Publications 📃

Rıza Özçelik, Laura van Weesep, Sarah de Ruiter, Francesca Grisoni (2025). peptidy: A light-weight Python library for peptide representation in machine learning. peptidy.

Rıza Özçelik, Francesca Grisoni (2024). The Jungle of Generative Drug Discovery: Traps, Treasures, and Ways Out. Jungle.

Rıza Özçelik, Francesca Grisoni (2024). A Hitchhiker's Guide to Deep Chemical Language Processing for Bioactivity Prediction. Hitchhiking.

Rebecca Birolo, Rıza Özçelik, Andrea Aramini, Roberto Gobetto, Michele Remo Chierotti, Francesca Grisoni (2024). Deep Supramolecular Language Processing for Co-crystal Prediction. DeepCocrystal.

Emanuele Crusciolo, Rıza Özçelik, Derek van Tilborg, Francesca Grisoni (2024). The surprising ineffectiveness of molecular dynamics coordinates for predicting bioactivity with machine learning. Ineffective MD.

Rıza Özçelik, Sarah de Ruiter, Emanuele Crusciolo, Francesca Grisoni (2024). Chemical Language Modeling with Structured State Space Sequence Models. S4.

Derek van Tilborg, Helena Brinkman, Emanuele Criscuolo, Luke Rossen, Rıza Özçelik, Francesca Grisoni (2024). Deep learning for low-data drug discovery: hurdles and opportunities. Low-data Review.

Emrah Budur, Rıza Özçelik, Dilara Soylu, Omar Khattab, Tunga Güngör, Christopher Potts (2024). Building Efficient and Effective OpenQA Systems for Low-Resource Languages. squad-tr.

Asu Büşra Temizer, Gökçe Uludoğan. Rıza Özçelik, Taha Koulani, Elif Ozkirimli, Kutlu O. Ulgen, Nilgün Karalı, Arzucan Özgür (2024). Exploring Data‐Driven Chemical SMILES Tokenization Approaches to Identify Key Protein‐Ligand Binding Moieties. Interpreting CW.

Rıza Özçelik, Alperen Bağ, Berk Atıl, Melih Barsbey, Arzucan Özgür, Elif Ozkirimli (2023). A Computational Software for Training Robust Drug-Target Affinity Prediction Models: pydebiaseddta. DebiasedDTA.

Rıza Özçelik, Derek van Tilborg, Jose Jimenez-Luna, Francesca Grisoni (2022). Structure-based Drug Discovery with Deep Learning. SBDD Review.

Rıza Özçelik, Alperen Bağ, Berk Atıl, Melih Barsbey, Arzucan Özgür, Elif Ozkirimli (2021). DebiasedDTA: A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models. DebiasedDTA.

Silvia Multari, Rıza Özçelik, Angelica Mazzolari, Marco Salvatore Nobile, Elif Francesca Grisoni (2020). Predicting Metabolic Reactions with a Molecular Transformer for Drug Design Optimization. Metabolic Reactions.

Rıza Özçelik, Hakime Öztürk, Arzucan Özgür, Elif Ozkirimli (2020). ChemBoost: A chemical language based approach for the prediction of protein - ligand binding affinity. ChemBoost.

PDF Code Poster Slides

Abdullatif Köksal, Hilal Dönmez, Rıza Özçelik, Elif Ozkirimli, Arzucan Özgür (2020). Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature. Vapur.

PDF Code Project

Emrah Budur, Rıza Özçelik, Tunga Güngör, Christopher Potts (2020). Data and Representation for Turkish Natural Language Inference. NLI-TR.

PDF Code Dataset

Rıza Özçelik, Gökçe Uludoğan, Selen Parlar, Özge Bakay, Özlem Ergelen, Olcay Taner Yıldız (2019). User Interface for Turkish Word Network KeNet. KeNet.

Gökçe Uludoğan, Rıza Özçelik, Selen Parlar, Gökhan Ercan, Olcay Taner Yıldız (2019). User Interfaces for Turkish Natural Language Processing. Nlptoolkit.

Gökhan Ercan, Orçun Erkek, Onur Açıkgöz, Rıza Özçelik, Selen Parlar, Olcay Taner Yıldız (2018). Data Set Generation for Analysis of Turkish Semantic and Sentence Similarity. Data Set Generation for Analysis of Turkish Semantic and Sentence Similarity.