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Usage

This chapter demonstrates the most important processing steps of an AUCMEDI AutoML Docker usage.

Docker Call¤

The Docker call to run AUCMEDI is formatted as follows:

docker run \
  -v <ABSOLUTE_HOST_PATH>:/data \
  --rm \
  ghcr.io/frankkramer-lab/aucmedi:latest \
  <AUTOML_MODE> \
  <PARAMETERS>
  • Parameter -v: Docker parameter to mount a host directory (left) into the Docker container (right). The container directory must be /data as expected working directory.
  • Parameter --rm: Docker parameter to clean up the created container after execution.
  • Parameter ghcr.io/frankkramer-lab/aucmedi:latest: AUCMEDI Docker Image hosted on GitHub Container Registry.
  • Parameter <AUTOML_MODE>: AUCMEDI AutoML mode (hub) ["training", "prediction", "evaluation"].
  • Parameter <PARAMETERS>: Optional arugments for AUCMEDI AutoML. See AutoML - Parameters.

Dataset Setup¤

For the Docker interface, data has to be mounted into the Docker container in order to be accessible for AUCMEDI.

In this example usage, the directory aucmedi.data/ is utilized as Docker Volume mount later.

A example dataset structure will look like this:

aucmedi.data/
└── training/                     # Required for training/
    ├── 01_TUMOR/
    │   ├── 10009_CRC-Prim-HE-03_009.tif_Row_301_Col_151.tif
    │   ├── 10062_CRC-Prim-HE-02_003b.tif_Row_1_Col_301.tif
    │   ├── 100B0_CRC-Prim-HE-09_009.tif_Row_1_Col_301.tif
    │   └── ...
    ├── 02_STROMA/
    │   └── ...
    ├── 03_COMPLEX/
    │   └── ...
    ├── 04_LYMPHO/
    │   └── ...
    ├── 05_DEBRIS/
    │   └── ...
    ├── 06_MUCOSA/
    │   └── ...
    ├── 07_ADIPOSE/
    │   └── ...
    └── 08_EMPTY/
        └── ...

Danger

Passing a host directory into the container as Volume, requires absolute paths!

More information about Docker Volumes can be found here: https://docs.docker.com/storage/bind-mounts/

Warning

Be aware that newly created files in a Docker container have the user permission root.

This can lead to issues in automatic processing pipelines.

More information about the dataset structure can be found here: AutoML - Dataset.

Training¤

For the start, our Volume directory must contain the subdirectory training. The training directory must contain all images for model training, sorted class subdirectories.

In order to create a high-performance model for clinical decision support, it is required to have one or multiple already fitted models for this imaging task.

In our usage example, we will train a ResNet50 model from scratch.

run AUCMEDI AutoML training hub

console
docker run \
  -v /root/aucmedi.automl.docker/aucmedi.data:/data \
  --rm \
  ghcr.io/frankkramer-lab/aucmedi:latest \
  training \
  --architecture ResNet50 \
  --epochs 25
output
2022-07-18 12:57:25.282772: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
Epoch 1/10
2022-07-18 12:57:32.516662: I tensorflow/stream_executor/cuda/cuda_dnn.cc:368] Loaded cuDNN version 8100
177/177 [==============================] - ETA: 0s - loss: 0.5103 - auc: 0.9563 - f1_score: 0.7556   
Epoch 1: val_loss improved from inf to 0.20766, saving model to model/model.best_loss.hdf5
177/177 [==============================] - 21s 92ms/step - loss: 0.5103 - auc: 0.9563 - f1_score: 0.7556 - val_loss: 0.2077 - val_auc: 0.9864 - val_f1_score: 0.8958 - lr: 1.0000e-04
Epoch 2/10
177/177 [==============================] - ETA: 0s - loss: 0.1932 - auc: 0.9893 - f1_score: 0.8842
Epoch 2: val_loss improved from 0.20766 to 0.18348, saving model to model/model.best_loss.hdf5
177/177 [==============================] - 15s 84ms/step - loss: 0.1932 - auc: 0.9893 - f1_score: 0.8842 - val_loss: 0.1835 - val_auc: 0.9891 - val_f1_score: 0.9010 - lr: 1.0000e-04
...
Epoch 23/25
177/177 [==============================] - ETA: 0s - loss: 0.0087 - auc: 0.9999 - f1_score: 0.9894
Epoch 23: val_loss did not improve from 0.12966
Epoch 23: ReduceLROnPlateau reducing learning rate to 9.999999747378752e-07.
177/177 [==============================] - 22s 126ms/step - loss: 0.0087 - auc: 0.9999 - f1_score: 0.9894 - val_loss: 0.1477 - val_auc: 0.9933 - val_f1_score: 0.9374 - lr: 1.0000e-05
Epoch 24/25
177/177 [==============================] - ETA: 0s - loss: 0.0051 - auc: 1.0000 - f1_score: 0.9950
Epoch 24: val_loss did not improve from 0.12966
177/177 [==============================] - 22s 125ms/step - loss: 0.0051 - auc: 1.0000 - f1_score: 0.9950 - val_loss: 0.1377 - val_auc: 0.9934 - val_f1_score: 0.9413 - lr: 1.0000e-06
Epoch 25/25
177/177 [==============================] - ETA: 0s - loss: 0.0061 - auc: 1.0000 - f1_score: 0.9941
Epoch 25: val_loss did not improve from 0.12966
177/177 [==============================] - 22s 125ms/step - loss: 0.0061 - auc: 1.0000 - f1_score: 0.9941 - val_loss: 0.1374 - val_auc: 0.9941 - val_f1_score: 0.9400 - lr: 1.0000e-06
/usr/local/lib/python3.8/dist-packages/plotnine/ggplot.py:719: PlotnineWarning: Saving 6.4 x 4.8 in image.
/usr/local/lib/python3.8/dist-packages/plotnine/ggplot.py:722: PlotnineWarning: Filename: model/plot.fitting_course.png

