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DOE OSTI2022

Redox Biochemistry of Energy Conservation in Methanogens and their Syntrophic Partners

The primary objective of this project was to uncover previously unknown modes by which living organisms harvested energy. Specifically, it queried microbial systems, which were once thought to not be able to utilize oxygen. Through the use of cutting-edge approaches, we were able to identify novel mechanistic processes that allow organisms to thrive under varying environmental conditions. This constitutes a paradigm shift in the field. Our work has opened new vistas for expanding the horizons of energy conservation in biological systems, as well as shed light on green energy innovations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

PV Degradation Modeling: Applying Geospatial Workflows with "PVDeg"

Accurate degradation modeling is essential for predicting photovoltaic (PV) module performance, estimating longevity and informing design decisions. With degradation rates varying significantly by location, geospatial analysis is critical for PV and broader applications, such as agrivoltaics, weathering and environmental data analysis. This work presents PVDeg, an open-source tool designed for geospatial degradation analysis. PVDeg integrates meteorological data from global sources, including the National Solar Radiation Database (NSRDB) and Photovoltaic Geographical Information System (PVGIS), with degradation models. The toolkit enables users to customize geospatial workflows by integrating weather data, material parameters, and user-defined Python functions. It facilitates accelerated downloads of NSRDB and PVGIS datasets and optimizes geospatial point selection to preserve data density in regions of interest. Additionally, PVDeg provides a local database for storage and spatial queries, supporting large-scale analyses without the need for high-performance computing (HPC) resources. PVDeg provides a foundational workflow that extends its utility beyond PV applications, enabling researchers to analyze geospatial processes across discipline.

14 SOLAR ENERGY↗

DOE OSTI2025

RAG for FLAG: AI Assistance for a Physics Code

Artificial intelligence (AI) has quickly become an important tool in scientific research, where significant efforts are underway to develop tools that will expedite the research process. One area of particular impact is scientific software, which can be particularly complex, and therefore time consuming to learn and use effectively. AI assistants are increasingly helping to streamline the process by performing tasks such as interactively answering user questions or suggesting solutions. Los Alamos National Laboratory (LANL) develops several advanced scientific codes, such as FLAG, which can be used to run multiphysics simulations. With this study, our goal was to develop an AI assistant for FLAG that could help make the process of understanding the software and running physics simulations more efficient. To develop an AI assistant for FLAG, we used a method called retrieval-augmented generation (RAG), which is a technique that uses information from relevant data sources to enhance the accuracy of large language models (LLMs). We used the FLAG user manual and other FLAG documentation as the knowledge base for the RAG system. When a user provides a query, RAG retrieves relevant sections from the knowledge base in response, then uses those excerpts to generate grounded and contextually rich answers. We found that our AI assistant was able to provide context aware answers and source references to user queries. To evaluate performance, we developed a set of 40 benchmark questions and compared the accuracy of the responses to those of two standard LLMs without retrieval. Our AI assistant significantly outperformed the standard LLMs at answering FLAG-related questions, with an 82.5% accuracy rate, compared to 47.5% for both of the standard LLMs. This has the potential to make the process of learning and using FLAG much easier, especially for new users. Ultimately, it supports LANL’s broader mission by empowering scientists and engineers to focus more on discovery and analysis rather than on navigating complex software systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

A Flang Plugin for Fortran Feature Characterization

As new compute systems are developed, there is still a need to compile and execute codes authored in Fortran on these leading edge systems. In order to achieve this, development of compilers that support the latest hardware is continuously under development. Though the specification of Fortran is extensive, it is helpful to compiler authors to be able to prioritize the development of key features in order to get certain codes deemed important, e.g., applications of interest to leadership computing facilities, executable on leading edge compute systems. Identifying key features though is largely done through querying software experts or users of the Fortran applications of interest, who then manually report what features are and are not present. This exercise can both time consuming and error prone. To automate this process, we present a compiler plugin to Flang, the Fortran frontend for LLVM. This plugin is a tool that operates on the parse tree representation generated by Flang and detects key features based on walking parse tree nodes that correspond to features of interest. We show the result of our tool on four applications, three of which were manually profiled by software experts. We show the discrepancies between our tool and the manual characterization of the three applications, as well as generate a characterization for an application not yet profiled. We intend to open-source our tool in order to invite the community to benefit from the tool and make contributions for other features.

