SIIM-ISIC-Melanoma-Classification-1st-Place-Solution: A Python repository from haqishen

SIIM-ISIC-Melanoma-Classification-1st-Place-Solution

Competition Leaderboard: https://www.kaggle.com/c/siim-isic-melanoma-classification/leaderboard

SOFTWARE (python packages are detailed separately in `requirements.txt`)

Python 3.6.9

CUDA Version 10.2.89

cuddn 7.6.5

nvidia Driver Version: 418.116.00

DATA SETUP (assumes the Kaggle API is installed)

Download and unzip resized 2020 and 2019 data (including 2018) of 3 sizes by Chris Deotte.

mkdir ./data
cd ./data
for input_size in 512 768 1024
do
  kaggle datasets download -d cdeotte/jpeg-isic2019-${input_size}x${input_size}
  kaggle datasets download -d cdeotte/jpeg-melanoma-${input_size}x${input_size}
  unzip -q jpeg-melanoma-${input_size}x${input_size}.zip -d jpeg-melanoma-${input_size}x${input_size}
  unzip -q jpeg-isic2019-${input_size}x${input_size}.zip -d jpeg-isic2019-${input_size}x${input_size}
  rm jpeg-melanoma-${input_size}x${input_size}.zip jpeg-isic2019-${input_size}x${input_size}.zip
done

Model Illustration

More details can be found here:

https://www.kaggle.com/c/siim-isic-melanoma-classification/discussion/175412

http://arxiv.org/abs/2010.05351

Training

Training commands of the 18 models. Training time for a single model ranges from 15 to 45 hours for all 5 folds in our setup.

After training, models will be saved in ./weights/ Tranning logs will be saved in ./logs/

python train.py --kernel-type 9c_meta_b3_768_512_ext_18ep --data-dir ./data/ --data-folder 768 --image-size 512 --enet-type efficientnet_b3 --use-meta --n-epochs 18 --use-amp --CUDA_VISIBLE_DEVICES 0,1

python train.py --kernel-type 9c_b4ns_2e_896_ext_15ep --data-dir ./data/ --data-folder 1024 --image-size 896 --enet-type tf_efficientnet_b4_ns --use-amp --init-lr 2e-5 --CUDA_VISIBLE_DEVICES 0,1,2,3,4,5

python train.py --kernel-type 9c_b4ns_448_ext_15ep-newfold --data-dir ./data/ --data-folder 512 --image-size 448 --enet-type tf_efficientnet_b4_ns --use-amp --CUDA_VISIBLE_DEVICES 0

python train.py --kernel-type 9c_b4ns_768_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b4_ns --use-amp --CUDA_VISIBLE_DEVICES 0,1,2

python train.py --kernel-type 9c_b4ns_768_768_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 768 --enet-type tf_efficientnet_b4_ns --use-amp --CUDA_VISIBLE_DEVICES 0,1,2

python train.py --kernel-type 9c_meta_b4ns_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b4_ns --use-meta --use-amp --CUDA_VISIBLE_DEVICES 0,1,2,3

python train.py --kernel-type 4c_b5ns_1.5e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b5_ns --out-dim 4 --init-lr 1.5e-5 --use-amp --CUDA_VISIBLE_DEVICES 0,1,2

python train.py --kernel-type 9c_b5ns_1.5e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b5_ns --init-lr 1.5e-5 --use-amp --CUDA_VISIBLE_DEVICES 0,1,2

python train.py --kernel-type 9c_b5ns_448_ext_15ep-newfold --data-dir ./data/ --data-folder 512 --image-size 448 --enet-type tf_efficientnet_b5_ns --use-amp --CUDA_VISIBLE_DEVICES 0,1

python train.py --kernel-type 9c_meta128_32_b5ns_384_ext_15ep --data-dir ./data/ --data-folder 512 --image-size 384 --enet-type tf_efficientnet_b5_ns --use-meta --n-meta-dim 128,32 --use-amp --CUDA_VISIBLE_DEVICES 0

