Vienna University of Technology

Interdisciplinary Project Report

2023S

Mihai Cata (12045439)

March 27, 2023

1 Motivation
The goal of this project is to apply all the knowledge obtained during the Data Science Masters
I am studying and apply it for solving a domain specific task. This includes successfully working
with data from the chosen domain, selecting the appropriate methods to use and applying them
on real data.
In order to achieve this, I first had to choose a domain, and my choice was the medical field. There
are several reasons for this. First of all, it is a domain where Machine Learning could automatize
many of the tasks currently performed by doctors, and perhaps even perform them with a higher
accuracy. Secondly, it is a domain in which innovations can save people’s lives, which makes it a
very noble and motivating pursuit.
The topic of my project is brain tumor classification using Machine Learning. In order to achieve
the required domain knowledge, I first had to complete the course Brain Modeling (101.152), which
was also a requirement of the project. By attending this course I learned about the different parts of
the brain and their functions, the basics of neuroscience (how to use simulations and mathematical
models to increase our understanding of the nervous system) and improved my skills of scientific
literature review. This proves to be useful also in the context of using Neural Networks, since
this type of Machine Learning model is inspired by the human brain and tries to mimic the way
biological neurons communicate.

2 Background
Various medical procedures are needed for various forms of brain tumors. The tumor mass must
first be recognized and segmented in conventional computer-aided diagnosis systems before it can
be classified into other categories. Following tumor mass segmentation, feature extraction and
classification are applied to the segmented area.
Brain and Central Nervous System tumors are the third most common cancer occurring among
teenagers and young adults (ages 15-38) [Cheng et al. (2016)]. In order to prevent prevent these
tumors as soon as possible, attempts have been made to create a tumor detection system regardless
of the tumor’s location, shape, and intensity, however without success [Siegel (2016)].
Detecting a tumor’s type plays a very important role for cancer patients because misdiagnosis of
brain tumor types will prevent effective response to medical intervention and therefore decrease
their chances of survival. This process is currently performed manually by doctors, being a very
tedious and prone to errors task. Furthermore, doctors require a lot of training in order to be
able to correctly identify brain tumors. It would be of great help for them to make use of Deep
Learning solutions to automate this task and simplify their work.
Attempts to perform this task have already been made by other researchers, both using classical
image processing and neural networks [Cheng et al. (2015), He et al. (2015), Pereira et al. (2016)].
We will focus on the later approach and use Convolutional Neural Networks, since the data is in
image format and this type of neural network performs great on image classification.

3 Experiments
The experimental part consisted of multiple steps which were performed and were structured in
the following way:
1. Data exploration
2. Data preprocessing
3. Training and testing classification networks
4. Data expansion and hyperparameter optimization
5. Demo web app

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3.1 Data exploration
The data used consisted of two Kaggle datasets (1 ,2 ).
The initial idea was to use only the first dataset for all of the experiments. However, when trying
to improve the model’s results, I wanted to check whether that could be achieved by training it
on more data. I was able to find a very similar dataset, containing the same kind of images and
classified into the same 4 categories. I then merged the two datasets by combining the images
from each of the four possible classes.
The images have 4 possible classes (meningioma tumor, glioma tumor, pituitary tumor or no tu-
mor), which are the target variables that we want to classify later.
The class distribution shows that the notumor class is slightly misrepresented (16% of the images
have these class), whereas the other three classes appear in 28% of the data each.
Both datasets consist of images containing slices of MRI brain scans of different patients. Ex-
ploratory analysis reveals that the initial dataset contains 3267 images, having different resolutions.
A sample image can be seen below.

Figure 1: Image sample

A further analysis of the resolutions of the images shows that the most common resolution is 512
by 512 pixels, and occurs in 31.17% of all the images. The minimum resolution is 167x167, while
the maximum resolution is 1375x1446. Only 35.64% percent of all the images have a "square"
resolution (width=height).
For contrast analysis, the Michelson contrast was used(3 ). The analysis shows that all images have
a constrast of 1.

