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All sources NASA NTRS DOE OSTI

DOE OSTI2025

PySIDT: Subgraph Isomorphic Decision Trees for Molecular Property Prediction

Accurate molecular property prediction is important across all fields of chemistry. Deep neural networks (DNNs) have become increasingly popular due to their ability to train automatically, avoiding the incredibly tedious process of constructing and extending traditional property estimation schemes. However, DNNs require large amounts of training data, are challenging to interpret, require large amounts of memory to load even during inference, and have severe difficulties incorporating qualitative chemical knowledge, which are often desired for molecular property prediction tasks. Here, in this study, we present PySIDT (https://github.com/zadorlab/PySIDT), a software for training and running inference on Subgraph Isomorphic Decision Trees (SIDTs). SIDTs are graph-based decision trees made of nodes associated with molecular substructures. Inference is done by descending target molecular structures down the decision tree to nodes with matching subgraph isomorphic substructures and making predictions based on the final (most specific) nodes matched. SIDTs scale down well to dataset sizes much smaller than is feasible for DNNs. As trees of molecular substructures, SIDTs are inherently readable and easy to visualize, making them easy to analyze. They are also straightforward to extend and retrain, facilitate uncertainty estimation, and enable easy integration of expert knowledge. We demonstrate the SIDT approach discussing its application to a diverse range of molecular prediction tasks: rate coefficient estimation, diffusion coefficient estimation, thermochemistry estimation, transition state bond stretch prediction, p K a prediction, stability of molecular structures, stability of surface structures, and prediction of surface lateral interaction energetics. Additionally, we demonstrate the power of the SIDT algorithms in two direct learning curve vanilla comparisons with the popular DNN-based software Chemprop and the popular gradient boosted trees-based software XGBoost on enthalpy of formation and rate coefficient prediction tasks. In particular, in the enthalpy of formation case, vanilla PySIDT is able to outperform vanilla Chemprop and XGBoost across the full range of training/validation set sizes out to 11,560 data points.

Johnson, Matthew Sean [Sandia National Laboratorie↗

DOE OSTI2014

Emergence of microbial networks as response to hostile environments

The majority of microorganisms live in complex communities under varying conditions. One pivotal question in evolutionary biology is the emergence of cooperative traits and their sustainment in altered environments or in the presence of free-riders. Co-occurrence patterns in the spatial distribution of biofilms can help define species’ identities, and systems biology tools are revealing networks of interacting microorganisms. However, networks of inter-dependencies involving micro-organisms in the planktonic phase may be just as important, with the added complexity that they are not bounded in space. An integrated approach linking imaging, “Omics” and modeling has the potential to enable new hypothesis and working models. In order to understand how cooperation can emerge and be maintained without abilities like memory or recognition we use evolutionary game theory as the natural framework to model cell-cell interactions arising from evolutive decisions. We consider a finite population distributed in a spatial domain (biofilm), and divided into two interacting classes with different traits. This interaction can be weighted by distance, and produces physical connections between two elements allowing them to exchange finite amounts of energy and matter. Available strategies to each individual of one class in the population are the propensities or “willingness” to connect any individual of the other class. Following evolutionary game theory, we propose a mathematical model which explains the patterns of connections which emerge when individuals are able to find connection strategies that asymptotically optimize their fitness. The process explains the formation of a network for efficiently exchanging energy and matter among individuals and thus ensuring their survival in hostile environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