Cabrera, Anthony [ORNL]↗

DOE OSTI2025

SlimIO: Lightweight I/O Path Design for Write Isolation in FDP-backed In-Memory Databases

In-Memory Databases (IMDBs) are widely used with HPC applications to manage transient data, often using snapshot-based persistence for backups. Redis, a representative IMDB, employs both snapshot and Write-Ahead Log (WAL) mechanisms, storing data on persistent devices via the traditional kernel I/O path. This method incurs syscall overhead, I/O contention between processes, and SSD garbage collection (GC) delays. To address these issues, we propose SlimIO, which adopts I/O passthru to minimize syscall overhead and inter-process I/O interference. Additionally, it leverages Flexible Data Placement (FDP) SSDs as backup storage to avoid performance degradation from SSD GC. Experimental results show that SlimIO reduces snapshot time by up to 25%, increases query throughput by up to 30% during non-snapshot periods, and lowers 99.9%-ile latency by up to 50%. Furthermore, it achieves a write amplification factor (WAF) of 1.00, indicating no redundant internal writes, thus extending SSD lifespan.

Lee, Sangyun [Sogang University]↗

DOE OSTI2025

On-Demand Column Joining for High Energy Physics

As the Large Hadron Collider (LHC) transitions into the High-Luminosity LHC (HL-LHC) era, the volume of data to be processed is expected to increase significantly. The CMS Experiment currently utilizes various data formats, including AOD, MiniAOD, and NanoAOD, each with different levels of detail and storage requirements. This paper addresses the challenges of data duplication and storage inefficiencies in high-energy physics (HEP) analyses by proposing an on-demand column-joining solution. This approach aims to reduce data duplication by enabling the dynamic combination of NanoAOD data with auxiliary information from larger data tiers, such as MiniAOD. The proposed solution leverages Trino, a high-performance distributed SQL query engine, to perform efficient and scalable data joins. Benchmarks using CMS OpenData demonstrate the feasibility of this approach, showing that it can handle large datasets with low latency. Integration with the scikit-hep ecosystem and the coffea analysis framework is also discussed, highlighting the potential for seamless end-to-end data processing and analysis. Ongoing and future work focuses on expanding benchmarks, integrating ServiceX for data transformation, and exploring the use of native object storage solutions.

Manganelli, Nicholas [Northeastern U.]↗

DOE OSTI2022

Deep Lynx Unidirectional Network Connector

The Deep Lynx UNC is a small utility written in Python that uses only basic Python libraries and the Deep Lynx Python Software Development Kit (SDK). It queries Deep Lynx for tasks that indicate some data to be run in the UNC's environment. Once a task is acquired, the UNC retrieves the associated data and provides it to some other application for processing, waits for output, and sends the output from the other application to Deep Lynx. As data flows only from the UNC to Deep Lynx, this software solves the problem of connecting Deep Lynx with applications and resources that exist in a network where the network can reach Deep Lynx, but Deep Lynx cannot reach that network (unidirectional network).

Browning, JerenM↗

DOE OSTI2025

Benchmark Tracking System for Performance Monitoring

Benchmarking is essential for high-performance software development, particularly for monitoring performance across code iterations. This project focused on enhancing the benchmarking process for Lamellar, an asynchronous runtime for High-Performance Computing (HPC) systems developed at Pacific Northwest National Laboratory. Prior to this work, benchmark results were difficult to track and compare across code versions, presenting significant challenges in identifying performance regressions and long-term trends. The primary objective was to establish a systematic, reproducible approach for measuring performance and detecting regressions following code commits. Our methodology involved three key components: standardizing benchmark outputs, implementing data versioning, and developing analysis tools. We standardized the benchmark output format to JSON Line records containing specific fields (execution time, hardware specifications, and environmental variables). To address data management challenges, we evaluated several options and eventually chose a git repository dedicated to benchmark data. We developed a suite of Python tools that processed benchmark results, enriched them with metadata, and facilitated search in the repository. The resulting system enables more efficient filtering and comparison of performance metrics across commit histories, hardware configurations, and benchmark variants through a unified query interface. Our implementation reduces computational overhead by first checking for existing results through configuration matching before initiating new benchmark runs, thereby conserving resources. The system has been validated by Lamellar developers. It organizes results by benchmark type and build configurations for efficient retrieval. Future developments include a planned Large Language Model interface for predicting benchmark performance, incorporating the criterion package for statistical analysis, which will enable automated detection of statistically significant performance changes, and integration with continuous integration pipelines. Despite these enhancements being reserved for future work, this project has successfully provided the Lamellar development team with a framework for maintaining consistent performance standards and identifying optimization opportunities across workloads and hardware environments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

