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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

PlasmoData.jl — A Julia framework for modeling and analyzing complex data as graphs

Datasets encountered in scientific and engineering applications appear in complex formats (e.g., images, multivariate time series, molecules, video, text strings, networks). Graph theory provides a unifying framework to model such datasets and enables the use of powerful tools that can help analyze, visualize, and extract value from data. In this work, we present PlasmoData.jl, an open-source, Julia framework that uses concepts of graph theory to facilitate the modeling and analysis of complex datasets. The core of our framework is a general data modeling abstraction, which we call a DataGraph. We show how the abstraction and software implementation can be used to represent diverse data objects as graphs and to enable the use of tools from topology, graph theory, and machine learning (e.g., graph neural networks) to conduct a variety of tasks. We illustrate the versatility of the framework by using real datasets: (i) an image classification problem using topological data analysis to extract features from the graph model to train machine learning models; (ii) a disease outbreak problem where we model multivariate time series as graphs to detect abnormal events; and (iii) a technology pathway analysis problem where we highlight how we can use graphs to navigate connectivity. Further, our discussion also highlights how PlasmoData.jl leverages native Julia capabilities to enable compact syntax, scalable computations, and interfaces with diverse packages. Overall, we show that the DataGraph abstraction and PlasmoData.jl Julia package are able to model data within graphs and enable useful analysis.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2019

Deep Transfer Learning Across Cancer Registries for Information Extraction from Pathology Reports

Automated text information extraction from cancer pathology reports is an active area of research to support national cancer surveillance. A well-known challenge is how to develop information extraction tools with robust performance across cancer registries. In this study we investigated whether transfer learning (TL) with a convolutional neural network (CNN) can facilitate cross-registry knowledge sharing. Specifically, we performed a series of experiments to determine whether a CNN trained with single-registry data is capable of transferring knowledge to another registry or whether developing a cross-registry knowledge database produces a more effective and generalizable model. Using data from two cancer registries and primary tumor site and topography as the information extraction task of interest, our study showed that TL results in 6.90% and 17.22% improvement of classification m acro F -score o ver the baseline single-registry models. Detailed analysis illustrated that the observed improvement is evident in the low prevalence classes.

Alawad, Mohammed↗
DOE OSTI2019

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variablelength protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw amino acids k-mer features.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

ABSTRACT In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variable-length protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw k-mer features. Availability Implementations of our method will be available under the Apache 2 licence at http://llp.berkeley.edu/dimotif and http://llp.berkeley.edu/protvecx .

Asgari, Ehsaneddin↗
DOE OSTI2026

Fungal mat growth and leaf colonization at the TRACE warming experiment, Mar - Aug 2024, Luquillo, Puerto Rico

This data package contains processed measurements on the growth of litter mat-forming fungi and the time to leaf colonization at the Tropical Responses to Altered Climate Experiment (TRACE). Located near the Sabana Field Research Station in Luquillo, Puerto Rico, the TRACE site is located in a mature, closed-canopy tropical rainforest within the Luquillo Experimental Forest (LEF). These data quantify fungal mat growth and the time to leaf colonization of fungi species Gymnopus johnstonii and Marasmius crinis-equi. The experiment was conducted in ambient (control) and experimentally warmed plots (4°C above ambient) during spring and summer periods to assess how litter mat-forming fungi respond to a range of environmental conditions of tropical wet forests. The data files include tables of relative fungal mat growth rates, time to leaf colonization, averages of soil temperature (°C), and number of dry days before leaf attachment. The data are stored in comma-separated values (CSV) format and viewable with any text editor, spreadsheet, or statistical software (e.g., R, Python, Excel). Associated metadata describe plot identifiers, measurement descriptions, and processing steps.