The result of the AUCMEDI AutoML training hub is a model directory in the Volume directory.

It contains one or multiple AUCMEDI models with other metadata created during the fitting process.

aucmedi.data/
├── training/
│   └── ...
└── model/
    ├── logs.training.csv
    ├── meta.training.json
    ├── model.best_loss.hdf5
    ├── model.last.hdf5
    └── plot.fitting_course.png

More information about the parameters for training can be found here: AutoML - Parameters - training.

Prediction¤

For predicting the classification of unknown images, the images should be stored in the test directory.

aucmedi.data/
├── training/
├── model/
│   └── ...
└── test/
    ├── UNKNOWN_IMAGE.0001.tif
    ├── UNKNOWN_IMAGE.0002.tif
    ├── UNKNOWN_IMAGE.0003.tif
    └── UNKNOWN_IMAGE.0004.tif

The AUCMEDI AutoML prediction hub read out the pipeline configuration and fitted models from the provided model directory.

run AUCMEDI AutoML prediction hub

console
docker run \
  -v /root/aucmedi.automl.docker/aucmedi.data:/data \
  --rm \
  ghcr.io/frankkramer-lab/aucmedi:latest \
  prediction
output
2022-07-18 13:13:47.334439: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2022-07-18 13:13:52.783231: I tensorflow/stream_executor/cuda/cuda_dnn.cc:368] Loaded cuDNN version 8100
4/4 [==============================] - 3s 87ms/step

The results will be stored in a CSV file called preds.csv (by default).

The CSV file shows the classification probability for an image for each class.

aucmedi.data/
├── training/
├── model/
│   └── ...
├── test/
│   ├── UNKNOWN_IMAGE.0001.tif
│   ├── UNKNOWN_IMAGE.0002.tif
│   ├── UNKNOWN_IMAGE.0003.tif
│   └── UNKNOWN_IMAGE.0004.tif
└── preds.csv

show inference content of prediction file

$ cat aucmedi.data/preds.csv
SAMPLE,01_TUMOR,02_STROMA,03_COMPLEX,04_LYMPHO,05_DEBRIS,06_MUCOSA,07_ADIPOSE,08_EMPTY
UNKNOWN_IMAGE.0001,0.9947149,5.093858e-05,0.0032877475,0.0004719145,0.00061258266,0.0005081127,1.5236534e-05,0.0003385503
UNKNOWN_IMAGE.0002,0.12757735,0.3084325,0.52998906,0.008813165,0.012200621,0.01229311,0.00034778274,0.00034644845
UNKNOWN_IMAGE.0003,0.9978336,4.6700584e-06,0.000806501,6.4442225e-05,0.0011141102,6.125228e-05,5.657194e-05,5.8843718e-05
UNKNOWN_IMAGE.0004,9.7639786e-05,0.0030071975,0.7069594,0.27908832,0.0037088492,0.0069722794,3.9823564e-05,0.00012642879

More information about the parameters for training can be found here: AutoML - Parameters - prediction.

Evaluation¤

For performance estimation of the model, a validation set is required which means the classification prediction of images with a known class annotation.

