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Teuku Rizky Noviandy
Interdisciplinary Innovation Research Unit, Graha Primera Saintifika, Aceh Besar 23771, Indonesia
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Journal : Grimsa Journal of Science Engineering and Technology

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Fine-Tuning ChemBERTa for Predicting Activity of AXL Kinase Inhibitors in Oncogenic Target Modeling Noviandy, Teuku Rizky; Idroes, Ghazi Mauer; Patwekar, Mohsina; Idroes, Rinaldi
Grimsa Journal of Science Engineering and Technology Vol. 3 No. 2 (2025): October 2025
Publisher : Graha Primera Saintifika

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.61975/gjset.v3i2.98

Abstract

The development of selective kinase inhibitors remains a key objective in cancer drug discovery, where predictive computational models can significantly accelerate the identification of leads. In this study, we investigate the fine-tuning strategies of the transformer-based ChemBERTa model for quantitative structure–activity relationship (QSAR) modeling of AXL receptor tyrosine kinase inhibitors, an important therapeutic target implicated in tumor progression and metastasis. A dataset of AXL inhibitors was curated from the ChEMBL database. Three fine-tuning configurations, namely baseline, full fine-tune, and aggressive, were implemented to examine the influence of learning rate, weight decay, and the number of frozen transformer layers on model performance. Models were evaluated using accuracy, precision, recall, F1-score, and calibration metrics. Results showed that both the full fine-tune and aggressive configurations outperformed the baseline model, achieving higher precision and F1-scores while maintaining robust recall. The aggressive configuration achieved the most balanced performance, with improved calibration and the lowest expected calibration error, indicating reliable probabilistic predictions. Overall, this study highlights that controlled fine-tuning of ChemBERTa significantly enhances predictive performance and confidence estimation in QSAR modeling, offering valuable insights for optimizing transformer-based chemical language models in kinase-targeted drug discovery.
Co-Authors Abas, Abdul Hawil Abd Rahman, Sunarti Abrar , Tajul Adi Purnawarman, Adi Afidh, Razief Perucha Fauzie Afjal, Mohd Ahmad Watsiq Maula Ahmad, Noor Atinah Ahsya, Yahdina Alfharijy, Muhammad Daffa Amalina, Faizah Amirah, Kelsy Amri Amin Anisah Aprianto . Apriliansyah, Feby Asep Rusyana Azhar, Fauzul Azzuhry , Haikal Baehaqi Bahri, Ridzky Aulia BAKRI, TEDY KURNIAWAN Dahlawy, Arriz Dharma, Aditia Dian Handayani Dian Lestari, Nova Dimas Chaerul Ekty Saputra Earlia, Nanda Effendy, Amalia Eko Suhartono El-Shazly, Mohamed Emran, Talha Bin Enitan, Seyi Samson Erkata Yandri Essy Harnelly Faisal, Farassa Rani Fajri, Irfan Fatani, Muhammad Fauzi, Fazlin Mohd Furqan, Nurul Ghazi Mauer Idroes Hafizah, Iffah Hardia, Natasha Athira Keisha Hewindati, Yuni Tri Hidayatullah, Ferdy Hizir Sofyan Husdayanti, Noviana Idroes, Ghalieb Mutig Idroes, Ghifari Maulana Iin Shabrina Hilal Imelda, Eva Imran Imran Irma Sari Irsan Hardi Irvanizam, Irvanizam Isa, Illyas Md Isra Firmansyah, Isra Kadri, Mirzatul Khairan Khairan Khairul, Mhd Khairul, Moh Khairun Nisa Kruba, Rumaisa Kurniadinur, Kurniadinur Kusumo, Fitranto Lala, Andi Lindawati Lindawati Maimun Syukri, Maimun Mardalena, Selvi Maria Paristiowati Marwan Marwan Maulana, Aga Maulydia, Nur Balqis Misbullah, Alim Mohamed Yusof, Nur Intan Saidaah Mohd Fauzi, Fazlin Muhammad Adam, Muhammad Muhammad Faisal Muhammad Subianto Muhammad Yanis Muhammad Yusuf Muhtadin Muhtadin Mukhlisuddin Ilyas Muksalmina Muksalmina Muliadi Mursyida, Waliam Muslem Muslem, Muslem Mutaqin, Raihan Nainggolan, Sarah Ika Niode, Nurdjannah Jane Nizamuddin Nizamuddin Nurleila, Nurleila Patwekar, Faheem Patwekar, Mohsina Rahmawati, Cut Raihan Raihan, Raihan Ramadeska, Siti Raudhatul Jannah Ray, Samrat Razief Perucha Fauzie Afidh Rinaldi Idroes Ringga, Edi Saputra Rizkia, Tatsa Ryan Setiawan Safhadi, Aulia Al-Jihad Sasmita, Novi Reandy Satrio, Justinus Sofyan, Rahmi Solly Aryza Souvia Rahimah Sufri, Rahmat sufriani, sufriani Sugara, Dimas Rendy Suhendra , Rivansyah Suhendra, Rivansyah Suhendrayatna Suhendrayatna Suryadi Suryadi Syahyana, Ahmad Taufiq Karma Teuku Zulfikar TRINA EKAWATI TALLEI Utami, Resty Tamara Zahriah, Zahriah Zhilalmuhana, Teuku Zuchra Helwani, Zuchra Zulkarnain Jalil Zurnila Marli Kesuma