Agaric fungi↗
DOE OSTI2018

Scalable deep text comprehension for Cancer surveillance on high-performance computing

Background: Deep Learning (DL) has advanced the state-of-the-art capabilities in bioinformatics applications which has resulted in trends of increasingly sophisticated and computationally demanding models trained by larger and larger data sets. This vastly increased computational demand challenges the feasibility of conducting cutting-edge research. One solution is to distribute the vast computational workload across multiple computing cluster nodes with data parallelism algorithms. In this study, we used a High-Performance Computing environment and implemented the Downpour Stochastic Gradient Descent algorithm for data parallelism to train a Convolutional Neural Network (CNN) for the natural language processing task of information extraction from a massive dataset of cancer pathology reports. We evaluated the scalability improvements using data parallelism training and the Titan supercomputer at Oak Ridge Leadership Computing Facility. To evaluate scalability, we used different numbers of worker nodes and performed a set of experiments comparing the effects of different training batch sizes and optimizer functions.Results: We found that Adadelta would consistently converge at a lower validation loss, though requiring over twice as many training epochs as the fastest converging optimizer, RMSProp. The Adam optimizer consistently achieved a close 2nd place minimum validation loss significantly faster; using a batch size of 16 and 32 allowed the network to converge in only 4.5 training epochs.Conclusions: We demonstrated that the networked training process is scalable across multiple compute nodes communicating with message passing interface while achieving higher classification accuracy compared to a traditional machine learning algorithm.

Qiu, John X.↗
DOE OSTI2023

Classification of River Catchments in the Contiguous United States: Code, Dataset, Similarity Patterns, and Resulting Classes

This dataset serves as supplementary information for the paper by Ciulla F. and Varadharajan C. A Network Approach for Multiscale Catchment Classification using Traits (see reference 1). It contains environmental and physical catchment traits, such as temperatures, precipitation, land use and human interference, from 9067 sites across the contiguous United States (CONUS). The purpose of this dataset is to provide information for a better trait-based categorization of river catchments in the CONUS using networks as an analytical tool. The traits variables match the ones present in the GAGES-II dataset and the preprocessing steps are described in the Methods section (processed_dataset.csv). Additionally we include the topologies (nodes, edges and clusters, also referred as classes) of the catchment network and traits network generated by said dataset (csv and json files). A series of tables support the information carried by the network providing more detailed descriptions of cluster components (SI1.pdf). A summary of all the plots of clusters of catchments with at least 50 nodes is provided (SI2.pdf). The characteristic traits for each cluster of catchments is presented as z-score (traits_categories_zscores_per_catchment_class.csv). The link to the hydrological behavior of clusters of catchments is displayed by boxplots, each describing a particular river discharge index (SI3.pdf). Both csv and json files can be read by common text editors but the data contained into them can be better handled using programming languages like python and database oriented libraries like pandas. Pdf files can be read by any pdf reader software.[02-23-2024] Update: The code and datasets necessary to reproduce the results of the study are available as a zipped repository (code_datasets_catchments_similarity.zip).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

