Skin Lesion Detection from Dermoscopic Images using Convolutional Neural Networks
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Transcript of Skin Lesion Detection from Dermoscopic Images using Convolutional Neural Networks
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SKIN LESION DETECTION FROM DERMOSCOPIC IMAGES USING
CONVOLUTIONAL NEURAL NETWORKS
Adrià Romero López Oge Marques Xavier Giró-i.Nieto
AUTHOR ADVISORS
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Acknowledgments
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MIDDLE Research Group
Víctor Campos Albert Gil
Jack Burdick Janet Weinthal Adam Lovett
Oge Marques Borko Furht Xavier Giró-i.Nieto Albert Jiménez
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‘’Outline
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1. Motivation2. State of the art3. Methodology4. Experimental Results5. Conclusions
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1.Motivation
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Background of the problem
▣ Skin cancer: most predominant type of cancer ▣ The frequency of melanoma doubles every 20 years ▣ Each year (in USA):
□ 76,380 new cases of melanoma □ 6,750 deaths
▣ Melanoma is a deadly form of skin cancer, but survival rates are high if detected and diagnosed early
▣ Melanoma detection: rely on hand-crafted features □ ABCDE rule (Asymmetry, Border, Color, Dermoscopic
structure, and Evolving)□ CASH rule (Color, Architecture, Symmetry, and
Homogeneity)
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Background of the problem
▣ Discriminating between benign and malignant skin lesions is challenging
▣ Without computer-based assistance: 60~80% detection accuracy
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Scope and goals
▣ Scope:□ Assist physicians in classifying skin lesions (especially in
melanoma detection: 2-class classifier problem) ▣ Goal:
□ Use state-of-the-art techniques, called Deep Learning, to design an intelligent medical imaging-based skin lesion diagnosis system
□ Achieve (or improve upon) state-of-the-art results for:■ skin lesion segmentation, and■ skin lesion classification
□ Evaluate the impact of skin lesion segmentation on the accuracy of the classifier
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Hypothesis
Previous segmentation of an image containing a skin lesion (i.e., isolating the lesion from the background) improves the accuracy and sensitivity of a Deep Learning classification model approach.
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Challenges
▣ Dermoscopic images may:■ Contain artifacts, such as: moles, freckles, hair,
patches, shading and noise.■ Present low contrast images between lesion and
background■ Contain multiple skin lesions
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Related work
•Typical block diagram (Non-Deep Learning approach from [Glaister2013])
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2.State of the art
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State-of-the-art hierarchy
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CNNs
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Deep learning motivation
▣ Image representations to:□ Image classification□ Object detection and recognition□ Semantic Segmentation
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Self-driving cars[Goodfellow et al. 2014]
[Ciresan et al. 2013]
[Turaga et al 2010]
Slide credit: Bay Area Deep Learning School Presentation by A. Karpathy
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Supervised learning
14[Car] [Dog]
Parameters
Slide credit: “Artificial Intelligence, revealed” by Facebook Research
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Why deep learning now?
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Large datasets GPUs (Graphics Processing Unit)
* Not applicable to medical imaging
[Deng et al. Russakovsky et al.]
[NVIDIA et al.]
Framework
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Convolutional Neural Networks
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Some input vector (our images).
Also known as ConvNets or CNNs
Our class label
▣ Convolutional Layers▣ Activation Layers▣ Pooling Layers
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Convolution layer
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32
32
3
5x5x3 filter
32x32x3 image
Convolve the filter with the imagei.e. “slide over the image spatially, computing dot products”
Filters always extend the full depth of the input volume
Slide credit: Bay Area Deep Learning School Presentation by A. Karpathy
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Convolution layer
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32
32
3
32x32x3 image
1 number: the result of taking a dot product between the filter and a small 5x5x3 chunk of the image(i.e. 5*5*3 = 75-dimensional dot product + bias)
Slide credit: Bay Area Deep Learning School Presentation by A. Karpathy
Linear function
5x5x3 filter → weights (Learnt by Backpropagation algorithms)
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Activation layer
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32
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3
32x32x3 image5x5x3 filter
Convolve (slide) over all spatial locations
ReLU (Rectified Linear Units)
1
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Slide credit: Bay Area Deep Learning School Presentation by A. Karpathy
activation map
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Pooling layer
▣ Undersampling task□ Makes the representation smaller and more
manageable□ Operates over each activation map independently
20Slide credit: Bay Area Deep Learning School Presentation by A. Karpathy
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Fully-Connected (FC) layer
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Main scheme
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Input image[Yann LeCun et al.]
