| Literature DB >> 35807337 |
Yan He1, Wei Zhang1, Yongcai Ma1, Jinyang Li1, Bo Ma2.
Abstract
Rice blast is a serious threat to rice yield. Breeding disease-resistant varieties is one of the most economical and effective ways to prevent damage from rice blast. The traditional identification of resistant rice seeds has some shortcoming, such as long possession time, high cost and complex operation. The purpose of this study was to develop an optimal prediction model for determining resistant rice seeds using Ranman spectroscopy. First, the support vector machine (SVM), BP neural network (BP) and probabilistic neural network (PNN) models were initially established on the original spectral data. Second, due to the recognition accuracy of the Raw-SVM model, the running time was fast. The support vector machine model was selected for optimization, and four improved support vector machine models (ABC-SVM (artificial bee colony algorithm, ABC), IABC-SVM (improving the artificial bee colony algorithm, IABC), GSA-SVM (gravity search algorithm, GSA) and GWO-SVM (gray wolf algorithm, GWO)) were used to identify resistant rice seeds. The difference in modeling accuracy and running time between the improved support vector machine model established in feature wavelengths and full wavelengths (200-3202 cm-1) was compared. Finally, five spectral preproccessing algorithms, Savitzky-Golay 1-Der (SGD), Savitzky-Golay Smoothing (SGS), baseline (Base), multivariate scatter correction (MSC) and standard normal variable (SNV), were used to preprocess the original spectra. The random forest algorithm (RF) was used to extract the characteristic wavelengths. After different spectral preproccessing algorithms and the RF feature extraction, the improved support vector machine models were established. The results show that the recognition accuracy of the optimal IABC-SVM model based on the original data was 71%. Among the five spectral preproccessing algorithms, the SNV algorithm's accuracy was the best. The accuracy of the test set in the IABC-SVM model was 100%, and the running time was 13 s. After SNV algorithms and the RF feature extraction, the classification accuracy of the IABC-SVM model did not decrease, and the running time was shortened to 9 s. This demonstrates the feasibility and effectiveness of IABC in SVM parameter optimization, with higher prediction accuracy and better stability. Therefore, the improved support vector machine model based on Ranman spectroscopy can be applied to the fast and non-destructive identification of resistant rice seeds.Entities:
Keywords: artificial bee colony algorithm; optimize support vector machine algorithm; ranman spectroscopy; resistant varieties; rice blast
Mesh:
Year: 2022 PMID: 35807337 PMCID: PMC9268727 DOI: 10.3390/molecules27134091
Source DB: PubMed Journal: Molecules ISSN: 1420-3049 Impact factor: 4.927
Figure 1Original Ranman spectra (a) and Ranman spectra modified by removing the noise signal for 240 rice seed samples using Savitzky–Golay 1-Der (b), Savitzky–Golay smoothing (c), baseline (d), multivariable scatter correction (e) and standard normal variable (f).
Figure 2Random forest algorithm was used to extract 90 characteristic variables from the original Ranman spectra.
Support vector machine, BP neural network and probabilistic neural network resistant-rice-classification models established using original Ranman spectra.
| Model | Input Units | Time (s) | Accuracy (%) |
|---|---|---|---|
| Raw − SVM | 3202 | 3 | 45 |
| Raw + BP | 3202 | 487 | 50 |
| Raw + PNN | 3202 | 2 | 25 |
Figure 3Relationship between classification accuracy and iteration times of the ABC-SVM, IABC-SVM, GSA-SVM and GWO-SVM models.
