Hi! I am Nuriye Özlem ÖZCAN ŞİMŞEK.

I am a Ph.D. graduate from Computer Engineering at Boğaziçi University, 2024. My thesis title is “Genomic Data Analysis using Machine Learning Methods For Disease and Disease-Gene Prediction”. My thesis advisors are Prof. Fikret Gürgen and Prof. Arzucan Özgür. The aim of my thesis was to detect genomic diseases based on gene mutations and detect novel gene-disease associations. I applied and compared term weighting methods from information retrieval domain to weight the effects of gene mutations on disease development. I proposed a neural network architecture for disease classification based on weighted mutations and an explainer method for this neural network (before the release of explainer modules like GNNExplainer). With the proposed explainer method, I identified the most effective genes in disease prediction. When I searched these genes in the literature, I found that nearly half of them have been published as drivr or target genes for the related diseases. Then, I transfered these most effective gene knowledge to gene expression domain and proposed a novel and disease specific gene selection method. I compared the proposed gene selection method with similar computational and manually curated disease related gene sets for the task of disease prediction. The results showed that the proposed method achieved similar and better classification performance. Finally, I proposed a heterogeneous graph structure for representing the gene mutations and protein interactions together. Proteins have important roles in most cell functions and therefore are related to disease development. In this novel graph structure, I ensembled the effects of mutations and protein interactions to detect diseases. The test results show that the proposed graph structure leads to significantly better disease prediction. I published the results of my thesis studies in SCIE indexed journals.

During my PhD studies, I worked as a teaching assistant at The Department of Computer Engineering at Boğaziçi University, 2017-2022. Then, I worked as a research assistant at The Department of Computer Engineering at Boğaziçi University, 2022-2024.

I received my M.S. degree from Systems and Control Engineering at Boğaziçi University, 2010. My thesis title is “A Fuzzy Support Vector Machine Approach For ECG Analysis”. My thesis advisors is Prof. Fikret Gürgen.

I received my B.S. degree from Computer Engineering at Middle East Technical University, 2005.