Teaching

UNIVERSITY OF COLOGNE

  • Data Driven Medicine (DDM):
    ♦  Theoretical background and origins: 2021-2022 (SS)
    ♦  Hands-on implementation with KNIME: 2021-2022 (SS)
    ♦  Introducton to Medical Data Science: 2022-2023 (WS)
    ♦  Teaching machines how to make a decision: Supervised Machine Learning: 2022-2023 (WS)
    ♦  How machines can self learn: Unsupervised Machine Learning: 2022-2023 (WS)
    ♦  Diagnosing AI algorithms: Visualisation and Evaluation: 2022-2023 (WS)
  • Data Analytics with Python for Medical Doctors: 2022-2023 (WS)
  • AI Ethics (AIE): 2021-2022 (SS), 2022-2023 (WS)
  • MedTech, medical technology-based entrepreneurship and innovation: 2021-2022 (SS), 2022-2023 (WS)
  • Semantic Interoperability (SI): 2021-2022 (SS)
  • Semantic Interoperability in Health: 2022-2023 (WS)
  • Medical Image Processing: 2022-2023 (WS)

RWTH AACHEN UNIVERSITY

  • Data Driven Medicine (Lecture): 2017 (SS), 2017-2018 (WS), 2018-2019 (WS), 2020-2021 (WS)
  • Big Data in Medical Informatics (Lecture): 2016-2017 (WS)
  • Knowledge Graphs Praktikum (Practical Course): 2018 (SS), 2019 (SS), 2020-2021 (WS)
  • Methods for Data Reusability (Seminar): 2018-2019 (WS), 2019-2020 (WS), 2020-2021 (WS)
  • Big Data in Personalized Medicine (Seminar): 2016 (SS), 2016-2017 (WS), 2017 (SS), 2017-2018 (WS)
  • Research Data Management (Seminar): 2017 (SS)
  • Linked Data (Seminar): 2015-2016 (WS), 2016 (SS), 2016-2017 (WS), 2017 (SS)

ATILIM UNIVERSITY (TÜRKİYE)

  • COMPE 111- Introduction to Computer Engineering: 2011-2012 (1)
  • SE 112- Introduction to Software Engineering: 2011-2012 (2)
  • SE 322- Software Design and Architecture: 2011-2012 (2)
  • COMPE 343- Database Systems and Programming: 2011-2012 (3)
  • COMPE 491- Senior Project: 2011-2012 (1), 2011-2012 (2)

MIDDLE EAST TECHNICAL UNIVERSITY-METU (TÜRKİYE)

  • IS 503- Database Concepts and Applications: 2010-2011 (2)
  • IS 580- Knowledge Representation and Data Mining: 2009-2010 (1), 2010-2011 (1)
  • MIN 502- Introduction to Medical Informatics: 2008-2009 (2), 2009-2010 (2)
  • IS 100- Introduction to Information Technologies and Applications: 2000 through 2003

RUNNING THESES:

Generative Deep Learning Modeling for Medical Image Transformation Application in Federated Learning Framework. (Feifei Li; Supervisor: Prof. Dr. Oya Deniz Beyan) (Ph.D. Thesis) 

Classification of CUP Patients with Retrospective Data Analyzed by Using Machine Learning. (Devina Johanna Soenarto; Supervisor: Prof. Dr. Oya Deniz Beyan) (Doctoral Studies)

Modeling an AI-enabled Crowdsourcing Platform for Rare Diseases. How to Extend Clinic-Integrated Crowdsourcing Systems with AI & Machine Learning Approaches to Support Better Diagnosis with Rare Diseases. (Adam Graefe; Supervisor: Prof. Dr. Oya Deniz Beyan) (Doctoral Studies)

FINISHED THESES:

Bridging the gap between design and deployment of statistical analyses in Distributed Analytics. (Completed by Sven Weber in 2022; Supervised by Prof. Dr. Stefan Decker, Prof. Dr. Oya Deniz Beyan) (Bachelor Thesis)

Design and Evaluation of a Federated Machine Learning Model on Vertically Partitioned Data. (Completed by Mehrshad Jaberansary in 2022; Supervised by Prof. Dr. Stefan Decker, Prof. Dr. Oya Deniz Beyan) (Master’s Thesis)

Fostering interoperability of unstructured radiology reports by designing and implementing an annotation guideline in oncology. (Completed by Matthias Thelen in 2022; Supervised by Prof. Dr. Stefan Decker, Prof. Dr. Oya Deniz Beyan) (Master’s Thesis)