A Data Processing Pipeline To Extract A Knowledge Graph From Heterogeneous Data For Socio-technical Analysis Of Critical Infrastructure Influence

The code is written in Python and consists of the following pipeline that is implemented in Apache Airflow. This pipeline intends to understand the companies that are directly or indirectly involved with a type of critical infrastructure system at some point in that system's lifecycle. The pipeline takes a configuration file that specifies a list of initial companies to consider, a geographic region of interest, and a set of SEC form types as well as other data sources (e.g. CrunchBase) from which to extract entities and relations. There are four main components to this pipeline as currently implemented: Entity Extraction, Network Construction, Analysis, and Visualization. First, Entity Extraction, is implemented as the `topear-extract_organizations` Apache Airflow workflow. Given an initial query that specifies a geographic region of interest and a time interval, the software will extract CI facilities of interest and organizations that have a direct influence relationship to those facilities (e.g. ownership). During the course of the LDRD, we focused on Electric Vehicle charging stations and this information is available via the Department of Energy (DOE) database on fueling stations maintained by NREL. Within the context of the DOE CESER project, we have focused on Battery Energy Storage Systems (BESS). Second, the Network Extraction component will iteratively construct a social network graph given the set of organizations and people extracted in the previous step. Organizations (and eventually People if desired) are then fed as a query to the `topgear-construct_social_network` Apache Airflow workflow which given a set of initial companies and data sets (e.g. SEC EDGAR form types, OpenCorporates, Crunchbase). This Airflow workflow will iteratively query such data sources to discover relationships with new organizations and people. For example, this module can iteratively query SEC EDGAR for metadata that documents the number of each type of form for the given set of companies and their location. This forms metadata represents a catalog of data sources from SEC EDGAR for the extracted social network knowledge graph. The pipeline then downloads these forms from the website and saves them in a build directory for further processing. These documents are then parsed for entities and relations. Again, we note that in additional to SEC data sources, this step can also pull in information on organizations via API services such as CrunchBase and OpenCorporates or bulk data sources. At the end of this step, the resultant social network, the Critical Infrastructure network, and the edges that encode relationships between organizations and CI facilities, form the Adversarial Socio-Technical Network (ASTN) that informs the analysis. Third, the Analysis component processes these generated ASTN. Previously, that has included the ability to compare prevalence of different vendors for a given infrastructure component type across different regions as well as identify common public and private investors across those vendors. This was demonstrated for EV Charging Stations across several different metropolitan areas within an IEEE PES GridEdge publication. More recently, we have looked at ways to identify infrastructure owners and operators of BESS with the most nameplate capacity across different states as well as other indictors of risk resulting from changes in ownership over time. Finally, the Visualization component consists of an HTML/CSS/JS framework by which users can interact geospatial, operational, and organizational relationships across a given portfolio of Critical Infrastructure facilities. The objective is to provide a library of UI/UX modules that can be repurposed for stakeholder-specific dashboards. All of the modules are related via a common event model that enables UI actions in one view to percolate across the other views.

Weaver, Gabriel [Idaho National Laboratory (INL), ↗

DOE OSTI2021

Development of a Framework for Data Integration, Assimilation, and Learning for Geological Carbon Sequestration (DIAL-GCS) (Final Report)

This project aimed to develop and demonstrate a Data Integration, Assimilation, and Learning framework for geologic carbon sequestration projects (DIAL-GCS). DIAL-GCS is an intelligence monitoring system (IMS) for automating GCS closed-loop management by leveraging recent developments in machine learning technologies, complex event processing (CEP), and reduced-order modeling. The safe and efficient operation of GCS repositories requires integrated monitoring to track the injected CO¬2 as it moves within a storage reservoir. GCS projects are data intensive, as a result of proliferation of digital instrumentation and smart-sensing technologies. GCS projects are also resource intensive, often requiring multidisciplinary teams performing different monitoring, verification, accounting (MVA) tasks throughout the lifecycle of a project to ensure secure containment of injected CO2. The success of GCS thus depends in a large part on our ability to access, assimilate, and analyze heterogeneous data and information sources in a timely manner. This project included a number of meaningful and necessary tasks to transform the human domain knowledge into machine-interpretable rules for automating knowledge extraction and discovery in GCS. The specific technical objectives of the proposed DIAL-GCS project were to develop an ontology-driven GCS data management module for storing, querying, and exchanging GCS data (both historic and live sensor data) from multiple sources and in heterogeneous formats. Incorporate a CEP engine for detecting abnormal situations by seamlessly combining expert knowledge, rule-based reasoning, and machine learning. Enable uncertainty quantification and predictive analytics using a combination of coupled-process modeling, AI/ML methods, and reduced-order modeling, and integrate and demonstrate the system’s capabilities with both real and simulated data. As far as we know, this is one of the first projects aimed to develop intelligent monitoring systems (IMS) targeting the GCS. Under this project, the team had developed a large number of web applications and scientific algorithms that contribute the main theme of intelligent monitoring. The team has published more than a dozen peer reviewed papers and disseminated the research results at multiple technical meetings.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