HarDWR - Harmonized Water Rights Records

A dataset within the Harmonized Database of Western U.S. Water Rights (HarDWR). For a detailed description of the database, please see the meta-record v2.0. Changelog v2.0 - Recalculated based on data sourced from WestDAAT - Changed using a Site ID column to identify unique records to using aa combination of Site ID and Allocation ID - Removed the Water Management Area (WMA) column from the harmonized records. The replacement is a separate file which stores the relationship between allocations and WMAs. This allows for allocations to contribute to water right amounts to multiple WMAs during the subsequent cumulative process. - Added a column describing a water rights legal status - Added "Unspecified" was a water source category - Added an acre-foot (AF) column - Added a column for the classification of the right's owner v1.02 - Added a .RData file to the dataset as a convenience for anyone exploring our code. This is an internal file, and the one referenced in analysis scripts as the data objects are already in R data objects. v1.01 - Updated the names of each file with an ID number less than 3 digits to include leading 0s v1.0 - Initial public release Description Here we present an updated database of Western U.S. water right records. This database provides consistent unique identifiers for each water right record, and a consistent categorization scheme that puts each water right record into one of seven broad use categories. These data were instrumental in conducting a study of the multi-sector dynamics of inter-sectoral water allocation changes though water markets (Grogan et al., *in review*). Specifically, the data were formatted for use as input to a process-based hydrologic model, Water Balance Model (WBM), with a water rights module (Grogan et al., *in review*). While this specific study motivated the development of the database presented here, water management in the U.S. West is a rich area of study (e.g., Anderson and Woosly, 2005; Tidwell, 2014; Null and Prudencio, 2016; Carney et al., 2021) so releasing this database publicly with documentation and usage notes will enable other researchers to do further work on water management in the U.S. West. We produced the water rights database presented here in four main steps: (1) data collection, (2) data quality control, (3) data harmonization, and (4) generation of cumulative water rights curves. Each of steps (1)-(3) had to be completed in order to produce (4), the final product that was used in the modeling exercise in Grogan et al. (*in review*). All data in each step is associated with a spatial unit called a Water Management Area (WMA), which is the unit of water right administration utilized by the state in which the right came from. Steps (2) and (3) required use to make assumptions and interpretation, and to remove records from the raw data collection. We describe each of these assumptions and interpretations below so that other researchers can choose to implement alternative assumptions an interpretation as fits their research aims. Motivation for Changing Data Sources The most significant change has been a switch from collecting the raw water rights directly from each state to using the water rights records presented in WestDAAT, a product of the Water Data Exchange (WaDE) Program under the Western States Water Council (WSWC). One of the main reasons for this is that each state of interest is a member of the WSWC, meaning that WaDE is partially funded by these states, as well as many universities. As WestDAAT is also a database with consistent categorization, it has allowed us to spend less time on data collection and quality control and more time on answering research questions. This has included records from water right sources we had previously not known about when creating v1.0 of this database. The only major downside to utilizing the WestDAAT records as our raw data is that further updates are tied to when WestDAAT is updated, as some states update their public water right records daily. However, as our focus is on cumulative water amounts at the regional scale, it is unlikely most records updates would have a significant effect on our results. The structure of WestDAAT led to several important changes to how HarWR is formatted. The most significant change is that WaDE has calculated a field known as `SiteUUID`, which is a unique identifier for the Point of Diversion (POD), or where the water is drawn from. This separate from `AllocationNativeID`, which is the identifier for the allocation of water, or the amount of water associated with the water right. It should be noted that it is possible for a single site to have multiple allocations associated with it and for an allocation to be able to be extracted from multiple sites. The site-allocation structure has allowed us to adapt a more consistent, and hopefully more realistic, approach in organizing the water right records than we had with HarDWR v1.0. This was incredibly helpful as the raw data from many states had multiple water uses within a single field within a single row of their raw data, and it was not always clear if the first water use was the most important, or simply first alphabetically. WestDAAT has already addressed this data quality issue. Furthermore, with v1.0, when there were multiple records with the same water right ID, we selected the largest volume or flow amount and disregarded the rest. As WestDAAT was already a common structure for disparate data formats, we were better able to identify sites with multiple allocations and, perhaps more importantly, allocations with multiple sites. This is particularly helpful when an allocation has sites which cross WMA boundaries, instead of just assigning the full water amount to a single WMA we are now able to divide the amount of water between the number of relevant WMAs. As it is now possible to identify allocations with water used in multiple WMAs, it is no longer practical to