Hyperspectral Sensing and Machine Learning for Early Detection of Cereal Leaf Beetle Damage in Wheat: Insights for Precision Pest Management
Abstract
1. Introduction
2. Materials and Methods
- data acquisition;
- data analysis;
- ML modeling.
2.1. Data Acquisition
2.1.1. Study Site and Experimental Design
2.1.2. Visual Assessment of Damage on Flag Leaves
- healthy leaf samples with no visible symptoms, representing 0% damage;
- slightly damaged leaves, with 10–15% leaf tissue loss; corresponding to the treatment threshold of 1 larva per flag leaf;
- moderately damaged leaves, exhibiting 15–30% leaf tissue loss, corresponding to the treatment threshold of 2–3 larvae per flag leaf (aligns with central European economic thresholds, where farmers can often tolerate yield losses from damage levels below this threshold);
- severely damaged leaves, showing extensive feeding, with 30–60% leaf tissue loss.
2.1.3. Spectral Data Acquisition
2.2. Data Analysis
2.2.1. Data Processing
- Healthy plants: 52;
- Slightly damaged plants: 52;
- Moderately damaged plants: 46;
- Severely damaged plants: 60.
2.2.2. Data Segmentation
Spectral Reflectance Data
Vegetation Indices (VI)
Uniform Manifold Approximation (UMAP)
2.2.3. Visual and Statistical Analysis
2.3. Machine Learning (ML) Analysis
2.3.1. Data Splitting and Processing
2.3.2. Machine Learning Models and Models Training
2.3.3. Models Validation
2.3.4. Feature Importance Analysis
3. Results and Discussion
3.1. Visual and Statistical Analysis
3.1.1. Response of Leaf Reflectance Spectra to CLB Damage
3.1.2. Vegetation Indices (VI)
3.1.3. Uniform Manifold Approximation and Projection (UMAP) Transformation
3.2. Machine Learning (ML) Modelling
3.2.1. ML Models Validation
3.2.2. ML Models Feature Importance Analysis
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
| CLB | Cereal Leaf Beetle |
| ML | Machine learning |
| RS | Remote sensing |
| VI | Vegetation index/indices |
| LR | Linear regression |
| KNN | k-nearest neighbor |
| RF | Random Forest |
| LGBM | Light Gradient-Boosting Machine |
| XGBM | Extreme Gradient Boosting Machine |
| LAI | Leaf area index |
Appendix A. Implementation Aspects
Appendix B
| Model | Hyperparameter | Range |
|---|---|---|
| UMAP | No. of neighbors | [5, 10, 15, 20, 30] |
| Minimum distance | [0.0, 0.01, 0.05, 0.1, 0.2, 0.5] | |
| Logistic regression | C | [1 × 10−3, 50], uniform distribution in the log domain |
| Tolerance | [1 × 10−6, 1 × 10−3], uniform distribution | |
| Penalty | [l1, l2, elasticnet] | |
| K-nearest neighbors | No. of neighbors | [1, 50], integer |
| Weights | [uniform, distance] | |
| Metric | [Euclidean, Manhattan, Minkowski] | |
| Support vector machine | Kernel | [linear, rbf, poly, sigmoid] |
| C | [0.1, 50], float | |
| Gamma | [0.0001, 0.001, 0.01, 0.1, 1, scale, auto] | |
| Degree | [2, 3, 4, 5], if kernel = poly | |
| Random forest | No. of estimators | [1, 500], integer |
| Max features | [auto, sqrt] | |
| Max depth | [10, 110], integer, step = 10 | |
| Min samples split | [2, 10], integer, step = 2 | |
| Min samples leaf | [1, 4], integer | |
| Light gradient-boosting machine | Objective | Multiclass |
| Boosting type | GBDT | |