The ABC-SVM classification models established by the original Ranman spectra and the Ranman spectra after five different kinds of pretreatments.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| Raw-ABC-SVM | 0/39 | 28 | 100 | 60 |
| SNV-ABC-SVM | 0/5 | 28 | 100 | 91 |
| MSC-ABC-SVM | 0/5 | 31 | 100 | 91 |
| BASE-ABC-SVM | 0/35 | 33 | 100 | 41 |
| SGS-ABC-SVM | 0/19 | 29 | 100 | 68 |
| SGD-ABC-SVM | 0/45 | 34 | 100 | 25 |
The IABC-SVM classification models established by the original Ranman spectra and the Ranman spectra after after five different kinds of pretreatments.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| Raw-IABC-SVM | 0/17 | 12 | 100 | 71 |
| SNV-IABC-SVM | 0/0 | 13 | 100 | 100 |
| MSC-IABC-SVM | 0/0 | 15 | 100 | 100 |
| BASE-IABC-SVM | 0/16 | 15 | 100 | 73 |
| SGS-IABC-SVM | 0/17 | 15 | 100 | 71 |
| SGD-IABC-SVM | 0/35 | 18 | 100 | 41 |
The GSA-SVM classification models established by the original Ranman spectra and the Ranman spectra after after five different kinds of pretreatments.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| Raw-GSA-SVM | 0/45 | 36 | 100 | 25 |
| SNV-GSA-SVM | 0/33 | 35 | 100 | 45 |
| MSC-GSA-SVM | 0/36 | 16 | 100 | 40 |
| BASE-GSA-SVM | 0/45 | 16 | 100 | 25 |
| SGS-GSA-SVM | 0/45 | 16 | 100 | 25 |
| SGD-GSA-SVM | 0/45 | 16 | 100 | 25 |
The GWO-SVM classification models established by the original Ranman spectra and the Ranman spectra after after five different kinds of pretreatments.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| Raw-GWO-SVM | 0/16 | 2 | 100 | 73 |
| SNV-GWO-SVM | 0/7 | 24 | 100 | 88 |
| MSC-GWO-SVM | 0/9 | 21 | 100 | 85 |
| BASE-GWO-SVM | 0/35 | 16 | 100 | 41 |
| SGS-GWO-SVM | 0/45 | 17 | 100 | 25 |
| SGD-GWO-SVM | 0/37 | 16 | 100 | 38 |
The Ranman spectra after five different pretreatments are extracted using the random forest algorithm, and the ABC-SVM classification models are established using the extracted feature variables.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| RF-ABCSVM | 0/18 | 18 | 100 | 70 |
| RF-SNV-ABCSVM | 0/5 | 19 | 100 | 92 |
| RF-MSC-ABCSVM | 0/4 | 14 | 100 | 93 |
| RF-Base-ABCSVM | 0/19 | 12 | 100 | 68 |
| RF-SGS-ABCSVM | 0/15 | 12 | 100 | 75 |
| RF-SGd-ABCSVM | 0/37 | 14 | 100 | 33 |
The Ranman spectra after five different pretreatments are extracted using the random forest algorithm, and the IABC-SVM classification models are established using the extracted feature variables.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| RF-IABCSVM | 0/18 | 9 | 100 | 70 |
| RF-SNV-IABCSVM | 0/0 | 9 | 100 | 100 |
| RF-MSC-IABCSVM | 0/4 | 7 | 100 | 93 |
| RF-Base-IABCSVM | 0/16 | 6 | 100 | 73 |
| RF-SGS-IABCSVM | 0/15 | 6 | 100 | 75 |
| RF-SGd-IABCSVM | 0/37 | 8 | 100 | 33 |
The Ranman spectra after five different pretreatments are extracted using the random forest algorithm, and the GSA-SVM classification models are established using the extracted feature variables.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| RF-GSASVM | 0/32 | 10 | 100 | 46 |
| RF-SNV-GSASVM | 0/33 | 10 | 100 | 45 |
| RF-MSC-GSASVM | 0/30 | 8 | 100 | 50 |
| RF-Base-GSASVM | 0/29 | 8 | 100 | 52 |
| RF-SGS-GSASVM | 0/28 | 8 | 100 | 53 |
| RF-SGd-GSASVM | 0/45 | 7 | 100 | 25 |
The Ranman spectra after five different pretreatments are extracted using the random forest algorithm, and the GWO-SVM classification models are established using the extracted feature variables.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| RF-GWOSVM | 0/45 | 10 | 100 | 70 |
| RF-SNV-GWOSVM | 0/4 | 10 | 100 | 93 |
| RF-MSC-GWOSVM | 0/5 | 7 | 100 | 92 |
| RF-Base-GWOSVM | 0/46 | 8 | 100 | 23 |
| RF-SGS-GWOSVM | 0/45 | 7 | 100 | 25 |
| RF-SGd-GWOSVM | 0/39 | 7 | 100 | 35 |
After SNV preprocessing, the random forest algorithm is used for feature extraction, and the resistance–susceptibility classification models are established by four optimized support vector machine algorithms.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| RF-SNV-SVM | 0/27 | 3 | 100 | 55 |
| RF-SNV-ABCSVM | 0/0 | 17 | 100 | 100 |
| RF-SNV-IABCSVM | 0/0 | 8 | 100 | 100 |
| RF-SNV-GSASVM | 0/14 | 9 | 100 | 77 |
| RF-SNV-GWOSVM | 0/1 | 9 | 100 | 98 |
After SNV preprocessing, the random forest algorithm is used for feature extraction, and the actual breeding resistance–susceptibility classification models established by four optimized support vector machine algorithms.
| Model | Misjudgment (Train/Test) | Time (s) | Train (%) | Test (%) |
|---|---|---|---|---|
| RF-SNV-SVM | 0/40 | 5 | 100 | 75 |
| RF-SNV-ABCSVM | 0/3 | 59 | 100 | 98 |
| RF-SNV-IABCSVM | 0/0 | 17 | 100 | 100 |
| RF-SNV-GSASVM | 0/30 | 30 | 100 | 81 |
| RF-SNV-GWOSVM | 0/18 | 23 | 100 | 89 |