3.2 Data preprocessing

An important aspect that we noted in the previous section is that the images have different
resolutions. In order to be able to feed them to a classification network, we need to make sure
that all of them have the same resolution, so the next step consisted of resizing all of the images
to the same width and height.
1 https://www.kaggle.com/datasets/sartajbhuvaji/brain-tumor-classification-mri?resource=download
2 https://www.kaggle.com/datasets/masoudnickparvar/brain-tumor-mri-dataset?resource=download
3 https://www.schorsch.com/en/kbase/glossary/contrast.html

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After analyzing all the resolutions, we choose to resize all the images to 167x167 pixels, which is
the smallest image resolution present in our dataset.
Other steps applied were splitting the data into training, validation and testing (70/10/20) and
rescaling the pixel values between 0 and 1.

3.3 Training and testing classification networks

Several architectures were selected for the classification model: 2 layer CNN, 3 layer CNN and
Resnet50. The lack of computational power that I had to deal with greatly influenced the choice
of networks. The first two were chose since they are very lightweight, don’t have many neuron
layers and therefore don’t need a lot of RAM memory for training. The latter was chosen because
it allows me to perform Transfer Learning (transfering the knowledge obtained by a model from a
dataset to another dataset). Among the more complex Deep Learning networks, it also has fewer
layers of neurons (only 50).
The results of my experiments can be seen below.

Figure 2: Experiment results

The metric chosen for evaluating the performance of the models was accuracy, and below we can
see the accuracy scores for the test data. My goal while carrying out the experiments was to try
and get the highest possible test accuracy. Among the first experiments, we can see the the CNN
with 3 layers performed the best, and this is why I have chosen this network for hyperparameter
optimization and applied it on the expanded dataset, described in the next section.

3.4 Data expansion and hyperparameter optimization

After further research, I was able to find a second dataset, having the same structure, format and
labels as the initial one, but containing around 7000 more images. This more than tripled the
initial number of images.
I merged the two datasets by combining together all the images from each class in a separate
folder and then applied all the steps described above, and additionally some hyperparameter
optimization. The hyperparameters I played around with were:
• learning rate

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 • optimizer
• number of epochs
• number of layers
The best accuracy I obtained was 92.13%.

3.5 Demo web app

To showcase my result and enable people to make use of the classification system I developed,
I created a web app using the Flask Python library4 . It consists of a client part that the user
interacts with, which sends a request a server which runs the selected image on the classification
model and returns the result to the client, which then displays it to the user.
The app allows the user to select an image by its id, run the classification model and see the actual
class of the image, the class predicted by the classifier and the prediction confidence.

Figure 3: Demo app showcase

4 Conclusions
To conclude, while working on this project I combine the knowledge obtained while taking the
Brain Modeling course and the curriculum of my Data Science Master’s. I successfully developed
an AI-based web application that can classify 3 types of brain tumors (or no tumor) with an
accuracy of 92.2%.

References
Cheng, J., Huang, W., Cao, S., Yang, R., Yang, W., Yun, Z. and Feng, Q. (2015), ‘Enhanced
performance of brain tumor classification via tumor region augmentation and partition’, PLoS
ONE 10.
4 https://flask.palletsprojects.com/en/2.2.x/

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Cheng, J., Yang, W., Huang, M., Huang, W., Jiang, J., Zhou, Y., Yang, R., Jie, Z., Feng, Y.,
Feng, Q. and Chen, W. (2016), ‘Retrieval of brain tumors by adaptive spatial pooling and fisher
vector representation’, PLoS ONE 11.
He, K., Zhang, X., Ren, S. and Sun, J. (2015), ‘Deep residual learning for image recognition’.
URL: https://arxiv.org/abs/1512.03385
Pereira, S., Pinto, A., Alves, V. and Silva, C. A. (2016), ‘Brain tumor segmentation using convolu-
tional neural networks in mri images’, IEEE Transactions on Medical Imaging 35(5), 1240–1251.
Siegel, R. (2016), ‘Cancer statistics 2016’, CA: A Cancer Journal for Clinicans, 66.