In order to demonstrate the CSV annotation, as well, the validation data is encoded in the following file structure:

aucmedi.data/
├── training/
├── model/
│   └── ...
├── test/
├── validation/
│   ├── images/
│   │   ├── 10070_CRC-Prim-HE-04_036.tif_Row_601_Col_601.tif
│   │   ├── 10078_CRC-Prim-HE-03_001.tif_Row_151_Col_601.tif
│   │   ├── 1012B_CRC-Prim-HE-10_016.tif_Row_1_Col_301.tif
│   │   └── ...
│   └── annotations.csv
└── preds.csv

show annotation content of validation CSV file

$ cat aucmedi.data/validation/annotations.csv
SAMPLE,CLASS
101A0_CRC-Prim-HE-03_034.tif_Row_151_Col_1.tif,01_TUMOR
1012B_CRC-Prim-HE-10_016.tif_Row_1_Col_301.tif,05_DEBRIS
13111_CRC-Prim-HE-05_009a.tif_Row_751_Col_1351.tif,03_COMPLEX
...

The evaluation mode of AUCMEDI requires another prediction call for the new validation images.

Compute predictions for validation images with a specific input & output path

console
docker run \
  -v /root/aucmedi.automl.docker/aucmedi.data:/data \
  --rm \
  ghcr.io/frankkramer-lab/aucmedi:latest \
  prediction \
  --path_imagedir validation/images/ \
  --path_pred validation/preds.csv
output
2022-07-18 13:26:25.699603: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2022-07-18 13:26:31.281593: I tensorflow/stream_executor/cuda/cuda_dnn.cc:368] Loaded cuDNN version 8100
20/20 [==============================] - 4s 50ms/step

show inference content of prediction file

$ cat aucmedi.data/validation/preds.csv
SAMPLE,01_TUMOR,02_STROMA,03_COMPLEX,04_LYMPHO,05_DEBRIS,06_MUCOSA,07_ADIPOSE,08_EMPTY
10070_CRC-Prim-HE-04_036.tif_Row_601_Col_601,0.0002848482,0.031636566,0.00048324154,0.00043562692,0.042952724,0.00074527983,0.92224264,0.001219118
10078_CRC-Prim-HE-03_001.tif_Row_151_Col_601,0.0065458445,0.486334,0.20805378,8.415832e-05,0.27862436,0.019759992,4.8646994e-05,0.0005491826
1012B_CRC-Prim-HE-10_016.tif_Row_1_Col_301,0.0030586768,0.13436078,0.030891698,0.004924605,0.7850058,0.021087538,0.015678901,0.00499198
...

Afterwards, it is possible to estimate the performance based on the annotations and predicted classifications of the validation set.

compute performance via AUCMEDI AutoML evaluation

console
docker run \
  -v /root/aucmedi.automl.docker/aucmedi.data:/data \
  --rm \
  ghcr.io/frankkramer-lab/aucmedi:latest \
  evaluation \
  --path_imagedir validation/images/ \
  --path_gt validation/annotations.csv \
  --path_pred validation/preds.csv
output
/usr/local/lib/python3.8/dist-packages/plotnine/ggplot.py:719: PlotnineWarning: Saving 12 x 9 in image.
/usr/local/lib/python3.8/dist-packages/plotnine/ggplot.py:722: PlotnineWarning: Filename: evaluation/plot.performance.barplot.png
/usr/local/lib/python3.8/dist-packages/plotnine/ggplot.py:719: PlotnineWarning: Saving 10 x 9 in image.
/usr/local/lib/python3.8/dist-packages/plotnine/ggplot.py:722: PlotnineWarning: Filename: evaluation/plot.performance.confusion_matrix.png
/usr/local/lib/python3.8/dist-packages/plotnine/ggplot.py:719: PlotnineWarning: Saving 10 x 9 in image.
/usr/local/lib/python3.8/dist-packages/plotnine/ggplot.py:722: PlotnineWarning: Filename: evaluation/plot.performance.roc.png

show file structure of Volume directory (after evaluation)

aucmedi.data/
├── training/
├── model/
│   └── ...
├── test/
├── validation/
│   ├── images/
│   │   └── ...
│   └── annotations.csv
├── evaluation/
│   ├── metrics.performance.csv
│   ├── plot.performance.barplot.png
│   ├── plot.performance.confusion_matrix.png
│   └── plot.performance.roc.png
└── preds.csv

Figure: Results Resulting evaluation result of AUCMEDI AutoML CLI usage example. File: evaluation/plot.performance.confusion_matrix.png.

More information about the parameters for training can be found here: AutoML - Parameters - evaluation.