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DOE OSTI2024

Functionally Assembled Terrestrial Ecosystem Simulator (FATES) for Hurricane Disturbance and Recovery

Tropical cyclones are an important cause of forest disturbance, and major storms caused severe structural damage and elevated tree mortality in coastal tropical forests. Model capabilities that can be used to understand post-hurricane forest recovery are still limited. We use a vegetation demography model, the Functionally Assembled Terrestrial Ecosystem Simulator, coupled with the Energy Exascale Earth System Model Land Model (ELM-FATES) to study the processes and the key factors regulating post-hurricane forest recovery. We implemented hurricane-induced forest damage, including defoliation, structural biomass reduction, and tree mortality, performed ensemble model simulations, and used random forest feature importance. For the simulation in the Luquillo Experimental Forest, Puerto Rico, we identified factors controlling the post-hurricane forest recovery, and quantified the sensitivity of key model parameters to the post-hurricane forest recovery. The results indicate a tendency for the Bisley forests to shift toward the light demanding plant functional type (PFT) when the pre-hurricane biomass between the light demanding and shade tolerant PFTs is nearly equal and forests experience hurricane disturbance with mortality >60% for both the two PFTs. Under more realistic conditions where the shade tolerant PFT is initially dominant, mortality >80% is required for a shift toward dominance of the light demanding PFT at Bisley. Hurricane mortality and background mortality are the two major factors regulating post-hurricane forest recovery in simulations. This research improves understanding of the ELM-FATES model behavior associated with hurricane disturbance and provides guidance for dynamic vegetation model development in representing hurricane induced forest damage with varied intensities.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRSDate not supplied

Mapping National Forest Aboveground Biomass in Mexico by Integrating GEDI, Sentinel‐1 and Sentinel‐2 Data

Accurate mapping of forest aboveground biomass density (AGBD) is required to better understand the role of forests in the global carbon cycle and to support international policies for climate change mitigation and adaptation. Mexico is one of the countries having great potential for the United Nations Programme on Reducing Emissions from Deforestation and Forest Degradation (or UN-REDD program) and there is a growing demand for unbiased Monitoring Reporting Verification systems at a national level. As an effort under NASA’s Carbon Monitoring System (CMS) program, we developed a machine learning model using multi-stream remote sensing measurements as well as topographic data to create a high spatial resolution AGBD map (~100 m) over Mexico (circa 2020). The remote sensing data includes Global Ecosystem Dynamic Investigation (GEDI) lidar, Sentinel 1 Synthetic-Aperture Radar (SAR), and Sentinel-2 multispectral imagery (MSI). GEDI onboard the International Space Station provides unprecedented forest structure and AGBD sampling datasets for model training and validation practices. Our analysis indicates that the developed random forest model can capture 63 % of the spatial variation (RMSE = 33.7 Mg/ha) of AGBD of Mexican forests. We find that shortwave infrared bands of Sentinel-2 MSI and topographical variables from elevation data are the most important variables in the developed AGBD model. Our study highlights methodological opportunities in synergistic uses of multiple sensors for large-scale forest AGBD mapping and shows potential for retrospective analysis and operational monitoring of forest AGBD and its dynamics.

Taejin Park↗

NASA NTRS2015

Mapping Species Composition of Forests and Tree Plantations in Northeastern Costa Rica with an Integration of Hyperspectral and Multitemporal Landsat Imagery

An efficient means to map tree plantations is needed to detect tropical land use change and evaluate reforestation projects. To analyze recent tree plantation expansion in northeastern Costa Rica, we examined the potential of combining moderate-resolution hyperspectral imagery (2005 HyMap mosaic) with multitemporal, multispectral data (Landsat) to accurately classify (1) general forest types and (2) tree plantations by species composition. Following a linear discriminant analysis to reduce data dimensionality, we compared four Random Forest classification models: hyperspectral data (HD) alone; HD plus interannual spectral metrics; HD plus a multitemporal forest regrowth classification; and all three models combined. The fourth, combined model achieved overall accuracy of 88.5%. Adding multitemporal data significantly improved classification accuracy (p less than 0.0001) of all forest types, although the effect on tree plantation accuracy was modest. The hyperspectral data alone classified six species of tree plantations with 75% to 93% producer's accuracy; adding multitemporal spectral data increased accuracy only for two species with dense canopies. Non-native tree species had higher classification accuracy overall and made up the majority of tree plantations in this landscape. Our results indicate that combining occasionally acquired hyperspectral data with widely available multitemporal satellite imagery enhances mapping and monitoring of reforestation in tropical landscapes.

