Tomato Leaf Disease Recognition on Leaf Images Based on Fine-Tuned Residual Neural Networks
Abstract
:1. Introduction
- A double form of data augmentation, using image transformations and the implementation of CutMix as a secondary form of data augmentation for model generalization.
- The effect of the train/test data split size ratio of our dataset on the network model for disease recognition on tomato leaf images. Train/test data split ratios of sizes 40/60, 50/50, 60/40, 70/30, and 80/20 were adopted and studied.
- The effect of varying batch sizes in training our network to correctly recognize tomato leaf diseases. According to the capacity of the GPU available, batch sizes of 40, 50, 60, 70, 80, 90, and 100 were adopted.
- The role of network depth in the effective recognition of tomato leaf disease. Residual networks with varying depths of 18, 34, 50, 101, and 152 layers were studied.
- The effect of tuning the learning rate while training the network and identification of a threshold to obtain suitable learning rates to effectively train the network to recognize tomato leaf diseases. The implementation of a discriminative learning rate for efficient training of residual models.
2. Related Work
3. Evaluation Metrics, Results, and Discussion
3.1. Evaluation Metrics
- Accuracy: Accuracy is the number of right predictions that are made by the model with respect to the total number of predictions that were made. It is mathematically represented by Equation (1).
- Precision: Precision is defined as the number of true positive results (TP) divided by the number of positive results (TP + FP) that are predicted by the model. The range of the precision is between 0 and 1 and is calculated using Equation (2). It is used to find the proportion of positive identifications that is true.
- Recall: The recall is the number of true positives (TP) divided by the number of all relevant sample data (TP + FN). Equation (3) represents the mode of calculation of the recall. It is used to determine the proportion of actual positives that were correctly identified. These concepts are represented mathematically by Equations (2) and (3), respectively:
- F1 Score: Being one of the widely used metrics for the performance evaluation of machine learning algorithms, the F1 score is the harmonic mean of precision and recall. The range of the F1 score is between 0 and 1, and it is calculated as shown by Equation (4). It reflects the number of instances that are correctly classified by the learning model.
3.2. Results and Discussion
3.2.1. Results on Varied Network Depth
3.2.2. Results on Varied Train-Validation Data Split Ratios
3.2.3. Results on Different Batch Sizes
3.2.4. Results on Computing Time
3.2.5. Benchmark against Other Models
4. Materials and Methods
4.1. Data Acquisition and Pre-Processing
4.1.1. Datasets
- The Flavia leaf dataset
- 2.
- The tomato leaf dataset
- Early blight is a fungal infection, and symptoms start as oval-shaped lesions with a yellow chlorotic region across the lesion; concentric leaf lesions may be seen on infected leaves.
- Late blight, being another fungal infection, affects all aerial parts of the tomato plant; initial symptoms of the disease appear as water-soaked green to black areas on leaves which rapidly change to brown lesions; fluffy white fungal growth may appear on infected areas and leaf undersides during wet weather.
- The leaf spot is another fungal infection. Infected plants exhibit bronzing or purpling of the upper sides of young leaves and develop necrotic spots; leaf spots may resemble those caused by bacterial spots, but a bacterial ooze test will be negative; leaves may cup downwards, and shoot tips may begin to die back.
- Septoria leaf spot is yet another fungal disease. Symptoms may occur at any stage of tomato development and begin as small, water-soaked spots or circular grayish-white spots on the underside of older leaves; spots have a grayish center and a dark margin, and they may coalesce.
- Leaf mold is still another fungal infection. The older leaves exhibit pale greenish to yellow spots (without distinguishable margins) on the upper surface, whereas, the lower portion of these spots exhibits green to brown velvety fungal growth. As the disease progresses, the spots may coalesce and appear brown. The infected leaves wither and die but stay attached to the plant.
- Bacterial spots are bacterial diseases, and lesions start as small water-soaked spots; lesions become more numerous and coalesce to form necrotic areas on the leaves giving them a blighted appearance; leaves drop from the plant, and severe defoliation can occur leaving the fruit susceptible to sunscald; mature spots have a greasy appearance and may appear transparent when held up to a light source; centers of lesions dry up and fall out of the leaf; blighted leaves often remain attached to the plant and give it a blighted appearance.
- Spider mites (two-spotted spider mites). Leaves stippled with yellow; leaves may appear bronzed; webbing covering leaves; mites may be visible as tiny moving dots on the webs or underside of leaves, best viewed using a hand lens; usually not spotted until there are visible symptoms on the plant; leaves turn yellow and may drop from the plant.
- Target spot is also caused by a fungus. The fungus infects all parts of the plant. Infected leaves show small, pinpoint, water-soaked spots initially. As the disease progresses, the spots enlarge to become necrotic lesions with conspicuous concentric circles, dark margins, and light brown centers. Whereas the fruits exhibit brown, slightly sunken flecks in the beginning, later the lesions develop a large, pitted appearance.
