Paddy Doctor Kaggle Competition - Part 7

deep learning
fastai
kaggle competition
paddy doctor
python
In this notebook I run the code from Jeremy Howard’s “Scaling Up - Road to the Top, Part 3” notebook.
Author

Vishal Bakshi

Published

February 5, 2024

Background

In the fastai course Part 1 Lesson 6 video Jeremy Howard walked through the notebooks First Steps: Road to the Top, Part 1 and Small models: Road to the Top, Part 2 where he builds increasingly accurate solutions to the Paddy Doctor: Paddy Disease Classification Kaggle Competition. In the video, Jeremy referenced a series of walkthrough videos that he made while working through the four-notebook series for this competition. I’m excited to watch these walkthroughs to better understand how to approach a Kaggle competition from the perspective of a former #1 Kaggle grandmaster.

In this blog post series, I’ll walk through the code Jeremy shared in each of the 6 Live Coding videos focused on this competition, submitting predictions to Kaggle along the way. My last two blog posts in this series reference Jeremy’s Scaling Up: Road to the Top, Part 3 notebook to improve my large model ensemble predictions. Here are the links to each of the blog posts in this series:

from google.colab import userdata
creds = userdata.get('kaggle')
from pathlib import Path

cred_path = Path("~/.kaggle/kaggle.json").expanduser()
if not cred_path.exists():
  cred_path.parent.mkdir(exist_ok=True)
  cred_path.write_text(creds)
  cred_path.chmod(0o600)
!pip install -qq timm==0.6.13
import timm
timm.__version__
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0.0/549.1 kB ? eta -:--:--     ━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 92.2/549.1 kB 2.8 MB/s eta 0:00:01     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━ 460.8/549.1 kB 7.0 MB/s eta 0:00:01     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 549.1/549.1 kB 6.5 MB/s eta 0:00:00
'0.6.13'
import zipfile,kaggle

path = Path('paddy-disease-classification')
if not path.exists():
  kaggle.api.competition_download_cli(str(path))
  zipfile.ZipFile(f'{path}.zip').extractall(path)
Downloading paddy-disease-classification.zip to /content

100%|██████████| 1.02G/1.02G [00:35<00:00, 30.9MB/s]
from fastai.vision.all import *
path.ls()
(#4) [Path('paddy-disease-classification/train.csv'),Path('paddy-disease-classification/sample_submission.csv'),Path('paddy-disease-classification/test_images'),Path('paddy-disease-classification/train_images')]
trn_path = path/'train_images'
# run this once and re-use for all trainings
tst_files = get_image_files(path/'test_images')
tst_files.sort()
tst_files[:5]
(#5) [Path('paddy-disease-classification/test_images/200001.jpg'),Path('paddy-disease-classification/test_images/200002.jpg'),Path('paddy-disease-classification/test_images/200003.jpg'),Path('paddy-disease-classification/test_images/200004.jpg'),Path('paddy-disease-classification/test_images/200005.jpg')]

Using lr_find for Large Models

One of the students in Live coding 12 faced the same problem as I did: their large model ensemble submission did not improve their Kaggle scores. Jeremy said this is probably because they ran some incorrect code somewhere, and suggested (among other things), to see if using a learning rate from lr_find improved their ensemble. This is what I’ll try next to improve my Kaggle score. If it doesn’t work, I’ll reference Jeremy’s Road to the Top notebook corresponding to large model training, and see what I coded wrong.

kwargs = {'bs': 16}
cbs = GradientAccumulation(2)
arch = 'swinv2_large_window12_192_22k'

I wasn’t getting a very promising learning rate result the first few times I rant it. The lr_find plot didn’t have a section that was steep and somewhat linear, so I’ll run lr_find a few times here to show what I was seeing:

dls = ImageDataLoaders.from_folder(
    trn_path,
    valid_pct=0.2,
    item_tfms=Resize(480, method='squish'),
    batch_tfms=aug_transforms(size=192, min_scale=0.75),
    **kwargs)

learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
learn.model_dir = '/tmp/model'
learn.lr_find()
SuggestedLRs(valley=0.0010000000474974513)

dls = ImageDataLoaders.from_folder(
    trn_path,
    valid_pct=0.2,
    item_tfms=Resize(480, method='squish'),
    batch_tfms=aug_transforms(size=192, min_scale=0.75),
    **kwargs)

learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
learn.model_dir = '/tmp/model'
learn.lr_find()
SuggestedLRs(valley=0.0008317637839354575)

dls = ImageDataLoaders.from_folder(
    trn_path,
    valid_pct=0.2,
    item_tfms=Resize(480, method='squish'),
    batch_tfms=aug_transforms(size=192, min_scale=0.75),
    **kwargs)

learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
learn.model_dir = '/tmp/model'
learn.lr_find()
SuggestedLRs(valley=0.0012022644514217973)

