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DOE OSTI2026

Challenges and Vision for Standardization of Biopolymer Data Sets for Machine Learning

Machine learning (ML) is transforming materials research, yet potential for biopolymer discovery remains constrained by fragmented data and nonstandardized reporting. Biopolymers differ significantly from synthetic polymers, requiring specialized approaches to represent their biosynthetic origins, hierarchical structures, and application-specific metrics. In this Perspective, we identify three core challenges limiting biopolymer representation: information encoding, data quality, and data sharing. We describe the most pressing issues and propose commensurate approaches to address each key challenge. Recommendations include the design and adoption of biopolymer-specific fingerprinting and representation frameworks, development of hybrid human-large language model (LLM) data extraction strategies, and expanding Findable, Accessible, Interoperable, Reusable (FAIR)-compliant repositories. We propose a robust foundation to define interoperable, high-quality data sets that capture the full context of biopolymer materials. Standardized metadata, shared ontologies, and community-driven infrastructure would enable scalable, reproducible workflows and accelerate the ML-driven development of biopolymers.

36 MATERIALS SCIENCE↗

DOE OSTI2024

fluxfinder: An R Package for Reproducible Calculation and Initial Processing of Greenhouse Gas Fluxes From Static Chamber Measurements

Fluxes of greenhouse gases are a critical component of the earth's natural climate, but anthropogenic emissions have created an imbalance and resulted in global climate change. Quantifying the emission of these gases is vital to our understanding of their sources and sinks, both natural and anthropogenic. The static chamber method, in which a system of interest is enclosed, and gas concentrations are measured over time, is widely used to estimate fluxes of greenhouse gases. With the development of instruments such as infrared gas analyzers (IRGAs) supporting high-frequency concentration data, there is a growing need for open-source workflows to calculate fluxes. Here we present fluxfinder, an R package designed to support reproducible calculations and processing of greenhouse gas fluxes measured with the static chamber method. The package includes raw data file parsing from widely used IRGAs, metadata matching, unit conversion, flux estimations, and initial quality assurance/quality control (QA/QC). Diagnostic graphical plots provide a transparent way to differentiate between measurement issues and nonlinear behavior. The package is also designed to be easily integrated with the gasfluxes package for further fitting of nonlinear concentration-time models, allowing alternative or additional flux QA/QC. The fluxfinder package offers a flexible workflow that is easily adaptable to promote open and reproducible greenhouse gas flux estimations.

Wilson, Stephanie J.↗

DOE OSTI2024

Prediction of Distributed River Sediment Respiration Rates Using Community-Generated Data and Machine Learning

River sediment microbial respiration is a key indicator of ecosystem functioning and the biogeochemical fluxes across this critical zone link surface and subsurface waters. As such, there is tremendous interest in measuring and mapping these respiration rates. Respiration observations are expensive and labor intensive; there is limited data available to the community. An open science, collaborative initiative is collecting samples for respiration rate analysis and multi-scale metadata; this evolving data set is being used for making machine learning (ML) predictions at unsampled sites to help inform continued community engagement. However, it is a challenge to find an optimum configuration for ML models to work with this feature-rich (i.e., 100+ possible input variables) data set. Here, we present results from a two-tiered approach to managing the analysis of this complex data set: (a) a stacked ensemble of models that automatically optimizes hyperparameters and manages the training of many models and (b) feature permutation importance to detect the most important features in the models. The major elements of this workflow are modular, portable, open, and cloud-based thus making this implementation a potential template for other applications. The models developed here predict that sediment organic matter chemistry is one of the most important features for predicting sediment respiration rate. Other larger-scale, important features fall into the categories of climatic, ecological, geological, and fluvial settings. Leveraging these larger-scale features to generate data-driven estimates of river sediment respiration rates reveals spatially consistent but heterogeneous patterns across the river network of the Columbia River Basin.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

A Performant, Scalable Processing Pipeline for High‐Quality and FAIR Environmental Sensor Data