Current state, challenges and recommendations for the use of data science and implementation of digital processes in psychiatry. (Completed by Tanja Veselinović in 2022; Supervised by Prof. Dr. Irene Neuner, Prof. Dr. Oya Deniz Beyan) (Master’s Thesis)

Designing a Data Access and Integration Workflow for Medical Data Science: A Use Case of Compilling a Reusable Data Set for Primary Tumor Discovery at MeDIC Cologne. (Completed by Julia Gehrmann in 2022; Supervised by Prof. Dr. Stefan Decker, Prof. Dr. Oya Deniz Beyan) (Master’s Thesis)

Methods to Improve Decentralised Incremental Learning (Completed by Madhavi Jouhari in 2021; Supervised by Prof. Dr. Stefan Decker, Prof. Dr. Markus Strohmaier; Advisors: Dr. Oya Deniz Beyan, Sascha Welten, Yongli Mou, Yeliz Ucer Yediel) (Master’s Thesis)

An ethics guideline for data scientists, Developing an executable guide for responsible data science (Completed by Dinh An Ho in 2020; Supervised by Prof. Dr. Stefan Decker, Prof. Dr. Markus Strohmaier; Advisor: Dr. Oya Deniz Beyan) (Master’s Thesis)

A Framework for Visual Configuration of Application-specific Presentation Views on Standardized Reference Master Data (Completed by Kevin Koopmann in 2020; Supervised by Prof. Dr. Stefan Decker; Advisors: Dr. Oya Deniz Beyan, Dr. Heiner Oberkampf, Jan Winkelmann) (Bachelor Thesis)

A Meta-Data Description for a Distributed Analytics Platform (Completed by Laurenz Neumann in 2020; Supervised by Prof. Dr. Stefan Decker, Prof. Dr. Markus Strohmaier; Advisors: Dr. Oya Deniz Beyan, Sascha Welten, Yeliz Ucer Yediel) (Bachelor Thesis)

Developing Data Quality Metrics for Power System Modeling (Completed by Merlin Bögershausen in 2020; Supervised by Prof. Dr. Stefan Decker, Prof. Dr. Bernhard Rumpe; Advisors: Dr. Oya Deniz Beyan, Dr. Christoph Lange-Bever, Dr. Oliver Scheufeld) (Bachelor Thesis)

FAIR Identifier Registry for Distributed Systems (Completed by Oleksandr Snizhko in 2019; Supervised by Prof. Dr. Stefan Decker; Advisors: Dr. Oya Deniz Beyan, Dr. Heiner Oberkampf, Jan Winkelmann) (Master’s Thesis)

Towards Automating Graph Data Cleansing Using Shapes (Completed by Erhard Eibl in 2019; Supervised by Prof. Dr. Stefan Decker; Advisors: Dr. Oya Deniz Beyan, Dr. Heiner Oberkampf, Jan Winkelmann) (Bachelor Thesis)

Classification of Cancer with Methylation Aware Motifs (Completed by Julia Gehrmann in 2019; Supervised by Prof. Dr. Stefan Decker, Prof. Dr. Ivan Gesteira Costa Filho; Advisors: Dr. Oya Deniz Beyan, Md. Rezaul Karim, M.Sc.) (Bachelor Thesis)

An Explainable and Fully Automated Localization and Semantic Segmentation Technique for Biomedical Imaging (Completed by Nazmi Shafin in 2019; Supervised by Prof. Dr. Stefan Decker; Advisors: Dr. Oya Deniz Beyan, Md. Rezaul Karim, M.Sc.) (Master’s Thesis)

Semantic Anomaly Detection in Medical Time Series (Completed by Sven Festag in 2019; Supervised by Prof. Dr. Stefan Decker, Dr. rer. nat. Cord Spreckelsen; Advisor: Dr. Oya Deniz Beyan) (Master’s Thesis)

Deep Learning-based Knee Osteoarthritis Diagnosis from Radiographs and Magnetic Resonance Images (Completed by Jiao Jiao  in 2019; Supervised by Prof. Dr. Stefan Decker; Advisors: Dr. Oya Deniz Beyan, Dr. Michael Cochez, Md. Rezaul Karim, M.Sc.) (Master’s Thesis)