python train.py --kernel-type 9c_b6ns_448_ext_15ep-newfold --data-dir ./data/ --data-folder 512 --image-size 448 --enet-type tf_efficientnet_b6_ns --use-amp --CUDA_VISIBLE_DEVICES 0,1

python train.py --kernel-type 9c_b6ns_576_ext_15ep_oldfold --data-dir ./data/ --data-folder 768 --image-size 576 --enet-type tf_efficientnet_b6_ns --use-amp --CUDA_VISIBLE_DEVICES 0,1,2,3

python train.py --kernel-type 9c_b6ns_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b6_ns --use-amp --CUDA_VISIBLE_DEVICES 0,1,2,3

python train.py --kernel-type 9c_b7ns_1e_576_ext_15ep_oldfold --data-dir ./data/ --data-folder 768 --image-size 576 --enet-type tf_efficientnet_b7_ns --init-lr 1e-5 --use-amp --CUDA_VISIBLE_DEVICES 0,1,2,3

python train.py --kernel-type 9c_b7ns_1e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b7_ns --init-lr 1e-5 --use-amp --CUDA_VISIBLE_DEVICES 0,1,2,3,4,5,6,7

python train.py --kernel-type 9c_meta_1.5e-5_b7ns_384_ext_15ep --data-dir ./data/ --data-folder 512 --image-size 384 --enet-type tf_efficientnet_b7_ns --use-meta --use-amp --CUDA_VISIBLE_DEVICES 0,1,2

python train.py --kernel-type 9c_nest101_2e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type resnest101 --init-lr 2e-5 --use-amp --CUDA_VISIBLE_DEVICES 0,1,2,3

python train.py --kernel-type 9c_se_x101_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type seresnext101 --use-amp --CUDA_VISIBLE_DEVICES 0,1

(Optional) Evaluating

Optionally, you can evaluate each model on 5 fold cross valiation sets. You can either use the models trained in previous step, or use the trained models we provided and specify the directory in --model-dir.

Evaluation results will be printed out and saved to ./logs/ Out-of-folds prediction results will be saved to ./oofs/

python evaluate.py --kernel-type 9c_meta_b3_768_512_ext_18ep --data-dir ./data/ --data-folder 768 --image-size 512 --enet-type efficientnet_b3 --use-meta

python evaluate.py --kernel-type 9c_b4ns_2e_896_ext_15ep --data-dir ./data/ --data-folder 1024 --image-size 896 --enet-type tf_efficientnet_b4_ns

python evaluate.py --kernel-type 9c_b4ns_448_ext_15ep-newfold --data-dir ./data/ --data-folder 512 --image-size 448 --enet-type tf_efficientnet_b4_ns

python evaluate.py --kernel-type 9c_b4ns_768_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b4_ns

python evaluate.py --kernel-type 9c_b4ns_768_768_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 768 --enet-type tf_efficientnet_b4_ns

python evaluate.py --kernel-type 9c_meta_b4ns_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b4_ns --use-meta

python evaluate.py --kernel-type 4c_b5ns_1.5e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b5_ns --out-dim 4

python evaluate.py --kernel-type 9c_b5ns_1.5e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b5_ns

python evaluate.py --kernel-type 9c_b5ns_448_ext_15ep-newfold --data-dir ./data/ --data-folder 512 --image-size 448 --enet-type tf_efficientnet_b5_ns

python evaluate.py --kernel-type 9c_meta128_32_b5ns_384_ext_15ep --data-dir ./data/ --data-folder 512 --image-size 384 --enet-type tf_efficientnet_b5_ns --use-meta --n-meta-dim 128,32

python evaluate.py --kernel-type 9c_b6ns_448_ext_15ep-newfold --data-dir ./data/ --data-folder 512 --image-size 448 --enet-type tf_efficientnet_b6_ns

python evaluate.py --kernel-type 9c_b6ns_576_ext_15ep_oldfold --data-dir ./data/ --data-folder 768 --image-size 576 --enet-type tf_efficientnet_b6_ns

python evaluate.py --kernel-type 9c_b6ns_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b6_ns