hyperspectral fusion↗

NASA NTRSDate not supplied

Quantifying Post-fire Vegetation Recovery on the Colorado Front Range

Forest composition and structure in the Colorado Front Range has been altered by changing wildfire regimes, particularly in response to increased fire severity. Subsequent reductions in post-fire tree regeneration can result in chronic impacts to ecological function and water quality. This project partnered with the U.S. Forest Service to estimate tree canopy recovery from 15 to 21 years after four Colorado Front Range fires that burned between 1996 and 2002— the Bobcat, Buffalo Creek, Hayman, and High Meadows fires—using Landsat 5 Thematic Mapper (TM), Landsat 7 Enhanced Thematic Mapper (ETM+), and Landsat 8 Operational Land Imager (OLI). First, we evaluated relationships between recovery metrics derived from spectral vegetation indices (i.e. post-fire vegetation, normalized burn ratio, percent unrecovered vegetation) and field-collected counts of post-fire tree seedling regeneration. Then, we used high-resolution imagery paired with Landsat timeseries spectral and geomorphometric data to map forest canopy cover 15-21 years post-fire. Finally, we assessed ecological drivers of recovery including topography, climate, soils, and fire severity using Random Forest. While we found that basic vegetation index metrics failed to distinguish field-measured tree regeneration, our data showed that both aspect and burn severity were important drivers of vegetation recovery. North-facing aspects tended to have higher pre-fire Normalized Difference Vegetation Index (NDVI) and thus higher burn severities. However, areas that burned at high severity experienced slower vegetation recovery, regardless of aspect suggesting that high severity fire can mute favorable site conditions on north-facing aspects (i.e. moister, more developed soils). While this work propels our understanding of variables that influence vegetative recovery, vegetation type, forest conversion, and watershed function, more work should focus on what vegetation indices identifying areas of recovery indicate across different forest types and burn severities.

NASA DEVELOP↗

NASA NTRS2021

Colorado Front Range Disasters: Understanding the Impact of Forest Management on the Cameron Peak and CalWood Fire

Along the Colorado Front Range, forest management has gained significant attention due to uncharacteristically large fires that burned late in 2020. The Cameron Peak Fire (largest in Colorado recorded history) and the CalWood Fire collectively burned an estimated 219,019 acres from August through December of 2020. Project partners at the Coalition for the Poudre River Watershed, Colorado State Forest Service, Ben Delatour Scout Ranch, The Nature Conservancy, Colorado Forest Restoration Institute, and Colorado State University were interested in understanding the effectiveness of previous forest treatments in reducing burn severity within the Cameron Peak Fire and the CalWood Fire. We first collated a forest treatment dataset from pre-existing datasets by reclassifying over 29,000 treatments, which occurred across the Northern Colorado Front Range between 1970-2020. Secondly, we mapped three burn severity indices using Landsat 8 OLI and Sentinel-2 MSI Earth observations and compared them to soil burn severity field data. Thirdly, a total of 35 topographic, disturbance, forest structure, and treatment predictor variables were generated across the fires. Finally, we assessed relationships between these predictor variables and burn severity using the random forest algorithm. Model results indicate that the primary drivers of burn severity were elevation and distance to treatment edge for the Cameron Peak Fire and fire area and forest canopy cover for the CalWood Fire. Further analysis of these variables paired with field data is necessary to understand the relationship between burn severity and treatments to guide future restoration efforts, improve forest resiliency, and mitigate fire risks.

Neal Swayze↗

DOE OSTI2020

Structure–activity relationship-based chemical classification of highly imbalanced Tox21 datasets

