18 Aug 2025

Bare Ground Classification Using a Spectral Index Ensemble and Machine Learning Models Optimized Across 12 International Study Sites

Abstract: This research investigates a global approach to map bare ground across diverse geographies with an ensemble of spectral indices using optimal thresholds identified in testing to train and evaluate machine learning models to extract bare ground pixels from Sentinel-2 imagery. Twelve locations in four Köppen climate zones with data from two seasons were evaluated. Accuracy assessment showed a mean F1 score of 80% and a mean Overall Accuracy (OA) of 81% for random forest and an F1 score of 78% and OA of 79% for support vector machine. Higher accuracies were observed in climate region-based models with mean F1 = 84% in three of four climate zones. Low accuracies occurred in winter imagery with leaf-off tree cover or building materials similar to bare ground. This framework provides a global approach to map bare ground without need for high-density time-series or deep learning models and moves beyond locally effective methods.

18 Sep 2024

Automated Mapping of Land Cover Type within International Heterogenous Landscapes Using Sentinel-2 Imagery with Ancillary Geospatial Data

Abstract: A near-global framework for automated training data generation and land cover classification using shallow machine learning with low-density time series imagery does not exist. This study presents a methodology to map nine-class, six-class, and five-class land cover using two dates of a Sentinel-2 granule across seven international sites. The approach uses a series of spectral, textural, and distance decision functions combined with modified ancillary layers to create binary masks from which to generate a balanced set of training data applied to a random forest classifier. For the land cover masks, stepwise threshold adjustments were applied to reflectance, spectral index values, and Euclidean distance layers, with 62 combinations evaluated. Global and regional adaptive thresholds were computed. An annual 95th and 5th percentile NDVI composite was used to provide temporal corrections to the decision functions, and these corrections were compared against the original model. The accuracy assessment found that the regional adaptive thresholds for both the two-date land cover and the temporally corrected land cover could accurately map land cover type within nine-class, six-class, and five-class schemes. Lastly, the five-class and six-class models were compared with a manually labeled deep learning model (Esri), where they performed with similar accuracies. The results highlight performance in line with an intensive deep learning approach, and reasonably accurate models created without a full annual time series of imagery.

28 Jul 2021

Deep Learning-Based Structure-Activity Relationship Modeling for Multi-Category Toxicity Classification: A Case Study of 10K Tox21 Chemicals with High-Throughput Cell-Based Androgen Receptor Bioassay Data

Abstract: Deep learning (DL) has attracted the attention of computational toxicologists as it offers a potentially greater power for in silico predictive toxicology than existing shallow learning algorithms. However, contradicting reports have been documented. To further explore the advantages of DL over shallow learning, we conducted this case study using two cell-based androgen receptor (AR) activity datasets with 10K chemicals generated from the Tox21 program. A nested double-loop cross-validation approach was adopted along with a stratified sampling strategy for partitioning chemicals of multiple AR activity classes (i.e., agonist, antagonist, inactive, and inconclusive) at the same distribution rates amongst the training, validation and test subsets. Deep neural networks (DNN) and random forest (RF), representing deep and shallow learning algorithms, respectively, were chosen to carry out structure-activity relationship-based chemical toxicity prediction. Results suggest that DNN significantly outperformed RF (p < 0.001, ANOVA) by 22–27% for four metrics (precision, recall, F-measure, and AUPRC) and by 11% for another (AUROC). Further in-depth analyses of chemical scaffolding shed insights on structural alerts for AR agonists/antagonists and inactive/inconclusive compounds, which may aid in future drug discovery and improvement of toxicity prediction modeling.