A Random Forest Machine Learning Approach for the Retrieval of Leaf Chlorophyll Content in Wheat
<p>Simple illustration of decision trees regression models, showing the building blocks for the Random Forest (<b>A</b>). Random Forest combines multiple randomized decision trees into a single output (<b>B</b>). The trees generated in the random forest are not interpreted individually, but are used collectively in predicting the response variable.</p> "> Figure 2
<p>Schematic of workflow of procedure for data processing and random forest machine learning analysis.</p> "> Figure 3
<p>Total leaf chlorophyll content (<span class="html-italic">Chl<sub>t</sub>)</span> as a function of the specific vegetation index, for the top four performing vegetation indices (out of 45 evaluated) based on regression analysis (<span class="html-italic">n</span> = 276). All spectral index‒chlorophyll relationships were best fitted using a second-order polynomial.</p> "> Figure 4
<p>Ensemble bagged trees operation using (<b>A</b>) all the spectral bands and (<b>B</b>) the 45 selected spectral vegetation indices as input features, showing the <span class="html-italic">Chl<sub>t</sub></span> predicted from the RF model plotted against the actual <span class="html-italic">Chl<sub>t</sub></span> obtained from chemical extraction of leaf tissues in the laboratory. The fitted 1:1 regression line and model metrics of RMSE and <span class="html-italic">R</span><sup>2</sup> values (<span class="html-italic">n</span> = 2760) are also included.</p> "> Figure 5
<p>Optimization of input parameters for the RF model training. The optimum number of trees (<b>A</b>) and optimum number of leaves (<b>B</b>) were selected based on the variation in error using all the VIs as input variable in analysis.</p> "> Figure 6
<p>Importance ranking of out-of-bag permuted predictor estimates of the vegetation indices. All 45 vegetation indices are ranked in descending order of importance values (<b>A</b>). The order changes slightly each time the model is run due to the permutation and the bootstrap procedure. (<b>B</b>–<b>D</b>) show the impact of narrowing the number of important variables (half each time) and the minimal change in the RMSE.</p> "> Figure 7
<p>Effect of repeating the predictive model 10 times (<span class="html-italic">n</span> = 10) on the relative importance of 15 selected features; (<b>A</b>) shows the histogram of the relative importance of the VIs; and (<b>B</b>) shows the variations in RMSE due to the repetition of the 10 runs. The average RMSE was 3.76 for <span class="html-italic">n</span> = 10.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Greenhouse Pot Experiment
2.2. Hyperspectral Data Acquisition
2.3. Chlorophyll Determination
2.4. Hyperspectral Data Processing and Extraction of Vegetation Indices
2.5. Statistical Analysis and Machine Learning
2.5.1. Simple Univariate Regression Analysis
2.5.2. Description of the Random Forest Approach
2.5.3. Implementing the Random Forest Approach
- Define the optimum number of trees (ntree) based on a bootstrapping sampling procedure.
- Optimal number of leaves (nodesize) was decided as a specified stop condition to reach during the data splitting process at all internal nodes. Leaves are the terminal nodes where the tree growth is stopped. If the trees are allowed to grow to full depth, it may be too variable (i.e., result in relatively high variance and low bias and a possible overfitting of the data). Thus, pruning of the tree is done by deciding upon the optimal number of leaves.
- At every node of the tree, the number of input variables (mtry) (i.e., number of individual bands or VIs) used for the split decisions were randomly selected out of the total (2102 individual spectral bands or 45 VIs).
- The stop condition of each tree growth in our method was determined by defining an optimum number of leaves. The number of trees and number of leaves were optimized by minimizing the RMSE. A diagram of the workflow is provided in Figure 2.