Abstract The specificity of toxicant-target biomolecule interactions lends to the very imbalanced nature of many toxicity datasets, causing poor performance in Structure–Activity Relationship (SAR)-based chemical classification. Undersampling and oversampling are representative techniques for handling such an imbalance challenge. However, removing inactive chemical compound instances from the majority class using an undersampling technique can result in information loss, whereas increasing active toxicant instances in the minority class by interpolation tends to introduce artificial minority instances that often cross into the majority class space, giving rise to class overlapping and a higher false prediction rate. In this study, in order to improve the prediction accuracy of imbalanced learning, we employed SMOTEENN, a combination of Synthetic Minority Over-sampling Technique (SMOTE) and Edited Nearest Neighbor (ENN) algorithms, to oversample the minority class by creating synthetic samples, followed by cleaning the mislabeled instances. We chose the highly imbalanced Tox21 dataset, which consisted of 12 in vitro bioassays for > 10,000 chemicals that were distributed unevenly between binary classes. With Random Forest (RF) as the base classifier and bagging as the ensemble strategy, we applied four hybrid learning methods, i.e., RF without imbalance handling (RF), RF with Random Undersampling (RUS), RF with SMOTE (SMO), and RF with SMOTEENN (SMN). The performance of the four learning methods was compared using nine evaluation metrics, among which F 1 score, Matthews correlation coefficient and Brier score provided a more consistent assessment of the overall performance across the 12 datasets. The Friedman’s aligned ranks test and the subsequent Bergmann-Hommel post hoc test showed that SMN significantly outperformed the other three methods. We also found that a strong negative correlation existed between the prediction accuracy and the imbalance ratio (IR), which is defined as the number of inactive compounds divided by the number of active compounds. SMN became less effective when IR exceeded a certain threshold (e.g., > 28). The ability to separate the few active compounds from the vast amounts of inactive ones is of great importance in computational toxicology. This work demonstrates that the performance of SAR-based, imbalanced chemical toxicity classification can be significantly improved through the use of data rebalancing.

Idakwo, Gabriel↗

NASA NTRS2017

Linear Subpixel Learning Algorithm for Land Cover Classification from WELD using High Performance Computing

In this work, we use a Fully Constrained Least Squares Subpixel Learning Algorithm to unmix global WELD (Web Enabled Landsat Data) to obtain fractions or abundances of substrate (S), vegetation (V) and dark objects (D) classes. Because of the sheer nature of data and compute needs, we leveraged the NASA Earth Exchange (NEX) high performance computing architecture to optimize and scale our algorithm for large-scale processing. Subsequently, the S-V-D abundance maps were characterized into 4 classes namely, forest, farmland, water and urban areas (with NPP-VIIRS-national polar orbiting partnership visible infrared imaging radiometer suite nighttime lights data) over California, USA using Random Forest classifier. Validation of these land cover maps with NLCD (National Land Cover Database) 2011 products and NAFD (North American Forest Dynamics) static forest cover maps showed that an overall classification accuracy of over 91 percent was achieved, which is a 6 percent improvement in unmixing based classification relative to per-pixel-based classification. As such, abundance maps continue to offer an useful alternative to high-spatial resolution data derived classification maps for forest inventory analysis, multi-class mapping for eco-climatic models and applications, fast multi-temporal trend analysis and for societal and policy-relevant applications needed at the watershed scale.

Subpixel↗

NASA NTRS2019

Modelling above-ground biomass stock over Norway using national forest inventory data with ArcticDEM and Sentinel-2 data

Boreal forests constitute a large portion of the global forest area, yet they are undersampled through field surveys, and only a few remotely sensed data sources provide structural information wall-to-wall throughout the boreal domain. ArcticDEM is a collection of high-resolution (2 m) space-borne stereogrammetric digital surface models (DSM) covering the entire land area north of 60° of latitude. The free-availability of ArcticDEM data offers new possibilities for aboveground biomass mapping (AGB) across boreal forests, and thus it is necessary to evaluate the potential for these data to map AGB over alternative open-data sources (i.e., Sentinel-2). This study was performed over the entire land area of Norway north of 60° of latitude, and the Norwegian national forest inventory (NFI) was used as a source of field data composed of accurately geolocated field plots (n=7710) systematically distributed across the study area. Separate random forest models were fitted using NFI data, and corresponding remotely sensed data consisting of either: i) a canopy height model (ArcticCHM) obtained by subtracting a high-quality digital terrain model (DTM) from the ArcticDEM DSM height values, ii) Sentinel-2 (S2), or iii) a combination of the two (ArcticCHM+S2). Furthermore, we assessed the effect of the forest- and terrain-specific factors on the models’ predictive accuracy. The best model (,i.e., ArcticCHM+S2) explained nearly 60% of the variance of the training set, which translated in the largest accuracy in terms of root mean square error (RMSE=41.4 t/ha). This result highlights the synergy between 3D and multispectral data in AGB modelling. Furthermore, this study showed that despite the importance of ArcticCHM variables, the S2 model performed slightly better than ArcticCHM model. This finding highlights some of the limitations of ArcticDEM, which, despite the unprecedented spatial resolution, is highly heterogeneous due to the blending of multiple acquisitions across different years and seasons. We found that both forest- and terrain-specific characteristics affected the uncertainty of the ArcticCHM+S2 model and concluded that the combined use of ArcticCHM and Sentinel-2 represents a viable solution for AGB mapping across boreal forests. The synergy between the two data sources allowed for a reduction of the saturation effects typical of multispectral data while ensuring the spatial consistency in the output predictions due to the removal of artifacts and data voids present in ArcticCHM data. While the main contribution of this study is to provide the first evidence of the best-case-scenario (i.e., availability of accurate terrain models) that ArcticDEM data can provide for large-scale AGB modelling, it remains critically important for other studies to investigate how ArcticDEM may be used in areas where no DTMs are available as is the case for large portions of the boreal zone.