The suggested learning rate (~0.001) is always conservative, so I’ll pick something larger for the swinv2_large_window12_192_22k architecture: 0.005.

arch = 'convnext_large_in22k'
dls = ImageDataLoaders.from_folder(
    trn_path,
    valid_pct=0.2,
    item_tfms=Resize((640,480)),
    batch_tfms=aug_transforms(size=(288,224), min_scale=0.75),
    **kwargs)

learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
learn.model_dir = '/tmp/model'
learn.lr_find()
Downloading: "https://dl.fbaipublicfiles.com/convnext/convnext_large_22k_224.pth" to /root/.cache/torch/hub/checkpoints/convnext_large_22k_224.pth
SuggestedLRs(valley=0.0014454397605732083)

dls = ImageDataLoaders.from_folder(
    trn_path,
    valid_pct=0.2,
    item_tfms=Resize((640,480)),
    batch_tfms=aug_transforms(size=(288,224), min_scale=0.75),
    **kwargs)

learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
learn.model_dir = '/tmp/model'
learn.lr_find()
SuggestedLRs(valley=0.0010000000474974513)

dls = ImageDataLoaders.from_folder(
    trn_path,
    valid_pct=0.2,
    item_tfms=Resize((640,480)),
    batch_tfms=aug_transforms(size=(288,224), min_scale=0.75),
    **kwargs)

learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
learn.model_dir = '/tmp/model'
learn.lr_find()
SuggestedLRs(valley=0.0008317637839354575)

For convnext_large_in22k, I’m tempted to use 0.02, but in the last run of lr_find the loss just starts to inflect upwards at this learning rate. I’ll go with 0.015.

arch = 'vit_large_patch16_224'
dls = ImageDataLoaders.from_folder(
    trn_path,
    valid_pct=0.2,
    item_tfms=Resize(480),
    batch_tfms=aug_transforms(size=224, min_scale=0.75),
    **kwargs)

learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
learn.model_dir = '/tmp/model'
learn.lr_find()
SuggestedLRs(valley=0.0010000000474974513)

dls = ImageDataLoaders.from_folder(
    trn_path,
    valid_pct=0.2,
    item_tfms=Resize(480),
    batch_tfms=aug_transforms(size=224, min_scale=0.75),
    **kwargs)

learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
learn.model_dir = '/tmp/model'
learn.lr_find()
SuggestedLRs(valley=0.0008317637839354575)

dls = ImageDataLoaders.from_folder(
    trn_path,
    valid_pct=0.2,
    item_tfms=Resize(480),
    batch_tfms=aug_transforms(size=224, min_scale=0.75),
    **kwargs)

learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
learn.model_dir = '/tmp/model'
learn.lr_find()
SuggestedLRs(valley=0.00363078061491251)

For vit_large_patch16_224, I’ll use a learning rate of 0.005. I was tempted to use 0.01 but the loss starts to enter instability in the second lr_find run.

Here is a summary of learning rates I’ll use for each architecture:

Architecture Learning Rate
swinv2_large_window12_192_22k 0.005
convnext_large_in22k 0.015
vit_large_patch16_224 0.005 
tta_res = []

Note that my train function now has the parameters lr and n_epochs to specify learning rate and number of training epochs, respectively.

def train(arch, item, batch, lr, n_epochs=24, accum=False):
    kwargs = {'bs': 16} if accum else {}
    dls = ImageDataLoaders.from_folder(trn_path, valid_pct=0.2, item_tfms=item, batch_tfms=batch, **kwargs)
    cbs = GradientAccumulation(2) if accum else []
    learn = vision_learner(dls, arch, metrics=error_rate, cbs=cbs).to_fp16()
    learn.fine_tune(n_epochs, lr)

