Description
I. Purpose:
This homework contains a large-scale classification task for skin lesion detection:
1. Develop a 2D deep neural network on >10,000 medical image classification.
2. You will use 9015 skin lesion images as training, and 1000 as testing with 7 classes.
3. Understand the basic metrics for classification (acc, precision, recall, confusion matrix).
4. Be able to refer the similar platform based on assignment 0, and assignment 1.
5. Have the processing pipeline for the following assignments.
The training data is large-scale, please use GPU since CPU is probably too slow.
II. Grading and Submission
1. The assignment will be evaluated in a total of 150 scores. The basic scores are generally
given based on the following table. Then, the scores will be further adjusted based on
requirements in “Tasks” (as red color scores in Tasks).
Basic Score (score can be adjusted based on the “Task” requirements)
Amazing Work
150 Design a new network with > 80% accuracy on testing
images.
140 Have substantial improvements on an existing network
with > 70% accuracy on testing images.
Solid Project
130 Some improvements or directly using an existing network
with > 60% accuracy on testing images.
120 Some improvements or directly using an existing network
with at least > 50% accuracy on testing images.
Significant Efforts 110 Some improvements or directly using an existing network
with no roughly correct predictions on testing images.
Much Work Needed 90 Propose a method with some implementation.
Show Understanding 70 Propose a method without implementation.
Turn in Something 50 Barely written report.
No Turn in 0
2. The assignment should be submitted in four formats:
i) Presentations should be submitted to brightspace as a ppt/pptx file with last name
and VUID (e.g., “Huo_huoy1.pptx”).
ii) A single PDF report file should be submitted to brightspace with last name and VUID
(e.g., “Huo_huoy1.pdf”). The PDF report consist presentation slides and code.
(Please do not write any extra words)
iii) The same PDF file should also be printed (color/black) and please bring it to class.
Don’t forget to put your name and VUID on the first page of the report.
iv) All source code should be submitted to brightspace as a single zip file with last name
and VUID (e.g., “Huo_huoy1.zip”).
3. The deadline of braightspace submission is 9:00am on Feb 13.
The deadline of hardcopy report is 4:00pm on Feb 13.
III. Description
This assignment is to implement a classification deep neural network. The link for
downloading the data is provided in BrightSpace.
1. 9015 training images are saved in “train” folder.
2. 1000 testing images are saved in “test” folder.
3. The class labels are saved in “labels” folder.
4. A set of withheld images are not released so that instructor is able to test the code on
such images when it is necessary.
Everything about the data can be found from ISIC website (https://challenge2018.isicarchive.com/task3/)
The lesion types are
The labels for train and testing images are provided. You can tune the network base on
train and testing images to obtain the good combinations of hyper-parameters (learning
rate, batch size etc.). The main training code should be named as “train.py”.
IV. Tasks:
The following tasks can be run on Windows, Mac or Linux, with/without GPU.
1. Presentation
Each presentation is presented in 3 minutes. Less than 3 is totally fine, but please try to
keep in within 3 minutes. (10 scores)
i) Title page with name, 1 slide. (5 scores)
ii) Introduction, 1 slide, (5 scores)
Summarize the task in 1 slide.
iii) Rationale, 1-2 slides (10 scores)
The method you referred and why did you use that.
iv) Method, 2 slides (40 scores)
Slide 1:
Show a figure of network structure. If you use existing networks (e.g. ResNet, VGG,
AlexNet etc.), you can even copy paste the figure from google/paper. The purpose
of the figure is to let the reader understand the method quickly.
Slide 2:
Show how did your format the input and output?
Slide 3:
Show did you use any interesting tricks for training? (e.g., preprocessing,
postprocessing, data augmentation etc.)
Slide 4:
Describe the hyper parameters used during training. (e.g., epoch number, batch
size, learning rate, loss function, parameters of layers, optimizer, input number of
channels, output number of channels, OS, GPU/CPU model).
v) Results, 3 slides (30 scores)
Slide 1:
One figure shows training and testing loss along with epochs, such as the following
example figure.
Slide 2:
One slide shows accuracy, recall, precision.
To get the scores, you can refer to the following websites.
The python code and definition of accuracy:
http://scikit-learn.org/stable/modules/generated/sklearn.metrics.accuracy_score.html#sklearn.metrics.accuracy_score
The python code and definition of recall:
http://scikit-learn.org/stable/modules/generated/sklearn.metrics.recall_score.html#sklearn.metrics.recall_score
The python code and definition of recall:
http://scikit-learn.org/stable/modules/generated/sklearn.metrics.precision_score.html#sklearn.metrics.precision_score
Slide 3:
One figure shows confusion matrix.
To get the matrix, you can refer to the following websites.
The python code and definition of confusion matrix:
http://scikit-learn.org/stable/modules/generated/sklearn.metrics.confusion_matrix.html
You can decide if you will present your results slides or not during in class
presentation.
vi) Conclusion, 1-2 slides (10 scores)
Summarize the experiments (e.g., difficulties, limitations, or thoughts).
2. Code
Paste your code at the end of the report and submitted the e-version as a zip file.
The consistency of the method, results and the code would be evaluated by
lecturer.
i) Code for training (15 scores)
The labels for > 9000 training images are provided. You can tune the network base
on train images to obtain the good combinations of hyper-parameters (learning
rate, batch size etc.). The main training code should be named as “train.py”.
ii) Code for testing (15 scores)
The trained model will be applied to 1000 testing images or withhold images, which
the labels are provided. You need to write a “test.py” file, which load the trained
model and apply to a single jpg image. For example, we would run test.py on a jpg
image and get coordinates with four digits precision.
>>> python test.py ~/test/ ISIC_0033321.jpg
>>> 3
Please make sure labels of testing images are ONLY used for calculating the metrics,
and NOT used during training or testing. If the lecturer feels the results are not
“real”, you might be asked to re-produce your training and testing on ACCRE in
lecturer’s office.
3. Submission (10 scores)
Submit report in both e-version and hardcopy.
Submit code in e-version.
Submit presentation in e-version.