Track Seeding and Labelling with Embedded-space Graph Neural Networks

To address the unprecedented scale of HL-LHC data, the Exa.TrkX project is investigating a variety of machine learning approaches to particle track reconstruction. The most promising of these solutions, graph neural networks (GNN), process the event as a graph that connects track measurements (detector hits corresponding to nodes) with candidate line segments between the hits (corresponding to edges). Detector information can be associated with nodes and edges, enabling a GNN to propagate the embedded parameters around the graph and predict node-, edge- and graph-level observables. Previously, message-passing GNNs have shown success in predicting doublet likelihood, and we here report updates on the state-of-the-art architectures for this task. In addition, the Exa.TrkX project has investigated innovations in both graph construction, and embedded representations, in an effort to achieve fully learned end-to-end track finding. Hence, we present a suite of extensions to the original model, with encouraging results for hitgraph classification. In addition, we explore increased performance by constructing graphs from learned representations which contain non-linear metric structure, allowing for efficient clustering and neighborhood queries of data points. We demonstrate how this framework fits in with both traditional clustering pipelines, and GNN approaches. The embedded graphs feed into high-accuracy doublet and triplet classifiers, or can be used as an end-to-end track classifier by clustering in an embedded space. A set of post-processing methods improve performance with knowledge of the detector physics. Finally, we present numerical results on the TrackML particle tracking challenge dataset, where our framework shows favorable results in both seeding and track finding.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

WELLBASE - An Interactive Platform for Wellbore Material Assessment

This project seeks to build an open-source wellbore material data repository with adequate material performance and contextual data to support Geological Carbon Storage (GCS). By appropriately evaluating the data types as mentioned earlier made available by the WELLBASE tool, stakeholders can make more informed decisions regarding well selections, risk assessment, and economic analysis for geologic carbon storage projects. Advanced Natural Language Processing models and other custom python scripts will be deployed in an automated process to extract unstructured data from documents, reports, and web applications and subsequently parse to more usable formats. The processed data will then be integrated into a robust and comprehensive database architecture, optimizing data accessibility, and usability for analytical purposes. The final data products will be accessible through a user-friendly visualization platform that will allow users to query and visualize the data, as well as download data in usable formats.

Tetteh, Daniel A.↗

DOE OSTI2024

A Data Processing Pipeline To Extract A Knowledge Graph From Sec Documents For Socio-technical Analysis Of Critical Infrastructure Influence

Weaver, GabrielA.↗

DOE OSTI2020

Active Learning for Anomaly Detection in Environmental data

Due to the growing amount of data from in-situ sensors in environmental monitoring, it becomes necessary to automatically detect anomalous data points. Nowadays, this is mainly performed using supervised machine learning models, which need a fully labelled data set for their training process. However, the process of labelling data is typically cumbersome and, as a result, a hindrance to the adoption of machine learning methods for automated anomaly detection. In this work, we propose to address this challenge by means of active learning. This method consists of querying the domain expert for the labels of only a selected subset of the full data set. We show that this reduces the time and costs associated to labelling while delivering the same or similar anomaly detection performances. Finally, we also show that machine learning models providing a nonlinear classification boundary are to be recommended for anomaly detection in complex environmental data sets.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Identification of Known and Novel Monomers for Poly(hydroxyurethanes) from Biobased Materials

