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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The Utility in Conjoint Analysis as a Fast Expert Elicitation Technique

This paper presents an interface and analysis technique for quickly conducting expert elicitation with the goal of determining entity importance. Our interface deploys a two-alternative choice experiment that is capable of representing knowledge graphs in an easy to interpret fashion for users with limited experience with knowledge graphs. Our analysis methodology takes advantage of conjoint analysis techniques and provides entity weights for many SMEs simultaneously. The results largely align with individual participant fits.

Conjoint Analysis, interface, Expert Elicitation, ↗
DOE OSTI2024

Geospatial Data Platform for All

Spatiotemporal data has evolved in scale due to augmented use in cross-domain applications. Simultaneously, there is substantial growth in the availability of Geographic Information Systems (GIS) data provided by the United States Geological Survey (USGS) along with other federal, state, county, or local agencies through open-data portals and public access APIs. However, data availability does not equate with accessibility. Large-scale analyses and applications require robust, performant data management with co-location of data storage and computing. The insufficiency of data management infrastructure compels researchers to adopt ad hoc project- specific GIS data storage solutions (e.g., copying data to High-Performance computer file systems). As an ad hoc storage strategy does not scale, it hampers cross-domain analyses causing difficulty in data reuse and utilizing existing code bases. Furthermore, GIS data is complex and requires expertise to analyze and manipulate due to its intricate data structures and data-specific projection transformations. Despite the challenges, we recognize that derived GIS data products, e.g., satellite or LIDAR-based images, can be used in downstream applications such as AI by domain, but non-GIS experts. To address the data needs and overcome the challenges, we are working towards a GIS Data Platform focused on efficient data storage, data discovery and access, and an API to enable common workflows. We propose a knowledge-graph (KG) approach for data discovery, whereby datasets are semantically linked to higher- level constructs such as projects and research areas. The semantic data links enable researchers to explore datasets in a top-down approach by specifying relevant and meaningful terms (assists in finding hidden data). An advantage is that the nodes and edges in a knowledge graph create built-in semantic documentation. Deeper spatiotemporal connections between data sources can be encoded via Graph Neural Networks (GNN) (Zhang et al., 2021). The KG approach can be extended to integrate the data itself in a Virtual KG (VKG). Our work will derive inspiration from large-scale VKG efforts that have been undertaken or are currently underway as part of the OpenStreetMap project (Ding et al., 2021). For DOE Data Days, we share the proposed geospatial data platform hybrid (cloud/on-prem) architecture, our work-to-date on storing, retrieving, and transforming LiDAR and raster data relevant to two important NREL use-cases, including the Renewable Energy Potential (reV) Model, and present our proposal for a KG based data discovery engine.

data platform↗
DOE OSTI2023

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

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

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Announcing the Biomedical Data Translator: Initial Public Release

ABSTRACT The growing availability of biomedical data offers vast potential to improve human health, but the complexity and lack of integration of these datasets often limit their utility. To address this, the Biomedical Data Translator Consortium has developed an open‐source knowledge graph–based system—Translator—designed to integrate, harmonize, and make inferences over diverse biomedical data sources. We announce here Translator's initial public release and provide an overview of its architecture, standards, user interface, and core features. Translator employs a scalable, federated, knowledge graph framework for the integration of clinical, genomic, pharmacological, and other biomedical knowledge sources, enabling query retrieval, inference, and hypothesis generation. Translator's user interface is designed to support the exploration of knowledge relationships and the generation of insights, without requiring deep technical expertise and gradually revealing more detailed evidence, provenance, and confidence information, as needed by a given user. To demonstrate Translator's application and impact, we highlight features of the user interface in the context of three real‐world use cases: suggesting potential therapeutics for patients with rare disease; explaining the mechanism of action of a pipeline drug; and screening and validating drug candidates in a model organism. We discuss strengths and limitations of reasoning within a largely federated system and the need for rich concept modeling and deep provenance tracking. Finally, we outline future directions for enhancing Translator's functionality and expanding its data sources. Translator represents a significant step forward in making complex biomedical knowledge more accessible and actionable, aiming to accelerate translational research and improve patient care.