store this information within a single column. Instead the stAllocationToWMATab.csv file was created, which is an allocation by WMA matrix containing the percent Place of Use area overlap with each WMA. We then use this percentage to divide the allocation's flow amount between the given WMAs during the cumulation process to hopefully provide more realistic totals of water use in each area. However, not every state provides areas of water use, so like HarDWR v1.0, a hierarchical decision tree was used to assign each allocation to a WMA. First, if a WMA could be identified based on the allocation ID, then that WMA was used; typically, when available, this applied to the entire state and no further steps were needed. Second was the spatial analysis of Place of Use to WMAs. Third was a spatial analysis of the POD locations to WMAs, with the assumption that allocation's POD is within the WMA it should belong to; if an allocation still had multiple WMAs based on its POD locations, then the allocation's flow amount would be divided equally between all WMAs. The fourth, and final, process was to include water allocations which spatially fell outside of the state WMA boundaries. This could be due to several reasons, such as coordinate errors / imprecision in the POD location, imprecision in the WMA boundaries, or rights attached with features, such as a reservoir, which crosses state boundaries. To include these records, we decided for any POD which was within one kilometer of the state's edge would be assigned to the nearest WMA. Other Changes WestDAAT has Allowed In addition to a more nuanced and consistent method of assigning water right's data to WMAs, there are other benefits gained from using the WestDAAT dataset. Among those is a consistent categorization of a water right's legal status. In HarDWR v1.0, legal status was effectively ignored, which led to many valid concerns about the quality of the database related to the amounts of water the rights allowed to be claimed. The main issue was that rights with legal status' such as "application withdrawn", "non-active", or "cancelled" were included within HarDWR v1.0. These, and other water rights status' which were deemed to not be in use have been removed from this version of the database. Another major change has been the addition of the "unspecified water source category. This is water that can come from either surface water or groundwater, or the source of which is unknown. The addition of this source category brings the total number of categories to three. Due to reviewer feedback, we decided to add the acre-foot (AF) column so that the data may be more applicable to a wider audience. We added the ownerClassification column so that the data may be more applicable to a wider audience. File Descriptions The dataset is a series of various files organized by state sub-directories. In addition, each file begins with the state's name, in case the file is separate from its sub-directory for some reason. After the state name is the text which describes the contents of the file. Here is each file described in detail. Note that st is a placeholder for the state's name. stFullRecords_HarmonizedRights.csv: A file of the complete water records for each state. The column headers for each of this type of file are: state - The name of the state to which the allocations belong to. FIPS - The two digit numeric state ID code. siteID - The site location ID for POD locations. A site may have multiple allocations, which are the actual amount of water which can be drawn. In a simplified hypothetical, a farm stead may have an allocation for "irrigation" and an allocation for "domestic" water use, but the water is drawn from the same pumping equipment. It should be noted that many of the site ID appear to have been added by WaDE, and therefore may not be recognized by a given state's water rights database. allocationID - The allocation ID for the water right. For most states this is the water right ID, and what is recommended to use should a right be looked up on a given state's water rights database. The water amounts associated with these IDs tend to be finer scaled than those associated with siteID. It should be noted that some allocations may be extracted from multiple sites, particularly for larger Places of Use. ownerClassification - A classification of the types of owners for water rights. The most common is `Private` which incorporates a wide range of entities. Several classifications would be grouped into a government category, most of which are for the U.S. Federal Government. These allocations could be listed as "Federal", "United States of America", or as the names of any number of federal agencies. The last major grouping of entities is for "Native American"s. priorityDate - The date we use as the water right priority date for our modeling analysis. This is the legal priority date when it is available. However, for some rights, specifically from California and New Mexico, we used a pseudo priority date (e.g. well completion date or start of well drilling date) when a legal priority date was not available. The most questionable dates come from New Mexico, where the only date associated with certain water right records was the date the allocation was recorded in the database. As the allocation record creation tended to be within a few months of the filing of the application of the water right, from manually double checking the water rights, and our analysis focuses on aggregating water rights on the timescale of years, we determined it was acceptable to use such dates to include as many records as possible. primaryBeneficialUse - From the numerous state water use categories, WaDE categorized them into 21 categories WestDAAT. This column is the original WaDE category for the primary water use at the PoD site. allocationBeneficialUse - From the numerous state water use categories, WaDE categorized them into 21 categories for WestDAAT. This column is the original WaDE category