graphenv: a Python library for reinforcement learning on graph search spaces

Many important and challenging problems in combinatorial optimization (CO) can be expressed as graph search problems, in which graph vertices represent full or partial solutions and edges represent decisions that connect them. Graph structure not only introduces strong relational inductive biases for learning (Battaglia et al., 2018) - in this context, by providing a way to explicitly model the value of transitioning (along edges) between one search state (vertex) and the next - but lends itself to problems both with and without clearly defined algebraic structure. For example, classic CO problems on graphs such as the Traveling Salesman Problem (TSP) can be expressed as either pure graph search or integer programs. Other problems, however, such as molecular optimization, do no have concise algebraic formulations and yet are readily implemented as a graph search (V. et al., 2022; Zhou et al., 2019). Such "model-free" problems constitute a large fraction of modern reinforcement learning (RL) research owing to the fact that it is often much easier to write a forward simulation that expresses all of the state transitions and rewards, than to write down the precise mathematical expression of the full optimization problem. In the case of molecular optimization, for example, one can use domain knowledge alongside existing software libraries to model the effect of adding a single bond or atom to an existing but incomplete molecule, and let the RL algorithm build a model of how good a given decision is by "experiencing" the simulated environment many times through. In contrast, a model-based mathematical formulation that fully expresses all the chemical and physical constraints is intractable. In recent years, RL has emerged as an effective paradigm for optimizing searches over graphs and led to state-of-the-art heuristics for games like Go and chess, as well as for classical CO problems such as the TSP. This combination of graph search and RL, while powerful, requires non-trivial software to execute, especially when combining advanced state representations such as Graph Neural Networks (GNN) with scalable RL algorithms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2013

Orders on Intervals Over Partially Ordered Sets: Extending Allen's Algebra and Interval Graph Results

To make a decision, we need to compare the values of quantities. In many practical situations, we know the values with interval uncertainty. In such situations, we need to compare intervals. Allen’s algebra describes all possible relations between intervals on the real line, and ordering relations between such intervals are well studied. In this paper, we extend this description to intervals in an arbitrary partially ordered set (poset). In particular, we explicitly describe ordering relations between intervals that generalize relation between points. As auxiliary results, we provide a logical interpretation of the relation between intervals, and extend the results about interval graphs to intervals over posets.

Zapata, Francisco↗

DOE OSTI2015

A Clustering Graph Generator

In very simple terms a network can be de ned as a collection of points joined together by lines. Thus, networks can be used to represent connections between entities in a wide variety of elds including engi- neering, science, medicine, and sociology. Many large real-world networks share a surprising number of properties, leading to a strong interest in model development research and techniques for building synthetic networks have been developed, that capture these similarities and replicate real-world graphs. Modeling these real-world networks serves two purposes. First, building models that mimic the patterns and prop- erties of real networks helps to understand the implications of these patterns and helps determine which patterns are important. If we develop a generative process to synthesize real networks we can also examine which growth processes are plausible and which are not. Secondly, high-quality, large-scale network data is often not available, because of economic, legal, technological, or other obstacles [7]. Thus, there are many instances where the systems of interest cannot be represented by a single exemplar network. As one example, consider the eld of cybersecurity, where systems require testing across diverse threat scenarios and validation across diverse network structures. In these cases, where there is no single exemplar network, the systems must instead be modeled as a collection of networks in which the variation among them may be just as important as their common features. By developing processes to build synthetic models, so-called graph generators, we can build synthetic networks that capture both the essential features of a system and realistic variability. Then we can use such synthetic graphs to perform tasks such as simulations, analysis, and decision making. We can also use synthetic graphs to performance test graph analysis algorithms, including clustering algorithms and anomaly detection algorithms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2013

Generative model selection using a scalable and size-independent complex network classifier

Real networks exhibit nontrivial topological features, such as heavy-tailed degree distribution, high clustering, and small-worldness. Researchers have developed several generative models for synthesizing artificial networks that are structurally similar to real networks. An important research problem is to identify the generative model that best fits to a target network. In this paper, we investigate this problem and our goal is to select the model that is able to generate graphs similar to a given network instance. By the means of generating synthetic networks with seven outstanding generative models, we have utilized machine learning methods to develop a decision tree for model selection. Our proposed method, which is named “Generative Model Selection for Complex Networks,” outperforms existing methods with respect to accuracy, scalability, and size-independence.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Multi-Agent Graph-Attention Deep Reinforcement Learning for Post-Contingency Grid Emergency Voltage Control

Grid emergency voltage control (GEVC) is paramount in electric power systems to improve voltage stability and prevent cascading outages and blackouts in case of contingencies. While most deep reinforcement learning (DRL)-based paradigms perform single agents in a static environment, real-world agents for GEVC are expected to cooperate in a dynamically shifting grid. Moreover, due to high uncertainties from combinatory natures of various contingencies and load consumption, along with the complexity of dynamic grid operation, the data efficiency and control performance of the existing DRL-based methods are challenged. To address these limitations, we propose a multi-agent graph-attention (GATT)-based DRL algorithm for GEVC in multi-area power systems. Here, we develop graph convolutional network (GCN)-based agents for feature representation of the graph-structured voltages to improve the decision accuracy in a data-efficient manner. Furthermore, a cutting-edge attention mechanism concentrates on effective information sharing among multiple agents, synergizing different-sized subnetworks in the grid for cooperative learning. We address several key challenges in the existing DRL-based GEVC approaches, including low scalability and poor stability against high uncertainties. Test results in the IEEE benchmark system verify the advantages of the proposed method over several recent multi-agent DRL-based algorithms.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2017

HodDB: Design and Analysis of a Query Processor for Brick.

