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kaggle-hpa

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Code for 3rd place solution in Kaggle Human Protein Atlas Image Classification Challenge.

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# kaggle-hpa-image-classification
Code for 3rd place solution in Kaggle Human Protein Atlas Image Classification Challenge.

To read the detailed solution, please, refer to [the Kaggle post](https://www.kaggle.com/c/human-protein-atlas-image-classification/discussion/77320)

## Hardware
The following specs were used to create the original solution.
- Ubuntu 16.04 LTS
- Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
- 3x NVIDIA TitanX

## Reproducing Submission
To reproduct my submission without retrainig, do the following steps:
1. [Installation](#installation)
2. [Download Official Image](#download-official-image)
3. [Make RGBY Images](#make-rgby-images) for official.
4. [Download Pretrained models](#pretrained-models)
5. [Inference](#inference)
6. [Make Submission](#make-submission)

## Installation
All requirements should be detailed in requirements.txt. Using Anaconda is strongly recommended.
```
conda create -n hpa python=3.6
source activate hpa
pip install -r requirements.txt
```

## Dataset Preparation
All required files except images are already in data directory.
If you generate CSV files (duplicate image list, split, leak.. ), original files are overwritten. The contents will be changed, but It's not a problem.

### Prepare Images
After downloading and converting images, the data directory is structured as:
```
data
  +- raw
  |  +- train
  |  +- test
  |  +- external
  +- rgby
  |  +- train
  |  +- test
  |  +- external
```
#### Download Official Image
Download and extract *train.zip* and *test.zip* to *data/raw* directory.
If the Kaggle API is installed, run following command.
```
$ kaggle competitions download -c human-protein-atlas-image-classification -f train.zip
$ kaggle competitions download -c human-protein-atlas-image-classification -f test.zip
$ mkdir -p data/raw
$ unzip train.zip -d data/raw/train
$ unzip test.zip -d data/raw/test
```

#### Download External Images
To download external images, run following command. The external images will be located in *data/raw/external*
```
$ python tools/download.py
```

#### Make RGBY Images
To train or inference, converting to RGBY image is required. Run following commands.

For official:
```
$ python tools/make_rgby.py --input_dir=data/raw/train --output_dir=data/rgby/train
$ python tools/make_rgby.py --input_dir=data/raw/test --output_dir=data/rgby/test
```
For external:
```
$ python tools/make_rgby.py --input_dir=data/raw/external --output_dir=data/rgby/external
```

### Generate CSV files
*You can skip this step. All CSV files are prepared in data directory.*

#### Duplicated Image List
There are duplicated images. To search them, run following commands. *duplicates.ahash.csv* and *duplicates.phash.csv* will be generated.
```
$ python tools/find_duplicate_images.py
```

#### Split Dataset
Create 5 folds CV set. One for training, the other for searching augmentation. *split.stratified.[0-4].csv* and *split.stratified.small.[0-4].csv* will be generated.
```
$ python stratified_split.py
$ python stratified_split.py --use_external=0
```

#### Search Data Leak
To learn more about data leak, please, refer to [this post](https://www.kaggle.com/c/human-protein-atlas-image-classification/discussion/72534). Following comand will create *data_leak.ahash.csv* and *data_leak.phash.csv*. [The other leak](https://www.kaggle.com/c/human-protein-atlas-image-classification/discussion/73395y) is already in *data* directory.
```
$ python find_data_leak.py
```

## Training
In configs directory, you can find configurations I used train my final models. My final submission is ensemble of resnet34 x 5, inception-v3 and se-resnext50, but ensemble of inception-v3 and se-resnext50's performance is better.

### Search augmentation
To find suitable augmentation, 256x256 image and resnet18 are used.
It takes about 2 days on TitanX. The result(best_policy.data) will be located in *results/search* directory.
The policy that I used is located in *data* directory.
```
$ python train.py --config=configs/search.yml
```

### Train models
To train models, run following commands.
```
$ python train.py --config={config_path}
```
To train all models, run `sh train.sh`

The expected training times are:

Model | GPUs | Image size | Training Epochs | Training Time
------------ | ------------- | ------------- | ------------- | -------------
resnet34 | 1x TitanX | 512 | 40 | 16 hours
inception-v3 | 3x TitanX | 1024 | 27 | 1day 15 hours
se-resnext50 | 2x TitanX | 1024 | 22 | 2days 15 hours

### Average weights
To average weights, run following commands.
```
$ python swa.py --config={config_path}
```
To average weights of all models, simply run `sh swa.sh`
The averages weights will be located in *results/{train_dir}/checkpoint*.

### Pretrained models
You can download pretrained model that used for my submission from [link](https://www.dropbox.com/s/qo65gw8kml5hgag/results.tar.gz?dl=0). Or run following command.
```
$ wget https://www.dropbox.com/s/qo65gw8kml5hgag/results.tar.gz
$ tar xzvf results.tar.gz
```
Unzip them into results then you can see following structure:
```
results
  +- resnet34.0.policy
  |  +- checkpoint
  +- resnet34.1.policy
  |  +- checkpoint
  +- resnet34.2.policy
  |  +- checkpoint
  +- resnet34.3.policy
  |  +- checkpoint
  +- resnet34.4.policy
  |  +- checkpoint
  +- inceptionv3.attention.policy.per_image_norm.1024
  |  +- checkpoint
  +- se_resnext50.attention.policy.per_image_norm.1024
  |  +- checkpoint
```

## Inference
If trained weights are prepared, you can create files that contains class probabilities of images.
```
$ python inference.py \
  --config={config_filepath} \
  --num_tta={number_of_tta_images, 4 or 8} \
  --output={output_filepath} \
  --split={test or test_val}
```
To make submission, you must inference test and test_val splits. For example:
```
$ python inference.py --config=configs/resnet34.0.policy.yml --num_tta=8 --output=inferences/resnet34.0.test_val.csv --split=test_val
$ python inference.py --config=configs/resnet34.0.policy.yml --num_tta=8 --output=inferences/resnet34.0.test.csv --split=test
```
To inference all models, simply run `sh inference.sh`

## Make Submission
Following command will ensemble of all models and make submissions.
```
$ python make_submission.py
```
If you don't want to use, modify *make_submission.py*.
For example, if you want to use inception-v3 and se-resnext50 then modify *test_val_filenames, test_filenames and weights* in *make_submission.py*.
```
test_val_filenames = ['inferences/inceptionv3.0.test_val.csv',
                      'inferences/se_resnext50.0.test_val.csv']
                      
test_filenames = ['inferences/inceptionv3.0.test.csv',
                  'inferences/se_resnext50.0.test.csv']
                  
weights = [1.0, 1.0]
```
The command generate two files. One for original submission and the other is modified using data leak.
- submissions/submission.csv
- submissions/submission.csv.leak.csv

kaggle-hpa

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