Economics↗
DOE OSTI2024

A Compound Data Poisoning Technique with Significant Adversarial Effects on Transformer-based Sentiment Classification Tasks

Transformer-based models have demonstrated much success in various natural language processing tasks. However, they are often vulnerable to adversarial attacks, such as data poisoning, which can intentionally fool the model into generating incorrect results. In this article, we present a novel, compound variant of a data poisoning attack on a transformer-based model that maximizes the poisoning effect while minimizing the scope of poisoning. Here we do so by combining the established data poisoning technique (label flipping) with a novel adversarial artifact selection and insertion technique aimed at minimizing detectability and the scope of the poisoning footprint. We find that by using a combination of these two techniques, we achieve a state-of-the-art attack success rate of approximately 90% while poisoning only 0.5% of the original training set, thus minimizing the scope and detectability of the poisoning action. These findings have the potential to advance the development of better data poisoning detection methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Nanomaterials in Extreme Environments: Fundamentals and Applications Rostislav A. Andrievski and Arsen V. Khatchoyan

Nanomaterials in Extreme Environments Rostislav A. Andrievski and Arsen V. Khatchoyan Springer, 2016 106 pages, $99.00 (e-book $69.99) ISBN 978–3-319–25331–2 This slim volume is an extensive review of our current understanding of the response of nanostructured materials to extreme operating conditions, such as high temperature, flux of high energy neutrons, high pressure, mechanical stress, and oxidizing environments. The emphasis is on metallic materials, especially Cu alloys. Graphene-based materials, fullerenes, polymeric materials, nano-glasses and glass-ceramics are not covered by this review. The book has six chapters including an introduction and a brief conclusion. The introduction documents the growth of scientific interest in nanostructured materials and stresses the need to study the behavior of nanomaterials under extreme conditions. This chapter also presents Herbert Gleiter’s classification of nanomaterials into twelve groups based on the shapes of the nanoscale features and chemical composition of the components of the nanostructure. The second chapter deals with the high temperature environment and the thermodynamics and kinetics of grain growth. The authors identify the lack of reliable thermodynamic data as a key limitation in this field. The discussion brings out the interplay of structural relaxation, redistribution of excess free volume, diffusion, and recrystallization in multicomponent nanostructures at elevated temperature. Chapter 3 focuses on the effects of ion and neutron irradiation on the structure and properties of nanomaterials. The authors do a good job of highlighting recent studies on the radiation tolerance of nanocrystalline oxides and rapid grain growth under irradiation. The material addresses both fission and fusion reactor applications. Chapter 4 reviews the effects of severe plastic deformation and cyclic loading on nanostructure formation and phase transformation. This chapter also explores the challenge of achieving high density while retaining nanostructural features during processing under extreme loads and high temperatures. Chapter 5 discusses the effects of corrosion on nanomaterials. The behavior of a variety of alloys and high melting point compounds in liquid media and high temperature oxidizing environments is reviewed. The concluding chapter identifies areas for further research. The book would have benefited from careful copy editing for use of the English language. Moreover, the excessive use of acronyms makes the text difficult to read. Each chapter ends with a section on the application of nanomaterials and a long list of references. The integration of theoretical approaches and simulation results with experimental data offers fresh insights into the behavior of nanomaterials. Overall, this book will serve as useful reference material for researchers interested in nanomaterials driven to extremes. Reviewer: Ram Devanathan is Technical Group Manager of Reactor Materials and Mechanical Design, Pacific Northwest National Laboratory, USA.