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Main scheme
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1. Convolutional Layers 2. Activation Layer 3. Pooling Layers
[Yann LeCun et al.]
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Main scheme
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[Yann LeCun et al.]
Fully-Connected Layer
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Main scheme
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[Yann LeCun et al.]
Output label
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ConvNets for classification
▣ Classification → Scoring:□ The CNN computes a class score {float} to each
image □ This score will be related to a class label {integer}
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[224x224x3]
f Class scores, indicating class labels
training
Slide credit: Bay Area Deep Learning School Presentation by A. Karpathy
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ConvNets for segmentation
▣ Segmentation → Localization:□ The CNN assigns a class label to each pixel (classify
all pixels)■ {0,1} → {absence of object, presence of object}
□
27Slide credit: CS231n
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ConvNets for segmentation
28Slide credit: CS231n
▣ Upsampling□ From labels {1x1} to Segmented Image {224x224} px
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Transfer learning
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1. Train on Imagenet
3. Medium dataset:finetuning
more data = retrain more of the network (or all of it)
2. Small dataset:feature extractor
Freeze these
Train this
Freeze these
Train this
Slide credit: Bay Area Deep Learning School Presentation by A. Karpathy
Medical Imaging case
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3.Methodology
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Framework
▣ Python environment:□ Keras - Deep Learning Library for Theano or TensorFlow□ OpenCV / PIL (Python Imaging Library)□ SciPy (Library for Mathematics, Science and Engineering) □ Scikit-learn (Machine Learning Library)□ CUDA library for the GPUs
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+ =
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ISIC Archive dataset
▣ ISBI 2016 Challenge dataset□ Skin Lesion Analysis towards melanoma detection□ 1279 RGB images□ Labeled as either benign or malignant□ Includes the binary mask for each image
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Class
Benign Malignant Total Images
Training subset 727 173 900
Validation subset 304 75 379
0 → outside lesion area255 → inside lesion area
Binary mask
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Method scheme
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Data augmentation
▣ Enlarge our few training examples:□ Re-scaling□ 40 degrees rotations □ Horizontal shifts□ Zooming□ Horizontal flips
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Original image Random transformations
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Preprocessing
▣ Mean subtraction: X -= np.mean(X, axis = 0)▣ Image Normalization: X /= np.std(X, axis = 0)
▣ Image cropping & resizing□ Segmentation model: 64 x 80 px□ Classification model: 224 x 224 px
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Segmentation model: U-Net architecture
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▣ Convolutional Networks for Biomedical Image Segmentation by Olaf Ronneberger et al.
Binary Mask
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Segmentation model: training parameters
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▣ U-Net trained from scratch (small image size)▣ Weights randomly initialized▣ Loss function:
□ Dice coefficient▣ Adam optimizer (Stochastic gradient-based
optimization):□ Learning rate: 10e-5
▣ Batch size: 32▣ Training epochs: 500 epochs▣ 13 sec / epoch on NVidia GeForce GTX TITAN X GPU
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Objective
To verify our hypothesis:1. Unaltered lesion classification2. Perfectly segmented lesion classification3. Automatically segmented lesion classification
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Logical AND operation
Logical AND operation
Original Binary Mask (perfect)
Binary Mask obtained with the U-Net
Previous segmentation of the skin lesion improves the accuracy and sensitivity of a Deep Learning classification model.
(1)
(2)
(3)
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Method Scheme (reminder)
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Classification Model: VGG-16 Architecture
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▣ Five Convolutional Blocks (2D conv.)
▣ 3 x 3 receptive field▣ ReLU as Activation
Functions▣ Max-Pooling▣ Classifier block:
□ 3 FC Layers at the top of the network
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Fine-tuning the VGG-16 Architecture
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▣ Weights initialized with the VGG-16 pretrained on Imagenet dataset
▣ Freeze bottom of the network
▣ Just train the top of the VGG-16 Train this
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Freeze these
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Classification Model: Loss function
▣ Problem: ISIC dataset classes not balanced□ Validation subset:
■ 304 benign images■ 75 malignant images
▣ Weighted Loss function:
where ρ is defined as 1−frequency appearance (minor class)
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Classification Model: Training parameters
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▣ VGG-16 fine-tuned▣ Weights initialized with the VGG-16 pretrained on
Imagenet dataset▣ Loss function:
□ Weighted Loss function▣ SGD optimizer (Stochastic gradient-based
optimization):□ Learning rate: 10e-5
▣ Batch size: 32▣ Training epochs: 50 epochs▣ 35 sec / epoch on NVidia GeForce GTX TITAN X GPU
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Overfitting
▣ When a model fits the training data too well□ Noise in the training data is learned by the model
▣ How to prevent it?□ Dropout□ Choosing a reduced network (VGG-16 with 138M
param. rather than VGG-19 with 144M param.)