space-borne imagery↗

NASA NTRS2018

Mapping Mangrove Extent and Change: A Globally Applicable Approach

This study demonstrates a globally applicable method for monitoring mangrove forest extent at high spatial resolution. A 2010 mangrove baseline was classified for 16 study areas using a combination of ALOS PALSAR and Landsat composite imagery within a random forests classifier. A novel map-to-image change method was used to detect annual and decadal changes in extent using ALOS PALSAR/JERS-1 imagery. The map-to-image method presented makes fewer assumptions of the data than existing methods, is less sensitive to variation between scenes due to environmental factors (e.g., tide or soil moisture) and is able to automatically identify a change threshold. Change maps were derived from the 2010 baseline to 1996 using JERS-1 SAR and to 2007, 2008 and 2009 using ALOS PALSAR. This study demonstrated results for 16 known hotspots of mangrove change distributed globally, with a total mangrove area of 2,529,760 ha. The method was demonstrated to have accuracies consistently in excess of 90% (overall accuracy: 92.2–93.3%, kappa: 0.86) for mapping baseline extent. The accuracies of the change maps were more variable and were dependent upon the time period between images and number of change features. Total change from 1996 to 2010 was 204,850 ha (127,990 ha gain, 76,860 ha loss), with the highest gains observed in French Guiana (15,570 ha) and the highest losses observed in East Kalimantan, Indonesia (23,003 ha). Changes in mangrove extent were the consequence of both natural and anthropogenic drivers, yielding net increases or decreases in extent dependent upon the study site. These updated maps are of importance to the mangrove research community, particularly as the continual updating of the baseline with currently available and anticipated spaceborne sensors. It is recommended that mangrove baselines are updated on at least a 5-year interval to suit the requirements of policy makers.

Thomas, Nathan↗

NASA NTRS2019

Evaluating Combinations of Sentinel-2 Data and Machine-Learning Algorithms for Mangrove Mapping in West Africa

Creating a national baseline for natural resources, such as mangrove forests, and monitoring them regularly often requires a consistent and robust methodology. With freely available satellite data archives and cloud computing resources, it is now more accessible to conduct such large-scale monitoring and assessment. Yet, few studies examine the reproducibility of such mangrove monitoring frameworks, especially in terms of generating consistent spatial extent. Our objective was to evaluate a combination of image processing approaches to classify mangrove forests along the coast of Senegal and The Gambia. We used freely available global satellite data (Sentinel-2), and cloud computing platform (Google Earth Engine) to run two machine learning algorithms, random forest (RF), and classification and regression trees (CART). We calibrated and validated the algorithms using 800 reference points collected using high-resolution images. We further re-ran 10 iterations for each algorithm, utilizing unique subsets of the initial training data. While all iterations resulted in thematic mangrove maps with over 90% accuracy, the mangrove extent ranges between 827-2807 km2 for Senegal and 245-1271 km2 for The Gambia with one outlier for each country. We further report "Places of Agreement" (PoA) to identify areas where all iterations for both methods agree (506.6 km2 and 129.6 km2 for Senegal and The Gambia, respectively), thus have a high confidence in predicting mangrove extent. While we acknowledge the time- and cost-effectiveness of such methods for the landscape managers, we recommend utilizing them with utmost caution, as well as post-classification on-the-ground checks, especially for decision making.