Research & Experimental Medicine↗
DOE OSTI2025

DOME: Directional medical embedding vectors from Electronic Health Records

Motivation: The increasing availability of Electronic Health Record (EHR) systems has created enormous potential for translational research. Recent developments in representation learning techniques have led to effective large-scale representations of EHR concepts along with knowledge graphs that empower downstream EHR studies. However, most existing methods require training with patient-level data, limiting their abilities to expand the training with multi-institutional EHR data. On the other hand, scalable approaches that only require summary-level data do not incorporate temporal dependencies between concepts. Methods: We introduce a DirectiOnal Medical Embedding (DOME) algorithm to encode temporally directional relationships between medical concepts, using summary-level EHR data. Specifically, DOME first aggregates patient-level EHR data into an asymmetric co-occurrence matrix. Then it computes two Positive Pointwise Mutual Information (PPMI) matrices to correspondingly encode the pairwise prior and posterior dependencies between medical concepts. Following that, a joint matrix factorization is performed on the two PPMI matrices, which results in three vectors for each concept: a semantic embedding and two directional context embeddings. They collectively provide a comprehensive depiction of the temporal relationship between EHR concepts. Results: We highlight the advantages and translational potential of DOME through three sets of validation studies. First, DOME consistently improves existing direction-agnostic embedding vectors for disease risk prediction in several diseases, for example achieving a relative gain of 5.5% in the area under the receiver operating characteristic (AUROC) for lung cancer. Second, DOME excels in directional drug-disease relationship inference by successfully differentiating between drug side effects and indications, correspondingly achieving relative AUROC gain over the state-of-the-art methods by 10.8% and 6.6%. Finally, DOME effectively constructs directional knowledge graphs, which distinguish disease risk factors from comorbidities, thereby revealing disease progression trajectories. The source codes are provided at https://github.com/celehs/Directional-EHRembedding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

GraphAide: Advanced Graph-Assisted Query and Reasoning System

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

Purohit, Sumit [BATTELLE (PACIFIC NW LAB)] (ORCID:↗
DOE OSTI2020

Topological Analysis of The SPOKE Graph

The SPOKE graph [2, 6] is a sparse decorated semantic graph representing a collection of knowledge collected in many scientific databases from the fields of healthcare, biochemistry, chemistry, biology, et cetera. This knowledge graph is stored as a relational dataset decorated with metadata on each constituent vertex and edge. Formally, the graph is G(V, E, D), where V is a set of n vertices V := {1, ..., n} and edges of the form (i, j) ϵ E for i, j ϵ V, and table D that for any item in V υ E stores unstructured data such as vertex/edge type, nature of a relationship, et cetera. D(i) = {data involving vertex i ϵ V}, and D(i, j) = {data involving edge (i, j) ϵ E}. Here, we treat the graph as undirected in the sense that a direct relationship for (i, j) causes a (possibly opposite) reverse direct relationship for (j, i). The SPOKE graph G(V, E, D) is formed by processing a collection of relational datasets from medicine, chemistry, and biology, connecting many entities. Here, we analyze an instance from 2019, Spoke-20190707, where a graph file contains 6.16M edges and associated metadata and a vertex file contains 2.15M vertices and the associated metadata. There are 12 different types of vertex entities; all edge types used are implicit (see §2). There is other metadata in D on edges and vertices, but we just use the topology and the vertex labels in this report. SPOKE is growing as more knowledge is gained and more datasets are added. SPOKE is likely to grow 10x during the next phase of this project, and we therefore would like to consider topoligical analysis techniques that are scalable to several orders of magnitude larger than the current dataset (say >1B edges).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

What Is the Agent Doing? Visualizing Agentic AI Querying Workflows

We explore how visualizations can help users understand what an AI agent is doing as it builds and runs queries over data. As part of the LinkQ system, a natural language interface for querying knowledge graphs with a large language model (LLM), we designed two complementary views: A State Diagram that shows where the agent is within a larger workflow, and a Live Action Display that gives real-time updates about the agent's current task. In a study with 14 practitioners, we found that these visuals helped participants build stronger mental models of the agent's behavior while also increasing their confidence in the system. However, we also observed that users sometimes trusted incorrect outputs simply because the agent appeared to be doing the "right" thing. Our findings point to both the value and risk of visualizing agent behavior in interactive AI systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Synthetic Data and Graph Generation for Modeling Adversarial Activity (Final Project Report)

The Data and Graph Generation for Modeling Adversary Activity (MAA) project developed a methodology along with scalable graph modeling and generation tools to produce realistic large-scale background activity graphs with embedded adversarial activity pathways. The technical report presents PNNL methodology, released datasets, lessons learned, and recommendations to develop graph analytic algorithms for structure-only and attributed knowledge graphs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Gene-Metabolite Association Prediction with Interactive Knowledge Transfer Enhanced Graph for Metabolite Production

