I am a PhD candidate in Computer Science at Case Western Reserve University, advised by Dr. Rong Xu and Dr. Mehmet Koyutürk. My thesis (anticipated May 2026) is titled Towards Precision Medicine, Personalizing Foundational Semantic Models.
Research
I enjoy working at the intersection of AI and biology. My research explores the parallels between computational processes and biological systems. Some questions I try to exlore:
- How can we adapt population-trained models to individual patient biology for drug repurposing? (NeurIPS AIDrugX ’24, JBI ’24, JBI ’25)
- How can we enable natural language querying of multimodal ML performance data? (GTAC (AMD) ’26)
- How can we better tokenize and visualize genomic data for discovery applications? (ICIBM '25)
- What factors predict treatment response and recidivism risk in intimate partner violence cases? (Psychosocial Intervention, AMIA '23, AMIA '25)
- How can we create better computational tools for transcription factor binding analysis? (Bioinformatics, Scientific Reports, Nature)
News
- 11/2025: AAAI 2026 (Singapore): 2 workshop papers + 2 bridge papers accepted (including one co-authored with my little brother)!
- 11/2025: Honored that our Precision Drug Repurposing (PDR) paper was featured in the AMIA 2025 Year in Review.
- 11/2025: Gave a talk on our interpretable ML for IPV work at the AMIA 2025 Annual Symposium in Atlanta, GA.
- 09/2025: Defended my PhD dissertation proposal.
- 08/2025: Gave a talk at the Oak Ridge National Laboratory (ORNL) AI Initiative on information sharing across multimodal data.
- 08/2025: Presented the Tokenvizz paper at ICIBM 2025 in Columbus, OH.
- 07/2025: Submitted “OmniHub-LAW” to AMD’s GTAC 2026 (internal venue).
- 06/2025: Joined AMD Research & Advanced Development (San Jose, CA) as a summer Research Associate. Thanks to Ashwin Aji for the opportunity.
- 05/2025: Presented research at the AMIA Clinical Informatics Conference (CIC 2025) in Anaheim, CA.
- 04/2023: Our work on disease-aware KG augmentation for semi-inductive reasoning accepted to JBI.
- 04/2025: AMIA 2025 paper on interpretable IPV risk factors accepted.
- 04/2025: Presented polymer glass-transition (Tg) prediction work at PiNO 2025 in Cleveland, OH.
- 12/2024: Presented spotlight work at the NeurIPS 2024 AIDrugX Workshop in Vancouver, Canada.
- 10/2024: Received an ACM-W Grace Hopper Celebration scholarship and attended the conference in Philly, PA.
- 06/2024: Joined Foundation Medicine (Roche) in San Diego, CA as a summer R&D ML Engineer intern. Thanks to Rain Sun for the opportunity.
- 03/2024: Published our first “Precision Drug Repurposing (PDR)” paper in JBI.
- 12/2023: Passed the Ph.D. qualifying exam and advanced to candidacy.
- 12/2023: Presented a Johnson & Johnson collaboration at the Genome Informatics 2023 meeting, Cold Spring Harbor Laboratory.
- 09/2023: Joined the Center for AI in Drug Discovery (CWRU) as a Research Assistant.
- 06/2023: Joined Janssen (Johnson & Johnson) in Philly, PA as a summer R&D ML Scientist intern. Thanks to Alex Javidi for the opportunity.
- 03/2023: Presented an AMIA paper on disparities in IPV treatment in Seattle, WA; received the AMIA LEAD Fund Trainee Scholarship.
- 03/2023: Published three papers on intimate partner violence (IPV).
- 10/2022: Presented our paper on neural method-name generation at IEEE STC.
- 06/2022: Joined the Experimental Drug Development Centre (A*STAR) in Singapore as a summer Computational Biology intern. Thanks to Sun Miao for the opportunity.
- 09/2021: Started a Ph.D. in Computer Science at Case Western Reserve University as a Research Assistant.
- 08/2021: Co-authored a paper in Scientific Reports, Nature.
- 05/2021: Graduated from Bilkent University with honors in Computer Engineering, with a minor in Molecular Biology and Genetics.
- 03/2021: Published my first paper, “MotifGenie,” in Bioinformatics.
- 06/2019: Joined Seven Bridges (Turkey) as a summer R&D intern. Thanks to Duygu Kabakci for the opportunity.
Selected Publications
KGiA: Drug repurposing through disease-aware knowledge graph augmentation — Journal of Biomedical Informatics, 2025.
Precision Drug Repurposing (PDR): Patient-Level Modeling and Prediction combining Foundational Knowledge Graph with Biobank Data — Journal of Biomedical Informatics, 2024.
Leveraging Disease-Specific Topologies and Counterfactual Relationships in Knowledge Graphs for Inductive Reasoning in Drug Repurposing — NeurIPS AIDrugX Workshop (Spotlight), 2024.
Interpretable Machine Learning to Identify Risk Factors for Recidivism in Intimate Partner Violence — AMIA Annual Symposium, 2025.
Tokenvizz: GraphRAG-Inspired Tokenization Tool for Genomic Data Discovery and Visualization — ICIBM, 2025.
Motifgenie: A python application for searching TF binding sequences using ChIP-seq — Bioinformatics, 2021.
A CpG island promoter drives the CXXC5 gene expression — Scientific Reports (Nature), 2021.