Potato Late Blight Outbreak: A Study on Advanced Classification Models Based on Meteorological Data
<p>Potato late blight: (<b>a</b>) Leaf form <span class="html-italic">P. infestans</span>; (<b>b</b>) Stem form of potato blight on late cv. ‘Amarant’; (<b>c</b>) Potato infection with late blight in ‘Boryna’ cv.; (<b>d</b>) <span class="html-italic">P. infestans</span> plantation infection, 2°, scale 9°, ‘Irga’ cv.; (<b>e</b>) Potato late blight on the tuber; (<b>f</b>) Potato blight on the cross-section of tubers; Source: own.</p> "> Figure 1 Cont.
<p>Potato late blight: (<b>a</b>) Leaf form <span class="html-italic">P. infestans</span>; (<b>b</b>) Stem form of potato blight on late cv. ‘Amarant’; (<b>c</b>) Potato infection with late blight in ‘Boryna’ cv.; (<b>d</b>) <span class="html-italic">P. infestans</span> plantation infection, 2°, scale 9°, ‘Irga’ cv.; (<b>e</b>) Potato late blight on the tuber; (<b>f</b>) Potato blight on the cross-section of tubers; Source: own.</p> "> Figure 2
<p>Analysis of meteorological data.</p> "> Figure 3
<p>First symptoms of <span class="html-italic">P. infestans</span> in the years 1987–1989.</p> "> Figure 4
<p>Linear regression model for predicting potato blight infection in period 1987–1989.</p> "> Figure 5
<p>Potato blight infections affecting different varieties of potato over the years 1987–1989. SA—Sencor before emergence; SB—Sencor after emergence in the 10–15 cm phase of potato plants; AF—Afalon 50 WP used before potato emergence as a control plant.</p> "> Figure 6
<p>Regression analysis based on potato blight infection data for the year 1987: (<b>a</b>) Anova; (<b>b</b>) Regression statistics.</p> "> Figure 7
<p>Regression analysis based on potato blight infection data for the year 1988: (<b>a</b>) Anova; (<b>b</b>) Regression statistics.</p> "> Figure 8
<p>Regression analysis based on potato blight infection data for the year 1989; (<b>a</b>) Anova; (<b>b</b>) Regression statistics.</p> ">
Abstract
:1. Introduction
1.1. Background
1.2. Significance of the Presented Work
2. Related Work
2.1. Survey on Potato Late Blight Infection
2.2. Survey on Prediction of Potato Blight Infection Using ML Models
- A real-life dataset containing meteorological data spanning twenty years from 1980 to 2000 is introduced.
- This dataset is a valuable resource for researchers interested in studying and analyzing meteorological patterns and trends over an extended period, because it contains eighteen different features related to windspeed, temperature, humidity, etc., which will be essential for predicting the emergence of late potato blight.
3. Materials and Methods
3.1. Dataset Description
- A fertilizer experiment;
- An experiment with the herbicide Sencor 70 WP on 44 potato varieties.
- Before emergence: Sencor 75 WP at 1 kg ha−1;
- After emergence: When shoots reached 10–15 cm, Sencor 75 WP at 0.75 kg ha−1;
- Standard practice: Afalon 50 WP at 2 kg ha−1.
3.2. Experimental Settings
3.3. Climatic Conditions
3.4. Conditions Favoring Occurrence of Potato Blight
3.5. Data Analysis and Prediction Model
3.6. Statistics Regarding Potato Blight Infection Data
- 9—Signifies no symptoms of the disease;
- 8—Indicates slight symptoms on individual leaves or plant units;
- 7—Signifies the spread of the disease to several leaves;
- 6—Indicates moderate plant infection but without apparent symptoms on tubers;
- 5—Signifies serious leaf infection and the appearance of initial symptoms on tubers;
- 4—Indicates moderately advanced infection, with visible symptoms on the tubers;
- 3—Signifies serious infection of both potato leaves and tubers;
- 2—Indicates severe infection of plants with visible symptoms on leaves and tubers;
- 1—Signifies destruction of the potato plant.
3.7. Description of Potato Blight Infection Data in Period 1987–1989
3.8. Regression Analysis of the Dataset 1987–1989
3.9. Proposed Algorithm
3.9.1. Machine Learning Methods
- Supervised learning;
- Unsupervised learning;
- Semi-supervised learning.
- (a)
- Regression: This captures the correlation between the dependent variable and one or more independent variables. There can be different types of regression, e.g., linear regression, non-linear regression, logistic regression, etc.;
- (b)
- Classification: This is used to predict distinct values such as True/False, etc. The different kinds of classification techniques are support vector machines (SVMs), k-nearest neighbors (k-NNs), etc.
- (a)
- Clustering techniques: K-means clustering, hierarchical clustering, etc.;
- (b)
- Dimensionality Reduction techniques: PCA, ICA, etc.
