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ORCIDOzan Gökdemir
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2020 – today
- 2026
[j1]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:
CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2. J. Chem. Inf. Model. 66(3): 1566-1581 (2026)- [c6]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, Daniel Schabacker, Venkatram Vishwanath, Rick Stevens, Ian T. Foster, Arvind Ramanathan:
Scalable Agentic Reasoning for Designing Biologics Targeting Intrinsically Disordered Proteins. PASC 2026: 28:1-28:13 - [i8]Blessy Antony, Amartya Dutta, Sneha Aggarwal, Vasu Gatne, Ozan Gökdemir, Samantha Grimes, Adam Lauring, Brian R. Wasik, Anuj Karpatne, T. M. Murali:
VILLA: Versatile Information Retrieval From Scientific Literature Using Large LAnguage Models. CoRR abs/2603.23849 (2026) - [i7]Brian Hsu, Ozan Gökdemir, Carlo Siebenschuh, Bruce D. Parrello, Neil Getty, Thomas S. Brettin, Rick L. Stevens, Ian T. Foster, Nicholas Chia, Arvind Ramanathan:
BioAlchemy: Distilling Biological Literature into Reasoning-Ready Reinforcement Learning Training Data. CoRR abs/2604.03506 (2026) - 2025
- [c5]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:
AdaParse: An Adaptive Parallel PDF Parsing and Resource Scaling Engine. MLSys 2025 - [c4]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:
HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights. PASC 2025: 1-13 - [c3]Ozan Gökdemir, Neil Getty, Robert Underwood, Sandeep Madireddy, Franck Cappello, Arvind Ramanathan, Ian T. Foster, Rick L. Stevens:
Automated MCQA Benchmarking at Scale: Evaluating Reasoning Traces as Retrieval Sources for Domain Adaptation of Small Language Models. SC Workshops 2025: 545-552 - [i6]Carlo Siebenschuh, Kyle Hippe, Ozan Gökdemir, Alexander Brace, Arham Khan, Khalid Hossain, Yadu N. Babuji, Nicholas Chia, Venkatram Vishwanath, Rick Stevens, Arvind Ramanathan, Ian T. Foster, Robert Underwood:
AdaParse: An Adaptive Parallel PDF Parsing and Resource Scaling Engine. CoRR abs/2505.01435 (2025) - [i5]Ozan Gökdemir, Carlo Siebenschuh, Alexander Brace, Azton Wells, Brian Hsu, Kyle Hippe, Priyanka Vasanthakumari, 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:
HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights. CoRR abs/2505.04846 (2025) - [i4]Ozan Gökdemir, Neil Getty, Robert Underwood, Sandeep Madireddy, Franck Cappello, Arvind Ramanathan, Ian T. Foster, Rick L. Stevens:
Automated MCQA Benchmarking at Scale: Evaluating Reasoning Traces as Retrieval Sources for Domain Adaptation of Small Language Models. CoRR abs/2509.10744 (2025) - [i3]Amin Tavakoli, Raswanth Murugan, Ozan Gökdemir, Arvind Ramanathan, Frances H. Arnold, Anima Anandkumar:
Self Distillation Fine-Tuning of Protein Language Models Improves Versatility in Protein Design. CoRR abs/2512.09329 (2025) - [i2]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:
Scalable Agentic Reasoning for Designing Biologics Targeting Intrinsically Disordered Proteins. CoRR abs/2512.15930 (2025) - 2024
- [c2]Archit Vasan, Ozan Gökdemir, Alexander Brace, Arvind Ramanathan, Thomas S. Brettin, Rick Stevens, Venkatram Vishwanath:
High Performance Binding Affinity Prediction with a Transformer-Based Surrogate Model. IPDPS (Workshops) 2024: 571-580 - [i1]Arham Khan, Robert Underwood, Carlo Siebenschuh, Yadu N. Babuji, Aswathy Ajith, Kyle Hippe, Ozan Gökdemir, Alexander Brace, Kyle Chard, Ian T. Foster:
LSHBloom: Memory-efficient, Extreme-scale Document Deduplication. CoRR abs/2411.04257 (2024) - 2020
- [c1]Diana Franklin, Merijke Coenraad, Jennifer Palmer, Donna Eatinger, Anna Zipp, Marco Anaya, Max White, Hoang Pham, Ozan Gökdemir, David Weintrop:
An Analysis of Use-Modify-Create Pedagogical Approach's Success in Balancing Structure and Student Agency. ICER 2020: 14-24
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