Rice Disease Classification through Self-Supervised Pretraining

Brian Muhia, July 2022

In this repository, we train a self-supervised encoder on images from this Zindi challenge , and fine-tune it on the challenge task of classifying diseases in rice leaves. In the dataset, each RGB image is paired with a corresponding RGNIR (RG-Near-Infra-Red) image of the same plant. Each image has a single label from the set S = ['brown', 'blast', 'healthy']. We want to make this, and other future challenges on this type of dataset simpler by utilising weight sharing: representing both images of the same object with the same weights, even if they're coming from two different cameras. After that, we can use those weights for the downstream task of classifying diseases. We can achieve this through self-supervised learning. For this task, we leave the labels alone and focus on training a model of the structure {ImageTensor , ImageTensor}.

In the standard self-supervised learning setup for computer vision, we take a single image from the training set, make a copy, suitably augment that copy, then train a neural network to minimize the distance between copies. When such a model is well trained to convergence, we have a task-agnostic encoder whose representations can be used for further downstream tasks by transfer learning. Since we have two cameras pointing at plants, we get two images per sample in the training set. We can therefore construct any self-supervised learning task by assuming the image's copy is given, and that the difference in appearance coming from the NIR channel might as well be another augmentation of the RGB image. The other augmentations from the SWAV paper/implementation are kind of a bonus but it would better to ablate them. We're also releasing one pretrained encoder from the best run, based on XResnet-34, which we're calling mwalimu-128, available here on Google Drive. Another one is in progress, based on Res2Net50 which will be made available soon.

installation

mamba install -c fastai fastai
pip install jupyter jupyterlab self-supervised wandb

Read the Notebooks for more

• Pretraining: self-supervised-learning-swav-eda.ipynb
• Classification: classifier.ipynb

mwalimu-128 details

• architecture: xresnet34,res2next50

• image size: 128px

• bs: 32

• training time: Approx. 2.5 hrs and 4 hours respectively. res2next50 trained faster, benefiting from a much higher batch size

• gpu: Nvidia GeForce RTX 3070 8GB | Tesla V100 16GB

New! Interpretability Research

Visualising Multi-Sensor Predictions from a Rice Disease Classifier https://www.qeios.com/read/U1Y01E

I have started a new project to interpret the representations learned by SwAV on this dataset. Watch this space, more coming soon.

Training loss curve

About 60% of the way into the training run mwalimu-128, the loss dropped dramatically, meaning the model escaped a saddle point that enabled it to solve the task significantly better. More results on wandb

Showcasing early generalization

During the transfer learning step of this challenge, early in training we observe that validation loss is lower than training loss, a sign of good generalization properties for this dataset. In the current set of experiments, the phenomenon disappears in later steps, and this observation survives for even more of the training time of a model if the batch size is higher.

Acknowledgments: @keremturgutlu for https://github.com/keremturgutlu/self_supervised, this would have not been possible so quickly without his work.