Devanathan, Ram↗
DOE OSTI2023

Data associated with “Different methods of estimating riverbed sediment grain size diverge at the basin scale ” (v2)

This data package is associated with the publication “Different methods of estimating riverbed sediment grain size diverge at the basin scale” published in Frontiers in Earth Science (Regier et al., 2025). The distribution of sediment grain size in streams and rivers is often quantified by the median grain size (d50), a key metric for understanding and predicting hydrologic and biogeochemical function of streams and rivers. Manual methods to measure d50 are time-consuming and ignore larger grains, while model-based methods to estimate d50 often over-generalize basin characteristics, and therefore cannot accurately represent site-scale heterogeneity. Here, we apply a machine learning-enabled photogrammetry methodology (You Only Look Once, or YOLO) for estimating d50 for grains > 2 mm based on images collected from streams and rivers throughout the Yakima River Basin (YRB). To understand how such methods may help bridge the gaps in resolution and accuracy between manual and catchment characteristics model-based d50 estimates, we compared YOLO d50 values to manual and model-based estimates across the YRB. We found distinct differences among methods for d50 averages and variability, and relationships between d50 estimates and basin characteristics. Source images can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1892052. This data package was originally published in May 2023. It was updated August 2025 (v2; new and modified files). File and folder names were not revised to indicate changes. See the change history section in the readme for more details. In addition to the readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) readme; (4) and subfolders containing data, figures, and scripts. The data folder contains datasets used for the analyses in the manuscript in image, text-delimited or geospatially-referenced formats. The figures folder contains the figures from the manuscript in different formats. The scripts folder contains all of the scripts used to complete the analyses in the manuscript. All files are .csv, .rds, .dbf, .prj, .shp, .shx, .jpg, .png, .R, .Rproj, or .pdf. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected some of these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Data from: 'Abiotic influences on continuous conifer forest structure across a subalpine watershed'

This package archives the core data used for analysis and inference in 'Abiotic influences on continuous conifer forest structure across a subalpine watershed' (Worsham et al., 2025). All data were collected in the East River, Washington Gulch, Slate River, and Coal Creek watersheds of Colorado. In the paper, we quantified the relative influence of climate, topographic, edaphic, and geologic factors on conifer stand structure and composition, and their functional relationships, at the watershed scale. We used waveform LiDAR data to derive spatially continuous stand structure metrics. We fused these with a species-level classification map to estimate tree species abundance. We applied generalized additive and generalized boosted models to evaluate the covariability of structural and compositional metrics with abiotic variables. The package contains the essential products required for reproducing our analysis and the tables and figures reported in the publication. The products comprise four classes: (1) geospatial data, (2) tabular data used for inferential analysis, (3) tabular data describing analytical results and performance statistics, and (4) a data user guide. (1) includes discretized waveform LiDAR data, locations and attributes of individual tree crowns, sampling locations and domain boundaries, a canopy height model, and raster files of estimated forest structural and compositional metrics at 100 m grid scale. (2) includes all response and explanatory variable values applied in inferential models. Response variables include conifer forest stand density, basal area, 95th percentile height, quadratic mean diameter, and others. Explanatory variables include climatic water deficit, actual evapotranspiration, elevation, heat load, soil available water content, and others. (3) includes results of training and testing several individual tree detection (ITD) algorithms, as well as inferential modeling results. (4) is a PDF user guide for this data package, including detailed descriptions and data dictionaries for all files. The data package root contains 17 assets: 8 compressed tape archive (.tar.gz) files, 5 comma-separated values (.csv) files, 3 Geographic Tagged Image File Format (GeoTIFF) (.tif) files, and 1 Portable Document Format (.pdf) file. The compressed .tar.gz archives contain ESRI shapefiles (.shp) .tif, compressed LASer (.laz), and .csv files. The archives must first be decompressed using the widely distributed command-line software utility TAR. All other files, including constituent files within the .tar.gz archives, can be opened in the open-source R statistical computing environment. Alternatively, .csv files may also be read in any simple text editor software or Microsoft Excel. Geospatial files including .shp and .tif files can also be opened in GIS software, such as QGIS (open-source) or ESRI ArcGIS (proprietary). The .pdf Data User Guide can be read with Adobe Acrobat Reader or other compatible readers.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2024

