Skin Lesion Classification: Transformation-based approach to CNNs

Installing / Getting started

A minimal setup you need to get running.

Requirements

• NVIDIA GPU
• cuda
• cudnn
• python 3
• pip

Setting up

Sonnet and TensorFlow

Compile and Install Sonnet and TensorFlow using their guides for use with at least 1 GPU.

Virtual Environment (Recommended)

The following commands are assuming several locations which may be different for your system. virtualenvwrapper

sudo -H pip install virtualenvwrapper
mkvirtualenv --python=/usr/bin/python3 isic_cnn
git clone https://github.gatech.edu/clehman31/isic_cnn.git
cd isic_cnn
workon isic_cnn
pip install [where ever you stored your TensorFlow and Sonnet .whl files]
pip install -R requirements.txt

Resources

Dataset

We modified the ISIC-archive by creating square crops registered on the legion in the images in order to remove large colored stickers and normalize the scale. Any images where the legion was smaller than 100px X 100px were not used. This resulted in ~6000 images.

Paper

Skin Lesion Classification: Transformation-based approach to CNNs

Experiment

Preparing input

First, download the data and generate the TFRecords using isic_input.py. This will build random 80/20 split for training/testing images, it does not care about distribution of labels. Be sure to indicate the where the images are located and what you want the TFRecords to be named.

isic_input.py

IMAGE_SHAPE = [220, 220, 3]
NUM_EXAMPLES_PER_EPOCH_FOR_TRAIN = 4540
NUM_EXAMPLES_PER_EPOCH_FOR_TEST = 1136
PATH_TO_IMAGES = 'isic_cnn_data'
TRAIN_NAME = 'isic_train'
TEST_NAME = 'isic_test'

python isic_input.py

Training & Evaluation

Though it is not necessary to edit the hyperparameters they are listed below.

isic_cnn.py

BATCH_SIZE = 10
EVAL_SIZE = 1136
NUM_CLASSES = 2
CHECKPOINT_DIR = '/tmp/experiments/tf/isic_cnn/'
CHECKPOINT_INTERVAL = 100
MAX_STEPS = 2000
REPORT_INTERVAL = 1
RGB_REDUCE_LEARNING_RATE_INTERVAL = 1000
FFT_REDUCE_LEARNING_RATE_INTERVAL = 1000
HSV_REDUCE_LEARNING_RATE_INTERVAL = 1000
RGB_LEARNING_RATE = 1e-2
FFT_LEARNING_RATE = 1e-2
HSV_LEARNING_RATE = 1e-2
LEARNING_RATE_MULTIPLIER = 0.95
NUM_GPU = 2

To evaluate only just comment out the train function.

def main(argv = None):
    train(MAX_STEPS, REPORT_INTERVAL, with_test=True)
    evaluate()

python isic_cnn.py