3.9.2. Data Preprocessing
Algorithm 1 Smote-Analysis |
Begin Smote-Analysis: |
Step 1: Randomly select two different numbers index1 and index2 |
Step 2: Select a random weight ‘β’ |
Step 3: New_point = β ∗ data[index1] + (1 − β) ∗ data[index2] |
Step 4: Add the ‘New_point’ to the original data-list |
End |
3.9.3. Evaluation Metrics
3.9.4. Model Implementation
- Decision tree classifier;
- Support vector classifier (SVC);
- K-nearest neighbors (KNN) classifier;
- Stacking classifier with logistic regression;
- Stacking classifier with gradient boosting;
- Voting classifier;
- Random forest classifier.
4. Results and Discussion
- Class 1: High sensitivity (98%) but lower specificity because many instances from other classes are misclassified into Class 1 (false positives);
- Class 2: Lower sensitivity (37%) indicates that many true instances of Class 2 are misclassified into Class 1, but its specificity is moderate since there are fewer false positives;
- Classes 3, 4, and 7: These have no true positives, leading to 0 sensitivity, but have a perfect specificity since no other class was classified as them.
- (a)
- Filter Methods: These use statistical techniques (like ANOVA) to evaluate the relationship between the features and the target variables based on their relevance. These methods are very efficient and independent of machine learning models. In this filter method, we used the top 17 features using ANOVA F-statistics.
- (b)
- Wrapper Methods: They evaluate the subset of features by training a machine learning model using the model’s performance as a criterion for selection. Normally, this model gives an optimal performance. Here, we used Recursive Feature Elimination (RFE) with Logistic Regression using n = 5 features.
- (c)
- Hybrid Methods: These combine the features of the filter, wrapper, and even embedded methods. Here, dimensionality reduction techniques like PCA are used. The problem with this method is that they can reduce the dimensionality but do not explicitly specify the features. Here, we reduced the dimensionality using logistic regression with a specific threshold.
5. Limitations and Future Work
6. Conclusions
- Machine learning models, particularly the stacking classifier with logistic regression, achieved high detection rates;
- Predictive accuracy can be enhanced using cross-validation and accumulating diverse datasets;
- Climate change significantly affects potato blight spread and severity, making the adaptive strategies essential.
- Traditional models can perform better with smaller datasets;
- Traditional models require less computational power and are faster;
- Models such as decision tree and linear regression offer more interpretability compared to deep learning.
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
CRISPR | Clustered Regularly Interspaced Short Palindromic Repeats |
P. infestans | Phytophthora infestans |
ML | Machine Learning |
AI | Artificial Intelligence |
ARIMA | Autoregressive Integrated Moving Average with exogenous variables |
NNAR | Neural Network Auto Regression |
SVR | Support Vector Regression |
CART | Classification and Regression Tree |
SA | Sencor before emergence |
SB | Sencor after emergence in the 10–15 cm phase of potato plants |
SMOTE | Synthetic Minority Oversampling Technique |
AF | Afalon 50 WP used before potato emergence as a control plant |
SVM | Support Vector Machine |
SVC | Support Vector Classifier |
KNN | K Nearest Neighbor |
RF | Random Forest |
Appendix A
Appendix B
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Specification | x1 | x2 | x3 | x4 | x5 | x6 | x7 | x8 | x9 | x10 | x11 | x12 | x13 | x14 | x15 | x16 | x17 | x18 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Mean | 10.82 | 13.42 | 18.35 | 15.14 | 13.66 | 19.75 | 16.00 | 1.90 | 92.58 | 83.30 | 58.74 | 74.78 | 2.36 | 3.54 | 1.53 | 14.43 | 16.47 | 77.35 |
Standard error | 0.11 | 0.11 | 0.12 | 0.11 | 0.11 | 0.13 | 0.13 | 0.09 | 0.18 | 0.22 | 0.34 | 0.28 | 0.04 | 0.05 | 0.03 | 0.10 | 0.11 | 0.19 |