    # view losses
    learn.recorder.plot_loss()

    # TTA predictions using test dataset
    tst_dl = dls.test_dl(tst_files)
    tta_res.append(learn.tta(dl=tst_dl))

    # Return error rate using validation dataset
    print(error_rate(*learn.tta(dl=dls.valid)))
    return learn, dls
def prep_submission(fn, tta_res):
    # pull out predictions from tta_res list
    tta_prs = first(zip(*tta_res))

    # convert tta_res from list to stacked tensor
    t_tta = torch.stack(tta_prs)

    # take mean of each item's predictions
    avg_pr = t_tta.mean(0)

    # get the index (class) of the maximum prediction for each item
    idxs = avg_pr.argmax(dim=1)

    # create DataLoaders to get its vocab
    dls = ImageDataLoaders.from_folder(trn_path, valid_pct=0.2, item_tfms=Resize(224))

    # convert indexes to vocab strings
    mapping = dict(enumerate(dls.vocab))

    # add vocab strings to sample submission file and export to CSV
    ss = pd.read_csv(path/'sample_submission.csv')
    results = pd.Series(idxs.numpy(), name='idxs').map(mapping)
    ss.label = results
    ss.to_csv(fn, index=False)
arch = 'swinv2_large_window12_192_22k'
train(
    arch,
    item=Resize(480, method='squish'),
    batch=aug_transforms(size=192, min_scale=0.75),
    lr=0.005,
    n_epochs=24,
    accum=True)
/usr/local/lib/python3.10/dist-packages/torch/functional.py:504: UserWarning: torch.meshgrid: in an upcoming release, it will be required to pass the indexing argument. (Triggered internally at ../aten/src/ATen/native/TensorShape.cpp:3526.)
  return _VF.meshgrid(tensors, **kwargs)  # type: ignore[attr-defined]
Downloading: "https://github.com/SwinTransformer/storage/releases/download/v2.0.0/swinv2_large_patch4_window12_192_22k.pth" to /root/.cache/torch/hub/checkpoints/swinv2_large_patch4_window12_192_22k.pth
epoch train_loss valid_loss error_rate time
0 1.070781 0.601547 0.201346 04:03
70.83% [17/24 1:33:49<38:38]
epoch train_loss valid_loss error_rate time
0 0.430227 0.230742 0.080250 05:29
1 0.336965 0.175396 0.056704 05:29
2 0.298998 0.187081 0.057665 05:30
3 0.307775 0.166967 0.055742 05:30
4 0.274865 0.170166 0.045651 05:34
5 0.314666 0.183352 0.049976 05:31
6 0.225893 0.139452 0.038924 05:31
7 0.209061 0.147105 0.039885 05:31
8 0.166353 0.107878 0.027871 05:31
9 0.220547 0.132710 0.033638 05:29
10 0.141531 0.133753 0.039404 05:31
11 0.076975 0.186801 0.036040 05:30
12 0.070114 0.119698 0.026910 05:30
13 0.086218 0.103130 0.025469 05:30
14 0.059969 0.075689 0.019702 05:31
15 0.064261 0.080532 0.018260 05:33
16 0.048361 0.083898 0.019222 05:33

15.58% [81/520 00:47<04:18 0.0468]
epoch train_loss valid_loss error_rate time
0 0.430227 0.230742 0.080250 05:29
1 0.336965 0.175396 0.056704 05:29
2 0.298998 0.187081 0.057665 05:30
3 0.307775 0.166967 0.055742 05:30
4 0.274865 0.170166 0.045651 05:34
5 0.314666 0.183352 0.049976 05:31
6 0.225893 0.139452 0.038924 05:31
7 0.209061 0.147105 0.039885 05:31
8 0.166353 0.107878 0.027871 05:31
9 0.220547 0.132710 0.033638 05:29
10 0.141531 0.133753 0.039404 05:31
11 0.076975 0.186801 0.036040 05:30
12 0.070114 0.119698 0.026910 05:30
13 0.086218 0.103130 0.025469 05:30
14 0.059969 0.075689 0.019702 05:31
15 0.064261 0.080532 0.018260 05:33
16 0.048361 0.083898 0.019222 05:33
17 0.031970 0.089230 0.019222 05:32
18 0.031545 0.079374 0.019222 05:30
19 0.026196 0.078567 0.018260 05:32
20 0.016311 0.070167 0.018260 05:31
21 0.022081 0.068992 0.016338 05:31
22 0.024040 0.073405 0.017780 05:32
23 0.016780 0.072001 0.017299 05:32 
TensorBase(0.0178)
(<fastai.learner.Learner at 0x782e6b00a860>,
 <fastai.data.core.DataLoaders at 0x782e6b00a740>)