High-resolution environmental monitoring is necessary to record, understand, and predict biogeochemical and ecological changes particularly in coastal systems but brings significant challenges in processing and making rapidly available the resulting data. The COMPASS-FME project established a network of coastal observational sites across the Chesapeake Bay and western Lake Erie regions extensively instrumented with soil, vegetation, and weather sensors logging data every 15 min. Our data processing framework, written in R and completely open source, prioritizes rapid model-experiment iteration and makes biogeochemical data rapidly available for quality assurance/quality control, analysis, and model ingestion. This pipeline is distinguished by a standardized and modular approach to data curation, extensive metadata and documentation, and its high performance. These attributes combine to make biogeochemical data rapidly accessible across COMPASS-FME and the broader community. Flexible, powerful, and reproducible approaches to handling high-volume environmental data are crucial for accelerating biogeosciences research.

Pennington, Stephanie C. [Pacific Northwest Nation↗

DOE OSTI2024

Predicting the heat release variability of Li-ion cells under thermal runaway with few or no calorimetry data

Accurate measurement of the variability of thermal runaway behavior of lithium-ion cells is critical for designing safe battery systems. However, experimentally determining such variability is challenging, expensive, and time-consuming. Here, we utilize a transfer learning approach to accurately estimate the variability of heat output during thermal runaway using only ejected mass measurements and cell metadata, leveraging 139 calorimetry measurements on commercial lithium-ion cells available from the open-access Battery Failure Databank. We show that the distribution of heat output, including outliers, can be predicted accurately and with high confidence for new cell types using just 0 to 5 calorimetry measurements by leveraging behaviors learned from the Battery Failure Databank. Fractional heat ejection from the positive vent, cell body, and negative vent are also accurately predicted. We demonstrate that by using low cost and fast measurements, we can predict the variability in thermal behaviors of cells, thus accelerating critical safety characterization efforts.

25 ENERGY STORAGE↗

DOE OSTI2025

Enabling pan-repository reanalysis for big data science of public metabolomics data

Public untargeted metabolomics data is a growing resource for metabolite and phenotype discovery; however, accessing and utilizing these data across repositories pose significant challenges. Therefore, here we develop pan-repository universal identifiers and harmonized cross-repository metadata. This ecosystem facilitates discovery by integrating diverse data sources from public repositories including MetaboLights, Metabolomics Workbench, and GNPS/MassIVE. Our approach simplified data handling and unlocks previously inaccessible reanalysis workflows, fostering unmatched research opportunities.

El Abiead, Yasin↗

DOE OSTI2026

Resolving root causes of experiment discrepancies guided by machine learning

Abstract Scientists rely on accurate experimental data to explain nature and then harness this knowledge for applications addressing human needs. However, discrepancies between experiments of the same observable can impede scientific progress if one does not understand the underlying causes. Here, we developed a process that unravels data discrepancies by first using Bayesian machine learning to relate discrepancies to few of many, potentially biasing metadata features that encode experiment procedures. This machine learning output guides human experts to study discrepancy causes by simulating suspicious aspects of historical experiments or designing modern ones to address open questions. The study findings then lead to rejecting or correcting historical data on firm scientific bases. This process is demonstrated for the energy spectrum of neutrons emitted promptly (<1 ns) after fission of 252 Cf, a trusted nuclear physics Standard. It reduces the spread in experimental 252 Cf spectra by up to a factor of 6.

Neudecker, D. (ORCID:0000000339200627)↗

DOE OSTI2024

The Arctic Plant Aboveground Biomass Synthesis Dataset

Plant biomass is a fundamental ecosystem attribute that is sensitive to rapid climatic changes occurring in the Arctic. Nevertheless, measuring plant biomass in the Arctic is logistically challenging and resource intensive. Lack of accessible field data hinders efforts to understand the amount, composition, distribution, and changes in plant biomass in these northern ecosystems. Here, we present The Arctic plant aboveground biomass synthesis dataset, which includes field measurements of lichen, bryophyte, herb, shrub, and/or tree aboveground biomass (g m -2 ) on 2,327 sample plots from 636 field sites in seven countries. We created the synthesis dataset by assembling and harmonizing 32 individual datasets. Aboveground biomass was primarily quantified by harvesting sample plots during mid- to late-summer, though tree and often tall shrub biomass were quantified using surveys and allometric models. Each biomass measurement is associated with metadata including sample date, location, method, data source, and other information. This unique dataset can be leveraged to monitor, map, and model plant biomass across the rapidly warming Arctic.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Aerial imagery dataset of lost oil wells