Identifying gene targets for enhancing metabolite production in metabolic engineering is challenging due to the vast research literature and the approximation in genome-scale metabolic model (GEM) simulations. Here, to address this, we propose the Gene-Metabolite Association Prediction task, which automates gene discovery for given metabolite-gene pairs, accompanied by a benchmark dataset of 2474 metabolites and 1947 genes for Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is complicated by incomplete metabolic graphs and metabolic heterogeneity. We introduce an Interactive Knowledge Transfer mechanism based on Metabolism Graphs (IKT4Meta) to enhance prediction accuracy by integrating cross-metabolism knowledge. Using Pretrained Language Models (PLMs) to generate inter-graph links mitigates heterogeneity issues, while intra-graph links are propagated via these anchors. Gene-metabolite predictions are then performed on the enriched graphs integrating multiple microorganisms’ knowledge. Experiments show that IKT4Meta outperforms baselines by up to 12.3% in link prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Session Introduction: Graph Representations and Algorithms in Biomedicine

Connectivity is a fundamental property of biological systems: on the cellular level, proteins interact with each other to form protein-protein interaction networks (PPIs); on the organism level, neurons are arranged in a network; and on a community-level, species can have complex relationships with one another that drive the development and balance of an ecosystem. Graphs, representations of systems consisting of entities as vertices and their connections as edges, are a useful structure to characterize many such systems. Such models can be used to understand biological systems that naturally have a network structure, including PPIs, biological neurons, and ecosystems. In today’s information age, graph representations and algorithms (often in combination with machine learning techniques) are used to organize massive amounts of related data, much of which may be heterogeneous or unstructured, and identify patterns that represent novel biological insights. PSB’s 2023 session “Graph Representations and algorithms in Biomedicine,” encompasses modern developments in graph theory and its applications to various fields of biomedicine. This session includes a wide range of research - knowledge graphs built from text-mined health data, heterogeneous networks using multi-omic databases, and graphs refined to represent uncertainty or improve memory usage.

Chrisman, Brianna S.↗
DOE OSTI2022

Generating and Analyzing Program Call Graphs using Ontology

Call graph or caller-callee relationships have been used for various kinds of static program analysis, performance analysis and profiling, and for program safety or security analysis such as detecting anomalies of program execution or code injection attacks. However, different tools generate call graphs in different formats, which prevents efficient reuse of call graph results. In this paper, we present an approach of using ontology and resource description framework (RDF) to create knowledge graphs for specifying call graphs to facilitate the construction of full-fledged and complex call graphs of computer programs, realizing more interoperable and scalable program analyses than conventional approaches. We create a formal ontology-based specification of call graph information to capture concepts and properties of both static and dynamic call graphs so different tools can collaboratively contribute to more comprehensive analysis results. Our experiments show that ontology enables merging of call graphs generated from different tools and flexible queries using a standard query interface. Index Terms—Callgraph, ontology, knowl

Dorta, E.↗
DOE OSTI2021

QLiG: Query Like a Graph For Subgraph Matching

A graph is a natural and flexible modeling approach to represent entities and relationships between them in real-world. A Knowledge Graphs (KG) is a specialized graph with formal and structured representation of facts, relationships, annotated with semantic descriptions. Subgraph matching is one of the fundamental graph problems to identify relationships, interactions and activities of interest within a large graph. A query specification is a collection of abstract components, operations, and constraints to express a pattern. The specification can be implemented in different ways based on underlying data model. Various graph query specifications have been developed over the years and have led to the development of different open-sourced and vendor-specific query languages. Such specification are modeled as an extension of relational algebra used to develop relational query languages such as SQL. Such relational concepts do not inherently support graph queries. There is a need to represent graph queries in terms on graph-based components to expedite query construction by non-database experts. We present a graph-based query approach QLiG (pronounced cleeg), to perform subgraph matching in Labeled Property Graph. We present the query specifications, salient features, and a use case to show functional examples.

