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Removal of external influences from on-line vis-NIR spectra for predicting soil organic carbon using machine learning

Muhammad Abdul Munnaf (UGent) and Abdul Mouazen (UGent)
(2022) CATENA. 211.
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Abstract
External factors including moisture content negatively affect the prediction accuracy of soil organic carbon (SOC) using on-line visible and near-infrared (vis-NIR) spectroscopy. This study compared the performances of four algorithms to remove the moisture content effect [direct standardization (DS), piecewise direct standardization (PDS), external parameter orthogonalization (EPO), and orthogonal signal correction (OSC)] against non corrected (NC) spectral models developed with partial least squares regression (PLSR), support vector machine (SVM), random forest (RF), and M5Rules regression. An on-line soil sensing platform coupled with a visNIR spectrophotometer (305-1700 nm) was used to scan twelve agricultural fields in Belgium and France. A total of 372 soil samples collected during the on-line measurement were divided into a calibration (260) and a prediction (112) dataset, using the Kennard-Stone algorithm. The latter set together with identical laboratory measured 112 dry soil spectra formed a transfer dataset to develop EPO, DS and PDS correction matrices. Results showed that models after EPO, PDS and OSC corrections resulted in improved accuracy [coefficient of determination (R-2) = 0.60-0.82, root mean square error (RMSE) = 16.1-5.7 g kg(-1))], compared to the NC models (R-2 = 0.58-0.73, RMSE = 16.5-6.8 g kg(-1)), whereas the DS (R-2 =-0.10 to 0.26, RMSE = 26.8-21.9 g kg 1) provided deteriorated prediction accuracy. The EPO and OSC models provided better prediction accuracy than that of the PDS corrected models. The OSC-M5Rules (R-2 = 0.82, RMSE = 5.7 g kg(-1)) obtained the highest accuracy followed by EPO-M5Rules (R-2 = 0.74, RMSE = 6.7 g kg(-1)) and NC-M5Rules (R-2 = 0.73, RMSE = 6.8 g kg(-1)), which outperformed all PLSR, RF and SVM models. Therefore, on-line vis-NIR spectra should be corrected with the OSC algorithm before calibrating a machine learning model for accurate prediction of SOC.
Keywords
Soil organic carbon, Vis-NIR spectroscopy, Machine learning, Spectra transfer, Orthogonality correction, DIFFUSE-REFLECTANCE SPECTROSCOPY, ORTHOGONAL SIGNAL CORRECTION, ARTIFICIAL NEURAL-NETWORKS, PARTIAL LEAST-SQUARES, RANDOM FORESTS, EPO-PLS, REGRESSION, MOISTURE, QUALITY, WATER

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MLA
Munnaf, Muhammad Abdul, and Abdul Mouazen. “Removal of External Influences from On-Line Vis-NIR Spectra for Predicting Soil Organic Carbon Using Machine Learning.” CATENA, vol. 211, 2022, doi:10.1016/j.catena.2022.106015.
APA
Munnaf, M. A., & Mouazen, A. (2022). Removal of external influences from on-line vis-NIR spectra for predicting soil organic carbon using machine learning. CATENA, 211. https://doi.org/10.1016/j.catena.2022.106015
Chicago author-date
Munnaf, Muhammad Abdul, and Abdul Mouazen. 2022. “Removal of External Influences from On-Line Vis-NIR Spectra for Predicting Soil Organic Carbon Using Machine Learning.” CATENA 211. https://doi.org/10.1016/j.catena.2022.106015.
Chicago author-date (all authors)
Munnaf, Muhammad Abdul, and Abdul Mouazen. 2022. “Removal of External Influences from On-Line Vis-NIR Spectra for Predicting Soil Organic Carbon Using Machine Learning.” CATENA 211. doi:10.1016/j.catena.2022.106015.
Vancouver
1.
Munnaf MA, Mouazen A. Removal of external influences from on-line vis-NIR spectra for predicting soil organic carbon using machine learning. CATENA. 2022;211.
IEEE
[1]
M. A. Munnaf and A. Mouazen, “Removal of external influences from on-line vis-NIR spectra for predicting soil organic carbon using machine learning,” CATENA, vol. 211, 2022.
@article{8735316,
  abstract     = {{External factors including moisture content negatively affect the prediction accuracy of soil organic carbon (SOC) using on-line visible and near-infrared (vis-NIR) spectroscopy. This study compared the performances of four algorithms to remove the moisture content effect [direct standardization (DS), piecewise direct standardization (PDS), external parameter orthogonalization (EPO), and orthogonal signal correction (OSC)] against non corrected (NC) spectral models developed with partial least squares regression (PLSR), support vector machine (SVM), random forest (RF), and M5Rules regression. An on-line soil sensing platform coupled with a visNIR spectrophotometer (305-1700 nm) was used to scan twelve agricultural fields in Belgium and France. A total of 372 soil samples collected during the on-line measurement were divided into a calibration (260) and a prediction (112) dataset, using the Kennard-Stone algorithm. The latter set together with identical laboratory measured 112 dry soil spectra formed a transfer dataset to develop EPO, DS and PDS correction matrices. Results showed that models after EPO, PDS and OSC corrections resulted in improved accuracy [coefficient of determination (R-2) = 0.60-0.82, root mean square error (RMSE) = 16.1-5.7 g kg(-1))], compared to the NC models (R-2 = 0.58-0.73, RMSE = 16.5-6.8 g kg(-1)), whereas the DS (R-2 =-0.10 to 0.26, RMSE = 26.8-21.9 g kg 1) provided deteriorated prediction accuracy. The EPO and OSC models provided better prediction accuracy than that of the PDS corrected models. The OSC-M5Rules (R-2 = 0.82, RMSE = 5.7 g kg(-1)) obtained the highest accuracy followed by EPO-M5Rules (R-2 = 0.74, RMSE = 6.7 g kg(-1)) and NC-M5Rules (R-2 = 0.73, RMSE = 6.8 g kg(-1)), which outperformed all PLSR, RF and SVM models. Therefore, on-line vis-NIR spectra should be corrected with the OSC algorithm before calibrating a machine learning model for accurate prediction of SOC.}},
  articleno    = {{106015}},
  author       = {{Munnaf, Muhammad Abdul and Mouazen, Abdul}},
  issn         = {{0341-8162}},
  journal      = {{CATENA}},
  keywords     = {{Soil organic carbon,Vis-NIR spectroscopy,Machine learning,Spectra transfer,Orthogonality correction,DIFFUSE-REFLECTANCE SPECTROSCOPY,ORTHOGONAL SIGNAL CORRECTION,ARTIFICIAL NEURAL-NETWORKS,PARTIAL LEAST-SQUARES,RANDOM FORESTS,EPO-PLS,REGRESSION,MOISTURE,QUALITY,WATER}},
  language     = {{eng}},
  pages        = {{14}},
  title        = {{Removal of external influences from on-line vis-NIR spectra for predicting soil organic carbon using machine learning}},
  url          = {{http://doi.org/10.1016/j.catena.2022.106015}},
  volume       = {{211}},
  year         = {{2022}},
}

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