Orphaned wells are wells for which the operator is unknown or insolvent. The location of hundreds of thousands of these wells remain unknown in the United States alone. Cost-effective techniques are essential to locate orphaned wells to address environmental problems. In this paper, we present a dataset consisting of 120,948 aerial images of recently documented orphan wells. Each of these 512 × 512 images is paired with segmentation masks that indicate the presence or absence of such well. These images, sourced from the National Agriculture Imagery Program, cover the continental United States with spatial resolutions ranging from 30 centimeters to 1 meter. Additionally, we included negative examples by selecting locations uniformly across the United States. Accompanying metadata includes the IDs and spatial resolution of the original images, which are available for free through the United States Geological Survey, and the pixel coordinates of documented orphaned wells identified in these images. This dataset is intended to support the development of deep-learning models that can help locating undocumented orphan wells from such imagery, thereby blunting the environmental damage they do.

Climate-change mitigation↗

DOE OSTI2025

International database of reference gamma spectra for nuclear safeguards applications

Nuclear safeguards missions use gamma spectroscopy as a non-destructive measurement technique for examining nuclear materials. Despite advances in the development of detection equipment as well as software codes, one of the concerns is the lack of well-documented spectra needed to test and validate isotopic analysis codes for their applicability. To address this need, this work introduces IDB, an international database of the reference gamma spectra of uranium, plutonium and mixed oxide nuclear material samples. IDB provides access to well-characterized sets of gamma spectra described by rich metadata, including information on the sample, measurement configuration and detector specifications. These spectra are accessible in different formats, also compatible with analysis code standards, thus promoting their sustainability and maintenance.

None, Dipti [International Atomic Energy Agency (I↗

DOE OSTI2025

A global database of soil microbial phospholipid fatty acids and enzyme activities

Abstract Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.

Science & Technology - Other Topics↗

DOE OSTI2025

dCache project status and update

The dCache project delivers an open-source, massively scalable, distributed storage system deployed internationally to satisfy today’s scientists’ ever-demanding storage requirements. Its multifaceted approach supports different use cases with the same storage, from high throughput data ingest, data sharing over wide area networks, efficient access from HPC clusters, and longterm data persistence on tertiary storage. Even though dCache was initially developed for HEP experiments, today, it is used by various scientific communities, including astrophysics, biomed, and life science, each with their specific requirements. To match the needs of these new communities and keep up with the scaling demands of existing experiments, dCache is permanently evolving. With this contribution, we would like to highlight the recent developments in dCache regarding integration with CERN Tape Archive (CTA), advanced metadata handling, token-based authorization support, bulk API for QoS transitions, REST API to control interaction with the tape system, and future development directions.

Mkrtchyan, Tigran [DESY]↗

DOE OSTI2025

Label-based Virtual Directories In dCache

Traditional filesystems organize data in directories. These directories are typically a collection of files whose grouping is based on a single criterion, e.g., the starting date of an experiment, experiment name, beamline ID, measurement device, or instrument. However, each file in a directory can belong to several logical groups, such as a special event type, experiment condition, or a part of a selected dataset. dCache is a storage system developed to store large amounts of scientific data, used by many HEP and Photon Science experiments. With recent developments in dCache, we have introduced a concept of file tagging, which dynamically groups files with the same label into virtual directories. The file labels can be added, removed, renamed, and deleted through the admin interface or via REST API. The files in virtual directories are exposed through all protocols supported by dCache. This contribution will describe the details of the implementation for file tagging in dCache and present our future development plans on automatic metadata extractions, a feature that will significantly simplify data management. Additionally, we are exploring the future use of virtual directories as a way to translate scientific data catalogs into filesystem views for direct data analysis.