3. Results
3.1. Regression Analysis Using Established Vegetation Indices for Chlt Estimation
3.2. RF Machine Learning Approach Using All Hyperspectral Bands as Input Features
3.3. Random Forest Approach Using Vegetation Indices as Input Features
3.3.1. Optimization of the Random Forest Model
3.3.2. Selective Reduction of Important Predictors
4. Discussion
4.1. Simple Regression Analysis of the Vegetation Indices for Chlt Determination
4.2. RF Machine Learning Approach Using Hyperspectral Bands and VIs as Input Features
4.3. Selection of Important Predictors
4.4. Limitations of the Experimental and Modeling Approach
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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No | Name | Vegetation Index | Application | |
---|---|---|---|---|
1 | Anthocyanin Reflectance Index [40] | Carotenoids | ||
2 | Atmospherically Resistant Vegetation Index [41] | Vegetation | ||
3 | Carotenoid Reflectance Index 1 [42] | Carotenoids | ||
4 | Carotenoid Reflectance Index 2 [42] | Carotenoids | ||
5 | Enhanced Vegetation Index [43] | Vegetation | ||
6 | Green Atmospherically Resistant Index [44] | Chlorophyll | ||
7 | Green Norm. Difference Vegetation Index [45] | Chlorophyll | ||
8 | Green Ratio Vegetation Index [46] | Pigments | ||
9 | Modified Chlorophyll Absorption Ratio Index [47] | Chlorophyll | ||
10 | Modified Chlorophyll Absorption Ratio Index Improved [48] | Vegetation | ||
11 | Plant Senescence Reflectance Index [49] | Pigments | ||
12 | MERIS Terrestrial Chlorophyll Index [50] | Chlorophyll | ||
13 | MERIS Terrestrial Chlorophyll Index 2 [51] | Chlorophyll | ||
14 | Modified Triangular Vegetation Index Improved [48] | Vegetation | ||
15 | Normalized Difference Red-edge Simple Ratio [52] | Chlorophyll | ||
16 | Normalized Difference Vegetation Index [53] | Vegetation | ||
17 | Normalized Difference Water Index [54] | Leaf water | ||
18 | Non-Linear Index [55] | Vegetation | ||
19 | Photochemical Reflectance Index [56] | Pigments | ||
20 | Photochemical Reflectance Index Improved [57] | Pigments | ||
21 | Red Edge Normalized Vegetation Index [49] | Chlorophyll | ||
22 | Red Green Ratio Index [58] | Pigments | ||
23 | Renormalized Difference Vegetation Index [59] | Chlorophyll | ||
24 | Red-edge Simple Ratio [52] | Chlorophyll | ||
25 | Soil Adjusted Vegetation Index [43] | Vegetation | ||
26 | Structure Insensitive Pigment Index [11] | Pigments | ||
27 | Simple Ratio Index [60] | Vegetation | ||
28 | Visible Atmospherically Resistant Index [42] | Vegetation | ||
29 | Vogelmann Red Edge Index [61] | Chlorophyll | ||
30 | Vogelmann Red Edge Index Improved [61] | Chlorophyll | ||
31 | Derivative Simple Ratio 02 | Vegetation | ||
32 | Derivative Simple Ratio 32 | Vegetation | ||
33 | Derivative Simple Ratio 12 | Vegetation | ||
34 | -----NDVIs based on the first derivatives (DND) over 650–750 nm domain----- | Maximum Derivative Index | Vegetation | |