Brick is a recently proposed metadata schema and ontology for describing building components and the relationships between them. It represents buildings as directed labeled graphs using the RDF data model. Using the SPARQL query language, building-agnostic applications query a Brick graph to discover the set of resources and relationships they require to operate. Latency-sensitive applications, such as user interfaces, demand response and modelpredictive control, require fast queries — conventionally less than 100ms. We benchmark a set of popular open-source and commercial SPARQL databases against three real Brick models using seven application queries and find that none of them meet this performance target. This lack of performance can be attributed to design decisions that optimize for queries over large graphs consisting of billions of triples, but give poor spatial locality and join performance on the small dense graphs typical of Brick. We present the design and evaluation of HodDB, a RDF/SPARQL database for Brick built over a node-based index structure. HodDB performs Brick queries 3-700x faster than leading SPARQL databases and consistently meets the 100ms threshold, enabling the portability of important latency-sensitive building applications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

Comparing Interaction Graphs on Cascading Outages under Different Loading Conditions

Interaction graphs on cascading outages of power systems provide valuable insights into how cascading outages evolve and propagate, and which components and links are critical to the propagation of cascading outages, enabling further development of mitigation strategies to support decision-making. However, the sensitivity of the interaction graph’s topology to the system’s loading condition has not been studied sufficiently. This paper compared interaction graphs under various loading conditions on the Northeastern Power Coordinating Council 140-bus system, and discovers the strong relationships between the graph topology, the cascade size distribution, and the load condition. Accordingly, three representative interaction graphs are constructed and illustrated.

Guo, Zhenping↗

DOE OSTI2023

Near-Optimal Distributed Linear-Quadratic Regulator for Networked Systems

This paper studies the trade-off between the degree of decentralization and the performance of a distributed controller in a linear-quadratic control setting. We study a system of interconnected agents over a graph and a distributed controller, called k-distributed control, which lets the agents make control decisions based on the state information within distance k on the underlying graph. This controller can tune its degree of decentralization using the parameter k and thus allows a characterization of the relationship between decentralization and performance. We show that under mild assumptions, including stabilizability, detectability, and a subexponentially growing graph condition, the performance difference between k-distributed control and centralized optimal control becomes exponentially small in k. Finally, this result reveals that distributed control can achieve near-optimal performance with a moderate degree of decentralization, and thus it is an effective controller architecture for large-scale networked systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

ACES-GNN: can graph neural network learn to explain activity cliffs?

Graph Neural Networks (GNNs) have revolutionized molecular property prediction by leveraging graph-based representations, yet their opaque decision-making processes hinder broader adoption in drug discovery. This study introduces the Activity-Cliff-Explanation-Supervised GNN (ACES-GNN) framework, designed to simultaneously improve predictive accuracy and interpretability by integrating explanation supervision for activity cliffs (ACs) into GNN training. ACs, defined by structurally similar molecules with significant potency differences, pose challenges for traditional models due to their reliance on shared structural features. By aligning model attributions with chemist-friendly interpretations, the ACES-GNN framework bridges the gap between prediction and explanation. Validated across 30 pharmacological targets, ACES-GNN consistently enhances both predictive accuracy and attribution quality for ACs compared to unsupervised GNNs. Our results demonstrate a positive correlation between improved predictions and accurate explanations, offering a robust and adaptable framework to better understand and interpret ACs. This work underscores the potential of explanation-guided learning to advance interpretable artificial intelligence in molecular modeling and drug discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Quantitative Risk Management - Risk Informed Decision Making on High-Risk Waste Remediation Projects - 19022