Sourcing polymers from biobased materials is desirable for a transition to a more sustainable world. However, finding new monomers sourced from biobased molecules requires extensive experimental effort, due to the fact that most biomolecules lack the functional groups or properties needed to serve as a monomer in a particular polymeric system without chemical modification. In this work, we demonstrate a computational screening method to obtain monomers of a non-isocyanate polyurethane (NIPU), polyhydroxyurethane (PHU), from biomolecules. Our method generates candidate monomers from a list of 15 selected biobased starting molecules by performing chemical transformations that are standard to chemical catalysis and organic synthesis on these starting molecules and then screening the results for molecules with moieties that can be used as monomers for a PHU. Product molecules from two generations of reaction, a total number of 20,057, were analyzed automatically to identify molecules that have two or more epoxy or cyclic carbonate functional groups as candidates for further derivatization. These 21 candidate molecules were then subjected to another two generations of reaction, producing a set of 17,913 additional molecules. Further scrutiny of this set for desired functional groups characterizing PHUs and querying against the PubChem database was carried out, and 15 known molecules that are commercially available were identified, with the desirable features that they are predicted to be derived from biobased starting molecules in four or fewer steps. Moreover, molecule space generated from this process was primarily comprised of molecules that were not known to PubChem, indicating the framework also has the ability to generate novel candidate monomers that originate from biobased starting points.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Selective Sampling for Sensor Type Classification in Buildings

A key barrier to applying any smart technology to a building is the requirement of locating and connecting to the necessary resources among the thousands of sensing and control points, i.e., the metadata mapping problem. Existing solutions depend on exhaustive manual annotation of sensor metadata --- a laborious, costly, and hardly scalable process. To reduce the amount of manual effort required, this paper presents a multi-oracle selective sampling framework to leverage noisy labels from information sources with unknown reliability such as existing buildings, which we refer to as weak oracles, for metadata mapping. This framework involves an interactive process, where a small set of sensor instances are progressively selected and labeled for it to learn how to aggregate the noisy labels as well as to predict sensor types. Two key challenges arise in designing the framework, namely, weak oracle reliability estimation and instance selection for querying. To address the first challenge, we develop a clustering-based approach for weak oracle reliability estimation to capitalize on the observation that weak oracles perform differently in different groups of instances. For the second challenge, we propose a disagreement-based query selection strategy to combine the potential effect of a labeled instance on both reducing classifier uncertainty and improving the quality of label aggregation. We evaluate our solution on a large collection of real-world building sensor data from 5 buildings with more than 11,000 sensors of 18 different types. The experiment results validate the effectiveness of our solution, which outperforms a set of state-of-the-art baselines.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2019

Dynamic Nested Tracking Graphs

This work describes an approach for the interactive visual analysis of large-scale simulations, where numerous superlevel set components and their evolution are of primary interest. The approach first derives, at simulation runtime, a specialized Cinema database that consists of images of component groups, and topological abstractions. This database is processed by a novel graph operation-based nested tracking graph algorithm (GO-NTG) that dynamically computes NTGs for component groups based on size, overlap, persistence, and level thresholds. Finally, the resulting NTGs are in turn used in a feature-centered visual analytics framework to query specific database elements and update feature parameters, facilitating flexible post hoc analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

BuildingQA: A Benchmark for Natural Language Question Answering over Building Knowledge Graphs

Graph-based representations of building metadata using ontologies like Brick are vital for smart building applications, but querying them remains a challenge for practitioners. Knowledge Graph Question Answering (KGQA) systems, meant to retrieve answers from natural language questions, traditionally require large-scale training data, making them ill-suited for the specialized and data-scarce building domain. The advent of Large Language Models (LLMs) offers a paradigm shift, enabling zero-shot natural language querying without building/domain-specific training. Yet, there is no standardized benchmark for building-specific KGQA which can guide and validate research in this area. To address this gap, our work makes three primary contributions. First, we introduce the BuildingQA Benchmark Dataset, constructed through a multi-stage process of collecting practitioner data, augmenting it with LLMs for linguistic diversity, and curating a final set of 188 questions across 4 buildings. Second, we characterize the benchmark's complexity and ambiguity, introducing a novel method to quantify its "lexical gap" and providing a four-stage diagnostic framework for analyzing how systems fail. Third, we benchmark zero-shot LLM-powered KGQA systems to establish baseline performance and analyze their failure modes. Our evaluation reveals that top-performing systems achieve a maximum F1 score of only 0.38. This result does not indicate a failure of these powerful systems, but rather underscores the unique challenges posed by our benchmark. It demonstrates a critical performance gap, showing that current methods successful on general KGs struggle with the specific lexical and structural nuances of the building domain. BuildingQA1 thus provides the benchmark dataset and foundational analysis needed to drive the development of novel, domain-aware methods required to unlock the use of semantic data in buildings.

Mulayim, Ozan Baris↗