Median | 11.00 | 14.20 | 18.80 | 15.80 | 14.75 | 20.20 | 17.20 | 0.00 | 95.00 | 85.00 | 56.00 | 75.50 | 2.00 | 3.00 | 1.00 | 15.13 | 17.42 | 77.75 |
Standard deviation | 6.00 | 5.97 | 6.52 | 5.87 | 6.01 | 6.74 | 6.99 | 4.71 | 9.24 | 11.56 | 17.66 | 14.82 | 2.01 | 2.41 | 1.75 | 5.18 | 6.04 | 10.26 |
Kurtosis | −0.16 | 0.19 | −0.19 | −0.21 | 0.12 | −0.26 | −0.36 | 26.75 | 5.41 | −0.17 | −0.63 | −0.71 | 3.16 | 1.21 | 4.86 | −0.10 | −0.42 | −0.07 |
Skewness | 0.01 | −0.30 | −0.33 | −0.47 | −0.29 | −0.33 | −0.54 | 4.47 | −2.20 | −0.62 | 0.45 | −0.29 | 1.34 | 0.96 | 1.94 | −0.47 | −0.44 | −0.31 |
Range | 30.70 | 39.00 | 38.60 | 31.10 | 34.20 | 36.60 | 30.70 | 52.00 | 65.00 | 60.00 | 81.00 | 71.00 | 17.00 | 17.00 | 12.00 | 30.70 | 30.13 | 66.50 |
Minimum | −4.70 | −4.20 | −3.20 | −3.00 | −0.40 | 0.10 | −0.10 | 0.00 | 35.00 | 40.00 | 19.00 | 29.00 | 0.00 | 0.00 | 0.00 | −2.85 | −0.10 | 33.00 |
Maximum | 26.00 | 34.80 | 35.40 | 28.10 | 33.80 | 36.70 | 30.60 | 52.00 | 100.00 | 100.00 | 100.00 | 100.00 | 17.00 | 17.00 | 12.00 | 27.85 | 30.03 | 99.50 |
Variation coefficients (%) | 55.45 | 44.47 | 35.54 | 38.80 | 44.00 | 34.14 | 43.72 | 247.45 | 9.98 | 13.88 | 30.07 | 19.82 | 85.10 | 68.05 | 114.15 | 35.92 | 36.65 | 13.26 |
Classifier Used | Train/Test Set Ratio | |||
---|---|---|---|---|
80:20 | 50:50 | 70:30 | 90:10 | |
Decision Tree Classifier | 78.04 | 76.56% | 77.68% | 78.56% |
SVC (Support Vector Classifier) | 82.30 | 81.43% | 82.25% | 80:59% |
KNN Classifier | 84.02 | 83.73% | 84.36% | 85.41% |
SC + Logistic Regression | 87.22 | 86.87% | 87.89% | 88.63% |
SC + Gradient Boosting | 87.15 | 86.83% | 87.81% | 88.26% |
Voting Classifier | 85.28 | 84.28% | 85.21% | 86.04% |
Random Forest Classifier | 85.96 | 85.37% | 86.06% | 86.56% |
Classification | Precision | Recall | F1-Score | Support | Sensitivity | Specificity |
---|---|---|---|---|---|---|
1 | 0.88 | 0.98 | 0.93 | 4448 | 0.97 | 0.37 |
2 | 0.80 | 0.37 | 0.51 | 947 | 0.37 | 0.97 |
3 | 0.00 | 0.00 | 0.00 | 1 | 0 | 1.0 |
4 | 0.00 | 0.00 | 0.00 | 2 | 0 | 1.0 |
7 | 0.00 | 0.00 | 0.00 | 2 | 0 | 1.0 |
Approximate accuracy | 87% | |||||
macro avg | 0.33 | 0.27 | 0.29 | 5400 | ||
weighted avg | 0.86 | 0.87 | 0.85 | 5400 |
PREDICTED CLASS | ||||||
TRUE CLASS | 1 | 2 | 3 | 4 | 7 | |
1 | 4357 | 91 | 0 | 0 | 0 | |
2 | 594 | 393 | 0 | 0 | 0 | |
3 | 1 | 0 | 0 | 0 | 0 | |
4 | 2 | 0 | 0 | 0 | 0 | |
7 | 2 | 0 | 0 | 0 | 0 |
Classifier Used | Filter Methods | Wrapper Methods | Hybrid Methods |
---|---|---|---|
Decision Tree Classifier | 79.41% | 73.89% | 76.89% |
SVC (Support Vector Classifier) | 83.67% | 82.56% | 82.56% |
KNN Classifier | 84.63% | 83.04% | 85.44% |
Stacking Classifier + Logistic Regression | 88.48% | 84.26% | 87.52% |
Stacking Classifier + Gradient Boosting | 88.11% | 84.00% | 87.15% |
Voting Classifier | 86.22% | 83.63% | 86.44% |
Random Forest Classifier | 86.74% | 83.85% | 86.85% |
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Bagchi, P.; Sawicka, B.; Stamenkovic, Z.; Marković, D.; Bhattacharjee, D. Potato Late Blight Outbreak: A Study on Advanced Classification Models Based on Meteorological Data. Sensors 2024, 24, 7864. https://doi.org/10.3390/s24237864
Bagchi P, Sawicka B, Stamenkovic Z, Marković D, Bhattacharjee D. Potato Late Blight Outbreak: A Study on Advanced Classification Models Based on Meteorological Data. Sensors. 2024; 24(23):7864. https://doi.org/10.3390/s24237864
Chicago/Turabian StyleBagchi, Parama, Barbara Sawicka, Zoran Stamenkovic, Dušan Marković, and Debotosh Bhattacharjee. 2024. "Potato Late Blight Outbreak: A Study on Advanced Classification Models Based on Meteorological Data" Sensors 24, no. 23: 7864. https://doi.org/10.3390/s24237864
APA StyleBagchi, P., Sawicka, B., Stamenkovic, Z., Marković, D., & Bhattacharjee, D. (2024). Potato Late Blight Outbreak: A Study on Advanced Classification Models Based on Meteorological Data. Sensors, 24(23), 7864. https://doi.org/10.3390/s24237864