For every $1 billion invested in projects, $97 million is wasted due to poor project performance. That means 9.7% of money spent on projects is wasted due to poor risk and uncertainty management. High-risk projects, similar to those in waste remediation, have the most to lose. A solid quantitative risk management program is one of the keys to increasing the likelihood that a project will succeed. A quantitative risk program solves two major problems that challenge the effective management of risk and uncertainty: 1. Risks arise at all levels of an organization; however, not all organizational levels have an effective way to identify and resolve them. This can lead to risks that, even if identified, are not reported. 2. Decision-makers are often forced to operate solely on intuition when implementing mitigation strategies, not fully understanding the effects that certain decisions have on the program's cost and schedule. A quantitative risk program uses a risk register and builds it into the project/program integrated schedule to assess the impact of these risks, typically at the 80% confidence contingency level for specific milestones and/or project completion. Implementing a quantitative risk program drives a forward-thinking, proactive mentality to problem solving into all levels of the organization. A healthy risk program for regular reporting and communication ensures that all members of an organization are thinking about risks and using their communication channels to resolve them. It gives a method of communication and incentive for all levels in the organization and helps to ensure that risks will be reported and resolved. Pacific Northwest National Laboratory (PNNL) has developed tools and methods that provide a level of realism for analyzing different scenarios and estimating contingency that does not exist in the standard industry risk tool kit. These tools and methods provide decision-makers with actionable, quantitatively based information to guide their decision making. The first tool is a probabilistic branching risk model for mitigation strategies. Current quantitative risk analysis tools in the industry simulate two cases: fully mitigated and un-mitigated. In the fully mitigated case, the user assumes that every planned mitigation activity is successful. In the un-mitigated case, the user assumes that none are successful. The truth lies between these two extremes. The PNNL team has developed a probabilistic risk model for mitigation scenarios that includes a probability that a mitigation activity will succeed and a probability that a mitigation action will be funded. These probabilities are elicited from subject matter experts and ensure that the contingency calculations at the specified confidence are approaching reality. The second tool developed at PNNL is the Risk Box, which is a tool that integrates with different scenarios in the risk register. For example, say the user is faced with two different and mutually exclusive mitigation actions to reduce a risk. The Risk Box methodology performs the contingency calculations and then displays them on a time-phased graph that shows how each scenario reduces the risk contingency needed on the project/program. This graph then provides quantitative information to show decision-makers which mitigation action provides the greatest reduction (cost and schedule) in risk contingency for the program. Implementing these and other tools within a structured risk program increases the likelihood that a project will come in on schedule and budget, ensures that all personnel are proactively thinking about problems and resolutions, creates communication channels for all members to submit and resolve potential problems, produces a prioritized list of risk rankings to focus leadership on issues that may cause the biggest problems, and implements processes that drive updates to the risk program as the risk profile changes. PNNL has been developing these methods and using them on projects for over 20 years. They have been successfully applied on waste management projects, high-tech research and development projects, and construction projects, and they continue to be used on a number of U.S. Department of Energy projects today. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

InterGraph-CPS: A Graph-Theoretic Approach to Characterize Cross-Domain Cyber-Physical Interdependencies and Uncertainties in Electric Grid Systems for Improved Decision-Making in Operation and Response

Critical infrastructure systems such as the electric grid are increasingly cyber-physical; yet, despite the cyber-physical characteristics of critical infrastructure systems, the physical process system and communication/control network system are traditionally analyzed in siloes. As these systems become more cyber-physical, it is crucial that models and methods are available to assess the cyber physical system (CPS) interdependencies, characteristics, and event propagation for improved planning, operation, and response. Thus, we proposed an integrated structural and temporal CPS interdependency analysis framework, InterGraph-CPS, that provides insight into the CPS function during normal operation as well as disturbances. This integrated structural and temporal interdependency framework is uniquely designed for assessing CPSs by account for the challenges of analyzing cyber and physical data streams together due to data availability, data type, and time scale differences. By leveraging both structural (e.g., graph analysis) and temporal (e.g., data analytics) techniques, different CPS behaviors and configurations can be accounted for.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Improving Trustworthiness of Data-Driven Power Grid Contingency Analysis With Bayesian Residual Graph Neural Networks