- Tomato mosaic virus is a viral infection. Symptoms can occur at any growth stage and any part of the plant can be affected; infected leaves generally exhibit a dark green mottling or mosaic; some strains of the virus can cause yellow mottling on the leaves; young leaves may be stunted or distorted; severely infected leaves may have raised green areas; dark necrotic streaks may appear on the petioles’ leaves.
- Tomato yellow leaf curl disease is another viral infection. The infected leaves become reduced in size, curl upward, appear crumpled, and show yellowing of veins and leaf margins.
4.1.2. Data Pre-Processing
- 1.
- Data Augmentation 1—Image Transformations
- 2.
- Data Augmentation 2—CutMix
4.2. Our Proposed Method
4.2.1. Convolutional Neural Networks
- 1.
- Convolutional Layer
- 2.
- Pooling Layer
- 3.
- Fully Connected Layer
4.2.2. Transfer Learning Approach
4.2.3. Overall Architecture of the Proposed Method
- To research the role of depth on the performance of such models, various residual convolutional neural networks, having different layers, such as ResNet-18, ResNet-34, ResNet-50, ResNet-102, and ResNet-152 were tested.
- Various train/test data split ratios were experimented on to determine the optimum value of the train/test split ratio for such a research area.
- Different batch sizes were selected based on the capacity of the GPU system obtainable in the laboratory to test for the influence of batch size on the training and if so on the result of the training and test processes of the model.
- The discriminative learning process was studied to determine the best learning rates to select in re-training the various models to achieve an optimal training process from one domain of data to a new domain of datasets: specific to this research is the tomato plant leaf dataset for disease recognition.
4.3. Training Procedure
4.3.1. Tuning the Learning Rate Schedule
4.3.2. Unfreezing and Re-Tuning the Learning Rate Schedule
4.4. Experimental Setup
5. Discussion
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
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Pathogen Group | Pathogen Name | Reference |
---|---|---|
Fungi | Alternaria solani, Botrytis cinerea, Cladosporium fulvum, Colletotrichum coccodes, Fusarium oxysporum, Fusarium clavum, Leveillula taurica, Oidium lycopersici, Pseudoidium neolycopersici, Pyrenochaeta lycopersici, Rhizoctonia solani, Septoria lycopersici, Sclerotinia sclerotiorum, Sclerotium rolfsii, Stemphylium spp., Verticillium dahliae | [4,6] |
Oomycetes | Phytophthora infestans, Phytophthora nicotianae, Phytophtora cryptogea, Pythium debaryanum, Pythium sylvaticum | [7] |
Bacteria | Clavibacter michiganensis subsp. michiganensis, Erwinia carotovora subsp. carotovora, Pseudomonas corrugata, Pseudomonas mediterranea, Pseudomonas syringae pv. tomato, Ralstonia solanacearum, Xanthomonas axonopodis pv. vesicatoria | [7] |
Phytoplasma | Candidatus Phytoplasma solani | [8] |
Viruses | Alfalfa mosaic virus, Chickpea chlorotic dwarf virus, Cucumber mosaic virus, Eggplant mottled dwarf virus, Parietaria mottle virus, Pelargonium zonate spot virus, Pepino mosaic virus, Potato virus Y, Southern tomato virus, Tobacco mosaic virus, Tomato brown rugose fruit virus, Tomato chlorosis virus, Tomato infectious chlorosis virus, Tomato leaf curl New Delhi virus, Tomato mosaic virus, Tomato spotted wilt virus, Tomato torrado virus, Tomato yellow leaf curl virus, Tomato yellow leaf curl Sardinia virus | [4,9] |
Viroids | Potato spindle tuber viroid, Tomato apical stunt viroid | [8] |
Batch Size | Performance (%) | ||||
