Rıza Özçelik

Rıza Özçelik

Research & Teaching Assistant

Dept. of Computer Engineering of Boğaziçi University

Biography

I am a research/teaching assistant and MSc student at the Dept. of Computer Engineering in Boğaziçi University, Istanbul, where I also hold a high-honor BSc degree 🎓. I conduct research on natural language processing and cheminformatics as a member of TabiLab, under the supervision of Arzucan Özgür and Elif Özkırımlı.👩‍🔬👩‍🔬

Besides research and teaching, I pen blogs in order to convey complex machine learning approaches accessibly. Join me!

Interests

  • Machine Learning
  • Natural Language Processing
  • Cheminformatics
  • Computational Drug Discovery

Education

  • MSc. in Computer Engineering, 2018 --

    GPA: 3.94/4.00. Thesis: Drug-only Representations for Drug - Target Affinity Prediction. Boğaziçi University.

  • BSc in Computer Engineering, 2013 -- 2018

    GPA: 3.57/4.00. Thesis: Disease Classification based on Genomic Data with Machine Learning. Boğaziçi University.

Employment 👨‍🔬

 
 
 
 
 

Research Assistant

Dept. of Computer Engineering, Boğaziçi University

July 2019 – Present İstanbul, Turkey
I have been leading and participating in research studies on machine learning for 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 data sets and representations, and an online search engine for Coronavirus researchers! 🎉🎉 Currently, we focus on improving our existing affinity prediction model, identifying lead drugs for COVID-19, and developing a joint named entity recognition and normalization model for biological text. The related publications are listed below. 👇
 
 
 
 
 

Teaching Assistant

Dept. of Computer Engineering, Boğaziçi University

July 2019 – Present İstanbul, Turkey
Being a teaching assistant allows me to share my research-driven knowledge with students 👨‍🏫. So, I have been instructing problem sessions, delivering assignments, and guiding senior projects. I always aim to make learning a fun and interactive experience and devise themed projects (such as helping Katniss Everdeen 🔥) and schedule additional sessions to interact with students as much as I can. I am happy that students appreciate my efforts with feedbacks such as: ‘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! 😎😎
 
 
 
 
 

Research Assistant

The Scientific and Technological Research Council of Turkey, TÜBİTAK

December 2018 – June 2019 İstanbul, Turkey
I worked in a team for 6 months on the project titled ‘Using Turkish WordNet for Machine Translation’ which was funded by The Scientific and Technological Research Council of Turkey (TUBITAK). We enhanced the accessibility of Turkish WordNet and nlptollkit, a Turkish natural language processing library, by creating online user interfaces and documentation 💻. We published our works in Turkish NLP oriented conferences. 📃
 
 
 
 
 

Data Scientist

ING Turkey

July 2018 – December 2018 İstanbul, Turkey
During my time at ING Turkey, I first collaborated with a large and interdisciplinary team to formulate autonomous branch cash management as a prediction problem. Second, I prepared in-depth data analysis reports and used data-driven insights to implement time-series clustering models 💹. The models successfully identified the branches with similar cash-flow patterns and based the prediction pipeline🔮. I left the position to work in a more research-oriented environment🔎.

Publications

ChemBoost: A chemical language based approach for the prediction of protein - ligand binding affinity

We exploit the chemical language in SMILES and aminoacid sequences to predict drug-target affinity and present state-of-the-art level affinity prediction models.

Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature

We create a search engine to identify bichemically related molecules in CORD-19 abstracts.

Data and Representation for Turkish Natural Language Inference

We present the first large labeled Turkish NLI dataset (NLI-TR) and models using machine translation.

User Interface for Turkish Word Network KeNet

We present the first UI that enables online traversal of Turkish WordNet: KeNet.

User Interfaces for Turkish Natural Language Processing

We develop a web application to use a Turkish NLP library (nlptoolkit) online.

News 📢📢

  • I presented our work ChemBoost at HIBIT 2020! It turned out that ChemBoost won a fierce competition to be a selected talk (~15 %acceptance rate)! 😎😎 Link to presentation Link to poster (October 22)
  • ChemBoost is accepted as a talk & poster to HIBIT 2020! Hope to see you during my presentations on October 22-23! 💊🧬👨‍🏫! Link to poster (October 19)
  • The senior project I guide jointly with my advisors Identifying Potential Treatments for COVID-19 with a Deep Learning Model is accepted as a poster to HIBIT 2020! Catch the presentation of Alperen and Berk for more information! 👨‍🎓👨‍🎓 Link to poster (October 19)
  • Emrah and I presented NLI-TR at a Kodluyoruz event. It was great to be among wonderful people! 🥰👨‍💻 (October 18, 2020)
  • Vapur is accepted to COVID-19 Workshop @ EMNLP 2020! 🚢🚢🚢 🥳 (October 2)
  • NLI-TR is accepted as a long paper to main conference of EMNLP 2020! 😎🎉🎊🥳 (September 14)
  • Attended ECCB 2020 virtually on. It was lovely to meet new people, even online… (September 7 & 8).
  • Joyfully presented NLI-TR at inzva community with Emrah. Thanks for the invite! 👨‍💻🐱‍💻 (August 29)

Coursework 👨‍🏫👨‍🎓

Taught

  • CMPE 250 - Data Structures & Algorithms - Fall ‘16, Fall ‘20
  • CMPE 462 - Machine Learning - Spring ‘18, Spring ‘20
  • CMPE 493 - Introduction to Information Retrieval - Spring ‘19, Spring ‘20
  • CMPE 344 - Computer Organization - Fall ‘19
  • CMPE 321 - Introduction to Database Systems - Spring ‘19
  • CMPE 150 - Introduction to Programming - Fall ‘15, Spring ‘16

Taken

  • CMPE 483 - Blockchain Programming
  • CMPE 484 - Introduction to Digital Video Systems
  • CMPE 493 - Introduction to Information Retrieval
  • CMPE 547 - Bayesian Statistics & Machine Learning
  • CMPE 58Z - Introduction to Biometrics
  • CMPE 593 - Multi-Agent Systems
  • CMPE 597 - Deep Learning
  • CMPE 58H - Social Semantic Web
  • CMPE 59H - Bioinformatics
  • IE 456 - Graph Theory & Applications
  • IE 515 - Graph Theory & Network Flows
  • IE 518 - Advanced Graph Theory

Contact 💭

  • riza.ozcelik@boun.edu.tr
  • Nispetiye, Rumeli Hisari, Istanbul.
  • Department of Computer Engineering, North Campus. Office: BM36