The output is unfortunately a bit messy, but here are my observations:

  • The TTA error rate is 0.0178 and the final epoch’s validation error rate is a bit lower. This is a good sign as this shows an improvement in error rate compared to the error rate (0.01862) when using a learning rate of 0.01. However, the improvement is only 5%, which seems unremarkable.
  • The training and validation losses look okay. The both decrease over epochs, and the validation loss does not seem to be increasing significantly at the end, so the model is not overfitting.

I’m not convinced that changing the learning rate from 0.01 to 0.005 has significantly improved my model, but I will go ahead and train the other two models in this ensemble and submit the predictions to Kaggle. If the private score does not improve, I’ll reference Jeremy’s “Road to the Top” notebook series to see how he trained his large models.

len(tta_res), len(tta_res[0][0])
(1, 3469)
arch = 'convnext_large_in22k'
learn, dls = train(
    arch,
    item=Resize((640,480)),
    batch=aug_transforms(size=(288,224), min_scale=0.75),
    lr=0.015,
    n_epochs=24,
    accum=True)
Downloading: "https://dl.fbaipublicfiles.com/convnext/convnext_large_22k_224.pth" to /root/.cache/torch/hub/checkpoints/convnext_large_22k_224.pth
epoch train_loss valid_loss error_rate time
0 1.350656 0.639466 0.192696 03:17
epoch train_loss valid_loss error_rate time
0 0.393383 0.226754 0.069678 05:01
1 0.278609 0.194963 0.054301 05:00
2 0.258872 0.242242 0.069678 04:59
3 0.272949 0.242155 0.070639 05:01
4 0.250942 0.288342 0.073042 04:59
5 0.256650 0.224654 0.060067 05:00
6 0.215623 0.242569 0.054781 04:59
7 0.204849 0.183193 0.049495 04:59
8 0.175016 0.224864 0.044210 04:58
9 0.179674 0.374226 0.078328 04:58
10 0.105390 0.209836 0.037482 04:57
11 0.088776 0.209220 0.039404 04:58
12 0.071399 0.180012 0.034118 04:57
13 0.066381 0.153438 0.030754 04:57
14 0.062488 0.146692 0.028832 04:58
15 0.062825 0.142316 0.026430 04:57
16 0.044528 0.153894 0.025949 04:57
17 0.043213 0.144824 0.024027 04:56
18 0.018004 0.145353 0.022585 04:57
19 0.024245 0.138911 0.021624 04:59
20 0.009057 0.139719 0.022105 04:57
21 0.015471 0.134287 0.020663 04:56
22 0.020319 0.135233 0.021624 04:56
23 0.011382 0.138716 0.019702 04:57
25.00% [1/4 00:24<01:12]
58.78% [77/131 00:14<00:09 0.0114] 
TensorBase(0.0197)

Here are my observations:

  • The larger learning rate of 0.015, although reasonably estimated from the lr_find plot, has decreased the performance of the model. The final validation error rate with lr=0.015 is 0.019702, which is larger than the final validation error rate with lr=0.01 (0.014416). I’ll stick with this for now—perhaps this difference in validation error rate can be attributed to the difference in validation sets. Again, if my large model ensemble does not result in an improved Kaggle score, I’ll reference Jeremy’s solution.
  • The training and validation losses are generally decreasing over the epochs, and are not showing signs of overfitting (i.e., validation loss increasing).

