About

I am a researcher working at the intersection of artificial intelligence, scientific reasoning, and biomedical natural language processing. My research explores how AI can support scientific understanding by extracting, structuring, and interpreting evidence, representing uncertainty, and making computational reasoning more transparent.

I focus on explainable, uncertainty-aware, and human-centered AI approaches that enable researchers to critically examine machine-generated outputs rather than simply rely on predictions. My work spans public health, biomedicine, and genomics, with a particular interest in evidence-based reasoning and knowledge discovery.

I am currently a postdoctoral researcher in the Phylogenomics Group at the Robert Koch Institute’s Centre for Artificial Intelligence in Public Health Research (ZKI-PH). Previously, I worked in the Visualization Group at ZKI-PH, where I also served as Deputy Research Group Leader.

Before joining the Robert Koch Institute, I was a postdoctoral researcher in the Language Technology Group at the University of Hamburg and an assistant professor at Istanbul Kültür University. I received my PhD in Computer Engineering from Istanbul Technical University.

Selected Publications

• İlgen, B., Shahid, A., & Kühnert, D. (2026). Interpretable Flavivirus Classification under Low-Coverage Conditions via ERF-Aware k-mer Attribution. EXPLIMED 2026 (IJCAI-ECAI Workshop).
• İlgen, B., Awotoro, E., & Hattab, G. (2026). VaxScope: Document-Level Structured Evidence Extraction from Immunization Systematic Reviews. BioNLP 2026 (ACL).
• Dubey, A., Anžel, A., İlgen, B., & Hattab, G. (2026). UbiQTree: Uncertainty Quantification in XAI with Tree Ensembles. Patterns.
• İlgen, B., & Hattab, G. (2026). Visualizing the Chain of Thought in Large Language Models. IEEE Computer Graphics and Applications.
• Köckritz, J., İlgen, B., Cohrdes, C., & Hattab, G. (2025). Current Applications and Future Directions in Natural Language Processing for News Media and Mental Health. Scientific Reports.

All publications →

Research

My research develops AI methods that help researchers extract and structure scientific evidence, quantify uncertainty, and critically examine computational results and their underlying explanations. Rather than treating model outputs as final answers, I investigate how evidence-grounded, explainable, and human-centered approaches can support scientific understanding. This work brings together three complementary research directions.

Scientific Evidence and AI-Assisted Reasoning

I develop computational methods for extracting, structuring, and interpreting scientific evidence, with a focus on biomedical literature and systematic reviews. My work explores how natural language processing, structured evidence representations, and interactive tools can support evidence synthesis, scientific reasoning, and the critical examination of research findings.

Explainability, Uncertainty, and Human-Centered AI

I investigate how AI systems can make their outputs more interpretable and their limitations more transparent. My research combines explainable AI, uncertainty quantification, and human-centered approaches to examine how explanations and uncertainty estimates can help researchers critically evaluate model outputs and AI-assisted reasoning.

Reliable AI for Biomedical and Genomic Applications

I study the reliability and robustness of machine learning methods applied to biomedical and genomic data. My work examines model behavior and generalization under limited or incomplete data, with particular attention to identifying genomic features and patterns that contribute to model predictions.

Research Interests

• Natural Language Processing
• Explainable and Interpretable Artificial Intelligence
• Uncertainty Quantification and Reliable AI
• Scientific Evidence Extraction and Computational Argumentation
• Human-Centered AI and Visualization
• Biomedical NLP and Computational Genomics

Academic Experience

• Robert Koch Institute, Germany
  Centre for Artificial Intelligence in Public Health Research (ZKI-PH)
  Postdoctoral Researcher (2023–Present)
  Deputy Research Group Leader, Visualization Group (04/2024–03/2026)
• University of Hamburg, Germany
  Postdoctoral Researcher, Language Technology Group (2021–2022)
• Istanbul Kültür University, Türkiye
  Assistant Professor, Department of Computer Engineering (2016–2021)

Research Leadership & Supervision

My experience includes serving as Deputy Research Group Leader at the Robert Koch Institute, co-supervising doctoral students, and supervising undergraduate and master’s students. I have also contributed to interdisciplinary research projects and funding proposals in biomedical and public health AI.

Teaching

Istanbul Kültür University

Assistant Professor, Department of Computer Engineering

Courses taught included:

• Programming Fundamentals & Object-Oriented Design
• Data Structures & Algorithms
• Machine Learning
• Data Mining
• Discrete Structures

Supervised undergraduate and graduate student projects in AI and software systems.

International Teaching Mobility

• Università degli Studi di Milano (2018) — Intelligent Systems
• Dennis Gabor College (2017) — Object-Oriented Software Development

Earlier Teaching Experience

Research & Teaching Assistant positions at Istanbul Kültür University and Izmir University of Economics (2005–2016), contributing to teaching in AI, programming, algorithms, operating systems, and computer organization.