DebiasedDTA: Model Debiasing to Boost Drug-Target Affinity Prediction. - Riza Özçelik; Alperen Bag; Berk Atil; Arzucan Özgür; Elif Özkirimli 001 (CoRR, 2021)

Prediction of new outlinks for focused Web crawling. - Thi Kim Nhung Dang; Doina Bucur; Berk Atil; Guillaume Pitel; Frank Ruis; Hamid Reza Kadkhodaei; Nelly Litvak (CoRR, 2021)

Look back, look around: A systematic analysis of effective predictors for new outlinks in focused Web crawling. - Thi Kim Nhung Dang; Doina Bucur; Berk Atil; Guillaume Pitel; Frank Ruis; Hamid Reza Kadkhodaei; Nelly Litvak (Knowl. Based Syst., 2023)

A Computational Software for Training Robust Drug-Target Affinity Prediction Models: pydebiaseddta. - Melih Barsbey; Riza Özçelik; Alperen Bag; Berk Atil; Arzucan Özgür; Elif Ozkirimli 001 (J. Comput. Biol., 2023)

A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models. - Riza Özçelik; Alperen Bag; Berk Atil; Melih Barsbey; Arzucan Özgür; Elif Ozkirimli 001 (J. Comput. Biol., 2023)

VerAs: Verify Then Assess STEM Lab Reports. - Berk Atil; Mahsa Sheikhi Karizaki; Rebecca J. Passonneau (AIED (1), 2024)

LLM Stability: A detailed analysis with some surprises. - Berk Atil; Alexa Chittams; Liseng Fu; Ferhan Ture; Lixinyu Xu; Breck Baldwin (CoRR, 2024)

Can LLMs Rank the Harmfulness of Smaller LLMs? We are Not There Yet. - Berk Atil; Vipul Gupta; Sarkar Snigdha Sarathi Das; Rebecca J. Passonneau (CoRR, 2025)

Something Just Like TRuST : Toxicity Recognition of Span and Target. - Berk Atil; Namrata Sureddy; Rebecca J. Passonneau (CoRR, 2025)