ISIC-2018

There are 3 parts to the ISIC 2018 challenge: Task 1: Lesion Boundary Segmentation Task 2: Lesion Attribute Detection Task 3: Disease Classification

Task 1: Lesion Boundary Segmentation

A ResNet50 based FCN network was used to segment the lesion from other skin areas. An off-the-shelf imagenet trained ResNet50 model was outfitted with upsampling layers, skip connections and trained with weighted loss functions to achive fscores of 0.89.

Sample Results

In the combined image:

• Purple: True Positive (model prediction matches lesion area marked by human)
• Blue: False Negative (model missed part of lesion in the area)
• Green: False Positive (model incorrectly predicted lesion in an area where there is none)

Dataset

The dataset, consisting of dermoscopic lesion images in JPEG format, was acquired from ISIC-2018 challenge Task-1 web page.

The dataset was augmented with the following steps to boost validation accuracy:

• adding random streaks
• randomly rotating image and corresponding mask
• adding variations to image saturation and hue

The data was preprocessed for training by:

• scalling to 224x224x3
• normalizing values to fall between [-1, 1], with to 0.5 mean and 0.5 std.dev.

Neural Net Architecture

ResNet-50 is a deep network with batch norms and identity shortcut connections that let gradients propogate well during backward propogation. 2D transpose convolutions up-sample tensors back to the original image's dimensions. A sigmoid layer generates 0/1 monochromatic image mask, where pixels corresponding to positive predictions are 1, the rest are 0. To improve precision, higher resolution tensor output from lower layers in ResNet are concatenated with input to 2D transpose convolution layers. This results in preditctions with finer details.

Model

Loss Functions and Metrics

During training the following metrics are computed after every 30 batches of training.

• IOU (Intersection over union) / Jaccard index

def iou(y_true, y_pred):
    intersection = torch.sum(y_true * y_pred)
    return (intersection + 1.) / 
                (torch.sum(y_true) + torch.sum(y_pred) - intersection + 1.)

• Dice Coefficient

def dice_coef(y_true, y_pred):
    intersection = torch.sum(y_true * y_pred)
    return (2. * intersection + 1.) / 
                (torch.sum(y_true) + torch.sum(y_pred) + 1.)

• [False Positive and False Negative]

def falsepos(y_true, y_pred):
    intersection = torch.sum(y_true * y_pred)
    return torch.sum(y_pred) - intersection

def falseneg(y_true, y_pred):
    intersection = torch.sum(y_true * y_pred)
    return torch.sum(y_true) - intersection

• Precision and Recall

def precision(y_true, y_pred):
    intersection = torch.sum(y_true * y_pred)
    return intersection / (torch.sum(y_pred) + 1.)

def recall(y_true, y_pred):
    intersection = torch.sum(y_true * y_pred)
    return intersection / (torch.sum(y_true) + 1.)

• F1-score

def fscore(y_true, y_pred):
    presci = precision(y_true, y_pred)
    rec = recall(y_true, y_pred)
    return 2*(presci * rec)/(presci + rec)

• Loss function:
  • Adapt F1-score function, weighted to improve recall as the loss function.
  • Returns negative f1 score, since larger fscore is preferable and optimizer will push it towards a larger negative value.

def weighted_fscore_loss(weight):
    def fscore_loss(y_true, y_pred):
        presci = precision(y_true, y_pred)
        rec = recall(y_true, y_pred)
        return -(1+weight)*(presci * rec) / (weight*presci + rec)
    return fscore_loss

Training

dataset.py: Data set is randomly split into training and validation sets - 80% training and 20% validation.

Batches of data are transformed with torchvision.transforms:

• Converting into tensors
• Normalized to values between -1 and 1 with mean 0.5 and std. dev 0.5.

train.py: Batches of training data are loaded intp the GPU for computing the forward pass and getting the output of the network, calculating losses by comparing with labeled data and updating gradients in the backward pass through the loss function.

for i, (inputs, labels) in enumerate(train_loader, 0):

    # map to gpu
    inputs, labels = inputs.cuda(), labels.cuda()

    # zero the parameter gradients
    optimizer.zero_grad()

    # forward + backward + optimize
    outputs = net(inputs)
    loss = criterion(outputs, labels)
    loss.backward()
    optimizer.step()

Since I chose not to resize the images, I could only fit 10 images per batch in the GPU. Resizing to smaller dimensions would have allowed larger batch sizes at the expense of precision.

At about 10 epochs of training, validation and training losses plateaued.

Optimizer and learning rate:

Torch offeres several optimization strategies, I used the popular Adam optimizer as it tends to converge quickly. Through trial and error, I arrived at a learning rate of 1e-5. Further, I used pytorch's learning rate scheduler ReduceLROnPlateau to automatically scale the learning rate when validation starts stagnating. But in testing 10 epochs, the learning rate was not reduced.

Evaluation

Metrics from training are sent to Visdom server for visualization.

Mean Training and Validation Losses

• Orange: Validation loss
• Blue: Training loss

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IOU and Dice Coefficient improves with training

• Orange: IOU
• Blue: Dice coefficient

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False Positives and False Negatives drop

• Orange: False negatives
• Blue: False positives

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Precision, Recall and F1-Score improve with training

• Orange: Recall
• Blue: Precision
• Green: F1-score

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Task 2: Lesion Attributes

Dataset:

Total numer of images: 2594

Mask Type	Mask Code	Number of blank images	% Blank images	Pixel Ratio (Ones / Ones + Zeroes)
Pigment network	0	1992	77	0.0309
Negative network	1	1915	74	0.01272
Streaks	2	2405	93	0.0067
Milia like cyst	3	1072	41	0.1370
Globules	4	2494	96	0.0042

Dataset is severely imbalanced, with very few instances of globules (100) and streaks (189) compared to the others. And with most of them, more than 75% of the masks are entirely blank.

Even in the images where they do appear, the relative sizes are small. This calls for augmenting the dataset considerably to boost the number of instances, specifically those of globules and streaks.