Sahakyan, Marina [DESY]↗

DOE OSTI2025

Mic-hackathon 2024: hackathon on machine learning for electron and scanning probe microscopy

Microscopy is one of the primary sources of information on materials structure and functionality at the nanometer and atomic scales. The data generated through microscopy is often contained in well-structured datasets, enriched with extensive metadata and sample histories, although not always with the same level of detail or storage format. The broad incorporation of data management plans by major funding agencies ensures the preservation and accessibility of this data. However, deriving insights from these rich datasets remains challenging due to the lack of established code ecosystems, standardized benchmarks, and integration strategies. Correspondingly, the efficiency of data usage is very low, and time expenditures at the analysis stage are enormous. In addition to post-acquisition data analysis, the emergence of application programming interfaces by major microscope manufacturers now creates opportunities for real-time ML-based data analytics to enable automated decision making, and particularly ML-agent controlled real-time microscope operation. Despite these opportunities, there is a significant gap in integrating the ML community with the broader microscopy community, limiting the value that these methods bring to physics and materials discovery and materials optimization. Hackathons address these challenges by fostering collaboration between ML experts and microscopy professionals, encouraging the development of innovative solutions that leverage ML for microscopy and preparing the workforce of the future both for microscopy-intensive domains areas, instrument manufacturers, and ML scientists interested in real world applications for fundamental research, materials optimization, and manufacturing. The hackathon generated benchmark datasets and digital twins of microscopes that further contribute to the development of the field and establish data analysis ecosystems. All the codes can be found at GitHub(https://github.com/KalininGroup/Mic-hackathon-2024-codes-publication/tree/1.0.0.1) and Zenodo (https://zenodo.org/records/15579940).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses in comparative genomic analyses, natural product discovery, and machine learning applications. We provide strategies and actionable lessons for adopting this model, supporting the sustainability of curated bioinformatics resources central to nucleic acid research and related fields.

biocuration↗

DOE OSTI2026

GenomeDepot: data management system for microbial comparative genomics

Summary GenomeDepot is an open-source web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of websites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, Basic Local Alignment Search Tool (BLAST) search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools. Availability and implementation GenomeDepot is open source and distributed under the GNU General Public License via GitHub (https://github.com/aekazakov/genome-depot). GenomeDepot is implemented in Python and was tested in Ubuntu Linux. Full installation instructions and documentation are available at https://aekazakov.github.io/genome-depot/. GenomeDepot demo server is freely accessible at https://iseq.lbl.gov/demogd/.

Kazakov, Alexey [Lawrence Berkeley National Labora↗

DOE OSTI2025

Scalable edge clustering of dynamic graphs via weighted line graphs

Timestamped relational datasets consisting of records (or connections) between pairs of entities are ubiquitous in network science. For applications like peer-to-peer communication, email, various social network interactions, and computer network security, it is useful to organize these records into groups based on how and when they are occurring. Weighted line graphs offer a natural way to model how records are related in such datasets but for large real-world graph topologies, building and utilizing the line graph is prohibitively expensive. Here, we present the framework to cluster the edges of a dynamic graph via the associated line graph that contains two major contributions. The first is a method to work with the line graph implicitly and the second is a distributed scale implementation of an agglomerative hierarchical graph clustering algorithm. We outline a novel hierarchical dynamic graph edge clustering approach that efficiently breaks massive relational datasets into small sets of edges containing events at various timescales. This is in stark contrast to traditional graph clustering algorithms that prioritize highly connected (clique-like) community structures. Our approach relies on constructing a sufficient subgraph of a weighted line graph and applying a hierarchical agglomerative clustering. This approach is related to scalable techniques from spatial clustering, nonlinear-dimension reduction, topological data analysis, and draws particular inspiration from HDBSCAN. As an edge clustering, this method yields an overlapping node clustering. Our algorithm is parallelizable and we demonstrate efficient clustering of a billion-scale, real-world dynamic graph into small edge sets that correlate in topology and time. The entire clustering process for a graph with tens of billions of edges takes just a few minutes of run time on 256 nodes of a distributed compute environment. We argue how the output of the edge clustering is useful for a multitude of data visualization and powerful machine learning tasks, both involving the original massive dynamic graph data and metadata associated with the nodes and edges. Finally, we describe how this approach can be extended to dynamic hypergraphs and dynamic graphs/hypergraphs with unstructured data living on vertices and edges.

Data Analysis↗

DOE OSTI2024

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