Mondal, Pinki↗

NASA NTRS2022

Southern Wyoming Ecological Forecasting: Monitoring Cheatgrass in Southern Wyoming and Northern Colorado to Inform Management Efforts Post-Mullen Fire

Cheatgrass (Bromus tectorum) is a prominent invasive species in the Intermountain West that has the potential to out-compete native plant species, reduce biodiversity, and reduce the quality of habitat for ungulates. Furthermore, because cheatgrass readily establishes in disturbed landscapes, it can potentially increase fuel loads and exacerbate wildfire risk. In 2020, the Mullen Fire burned 176,878 acres in Carbon and Albany Counties, Wyoming and Jackson County, Colorado. Large fires such as this one raise concern for partners at the United States Forest Service and the United States Geological Survey Fort Collins Science Center, who are tasked with rapidly detecting and controlling invasive species in the post-fire environment. We developed a Random Forest model trained by in-situ field data and spectral indices such as Normalized Difference Vegetation Index (NDVI), Soil Adjusted Vegetation Index, and Enhanced Vegetation Index derived from Landsat 8 Operational Land Imager, Sentinel-2 MultiSpectral Instrument, and Shuttle Radar Topography Mission to detect and map cheatgrass presence during the 2021 growing season. The team successfully created a spectral cheatgrass detection map in the study area (RMSE = 13.71, R2 = 0.34). We also produced a NDVI time-series derived from Sentinel-2 MSI to analyze vegetation recovery patterns.

Dahlia Shahin↗

DOE OSTI2023

Stand validation of lidar forest inventory modeling for a managed southern pine forest

We evaluated area-based approaches (ABAs) to light detection and ranging (lidar) predictions of plot- and stand-level forest attributes (tree count, height, basal area, volume, aboveground biomass, broadleaf/conifer, and diameter at breast height — “diameter”). ABA methods included post-stratification (PS), ordinary least squares (OLSs) regression, k nearest neighbors ( kNN), and random forest (RF). This study was conducted on the Savannah River Site in South Carolina, USA. Plot- and stand-level predictions were validated against fixed-radius 0.04 ha (0.1 acre) plots in 49 ≈2.0 ha (5 acre) stands. Our findings demonstrate that lidar can be incorporated operationally into forest inventory systems to provide stand-level inferences for a wide range of forest attributes. Volume predictions for specific diameter classes, however, often fared poorly (root mean squared error (RMSE) > 100%) for the methods we explored, especially for larger (less common) diameter trees. Stand-level results were consistently better than pixel-level results (10–200+ percentage points). kNN and RF performed similarly and better than OLS and PS, but RF was the most robust to model configurations, while kNN has practical advantages such as simultaneous predictions of many attributes.

Forestry↗

DOE OSTI2024

Forest Carbon Storage in the Western United States: Distribution, Drivers, and Trends

Abstract Forests are a large carbon sink and could serve as natural climate solutions that help moderate future warming. Thus, establishing forest carbon baselines is essential for tracking climate‐mitigation targets. Western US forests are natural climate solution hotspots but are profoundly threatened by drought and altered disturbance regimes. How these factors shape spatial patterns of carbon storage and carbon change over time is poorly resolved. Here, we estimate live and dead forest carbon density in 19 forested western US ecoregions with national inventory data (2005–2019) to determine: (a) current carbon distributions, (b) underpinning drivers, and (c) recent trends. Potential drivers of current carbon included harvest, wildfire, insect and disease, topography, and climate. Using random forests, we evaluated driver importance and relationships with current live and dead carbon within ecoregions. We assessed trends using linear models. Pacific Northwest (PNW) and Southwest (SW) ecoregions were most and least carbon dense, respectively. Climate was an important carbon driver in the SW and Lower Rockies. Fire reduced live and increased dead carbon, and was most important in the Upper Rockies and California. No ecoregion was unaffected by fire. Harvest and private ownership reduced carbon, particularly in the PNW. Since 2005, live carbon declined across much of the western US, likely from drought and fire. Carbon has increased in PNW ecoregions, likely recovering from past harvest, but recent record fire years may alter trajectories. Our results provide insight into western US forest carbon function and future vulnerabilities, which is vital for effective climate change mitigation strategies.