Maps of plant functional type (PFT), PFT fractional cover, and uncertainty derived from AVIRIS-NG data, 2019, Seward Peninsula

Remote sensing maps of plant functional type (PFT), PFT fractional cover (fCover), and fCover uncertainty maps derived from NASA’s Airborne Visible / Infrared Imaging Spectrometer – Next Generation (AVIRIS-NG). The AVIRIS-NG imaging spectroscopy data (380 ~ 2510 nm) was collected as a part of the collaboration between NASA’s Arctic-Boreal Vulnerability Experiment (ABoVE; Miller et al., 2019) and DOE’s Next Generation Ecosystem Experiment in the Arctic (NGEE-Arctic). This package includes maps for flights over Teller, Kougarok, and Council watersheds created using eight AVIRIS-NG imagery collected in July, 2019. The map data and metadata are provided as image (ENVI, *.png) and text (*.txt, *hdr) formats. Additional supporting map quicklooks are provided as GIS *.kml files. Detailed description of the methods for each map are provided in Yang et al., (2023). These datasets are provided in support of Yang et al., (In revision) “Topography and Functional Traits Control the Distribution of Key Shrub Plant Functional Types in Low-Arctic Tundra”.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Hot Droughts and Forest Tree Dynamics in the Amazon - Statistical Models, Scripts, Data, and Outputs

This package contains data, outputs, equations, and R scripts for analyses for manuscript entitled "Hot droughts in the Amazon: A window to a future hypertropical climate" by J. Chambers et al., in particular it contains statistical models and analyses for the INPA BIONTE tree mortality study. The Models folder contains details for all statistical models in PDF files. The Scripts folder contains the R scripts for Bayesian Hierarchical Models (two text files) and SEMs (one text file) are separate and reasonably annotated. All data associated with these scripts are in the data folder. The Data folder contains two of the three CSV files used for the analyses and are called by the R scripts. Two of them are part of published datasets (`BIONTE_mortality-rates.csv` from Lima et al. 2024, DOI:10.15486/ngt/1898910 and `SPEI.csv` from Pastorello et al. 2023 DOI:10.15486/ngt/1958257) and also provided in this package for convenience (please see the corresponding datasets for usage and citation terms). The third dataset (`BIONTE_gapfilled_wd.csv`) contains sensitive information and can be obtained by contacting the manuscript lead author. The Outputs folder contains the two output files that provide extra information about the analyses. The file `figuresFeb2025d.pdf` contains all the figures from the manuscript - captions are in the manuscript. The file `ChambersMS.pdf` contains primary results from Bayesian statistical models, regression analyses, and validation steps applied to the tree mortality data from the INPA experiments. The document includes visual summaries, model diagnostics, and leave-one-out (LOO) validation results. A breakdown of file contents can be found in the README file that is part of this package.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Maps of Arctic vegetation leaf nitrogen concentration, albedo and plant functional type (PFT) derived from imaging spectroscopy data, Council watershed, Seward Peninsula, Alaska, 2019

Remote sensing maps of surface albedo, leaf nitrogen content, and plant functional types (PFTs) derived from NASA's Airborne Visible / Infrared Imaging Spectrometer Next Generation (AVIRIS-NG) by the Terrestrial Ecosystem Science & Technology (TEST) group at Brookhaven National Laboratory. The AVIRIS-NG imaging spectroscopy data (380 ~ 2510 nm) was collected as a part of the collaboration between NASA's Arctic-Boreal Vulnerability Experiment (ABoVE; Miller et al., 2019) and DOE's Next Generation Ecosystem Experiment in the Arctic (NGEE-Arctic). This package includes maps for the NGEE-Arctic Council watershed created using AVIRIS-NG imagery collected on July 9th, 2019. The map data and metadata are provided as image (ENVI, *.png) and text (*.txt, *hdr) formats. Additional supporting map quicklooks are provided as *.png files and GIS *.kml files. Detailed description of the methods for each map are provided in this document. These datasets are provided in support of Figure 6 in Nelson et al., (2022), "Remote Sensing of Tundra Ecosystems using High Spectral Resolution Reflectance: Opportunities and Challenges". The full citation can be found within the references section. Note that the AVIRIS-NG leaf nitrogen product included in this dataset is a preliminary product and is provided for demonstration purposes only. It is not recommended that the map be used for scientific applications. For future updates on these products, please contact the authors.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