| No. of leaves | [2, 256], integer | |
| Learning rate | [1 × 10−4, 0.1], uniform distribution in the log domain | |
| No. of estimators | [10, 1000], integer | |
| Reg alpha | [1 × 10−8, 10], uniform distribution in the log domain | |
| Reg lambda | [1 × 10−8, 10], uniform distribution in the log domain | |
| Subsample | [0.5, 1], float, step = 0.01 | |
| Colsample bytree | [0.5, 1], float, step = 0.01 | |
| Min child samples | [5, 50], integer, step = 5 | |
| Min child weight | [1 × 10−3, 10], float, step = 1 × 10−3 | |
| Metric | Multi logloss | |
| Num of classes | 4 | |
| Max depth | −1 | |
| Subsample freq | 1 | |
| Early stopping rounds | 20 | |
| XGBoost | Objective | Multi:softmax |
| Booster | gbtree | |
| No. of leaves | [2, 256], integer | |
| Learning rate | [1 × 10−4, 0.1], uniform distribution in the log domain | |
| No. of estimators | [10, 1000], integer | |
| Alpha | [1 × 10−8, 10], uniform distribution in the log domain | |
| Lambda | [1 × 10−8, 10], uniform distribution in the log domain | |
| Subsample | [0.5, 1], float, step = 0.01 | |
| Colsample bytree | [0.5, 1], float, step = 0.01 | |
| Min child samples | [5, 50], integer, step = 5 | |
| Min child weight | [1 × 10−3, 10], float, step = 1 × 10−3 | |
| Metric | Multi logloss | |
| Num of classes | 4 | |
| Subsample freq | 1 | |
| Early stopping rounds | 20 |
Appendix C
| Model | Single Trial Time (s) | Total CV Tuning Time (s) | Inference Time per Sample (ms) |
|---|---|---|---|
| LR | 1.2879 ± 0.0643 | 64.39 ± 3.22 | 0.0155 ± 0.0015 |
| KNN | 0.3867 ± 0.0455 | 19.34 ± 2.28 | 0.0376 ± 0.0109 |
| SVM | 0.3224 ± 0.0398 | 16.11 ± 1.99 | 0.0237 ± 0.0058 |
| RF | 21.0088 ± 6.9670 | 1050.44 ± 348.35 | 0.0427 ± 0.0101 |
| LGBM | 1.0313 ± 0.1558 | 51.56 ± 7.79 | 0.0924 ± 0.0081 |
| XGBM | 8.4305 ± 2.9326 | 421.52 ± 146.63 | 0.0215 ± 0.0052 |
| Model | Single Trial Time (s) | Total CV Tuning Time (s) | Inference Time per Sample (ms) |
|---|---|---|---|
| LR | 0.1013 ± 0.0100 | 5.06 ± 0.50 | 0.0020 ± 0.0021 |
| KNN | 0.0570 ± 0.0153 | 2.85 ± 0.76 | 0.0030 ± 0.0032 |
| SVM | 0.0598 ± 0.0158 | 2.99 ± 0.79 | 0.0032 ± 0.0059 |
| RF | 1.8527 ± 0.3578 | 92.64 ± 17.89 | 0.0176 ± 0.0102 |
| LGBM | 0.2271 ± 0.0214 | 11.36 ± 1.07 | 0.0074 ± 0.0049 |
| XGBM | 1.2151 ± 0.3844 | 60.75 ± 19.22 | 0.0019 ± 0.0022 |
| Model | Single Trial Time (s) | Total CV Tuning Time (s) | Inference Time per Sample (ms) |
|---|---|---|---|
| LR | 0.0747 ± 0.0146 | 3.73 ± 0.73 | 0.0018 ± 0.0028 |
| KNN | 0.0592 ± 0.0215 | 2.96 ± 1.07 | 0.0018 ± 0.0023 |
| SVM | 0.0570 ± 0.0183 | 2.85 ± 0.91 | 0.0011 ± 0.0008 |
| RF | 2.2010 ± 0.2254 | 110.05 ± 11.27 | 0.0301 ± 0.0140 |
| LGBM | 0.2268 ± 0.0153 | 11.34 ± 0.76 | 0.0071 ± 0.0108 |
| XGBM | 1.0016 ± 0.3155 | 50.58 ±15.77 | 0.0034 ± 0.0031 |
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| Vegetation Index | Formula | Source |
|---|---|---|
| Normalized Difference Vegetation Index (NDVI) | [63] | |
| Red Edge Normalized Difference Vegetation Index (NDVI750) | [64] | |
| Green Normalized Difference Vegetation Index (GNDVI) | [65] | |
| Carotenoid Reflectance Index 1 (CRI1) | [66] | |
| Carotenoid Reflectance Index (CRI2) | [67] | |