Environmental Sciences & Ecology↗

NASA NTRS2021

Large-Scale High-Resolution Coastal Mangrove Forests Mapping Across West Africa With Machine Learning Ensemble and Satellite Big Data

Coastal mangrove forests provide important ecosystem goods and services, including carbon sequestration, biodiversity conservation, and hazard mitigation. However, they are being destroyed at an alarming rate by human activities. To characterize mangrove forest changes, evaluate their impacts, and support relevant protection and restoration decision making, accurate and up-to-date mangrove extent mapping at large spatial scales is essential. Available large-scale mangrove extent data products use a single machine learning method commonly with 30 m Landsat imagery, and significant inconsistencies remain among these data products. With huge amounts of satellite data involved and the heterogeneity of land surface characteristics across large geographic areas, finding the most suitable method for large-scale high-resolution mangrove mapping is a challenge. The objective of this study is to evaluate the performance of a machine learning ensemble for mangrove forest mapping at 20 m spatial resolution across West Africa using Sentinel-2 (optical) and Sentinel-1 (radar) imagery. The machine learning ensemble integrates three commonly used machine learning methods in land cover and land use mapping, including Random Forest (RF), Gradient Boosting Machine (GBM), and Neural Network (NN). The cloud-based big geospatial data processing platform Google Earth Engine (GEE) was used for pre-processing Sentinel-2 and Sentinel-1 data. Extensive validation has demonstrated that the machine learning ensemble can generate mangrove extent maps at high accuracies for all study regions in West Africa (92%–99% Producer’s Accuracy, 98%–100% User’s Accuracy, 95%–99% Overall Accuracy). This is the first-time that mangrove extent has been mapped at a 20 m spatial resolution across West Africa. The machine learning ensemble has the potential to be applied to other regions of the world and is therefore capable of producing high-resolution mangrove extent maps at global scales periodically.

coastal environment↗

DOE OSTI2021

A decreasing carbon allocation to belowground autotrophic respiration in global forest ecosystems

Belowground autotrophic respiration (RAsoil) depends on carbohydrates from photosynthesis flowing to roots and rhizospheres, and is one of the most important but least understood components in forest carbon cycling. Carbon allocation plays an important role in forest carbon cycling and reflects forest adaptation to changing environmental conditions. However, carbon allocation to RAsoil has not been fully examined at the global scale. To fill this knowledge gap, first, the spatio-temporal patterns of RAsoil from 1981 to 2017 were predicted by a Random Forest (RF) algorithm using the most updated Global Soil Respiration Database (v5) with global environmental variables; second, carbon allocation from photosynthesis to RAsoil (CAB), was calculated as the ratio of RAsoil to gross primary production; and its temporal and spatial patterns were assessed in global forest ecosystems. . Globally, mean RAsoil from forests was 8.9 ± 0.08 Pg C yr-1 (mean ± standard deviation) from 1981 to 2017 with strong spatial variabilities. Temporally, RAsoil increased at a rate of 0.0059 Pg C yr-2, paralleling broader soil respiration changes and indicating increasing carbon respired by roots. Mean CAB was 0.243 ± 0.016 and decreased over time. The temporal trend of CAB varied greatly in space, reflecting uneven responses of CAB to environmental changes. This study is the first attempt to predict global CAB and analyze its temporal and spatial patterns. With the linkage of carbon use efficiency, the developed CAB offers an completely independent approach to quantify global aboveground autotropic respiration spatially and temporally, which could provide crucial insights into carbon flux partition and global carbon cycling under climate change.

Tang, Xiaolu↗

DOE OSTI2022

Classification of bacterial plasmid and chromosome derived sequences using machine learning

Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer—including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements—were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2020

Southern Colorado Disasters: Using NASA Observations to Map Aspen Extent and Recovery Due to Wildfire

Quaking aspen (Populus tremuloides) is an important species for wildlife, watershed health, and ecosystem resilience across its range. Heavy ungulate browsing and factors influenced by a changing climate including seasonal temperature changes and moisture deficit have led to reduced post-fire aspen regeneration rates in southern Colorado. This project partnered with Trinchera Ranch and the Colorado State Forest Service to estimate aspen recovery after the Spring Creek Fire, which ignited in June of 2018. The Southern Colorado Disasters team utilized field measurements and satellite imagery from Landsat Operational Land Imager (OLI), Sentinel-2 MultiSpectral Instrument (MSI), and the Shuttle Radar Topography Mission (SRTM) to train and run several random forest models that detect pre- and post-fire aspen extent. Ocular sampling of over 500 points on high-resolution pre-fire and post-fire images identified percentage aspen cover in 30 x 30-meter grid cells. This process provided training data for regression models, which were able to detect aspen across the landscape for both time periods using multiple remote sensing vegetation health indices. In addition, landscape suitability for aspen regeneration was modeled to provide a guide for managers on where to monitor for aspen regeneration post-fire.

DEVELOP Project Summary↗

NASA NTRS2020

Southern Colorado Disasters: Using NASA Earth Observations to Map Aspen Extent and Recovery Due to Wildfire

DEVELOP Technical Paper↗