python evaluate.py --kernel-type 9c_b7ns_1e_576_ext_15ep_oldfold --data-dir ./data/ --data-folder 768 --image-size 576 --enet-type tf_efficientnet_b7_ns

python evaluate.py --kernel-type 9c_b7ns_1e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b7_ns

python evaluate.py --kernel-type 9c_meta_1.5e-5_b7ns_384_ext_15ep --data-dir ./data/ --data-folder 512 --image-size 384 --enet-type tf_efficientnet_b7_ns --use-meta

python evaluate.py --kernel-type 9c_nest101_2e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type resnest101

python evaluate.py --kernel-type 9c_se_x101_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type seresnext101

Predicting

Make predictions on test set. You can either use the models trained in the Training step, or use the trained models we provided and specify the directory in --model-dir

Each models submission file will be saved to ./subs/

python predict.py --kernel-type 9c_meta_b3_768_512_ext_18ep --data-dir ./data/ --data-folder 768 --image-size 512 --enet-type efficientnet_b3 --use-meta

python predict.py --kernel-type 9c_b4ns_2e_896_ext_15ep --data-dir ./data/ --data-folder 1024 --image-size 896 --enet-type tf_efficientnet_b4_ns

python predict.py --kernel-type 9c_b4ns_448_ext_15ep-newfold --data-dir ./data/ --data-folder 512 --image-size 448 --enet-type tf_efficientnet_b4_ns

python predict.py --kernel-type 9c_b4ns_768_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b4_ns

python predict.py --kernel-type 9c_b4ns_768_768_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 768 --enet-type tf_efficientnet_b4_ns

python predict.py --kernel-type 9c_meta_b4ns_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b4_ns --use-meta

python predict.py --kernel-type 4c_b5ns_1.5e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b5_ns --out-dim 4

python predict.py --kernel-type 9c_b5ns_1.5e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b5_ns

python predict.py --kernel-type 9c_b5ns_448_ext_15ep-newfold --data-dir ./data/ --data-folder 512 --image-size 448 --enet-type tf_efficientnet_b5_ns

python predict.py --kernel-type 9c_meta128_32_b5ns_384_ext_15ep --data-dir ./data/ --data-folder 512 --image-size 384 --enet-type tf_efficientnet_b5_ns --use-meta --n-meta-dim 128,32

python predict.py --kernel-type 9c_b6ns_448_ext_15ep-newfold --data-dir ./data/ --data-folder 512 --image-size 448 --enet-type tf_efficientnet_b6_ns

python predict.py --kernel-type 9c_b6ns_576_ext_15ep_oldfold --data-dir ./data/ --data-folder 768 --image-size 576 --enet-type tf_efficientnet_b6_ns

python predict.py --kernel-type 9c_b6ns_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b6_ns

python predict.py --kernel-type 9c_b7ns_1e_576_ext_15ep_oldfold --data-dir ./data/ --data-folder 768 --image-size 576 --enet-type tf_efficientnet_b7_ns

python predict.py --kernel-type 9c_b7ns_1e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type tf_efficientnet_b7_ns

python predict.py --kernel-type 9c_meta_1.5e-5_b7ns_384_ext_15ep --data-dir ./data/ --data-folder 512 --image-size 384 --enet-type tf_efficientnet_b7_ns --use-meta

python predict.py --kernel-type 9c_nest101_2e_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type resnest101

python predict.py --kernel-type 9c_se_x101_640_ext_15ep --data-dir ./data/ --data-folder 768 --image-size 640 --enet-type seresnext101

Ensembling

Ensemble the 18 single model's submission files (from previous step) into the final submission file.

The submission file final_sub1.csv will be saved in root directory.

python ensemble.py

Trained Weights

We published our trained weigths of the model settings above (which we won this competition):

https://www.kaggle.com/boliu0/melanoma-winning-models

Download it into ./weights/ then you can run evaluate.py and predict.py directly.

haqishen/SIIM-ISIC-Melanoma-Classification-1st-Place-Solution