Purohit, Sumit↗
DOE OSTI2024

Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning

Motivation: Graph representation learning is a family of related approaches that learn low-dimensional vector representations of nodes and other graph elements called embeddings. Embeddings approximate characteristics of the graph and can be used for a variety of machine-learning tasks such as novel edge prediction. For many biomedical applications, partial knowledge exists about positive edges that represent relationships between pairs of entities, but little to no knowledge is available about negative edges that represent the explicit lack of a relationship between two nodes. For this reason, classification procedures are forced to assume that the vast majority of unlabeled edges are negative. Existing approaches to sampling negative edges for training and evaluating classifiers do so by uniformly sampling pairs of nodes. Results: We show here that this sampling strategy typically leads to sets of positive and negative examples with imbalanced node degree distributions. Using representative heterogeneous biomedical knowledge graph and random walk-based graph machine learning, we show that this strategy substantially impacts classification performance. If users of graph machine-learning models apply the models to prioritize examples that are drawn from approximately the same distribution as the positive examples are, then performance of models as estimated in the validation phase may be artificially inflated. We present a degree-aware node sampling approach that mitigates this effect and is simple to implement. Availability and implementation: Our code and data are publicly available at https://github.com/monarch-initiative/negativeExampleSelection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

BrickQA: Bridging the Semantic Gap in Building Operations with Dynamic Graph Exploration

While standardized ontologies like the Brick schema address data heterogeneity in Building Automation Systems (BAS), accessing this semantic data remains a challenge as domain experts often lack the expertise to formulate complex SPARQL queries. To bridge this gap, we present BrickQA, a Large Language Model (LLM)-based framework that translates natural language into executable SPARQL queries through structured query decomposition, dynamic schema exploration, and inline validation. BrickQA utilizes an iterative reasoning agent to actively navigate graph topology through dynamic exploration actions without requiring exhaustive context injection or model fine-tuning. This approach effectively mitigates hallucinations, particularly in large-scale building knowledge graphs. Empirical evaluation on BuildingQA, a standardized benchmark, demonstrates that BrickQA significantly outperforms ReAct baselines, delivering a 0.291–0.355 absolute F1 improvement while achieving 3 × –12.7 × higher token cost-efficiency. Beyond these metrics, the framework maintains structural fidelity across heterogeneous buildings and remains resilient to ambiguous queries without requiring site-specific fine-tuning. Furthermore, a case study on operational analytics validates the framework’s capability to handle temporal and aggregation constraints, effectively transforming abstract semantic models into actionable facility management insights.1

Ko, Yun-Dam↗
DOE OSTI2025

FAIR to WISE (F2W) v1.0.0

FAIR to WISE (F2W) is an iterative, large-language model (LLM) driven pipeline that turns unstructured research PDFs into structured, queryable knowledge graphs (KGs). Core features include schema-driven extraction to a LinkML model; full provenance capture; ontology-grounded enrichment (e.g., chemical validation and ChEBI lookup); graph construction to JSON-LD with stable IDs; and KG-RAG question answering with evidence-aware retrieval. The system is engineered for reproducibility and accessibility (open-source Ollama models, temperature=0, NVTX/Nsight profiling) with robust QA (relation verification, deduplication, and deterministic outputs). Primary uses are literature-to-KG automation, knowledge-grounded Q&A, and experimental steering support. We demonstrate the approach in organic photovoltaics, where the pipeline ingests papers, builds a domain KG, and evaluates answers against expert competency questions to guide experimental planning and interpretation. Compared with off-the-shelf LLMs and ad-hoc NLP tools, F2W addresses ontology gaps and reduces hallucination risk by grounding responses in extracted evidence and enforcing schema constraints; it also offers deterministic, provenance-linked outputs and open, cost-aware deployment. Evidence-aware ranking further improves answer quality over pure vector search.

Abramov, David [Lawrence Berkeley National Laborat↗
DOE OSTI2026

Vulcan-Forge: Architecture and Design of a Multi-Modal Forensic Analysis Plugin for CALDERA

Forge and VULCAN together describe an open-architecture cybersecurity analysis ecosystem that unifies forensic artifact processing, detection engineering, and vulnerability intelligence within integrated platforms. Forge operates as a plugin for MITRE CALDERA, ingesting diverse evidence formats—including EVTX, PCAP/PCAPNG, CSV, JSON, YAML, XML, binaries, and archives—to construct a unified artifact graph enriched with severity scoring, TLP classification, and audit trails. It provides subsystems for artifact parsing, streaming structured-data visualization, NetworkMiner-based packet inspection, PE/.NET binary analysis, and LLM-assisted triage and rule generation, with outputs validated against CCCS-YARA and pySigma schemas. VULCAN complements this by serving as a cybersecurity analyst platform that integrates a Neo4j knowledge graph, Qdrant vector retrieval, SSVC-based triage, and a local LLM to deliver CVE intelligence and forensic analysis through a multi-source ingest pipeline drawing from NVD, CISA KEV, EPSS, MITRE ATT&CK, and CAPEC. Together, they bridge structured threat intelligence with automated forensic analysis and detection workflows.

97 MATHEMATICS AND COMPUTING↗
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↗