Rıza Özçelik

Ph.D. Candidate

Dept. of Biomedical Engineering, Eindhoven University of Technology

Hello, visitor!

I am Rıza! I am a lively Ph.D. candidate happy to be supervised by Francesca Grisoni 👩‍🔬 at the Molecular Machine Learning Group in Eindhoven University of Technology. I also hold high honor BSc. and MSc. degrees from the Dept. of Computer Engineering in Boğaziçi University, where I was lucky to work with Arzucan Özgür and Elif Özkırımlı👩‍🔬👩‍🔬.

Want to meet? Or just say something? Find me here!

Interests

Computational Drug Discovery
Generative Deep Learning
Natural Language Processing

Education

Ph.D. in Biomedical Engineering
Thesis: Advancing Chemical Language Models for De Novo Drug Design. Eindhoven University of Technology.
MSc. in Computer Engineering, 2022
GPA: 3.94/4.00. Thesis: Biomolecular Language Processing for Drug - Target Affinity Prediction.
BSc. in Computer Engineering, 2018
GPA: 3.57/4.00. Thesis: Disease Classification based on Genomic Data with Machine Learning.

Employment 👨‍🔬

Great Minds Research Intern

IBM Research

June 2021 – November 2021 Zurich, Switzerland

Discovering new research fields and environments is a joy for me. For 6 months, I worked on IBM’s AppConnect platform, to map natural text inputs to application flows. My research empowered a type-ahead component to hint users while typing, which was backed by a knowledge graph 🧠

Research Assistant

Dept. of Computer Engineering, Boğaziçi University

July 2019 – February 2022 İstanbul, Turkey

I make my living by processing the language; let it be natural, scientific, or biomolecular. During my time as a research assistant, I led and participated in research studies on computational drug discovery 💊, Turkish natural language processing 🇹🇷, and biological text mining 🧬. Our research resulted in novel machine learning approaches for binding affinity-prediction, first large-scale Turkish Natural Language Inference data sets and representations, and an online search engine for Coronavirus researchers. The linked publications are available below.

Teaching Assistant

Dept. of Computer Engineering, Boğaziçi University

July 2019 – October 2021 İstanbul, Turkey

I love sharing! And what is better your scientific knowledge to share? So I became a teaching assistant for an incredible audience: curious bachelor students. I instructed problem sessions, created assignments, and guided senior projects as a teaching assistant 👨‍🏫. I always made learning fun and interactive and devised themed projects (such as helping Katniss Everdeen 🔥) and scheduled additional sessions to interact with students as much as I can. I am happy that students appreciated my efforts with their feedback: ‘It is clear that you love and devote yourself to teaching’, ‘You are unexpectedly supportive, helpful and caring’, and ‘‘You are the best TA I have ever known! 😎😎

Publications

peptidy: A light-weight Python library for peptide representation in machine learning

We present a python library to encode peptides for machine learning applications. Non-canonical amino acids and post-translational modifications are supported.

Rıza Özçelik, Laura van Weesep, Sarah de Ruiter, Francesca Grisoni

PDF Code DOI