electronic structure quadratic unconstrained binary optimization problems (QUBOs) with Ocean and Mukai solvers

The most advanced D-Wave Advantage quantum annealer has 5000+ qubits, however, every qubit is connected to a small number of neighbors. As such, implementation of a fully-connected graph results in an order of magnitude reduction in qubit count. To compensate for the reduced number of qubits, one has to rely on special heuristic software such as qbsolv, the purpose of which is to decompose a large quadratic unconstrained binary optimization (QUBO) problem into smaller pieces that fit onto a quantum annealer. In this work, we compare the performance of the open-source qbsolv which is a part of the D-Wave Ocean tools and a new Mukai QUBO solver from Quantum Computing Inc. (QCI). The comparison is done for solving the electronic structure problem and is implemented in a classical mode (Tabu search techniques). The Quantum Annealer Eigensolver is used to map the electronic structure eigenvalue-eigenvector equation to a QUBO problem, solvable on a D-Wave annealer. We find that the Mukai QUBO solver outperforms the Ocean qbsolv with one to two orders of magnitude more accurate energies for all calculations done in the present work, both the ground and excited state calculations. This work stimulates the further development of software to assist in the utilization of modern quantum annealers.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Graph-Based Attention Mechanisms for Solving the AC Optimal Power Flow Problem in Electrical Power Networks

With the increasing complexity and data availability in modern power systems, learning-based approaches to AC Optimal Power Flow (AC OPF) have garnered significant attention. In particular, the structure of smart grids lends itself naturally to graph-based representations, where Graph Neural Networks (GNNs) can capture spatial and relational dependencies. This paper investigates attention-based GNN architectures tailored to heterogeneous graph representations of electric grids. We evaluate two major paradigms: relational attention, which distinguishes between edge types during message passing, and meta-path attention, which captures high-level semantics through multi-hop, typed paths. Using a large corpus of public AC OPF scenarios, we benchmark representative models of each type of attention. Our results demonstrate the benefits of heterogeneous attention-based models in accurately capturing grid dynamics; heterogeneous attention models achieve superior performance in both standard and perturbed settings. The findings highlight the importance of semantic-aware architectures for improving prediction robustness and interpretability in power system applications.

Trigui, Ali [Qubit Engineering Inc.]↗

DOE OSTI2022

Entanglement perspective on the quantum approximate optimization algorithm

Many quantum algorithms seek to output a specific bitstring solving the problem of interest—or a few if the solution is degenerate. It is the case for the quantum approximate optimization algorithm (QAOA) in the limit of large circuit depth, which aims to solve quadratic unconstrained binary optimization problems. Hence, the expected final state for these algorithms is either a product state or a low-entangled superposition involving a few bitstrings. What happens in between the initial N -qubit product state | 0 〉 ⊗ N and the final one regarding entanglement? Here, we consider the QAOA algorithm for solving the paradigmatic MaxCut problem on different types of graphs. We study the entanglement growth and spread resulting from randomized and optimized QAOA circuits and find that there is a volume-law entanglement barrier between the initial and final states. We also investigate the entanglement spectrum in connection with random matrix theory. In addition, we compare the entanglement production with a quantum annealing protocol aiming to solve the same MaxCut problems. Finally, we discuss the implications of our results for the simulation of QAOA circuits with tensor network-based methods relying on low-entanglement for efficiency, such as matrix product states.

Dupont, Maxime↗

DOE OSTI2021

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis

Counterfactual inference is a useful tool for comparing outcomes of interventions on complex systems. It requires us to represent the system in form of a structural causal model, complete with a causal diagram, probabilistic assumptions on exogenous variables, and functional assignments. Specifying such models can be extremely difficult in practice. The process requires substantial domain expertise, and does not scale easily to large systems, multiple systems, or novel system modifications. At the same time, many application domains, such as molecular biology, are rich in structured causal knowledge that is qualitative in nature. This manuscript proposes a general approach for querying a causal knowledge graph with a causal question and converting the qualitative result into a quantitative structural causal model that can learn from data to answer the question. Here, we demonstrate the feasibility, accuracy and versatility of this approach using two case studies in systems biology. The first demonstrates the appropriateness of the underlying assumptions and the accuracy of the results. The second demonstrates the versatility of the approach by querying a knowledge base for the molecular determinants of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storm and performing counterfactual inference to predict the causal effect of medical countermeasures for severely ill COVID-19 patients.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Sensory stimulation for upper limb amputations modulates adaptability of cortical large-scale systems and combination of somatosensory and visual inputs

Abstract Touch-like phantom limb sensations can be elicited through targeted transcutaneous electrical nerve stimulation (tTENS) in individuals with upper limb amputation. The corresponding impact of sensory stimulation on cortical activity remains an open question. Brain network research shows that sensorimotor cortical activity is supported by dynamic changes in functional connections between relevant brain regions. These groups of interconnected regions are functional modules whose architecture enables specialized function and related neural processing supporting individual task needs. Using electroencephalographic (EEG) signals to analyze modular functional connectivity, we investigated changes in the modular architecture of cortical large-scale systems when participants with upper limb amputations performed phantom hand movements before, during, and after they received tTENS. We discovered that tTENS substantially decreased the flexibility of the default mode network (DMN). Furthermore, we found increased interconnectivity (measured by a graph theoretic integration metric) between the DMN, the somatomotor network (SMN) and the visual network (VN) in the individual with extensive tTENS experience. While for individuals with less tTENS experience, we found increased integration between DMN and the attention network. Our results provide insights into how sensory stimulation promotes cortical processing of combined somatosensory and visual inputs and help develop future tools to evaluate sensory combination for individuals with amputations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees

Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the “first-infection tree,” a potentially counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our observation of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment, but also the four additional situations that can complicate the inference of reassortment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

The PetscSF Scalable Communication Layer

PetscSF, the communication component of the Portable, Extensible Toolkit for Scientific Computation (PETSc), is designed to provide PETSc's communication infrastructure suitable for exascale computers that utilize GPUs and other accelerators. PetscSF provides a simple application programming interface (API) for managing common communication patterns in scientific computations by using a star-forest graph representation. PetscSF supports several implementations based on MPI and NVSHMEM, whose selection is based on the characteristics of the application or the target architecture. An efficient and portable model for network and intra-node communication is essential for implementing large-scale applications. The Message Passing Interface, which has been the de facto standard for distributed memory systems, has developed into a large complex API that does not yet provide high performance on the emerging heterogeneous CPU-GPU-based exascale systems. Here, we discuss the design of PetscSF, how it can overcome some difficulties of working directly with MPI on GPUs, and we demonstrate its performance, scalability, and novel features.

97 MATHEMATICS AND COMPUTING↗