---|---|---|---|---|---|
40/60 | 50/50 | 60/40 | 70/30 | 80/20 | |
100 | 0.977447 | 0.984816 | 0.988378 | 0.992139 | 0.993655 |
90 | 0.97957 | 0.987927 | 0.993078 | 0.99241 | 0.99521 |
80 | 0.981349 | 0.987848 | 0.990103 | 0.992641 | 0.995611 |
70 | 0.984734 | 0.986958 | 0.988716 | 0.994496 | 0.994071 |
60 | 0.984338 | 0.987595 | 0.994316 | 0.993444 | 0.995579 |
50 | 0.987115 | 0.9893 | 0.993566 | 0.994769 | 0.994317 |
40 | 0.985295 | 0.990085 | 0.993045 | 0.994083 | 0.995048 |
Batch Size | Time (s) | ||||
---|---|---|---|---|---|
40/60 | 50/50 | 60/40 | 70/30 | 80/20 | |
100 | 162 | 196 | 221 | 234 | 249 |
90 | 179 | 188 | 218 | 237 | 253 |
80 | 169 | 193 | 222 | 235 | 247 |
70 | 176 | 188 | 211 | 232 | 240 |
60 | 172 | 193 | 217 | 236 | 259 |
50 | 188 | 208 | 221 | 242 | 275 |
40 | 200 | 204 | 226 | 248 | 281 |
Train Split (%) | Validation Split (%) | Train Loss | Valid Loss | Accuracy | Recall | Precision | F1 Score |
---|---|---|---|---|---|---|---|
90 | 10 | 0.052291 | 0.07908 | 0.976046 | 0.972897 | 0.972338 | 0.97166 |
80 | 20 | 0.049548 | 0.071533 | 0.976597 | 0.973958 | 0.973845 | 0.97321 |
70 | 30 | 0.045366 | 0.081245 | 0.97109 | 0.967464 | 0.966935 | 0.966463 |
60 | 40 | 0.042245 | 0.070298 | 0.975771 | 0.972307 | 0.97289 | 0.971938 |
50 | 50 | 0.033666 | 0.049622 | 0.984857 | 0.981165 | 0.982264 | 0.981518 |
40 | 60 | 0.002324 | 0.014366 | 0.996421 | 0.995781 | 0.995451 | 0.995611 |
Network Depth | Error Rate | F1 Score | Time (s) |
---|---|---|---|
18 | 0.037812 | 0.953628 | 35 |
34 | 0.028084 | 0.964552 | 53 |
50 | 0.025881 | 0.96916 | 83 |
101 | 0.01808 | 0.977994 | 126 |
152 | 0.018906 | 0.977447 | 160 |
Network Depth | Error Rate | F1 Score | Time (s) |
---|---|---|---|
18 | 0.027423 | 0.967306 | 40 |
34 | 0.024559 | 0.968959 | 59 |
50 | 0.018612 | 0.978017 | 91 |
101 | 0.015419 | 0.981207 | 139 |
152 | 0.013216 | 0.984816 | 187 |
Network Depth | Error Rate | F1 Score | Time (s) |
---|---|---|---|
18 | 0.021338 | 0.974903 | 41 |
34 | 0.015694 | 0.979904 | 63 |
50 | 0.015556 | 0.98172 | 97 |
101 | 0.010187 | 0.988444 | 152 |
152 | 0.009637 | 0.988378 | 217 |
Network Depth | Error Rate | F1 Score | Time (s) |
---|---|---|---|
18 | 0.016153 | 0.978283 | 43 |
34 | 0.011013 | 0.985728 | 69 |
50 | 0.011197 | 0.986037 | 105 |
101 | 0.009728 | 0.987897 | 160 |
152 | 0.006608 | 0.992139 | 228 |
Network Depth | Error Rate | F1 Score | Time (s) |
---|---|---|---|
18 | 0.015419 | 0.981407 | 47 |
34 | 0.011564 | 0.986212 | 73 |
50 | 0.009086 | 0.988667 | 112 |
101 | 0.006883 | 0.991295 | 179 |
152 | 0.005507 | 0.993655 | 243 |
Technique | Year | Objective | # Images | Methods | Accuracy (%) |
---|---|---|---|---|---|
Keivani et al. [50] | 2020 | Flavia dataset | 1907 | Decision Tree | 98.58 |
Li et al. [51] | 2021 | Flavia dataset | 1907 | DenseNet201 | 98.69 |
Kanda et al. [52] | 2021 | Flavia dataset | 1907 | DL + Logistic Regression | 99.0 |
Thanikkal et al. [53] | 2022 | Flavia dataset | 1907 | DL | 99.0 |
Twum et al. [54] | 2022 | Flavia dataset | 1907 | Log Gabor Filters | 97.0 |
Gajjar et al. [55] | 2022 | Flavia dataset | 1907 | Extreme learning machines | 99.10 |
Goyal et al. [56] | 2022 | Flavia dataset | 1907 | Hierarchical cluster | 96.24 |
Ganguly et al. [57] | 2022 | Flavia dataset | 1907 | ResNet + Bonferroni mean operator | 98.7 |
Proposed Network | 2022 | Flavia dataset | 1907 | ResNet + Discriminative Learning | 99.23 |
Technique | Year | Objective | # Images | Methods | Accuracy (%) |
---|---|---|---|---|---|
Too et al. [59] | 2019 | Plant leaf disease | 54,306 | VGG16 | 81.83 |
Gensheng et al. [60] | 2019 | Tea leaf disease | 4980 | VGG16 | 90 |
