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Defne Circi

Ph.D. Student
Duke University
defne.circi@duke.edu


About Me

I am a Ph.D. candidate at Duke University. I am very fortunate to be advised by Prof. Cate Brinson. Prior to starting my PhD, I was an undergraduate student in materials science and computer science at Sabanci University.

Research Interests

I am interested in the application of multimodal large language models (LLMs) in science, with a focus on knowledge extraction, question answering, and reasoning from scientific literature. Currently, I am working on extracting complex information from diverse scientific data sources, including charts, tables, and text, and evaluating LLM performance in these tasks. My goal is to automate the extraction of insights from scientific articles at scale and build comprehensive knowledge graphs and databases to accelerate discoveries in materials science. Additionally, I am interested in applying machine learning to materials property prediction tasks.

If you’re interested in discussing research ideas or just want to chat, please contact me via email!

News

🌟 Life Outside Research When I'm not working on research, you can find me: - 🧗‍♀️ Bouldering at the climbing gym - 🩰 Exploring movement through contact improvisation dance - 🏃‍♀️ Training for a 10-mile race (April 2025) - Follow my progress on Strava! - 🧘‍♀️ Practicing hot yoga

Selected Publications

  1. NAACL
    Evaluating Morphological Compositional Generalization in Large Language Models
    Ismayilzada, M., Circi, D., Saleva J., Sirin, H., Koksal, A., Dhingra, B., Bosselut A., Plas, L, Ataman, D.
    2025 Annual Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics
    PDF Code

  2. Language + Molecules at ACL
    Extracting Materials Science Data from Scientific Tables
    Circi, D., Khalighinejad, G., Chen, A., Dhingra, B., & Brinson, L.
    Language + Molecules Workshop at ACL, 2024
    PDF Code

  3. IMMI
    How Well Do Large Language Models Understand Tables in Materials Science?
    Circi, D., Khalighinejad, G., Chen, A., Dhingra, B., & Brinson, L.
    Integrating Materials and Manufacturing Innovation, 2024
    PDF Code

  4. AI4Materials at NeurIPS
    Retrieval of Synthesis Parameters of Polymer Nanocomposites Using LLMs
    Circi, D., Khalighinejad, G., Badhwar, S., Dhingra, B., & Brinson, L.
    AI4Materials Workshop at NeurIPS, 2023
    PDF

  5. Digital Discovery
    14 Examples of How LLMs Can Transform Materials Science and Chemistry
    Jablonka, K.M., Ai, Q., Al-Feghali, A., Badhwar, S., Bocarsly, J.D., Bran, A.M., Bringuier, S., Brinson, L.C., Choudhary, K., Circi, D., & Cox, S. et al.
    Digital Discovery, 2023
    PDF Code Won first place!

  6. Viruses
    The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense
    Azgari, C., Kilinc, Z., Turhan, B., Circi, D.., & Adebali, O.
    Viruses, 2021
    PDF Code

  7. Turkish Journal of Biology
    Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey
    Adebali, O., Bircan, A., Circi, D., Islek, B., Kilinc, Z., Selcuk, B., & Turhan, B.
    Turkish Journal of Biology, 2020
    PDF Code

Services

Reviewing Roles

Organizer and Volunteer Roles