Developing a machine-actionable process model for ethical approval workflows (Completed by Verena Schwaiger in 2019; Supervised by Prof. Dr. Stefan Decker; Advisor: Dr. Oya Deniz Beyan) (Master’s Thesis)

Unsupervised Anomaly Detection in Medical Time Series Data (Completed by Tobias Brockhoff in 2019; Supervised by Prof. Dr. Stefan Decker; Advisor: Dr. Oya Deniz Beyan) (Master’s Thesis)

Patterns zur Integration regel- und prozessbasierter Modellkomponenten bei der Operationalisierung klinischer Leitlinien. (Completed by  Florian Lammers in 2019; Supervised by Prof. Dr. Stefan Decker, Dr. rer. nat. Cord Spreckelsen; Advisor: Dr. Oya Deniz Beyan) (Master’s Thesis)

Arden Syntax in Use of Data Analysis Pipelines – Development of a DSL Based on the Arden Syntax, supporting recruitment for clinical trails (Completed by Felix Michael Fuchs in 2019; Supervised by Prof. Dr. Stefan Decker, Dr. rer. nat. Cord Spreckelsen; Advisor: Dr. Oya Deniz Beyan) (Bachelor Thesis)

Design and Implementation of an adaptable visual query tool for graph based health data (Completed by Maximilian Orth in 2019; Supervised by Prof. Dr. Stefan Decker; Advisor: Dr. Oya Deniz Beyan) (Master’s Thesis)

Implementation of Clinical Decision Support Services to Detect Drug Interactions using Clinical Quality Language (Completed by Binh-Phi Nguyen in 2019; Supervised by Prof. Dr. Stefan Decker; Advisor(s): Dr. Oya Deniz Beyan, Md. Rezaul Karim, M.Sc.) (Master’s Thesis)

Using Deep Neural Networks and Copy Number Variations for Cancer Detection (Completed by Md. Ashiqur Rahman in 2018; Supervised by Prof. Dr. Stefan Decker; Advisors: Dr. Oya Deniz Beyan, Md. Rezaul Karim, M.Sc.) (Master’s Thesis)

Semantic Data Profiling in Data Lake (Completed by Jasim Waheed Ansari in 2018; Supervised by Prof. Dr. Stefan Decker; Advisors: Dr. Oya Deniz Beyan, Naila Karim, Dr. Michael Cochez) (Master’s Thesis)

Analysis of Breast Cancer Genomic Data with Multimodal Deep Belief Network (Completed by Galih Gilang Wicaksono in 2018; Supervised by Prof. Dr. Stefan Decker; Advisors: Dr. Oya Deniz Beyan, Md. Rezaul Karim, M.Sc.) (Master’s Thesis)

Smart Quality Check for FHIR Resources System (Completed by Hareem Mughis in 2017; Supervised by Prof. Dr. Stefan Decker; Advisor: Dr. Oya Deniz Beyan) (Master’s Thesis)

The Design and Implementation of an Integrated Care Plan Application for Chronic Patients with the FHIR Standard (Completed by Maren Grüter in 2017; Supervised by Prof. Dr. Stefan Decker; Advisor: Dr. Oya Deniz Beyan) (Bachelor Thesis)

Development and Optimization of a STOPP/START Rule Base to Identify Potential Adverse Drug Reactions in Polypharmacy Cases (Completed by Jonas W. Könning in 2017; Supervised by Prof. Dr. Stefan Decker; Advisor: Dr. Oya Deniz Beyan) (Bachelor Thesis)

CONTRIBUTION TO STANDARDIZATION ACTIVITIES:

World Wide Web Consortium (W3C). A Minimum Representation of Potential Drug-Drug Interaction Knowledge and Evidence – Technical and User-centered Foundation. Final Community Group Report

HL7 FHIR. Potential Drug-Drug Interaction (PDDI) CDS IG R1/STU.

PROGRAM COORDINATION:

Sağlık Bilgi Sistemleri (SBS) Sertifika Programı (Healthcare Information Systems Certification Program), Middle East Technical University (METU) (in Turkish)

ION Informatics Online Master Program, Middle East Technical University (METU)

CURRICULUM & COURSE DEVELOPMENT:

Data Driven Medicine, RWHT Aachen University

Sağlık Bilgi Sistemleri (SBS) Sertifika Programı (Healthcare Information Systems Certification Program), Middle East Technical University (METU) (in Turkish)

Introduction to Information Technologies and Applications, Middle East Technical University (METU)