The evolving energy landscape requires novel tools to efficiently perform contingency analysis and reliability assessment of power grids, potentially in real-time. The high computational cost of traditional power flow solvers limits their applicability in practice. Machine learning (ML) surrogates such as deep neural networks (NNs) accelerate power flow solvers computations, enabling high-order contingency analysis and real-time decision-making by learning highly nonlinear functions and integrating grid topology via graph architectures. However, (graph) NNs lack predictive power away from training data and do not provide predictive confidence estimates. Here, we present a Bayesian residual graph NN that integrates knowledge from low-fidelity data via residual training and embeds granular quantification of uncertainties, improving trustworthiness critical for high-consequence decision-making. Applying Bayesian concepts to NNs is challenging due to the high-dimensionality of both the parameter space, complicating derivation of a meaningful prior, and the output space in large grid systems, requiring enhanced techniques to assess the predicted high-dimensional uncertainties. Our contributions include: (1) Deriving a prior for fully connected and graph NNs that leverages low-fidelity data to guide mean predictions and appropriately control prior predictive uncertainty. (2) Integrating this prior within an ensembling with anchoring scheme for efficient approximate posterior inference. (3) Deriving enhanced metrics to assess accuracy of both the mean and uncertainty predictions in high dimensions, appropriately accounting for correlations propagated through graph layers. The resulting Bayesian residual graph NN is tested on a contingency analysis task for 14-bus and 118-bus grids.

24 - POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2018

Human attitude analysis based on fuzzy soft differential equations with Bonferroni mean

In this paper, we model a system of fuzzy soft differential equations to analyze the behavior over the time of an individual depending on their companion’s actions under any particular situation against some decision. The Bonferroni mean (BM) is a very useful tool for group decision-making problems when arguments are interrelated to each other as Bonferroni mean can capture the interrelationship of the individual arguments. Using this ability of BM, we define Bonferroni fuzzy soft matrix (BFSM) and weighted Bonferroni fuzzy soft matrix (WBFSM) for data representation. WBFSM is a decision matrix and provide the optimum fuzzy soft constant (OFSC) which is the key element of fuzzy soft differential equation. By utilizing the OFSC, we develop a system of fuzzy soft differential equations to study a dynamical process with nonlinear uncertain and vague data. Second, we present a novel efficient technique for analyzing the future attitude of people due to their present decisions. To illustrate the practicality and feasibility of proposed technique an illustrative example is also discussed with the help of phase portrait and line graphs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Oak Ridge Graph Analytics for Medical Innovation (ORiGAMI)

In this era of data-driven decisions and discovery where Big Data is producing Bigger Data, data scientists at the Oak Ridge National Laboratory are leveraging unique leadership infrastructure (e.g., Urika XA and Urika GD appliances) to develop scalable algorithms for semantic, logical and statistical reasoning with Big Data (i.e., data stored in databases as well as unstructured data in documents). ORiGAMI is a next-generation knowledge-discovery framework that is: (a) knowledge nurturing (i.e., evolves seamlessly with newer knowledge and data), (b) smart and curious (i.e. using information-foraging and reasoning algorithms to digest content) and (c) synergistic (i.e., interfaces computers with what they do best to help subject-matter-experts do their best. ORiGAMI has been demonstrated using the National Library of Medicine's SEMANTIC MEDLINE (archive of medical knowledge since 1994).

Roberts, LarryW.↗

DOE OSTI2016

Oak Ridge Graph Analytics for Medical Innovation (ORiGAMI)

Roberts, Larry W.↗

DOE OSTI2019

Scalable Causal Graph Learning through a Deep Neural Network

Learning the causal graph in a complex system is crucial for knowledge discovery and decision making, yet it remains a challenging problem because of the unknown nonlinear interaction among system components. Most of the existing methods either rely on predefined kernel or data distribution, or they focus simply on the causality between a single target and the remaining system. This work presents a deep neural network for scalable causal graph learning (SCGL) through low-rank approximation. The SCGL model can explore nonlinearity on both temporal and intervariable relationships without any predefined kernel or distribution assumptions. Through low-rank approximation, the noise influence is reduced, and better accuracy and high scalability are achieved. Experiments using synthetic and real-world datasets show that our SCGL algorithm outperforms existing state-of-the-art methods for causal graph learning.

97 MATHEMATICS AND COMPUTING↗