I’ll train the final model next.

len(tta_res), len(tta_res[0][0]), len(tta_res[1][0])
(2, 3469, 3469)
# save_pickle("colab_tta_res.pkl", tta_res)
# tta_res = load_pickle("colab_tta_res.pkl")
arch = 'vit_large_patch16_224'
learn, dls = train(
    arch,
    item=Resize(480),
    batch=aug_transforms(size=224, min_scale=0.75),
    lr=0.005,
    n_epochs=24,
    accum=True)
epoch train_loss valid_loss error_rate time
0 1.163018 0.609755 0.195579 04:13
epoch train_loss valid_loss error_rate time
0 0.495968 0.220330 0.067756 06:21
1 0.365600 0.222172 0.073522 06:22
2 0.306510 0.231306 0.064873 06:22
3 0.312357 0.164647 0.044690 06:21
4 0.326301 0.223919 0.060548 06:21
5 0.291703 0.213934 0.057665 06:21
6 0.221403 0.221377 0.055262 06:18
7 0.234319 0.178601 0.044690 06:19
8 0.171401 0.246879 0.049976 06:18
9 0.194408 0.148840 0.035079 06:18
10 0.145152 0.149591 0.041326 06:17
11 0.113229 0.159672 0.032196 06:17
12 0.085892 0.125524 0.020663 06:17
13 0.053963 0.106966 0.023546 06:17
14 0.110243 0.099779 0.024507 06:16
15 0.048981 0.129755 0.031235 06:18
16 0.055013 0.106256 0.017299 06:17
17 0.043242 0.111034 0.021624 06:17
18 0.034097 0.097368 0.016819 06:16
19 0.035058 0.098730 0.017780 06:17
20 0.030310 0.098341 0.014897 06:17
21 0.019945 0.096790 0.013936 06:17
22 0.010267 0.095050 0.014416 06:18
23 0.015022 0.094428 0.014416 06:19
25.00% [1/4 00:45<02:16]
18.43% [40/217 00:08<00:38 0.0150] 
TensorBase(0.0139)

len(tta_res), len(tta_res[0][0]), len(tta_res[1][0]), len(tta_res[2][0])
(3, 3469, 3469, 3469)

Observations about this training:

  • The final validation error rate for lr=0.005 was 0.014416, which is about 35% less than when lr=0.01 (0.02215). That’s a good sign that this smaller learning rate was a better choice.
  • As with the other models, the training and validation losses generally decrease over epochs.
# save_pickle("final_tta_res.pkl", tta_res)

.

# tta_res = load_pickle("final_tta_res.pkl")

I’ll make a new submission with these predictions to Kaggle and see how it scores:

prep_submission("subm.csv", tta_res)
!head subm.csv
image_id,label
200001.jpg,hispa
200002.jpg,normal
200003.jpg,blast
200004.jpg,blast
200005.jpg,blast
200006.jpg,brown_spot
200007.jpg,dead_heart
200008.jpg,brown_spot
200009.jpg,hispa

The submission’s first few values are the same as before, so that’s a good sign.

This submission’s scores were:

  • Private: 0.98387 (previous best: 0.98617)
  • Public: 0.98577 (previous best: 0.98577)

The submissions with the best private score are still my small ensemble of these architectures that were trained for 12 epochs, and a large ensemble with the vit predictions with 3x the weight of the others.

I’ll triple the weight of the large vit model predictions and submit it to Kaggle to see if it improves the private score:

len(tta_res), len(tta_res[0][0]), len(tta_res[1][0]), len(tta_res[2][0])
(3, 3469, 3469, 3469)
tta_res += 2 * [tta_res[2]]
len(tta_res), len(tta_res[0][0]), len(tta_res[1][0]), len(tta_res[2][0]), len(tta_res[3][0]), len(tta_res[4][0])
(5, 3469, 3469, 3469, 3469, 3469)
prep_submission("subm.csv", tta_res)
!head subm.csv
image_id,label
200001.jpg,hispa
200002.jpg,normal
200003.jpg,blast
200004.jpg,blast
200005.jpg,blast
200006.jpg,brown_spot
200007.jpg,dead_heart
200008.jpg,brown_spot
200009.jpg,hispa

This submission matched my previous best Private score, and improved upon my previous best Public score:

  • Private score: 0.98617
  • Public score: 0.98654

It’s interesting to me that I can’t break this ceiling of 0.98617! I will now reference Jeremy’s large model ensemble and see if I can improve my score by following his methodology in my next blog post.