| Structural Independent Pigment Index (SIPI) | [68] | |
| Chlorophyll Reflectance Index green (RIgreen) | [69] | |
| Water Band Index (WBI) | [70] | |
| Photochemical Reflectance Index (PRI) | [71] | |
| Moisture Stress Index (MSI) | [72] | |
| Normalized Difference Water Index (NDWI) | [50] | |
| Red Edge Position (REP) | [73] | |
| Chlorophyll/Carotenoid Index (CCI) | [74] |
| LR | KNN | SVM | RF | LGBM | XGBM | Average | ||
|---|---|---|---|---|---|---|---|---|
| Wavelengths | Accuracy | 88.25 ± 2.50 | 86.98 ± 4.95 | 90 ± 2.37 | 89.52 ± 3.68 | 89.05 ± 2.84 | 87.94 ± 4.92 | 88.62 ± 3.54 |
| Precision | 0.89 ± 0.03 | 0.87 ± 0.05 | 0.90 ± 0.02 | 0.90 ± 0.03 | 0.89 ± 0.03 | 0.88 ± 0.05 | 0.88 ± 0.04 | |
| Recall | 0.88 ± 0.03 | 0.87 ± 0.05 | 0.90 ± 0.02 | 0.89 ± 0.04 | 0.89 ± 0.03 | 0.88 ± 0.05 | 0.89 ± 0.04 | |
| F1-score | 0.88 ± 0.03 | 0.87 ± 0.05 | 0.90 ± 0.02 | 0.89 ± 0.04 | 0.89 ± 0.03 | 0.88 ± 0.05 | 0.89 ± 0.04 | |
| VI | Accuracy | 87.78 ± 3.09 | 87.62 ± 2.68 | 90.63 ± 3.54 | 86.51 ± 4.18 | 85.71 ± 3.67 | 86.83 ± 3.43 | 87.51 ± 3.43 |
| Precision | 0.88 ± 0.03 | 0.88 ± 0.02 | 0.91 ± 0.03 | 0.87 ± 0.05 | 0.86 ± 0.04 | 0.87 ± 0.04 | 0.88 ± 0.04 | |
| Recall | 0.87 ± 0.03 | 0.87 ± 0.03 | 0.90 ± 0.04 | 0.86 ± 0.04 | 0.85 ± 0.04 | 0.86 ± 0.03 | 0.87 ± 0.04 | |
| F1-score | 0.87 ± 0.03 | 0.87 ± 0.03 | 0.90 ± 0.04 | 0.86 ± 0.04 | 0.85 ± 0.04 | 0.85 ± 0.04 | 0.87 ± 0.04 | |
| UMAP | Accuracy | 84.29 ± 3.92 | 85.55 ± 4.99 | 88.41 ± 5.55 | 85.71 ± 5.55 | 82.38 ± 6.75 | 81.43 ± 3.89 | 84.63 ± 5.10 |
| Precision | 0.85 ± 0.04 | 0.86 ± 0.05 | 0.89 ± 0.05 | 0.87 ± 0.05 | 0.84 ± 0.06 | 0.82 ± 0.04 | 0.86 ± 0.05 | |
| Recall | 0.84 ± 0.04 | 0.85 ± 0.05 | 0.88 ± 0.05 | 0.85 ± 0.06 | 0.82 ± 0.07 | 0.81 ± 0.04 | 0.84 ± 0.05 | |
| F1-score | 0.84 ± 0.04 | 0.85 ± 0.05 | 0.88 ± 0.05 | 0.86 ± 0.05 | 0.82 ± 0.07 | 0.81 ± 0.04 | 0.84 ± 0.05 | |
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Skendžić, S.; Novak, H.; Zovko, M.; Pajač Živković, I.; Lešić, V.; Maričević, M.; Lemić, D. Hyperspectral Sensing and Machine Learning for Early Detection of Cereal Leaf Beetle Damage in Wheat: Insights for Precision Pest Management. Agriculture 2025, 15, 2482. https://doi.org/10.3390/agriculture15232482
Skendžić S, Novak H, Zovko M, Pajač Živković I, Lešić V, Maričević M, Lemić D. Hyperspectral Sensing and Machine Learning for Early Detection of Cereal Leaf Beetle Damage in Wheat: Insights for Precision Pest Management. Agriculture. 2025; 15(23):2482. https://doi.org/10.3390/agriculture15232482
Chicago/Turabian StyleSkendžić, Sandra, Hrvoje Novak, Monika Zovko, Ivana Pajač Živković, Vinko Lešić, Marko Maričević, and Darija Lemić. 2025. "Hyperspectral Sensing and Machine Learning for Early Detection of Cereal Leaf Beetle Damage in Wheat: Insights for Precision Pest Management" Agriculture 15, no. 23: 2482. https://doi.org/10.3390/agriculture15232482
APA StyleSkendžić, S., Novak, H., Zovko, M., Pajač Živković, I., Lešić, V., Maričević, M., & Lemić, D. (2025). Hyperspectral Sensing and Machine Learning for Early Detection of Cereal Leaf Beetle Damage in Wheat: Insights for Precision Pest Management. Agriculture, 15(23), 2482. https://doi.org/10.3390/agriculture15232482

