Ozan Gökdemir

According to our database, Ozan Gökdemir authored at least 12 papers between 2020 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2026

BioAlchemy: Distilling Biological Literature into Reasoning-Ready Reinforcement Learning Training Data.

Brian Hsu, Ozan Gökdemir, Carlo Siebenschuh, Bruce D. Parrello, Neil Getty, Thomas S. Brettin, Rick L. Stevens, Ian T. Foster, Nicholas Chia, Arvind Ramanathan

CoRR, April, 2026

VILLA: Versatile Information Retrieval From Scientific Literature Using Large LAnguage Models.

Blessy Antony, Amartya Dutta, Sneha Aggarwal, Vasu Gatne, Ozan Gökdemir, Samantha Grimes, Adam Lauring, Brian R. Wasik, Anuj Karpatne, T. M. Murali

CoRR, March, 2026

CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2.

Oleksandra Herasymenko, Madhushika Silva, Galen J. Correy, Abd Al-Aziz A. Abu-Saleh, Suzanne Ackloo, Cheryl H. Arrowsmith, Alan Ashworth, Fuqiang Ban, Hartmut Beck, Kevin P. Bishop, Hugo J. Bohórquez, Albina Bolotokova, Marko Breznik, Irene Chau, Yu Chen, Artem Cherkasov, Wim Dehaen, Dennis Della Corte, Katrin Denzinger, Niklas Piet Doering, Kristina Edfeldt, Aled M. Edwards, Darren Fayne, Francesco Gentile, Elisa Gibson, Ozan Gökdemir, Anders Gunnarsson, Judith Guenther, John J. Irwin, Jan Halborg Jensen, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Ashley Hutchinson, Shubhangi Kandwal, Andrea Karlova, Kushal Koirala, Sergei Kotelnikov, Dima Kozakov, Juyong Lee, Soowon Lee, Uta F. Lessel, Sijie Liu, Xuefeng Liu, Peter Loppnau, Jens Meiler, Rocco Moretti, Yurii S. Moroz, Charuvaka Muvva, Tudor I. Oprea, Brooks Paige, Amit Pandit, Keunwan Park, Gennady Poda, Mykola V. Protopopov, Vera Pütter, Rahul Ravichandran, Didier Rognan, Edina Rosta, Yogesh Sabnis, Thomas Scott, Almagul Seitova, Purshotam Sharma, François Sindt, Minghu Song, Casper Steinmann, Rick Stevens, Valerij Talagayev, Valentyna V. Tararina, Olga O. Tarkhanova, Damon Tingey, John F. Trant, Dakota Treleaven, Alexander Tropsha, W. Patrick Walters, Jude Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Shuangjia Zheng, James S. Fraser, Matthieu Schapira

J. Chem. Inf. Model., 2026

2025

Scalable Agentic Reasoning for Designing Biologics Targeting Intrinsically Disordered Proteins.

Matthew Sinclair, Moeen Meigooni, Archit Vasan, Ozan Gökdemir, Xinran Lian, Heng Ma, Yadu N. Babuji, Alexander Brace, Khalid Hossain, Carlo Siebenschuh, Thomas S. Brettin, Kyle Chard, Christopher S. Henry, Venkatram Vishwanath, Rick L. Stevens, Ian T. Foster, Arvind Ramanathan

CoRR, December, 2025

Self Distillation Fine-Tuning of Protein Language Models Improves Versatility in Protein Design.

Amin Tavakoli, Raswanth Murugan, Ozan Gökdemir, Arvind Ramanathan, Frances H. Arnold, Anima Anandkumar

CoRR, December, 2025

HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights.

Ozan Gökdemir, Carlo Siebenschuh, Alexander Brace, Azton Wells, Brian Hsu, Kyle Hippe, Priyanka Vasanthakumari, Aswathy Ajith, J. Gregory Pauloski, Varuni Katti Sastry, Sam Foreman, Huihuo Zheng, Heng Ma, Bharat Kale, Nicholas Chia, Thomas Gibbs, Michael E. Papka, Thomas S. Brettin, Francis J. Alexander, Anima Anandkumar, Ian T. Foster, Rick Stevens, Venkatram Vishwanath, Arvind Ramanathan

CoRR, May, 2025

Automated MCQA Benchmarking at Scale: Evaluating Reasoning Traces as Retrieval Sources for Domain Adaptation of Small Language Models.

Ozan Gökdemir, Neil Getty, Robert Underwood, Sandeep Madireddy, Franck Cappello, Arvind Ramanathan, Ian T. Foster, Rick L. Stevens

Proceedings of the SC '25 Workshops of the International Conference for High Performance Computing, 2025

HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights.

Ozan Gökdemir, Carlo Siebenschuh, Alexander Brace, Azton Wells, Brian Hsu, Kyle Hippe, Priyanka Setty, Aswathy Ajith, J. Gregory Pauloski, Varuni Sastry, Sam Foreman, Huihuo Zheng, Heng Ma, Bharat Kale, Nicholas Chia, Thomas Gibbs, Michael E. Papka, Thomas S. Brettin, Francis J. Alexander, Anima Anandkumar, Ian T. Foster, Rick Stevens, Venkatram Vishwanath, Arvind Ramanathan

Proceedings of the Platform for Advanced Scientific Computing Conference, 2025

AdaParse: An Adaptive Parallel PDF Parsing and Resource Scaling Engine.

Carlo Siebenschuh, Kyle Hippe, Ozan Gökdemir, Alexander Brace, Arham Mushtaq Khan, Khalid Hossain, Yadu N. Babuji, Nicholas Chia, Venkatram Vishwanath, Arvind Ramanathan, Rick L. Stevens, Ian T. Foster, Robert Underwood

Proceedings of the Eighth Conference on Machine Learning and Systems, 2025

2024

LSHBloom: Memory-efficient, Extreme-scale Document Deduplication.

Arham Khan, Robert Underwood, Carlo Siebenschuh, Yadu N. Babuji, Aswathy Ajith, Kyle Hippe, Ozan Gökdemir, Alexander Brace, Kyle Chard, Ian T. Foster

CoRR, 2024

High Performance Binding Affinity Prediction with a Transformer-Based Surrogate Model.

Archit Vasan, Ozan Gökdemir, Alexander Brace, Arvind Ramanathan, Thomas S. Brettin, Rick Stevens, Venkatram Vishwanath

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2024

2020

An Analysis of Use-Modify-Create Pedagogical Approach's Success in Balancing Structure and Student Agency.

Diana Franklin, Merijke Coenraad, Jennifer Palmer, Donna Eatinger, Anna Zipp, Marco Anaya, Max White, Hoang Pham, Ozan Gökdemir, David Weintrop

Proceedings of the ICER 2020: International Computing Education Research Conference, 2020