I recently defended my PhD in Computer Science at Case Western Reserve University, advised by Dr. Rong Xu and Dr. Mehmet Koyutürk. My thesis 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
- 1/2026: I defended my PhD dissertation, Towards Precision Medicine: Personalizing Foundational Semantic Models!
- 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.