AI Model Benchmarking for Nonproliferation Applications: Steel Thread Benchmarking Task Force Technical Report (Rev. 2)

Steel Thread is a NA-22 venture that seeks to build trustworthy, reliable AI models that can be used in a wide variety of nonproliferation tasks. A key aspect of building these models is developing appropriate benchmarks and evaluation methods, which will enable the venture to identify and adapt models to provide the most value in the nonproliferation domain. Benchmarks must be relevant to key tasks in this domain, such as question answering, information retrieval, document summarization and classification, consensus analysis, and image and data analysis. This report 1) provides an overview of benchmark design, evaluation, and challenges; 2) reviews a variety of open benchmarks, with a focus on language models and tasks; and 3) identifies benchmarks that are most relevant to Steel Thread. This report is intended to serve as a basis for further efforts to classify and evaluate benchmarks and their correlation with success on nonproliferation-specific tasks. The Steel Thread venture has defined benchmarks to be a particular combination of a dataset (or datasets) and a metric (or metrics) conceptualized as representing one or more specific tasks or sets of abilities for a specific modality. It is adopted by a research community as a shared framework for comparing methods.1 It includes 1) Data: Labeled (a designated subset not used for training, which could be all the data), 2) Metric: A way to quantify performance, 3) Task/Ability: What the benchmark is testing, 4) Protocol: A structured and repeatable evaluation process, 5) Baseline/Reference Model: For comparison; could be statistical, rule-based, SME-derived, or another model, and 6) Maintenance Plan: to update with new information over time; important for long-term utility. For further clarity, the definition includes what a benchmark, in this context, is not. It is not a corpus of training data, specific to a model (it is intended to apply to a range of models), a universal evaluation of performance, a guarantee that the ‘top’ model on the leaderboard will be the best fit for every specific use case, an all-encompassing proof of a model’s universal quality, nor is it a one-size-fits-all measure of success. It does not cover every real-world constraint (like operational, ethical, or cost considerations), a systems integration test, or a unit test. This definition was inspired by and resulted from discussions within the Steel Thread Benchmarking Task Force. This group was formed to define what we would mean as a benchmark within Steel Thread but persisted as the need to develop a thorough understanding of the large and expanding existing benchmarking space. This technical report is a result of the group’s divide and conquer approach to exploring this space. The release of benchmarks might not be progressing as quickly as model development, but it is moving very fast, as many benchmarks quickly become saturated, when state-of-the-art models score so close to the benchmark’s ceiling that their results are virtually indistinguishable. At that point, the test no longer differentiates between new systems, so researchers usually stop reporting scores as the benchmark no longer informs about improvements from the next generation of models. In the OpenAI announcement of GPT-5, they reported results on six flagship public benchmarks (AIME 2025, SWE-bench Verified, Aider Polyglot, MMMU, HealthBench Hard, GPQA) but the full system-card covers roughly thirty-five separate evaluations, comprising hundreds of test task items in total. There have been some efforts to summarize benchmarks in specific fields, like for text-to-image generation, but these surveys have had a narrow methodology scope. Therefore, a comprehensive survey of all benchmarks or even all benchmarks that could be relevant to Steel Thread is outside of the scope of this report. We chose some specific benchmarks to investigate in detail.

97 MATHEMATICS AND COMPUTING↗