INDUSTRIAL ENGINEERING DEPARTMENT

IE 49M
Special Studies in Network Extraction and Analysis
Fall 2022

Type: IE elective
Credits/ECTS: 3 Credits / 6 ECTS (Letter Grade)
Class/Laboratory/PS: MWW / 323 Regular class
Place: TBA
Instructor: Tınaz Ekim (tinaz.ekim@boun.edu.tr)
Office Hours: TBA
Assistant: None
Prerequisite(s): Experience in image processing tools, good programming
skills, and consent of the instructor

Course Description:

This course is designed for students who have prior knowledge and experience in network
extraction methods using open source tools. The aim is to extract network representations of
blood vessels and to conduct a systematic study of their structure from a graph theoretical
perspective to enlighten several diseases including cancer. We hypothesize that there are
statistically meaningful differences between healthy and pathological tissues’ vascular
networks in terms of graph-theoretical parameters. This novel approach, proposed in
Vilanova et al (2017), has the potential to provide quantitative validation for the medical
expertise and imply high clinical applicability. However, it has not been fully explored yet.
This study will be conducted with the help of Assoc. Prof. Esin Öztürk Işık from the Institute
of Biomedical Engineering, Boğaziçi University.

Reference:

Vilanova, G., Colominas, I. & Gomez, H. Computational Modeling of Tumor-Induced

Angiogenesis. Arch Computat Methods Eng 24, 1071–1102 (2017).
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., … Cardona,
A. 2012. "Fiji: an open-source platform for biological-image analysis." Nature Methods 676–682.
Steps of the study:
1. Exploring Image Processing tools such as NEFI (http://nefi.mpi-inf.mpg.de ), ImageJ
(https://imagej.net/Welcome.), Fiji and Angiogenesis Analyzer.
2. Literature review on graph network approaches for brain and kidney diseases.
3. Meet up with clinicians
4. Applications for ethical approvals
5. Data gathering - kidney images from Koc University Hospital (Dr. Tarık Esen, Dr. Metin
Vural - Urology) and brain images from Acibadem Hospital (Dr. Alp Dinçer - Radiology)
6. Network extraction from biomedical images
7. Preprocessing and cleaning of the obtained networks
8. Choosing relevant graph parameters to distinguish vascular networks extracted from
healthy and pathological tissues
9. Computing relatively simple graph parameters such as number of cycles per vertex, the
average length of cycles, maximum/average degree, density, etc. using network packages
10. Developing practical and efficient algorithms to compute more sophisticated parameters
such as treewidth, minimum feedback vertex set, etc.
11. Algorithm implementation and experiments
12. Submission of the results to conferences and paper writing

Grading:

 10% - Applying for 2209 TÜBİTAK student research grant

https://www.tubitak.gov.tr/tr/burslar/lisans/burs-programlari/icerik-2209-a-universite-
ogrencileri-arastirma-projeleri-destekleme-programi

 15% - Submitting an abstract on the results about brain vascular networks to the Annual
Meeting ISMRM, 03-08 June 2023, Toronto
https://www.ismrm.org/meetings-workshops/future-ismrm-meetings/ . Abstract submission
deadline: November 2022

 15% - Submitting an abstract on the results about kidney vascular networks to SİU 2023
(IEEE Sinyal İşleme ve İletişim Uygulamaları Kurultayı 2023), May 2023, Turkey.
Expected submission deadline February 2023 https://siu2022.bau.edu.tr/tr/default.asp

 10% - Applying for 2224A and 2224B TÜBİTAK conference participation support
https://www.tubitak.gov.tr/tr/destekler/bilimsel-etkinlik/etkinliklere-katilma-
destekleri#destekler_bilimsel_etkinlik_ana_sayfa_akordiyon-block_1-1

 25% - Writing up a journal paper on the results about brain vascular networks

 25% - Writing up a journal paper on the results about kidney vascular networks