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4.Experimental
Results
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Segmentation Evaluation
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Participant Accuracy Dice Coef. Jaccard Index
Sensitivity Specificity
MIDDLE group
0.9176 0.8689 0.9176 0.9301 0.9544
▣ Comparing pixel by pixel of each masks:
Ground truth Mask obtained
JACCARD INDEX:
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Segmentation Examples
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▣ Satisfactory segmentation examples
▣ Poor segmentation examples
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Classification Evaluation
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Model Accuracy Loss Sensitivity Precision
Unaltered lesion clas.
0.8469 0.4723 0.8243 0.9523
Perfectly segmented lesion clas.
0.8390 0.4958 0.8648 0.9621
Automatically segmented lesion clas.
0.8174 0.5144 0.8918 0.9681
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Classification Evaluation
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Model Accuracy Loss Sensitivity Precision
Unaltered lesion clas.
0.8469 0.4723 0.8243 0.9523
Perfectly segmented lesion clas.
0.8390 0.4958 0.8648 0.9621
Automatically segmented lesion clas.
0.8174 0.5144 0.8918 0.9681
▣ With segmentation □ Accuracy decreases□ Loss increases
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Classification Evaluation
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Model Accuracy Loss Sensitivity Precision
Unaltered lesion clas.
0.8469 0.4723 0.8243 0.9523
Perfectly segmented lesion clas.
0.8390 0.4958 0.8648 0.9621
Automatically segmented lesion clas.
0.8174 0.5144 0.8918 0.9681
▣ But...with segmentation □ Sensitivity increases !□ Precision increases !
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Classification Evaluation
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Model Accuracy Loss Sensitivity Precision
Unaltered lesion clas.
0.8469 0.4723 0.8243 0.9523
Perfectly segmented lesion clas.
0.8390 0.4958 0.8648 0.9621
Automatically segmented lesion clas.
0.8174 0.5144 0.8918 0.9681
▣ But...with segmentation: □ Sensitivity increases !□ Precision increases !
SENSITIVITY = TP / (TP + FN)
PRECISION = TP / (TP + FP)
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Sensitivity in Medical Settings
▣ Sensitivity is often considered the most important metric in the medical setting
▣ For early diagnosis□ By missing a False Negatives (true melanoma case)
the model would fail in the early diagnosis□ It is better to raise a False Positive than to create a
False Negative
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Classification evaluation
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Model Accuracy Loss Sensitivity Precision
Unaltered lesion clas.
0.8469 0.4723 0.8243 0.9523
Perfectly segmented lesion clas.
0.8390 0.4958 0.8648 0.9621
Automatically segmented lesion clas.
0.8174 0.5144 0.8918 0.9681
▣ And the Automatically Segmented Model is even BETTER than the Perfectly Segmented□ Physicians can avoid Manual Segmentation tasks
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Confusion Matrices
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False Negatives descending
Unaltered Classifier Perfectly Classifier Segmented Classifier
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Classification Examples
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5.Conclusions
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Conclusions
▣ DL solution for assisting dermatologists with the diagnosis of skin lesions□ Specifically, for early melanoma detection
▣ Does a previous semantic segmentation improve the performance of a fine-tuned CNN for a 2-class classifier?□ Hypothesis verified
▣ Perfect Segmentation was not needed to obtain the best classification result of the model□ DL Segmentation approach obtained the best
sensitivity classification result
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Conclusions
▣ BioMed 2017 Conference → Paper Accepted□ Title: “Skin Lesion Classification from Dermoscopic
Images Using Deep Learning Techniques”▣ SIIM 2017 Meeting → Paper Accepted
□ Title: “The Impact of Segmentation on the Accuracy and Sensitivity of a Melanoma Classifier Based on Skin Lesion Images”
▣ MICCAI 2017 Conference → Intention of Paper ▣ MIUA 2017 Conference → Intention of Paper▣ ISBI 2017 Challenge → Intention of Participation
□ Skin Lesion Analysis Towards Melanoma Detection
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Thanks!Any questions?
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