Wang et al. [61] | 2017 | Plant leaf disease | 54,306 | VGG16 | 90.4 |
Agarwal et al. [62] | 2020 | Tomato leaf disease | 18,160 | VGG16 | 93.5 |
Wang et al. [61] | 2017 | Plant leaf disease | 54,306 | Inception-V3 | 80 |
Gandhi et al. [63] | 2018 | Plant leaf disease | 56,000 | Inception-V3 | 88.6 |
Agarwal et al. [62] | 2020 | Tomato leaf disease | 18,160 | Inception-V3 | 77.5 |
Elhassouny & Smarandache [64] | 2019 | Tomato leaf disease | 7176 | MobileNet | 88.4 |
Gandhi et al. [63] | 2018 | Plant leaf disease | 56,000 | Mobilenet | 92 |
Agarwal et al. [62] | 2020 | Tomato leaf disease | 18,160 | Mobilenet | 82.6 |
Darwish et al. [65] | 2019 | Maize leaf disease | 15,408 | VGG19 | 98.2 |
Karthik et al. [27] | 2020 | Tomato leaf disease | 5452 (4 classes) | ResNet + DenseNet | 98 |
Mishra et al. [66] | 2020 | Corn leaf disease | 3703 | CNN | 98.4 |
Lamba et al. [67] | 2021 | Tomato leaf disease | 16,012 | CNN | 98.2 |
Agarwal et al. [62] | 2020 | Tomato leaf disease | 18,160 | CNN | 98.4 |
Zhao et al. [68] | 2021 | Tomato leaf disease | 18,160 (10 classes) | ResNet50 + SeNet | 96.81 |
Li et al. [58] | 2022 | Tomato leaf disease | 4240 | FWDGAN + B-ARNet | 98.75 |
Paymode et al. [69] | 2022 | Tomato leaf disease | VGG16 | 95.71 | |
Devi et al. [47] | 2022 | Tomato leaf disease | 9281 | DensNet + Attention mechanism | 97.56 |
Bhujel et al. [48] | 2022 | Tomato leaf disease | 19,510 | Lightweight Attention-Based CNN | 99.34 |
Zaho et al. [49] | 2022 | Tomato leaf disease | 18,160 | Spatial attention with CNN | 95.20 |
Islam et al. [70] | 2022 | Tomato leaf disease | 15,989 | cGAN + CNN + Logistic Regression | 100 |
Tarek et al. [71] | 2022 | Tomato leaf disease | 16,004 | MobileNetV3 | 99.81 |
Tej et al. [72] | 2022 | Pepper and Tomato leaf diseases | 488 | CNN | 98.85 |
Özbılge et al. [73] | 2022 | Tomato leaf disease | 18,160 | Compact CNN | 98.49 |
Mukherjee et al. [74] | 2022 | Tomato leaf disease | 10,839 (7 classes) | Gray Wolf + MobileNetV2 | 98 |
Proposed Technique | 2022 | Tomato leaf disease | 18,160 | ResNet + Discriminative Learning | 99.51 |
Name | Parameter |
---|---|
Memory | 32 GB |
Processor | Intel(R) Xeon(R) Silver 4114 CPU @ 2.20 GHz |
Server model | DELL PowerEdge T640 Tower Server |
Graphics | CUDA-based video cards 4X 1080TI; GPU Video memory of 11 Gb |
OS | Linux |
Language | Python 3 |
Framework | Pytorch |
Name | Parameter |
---|---|
Solver type | Adam |
Batch sizes | 20, 30, 40, 50, 60, 70, 80, 90, 100 |
Image input size | 256 × 256 |
Train/Test-split ratio | 40/60, 50/50, 60/40, 70/30, 80/20 |
Learning rate | Discriminative ranges |
Drop out | 0.5 |
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Share and Cite
Kanda, P.S.; Xia, K.; Kyslytysna, A.; Owoola, E.O. Tomato Leaf Disease Recognition on Leaf Images Based on Fine-Tuned Residual Neural Networks. Plants 2022, 11, 2935. https://doi.org/10.3390/plants11212935
Kanda PS, Xia K, Kyslytysna A, Owoola EO. Tomato Leaf Disease Recognition on Leaf Images Based on Fine-Tuned Residual Neural Networks. Plants. 2022; 11(21):2935. https://doi.org/10.3390/plants11212935
Chicago/Turabian StyleKanda, Paul Shekonya, Kewen Xia, Anastasiia Kyslytysna, and Eunice Oluwabunmi Owoola. 2022. "Tomato Leaf Disease Recognition on Leaf Images Based on Fine-Tuned Residual Neural Networks" Plants 11, no. 21: 2935. https://doi.org/10.3390/plants11212935
APA StyleKanda, P. S., Xia, K., Kyslytysna, A., & Owoola, E. O. (2022). Tomato Leaf Disease Recognition on Leaf Images Based on Fine-Tuned Residual Neural Networks. Plants, 11(21), 2935. https://doi.org/10.3390/plants11212935