35 | DMAX Simple Ratio with D712 | Vegetation | ||
36 | DMAX Simple Ratio D722 | Vegetation | ||
37 | DMAX Simple Ratio D742 | Vegetation | ||
38 | Normalized Difference Derivative 1 | Vegetation | ||
39 | Normalized Difference Derivative 2 | Vegetation | ||
40 | Normalized Difference Derivative 3 | Vegetation | ||
41 | Normalized Difference Derivative 4 | Vegetation | ||
42 | Normalized Difference Derivative 5 | Vegetation | ||
43 | Normalized Difference Derivative 6 | Vegetation | ||
44 | Normalized Difference Derivative 7 | Vegetation | ||
45 | Normalized Difference Derivative 8 | Vegetation |
No. | Vegetation Index | R2 | RMSE (µg cm−2) | No. | Vegetation Index | R2 | RMSE (µg cm−2) |
---|---|---|---|---|---|---|---|
1 | D12 | 0.86 | 6.05 | 24 | DND3 | 0.43 | 12.41 |
2 | MTCI | 0.86 | 6.07 | 25 | SR | 0.39 | 12.74 |
3 | VREI1 | 0.85 | 6.24 | 26 | NDVI | 0.37 | 12.98 |
4 | VREI2 | 0.85 | 6.25 | 27 | DND4 | 0.35 | 13.22 |
5 | D02 | 0.85 | 6.26 | 28 | PSRI | 0.32 | 13.46 |
6 | MRENDVI | 0.85 | 6.34 | 29 | MCARI | 0.30 | 13.73 |
7 | DND1 | 0.85 | 6.36 | 30 | CRI1 | 0.27 | 13.96 |
8 | RSR | 0.85 | 6.38 | 31 | NLI | 0.26 | 14.03 |
9 | NDRSR | 0.85 | 6.39 | 32 | EVI | 0.24 | 14.22 |
10 | DND8 | 0.85 | 6.45 | 33 | ARI2 | 0.24 | 14.23 |
11 | DMAX22 | 0.85 | 6.47 | 34 | RNDVI | 0.24 | 14.25 |
12 | D32 | 0.83 | 6.71 | 35 | SAVI | 0.24 | 14.25 |
13 | DMAX42 | 0.82 | 6.91 | 36 | PRI4 | 0.24 | 14.30 |
14 | RENDVI | 0.82 | 6.97 | 37 | CRI2 | 0.22 | 14.49 |
15 | DND2 | 0.82 | 7.01 | 38 | MCARI2 | 0.20 | 14.63 |
16 | GRVI | 0.80 | 7.40 | 39 | MTVI | 0.20 | 14.63 |
17 | GNDVI | 0.79 | 7.42 | 40 | VARI | 0.17 | 14.88 |
18 | GARI | 0.79 | 7.55 | 41 | RGRI | 0.14 | 15.16 |
19 | DND7 | 0.78 | 7.64 | 42 | DMAX | 0.09 | 15.61 |
20 | DMAX12 | 0.62 | 10.09 | 43 | NDWI | 0.08 | 15.66 |
21 | PRI | 0.54 | 11.12 | 44 | DND5 | 0.02 | 16.21 |
22 | SIPI | 0.53 | 11.27 | 45 | DND6 | 0.01 | 16.30 |
23 | ARVI | 0.43 | 12.32 |
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Shah, S.H.; Angel, Y.; Houborg, R.; Ali, S.; McCabe, M.F. A Random Forest Machine Learning Approach for the Retrieval of Leaf Chlorophyll Content in Wheat. Remote Sens. 2019, 11, 920. https://doi.org/10.3390/rs11080920
Shah SH, Angel Y, Houborg R, Ali S, McCabe MF. A Random Forest Machine Learning Approach for the Retrieval of Leaf Chlorophyll Content in Wheat. Remote Sensing. 2019; 11(8):920. https://doi.org/10.3390/rs11080920
Chicago/Turabian StyleShah, Syed Haleem, Yoseline Angel, Rasmus Houborg, Shawkat Ali, and Matthew F. McCabe. 2019. "A Random Forest Machine Learning Approach for the Retrieval of Leaf Chlorophyll Content in Wheat" Remote Sensing 11, no. 8: 920. https://doi.org/10.3390/rs11080920
APA StyleShah, S. H., Angel, Y., Houborg, R., Ali, S., & McCabe, M. F. (2019). A Random Forest Machine Learning Approach for the Retrieval of Leaf Chlorophyll Content in Wheat. Remote Sensing, 11(8), 920. https://doi.org/10.3390/rs11080920