Resume

Education

Ph.D in Biology, The University of North Carolina at Chapel Hill 2017 - 2022
M.S. in Marine Technology, Istanbul Technical University 2012 - 2014
B.S. in Naval Architecture Engineering, University of Applied Sciences Kiel 2008 - 2009
B.S. in Naval Architecture Engineering, Yildiz Technical University 2005 - 2010

Work experience

Collaborations Pharmaceuticals Jan 2023 - Feb 2024
Data Science Postdoc
- Built state-of-the-art (SOTA) ML and DL models to discover selective compounds for Alzheimer’s Disease; improved the precision of models by 61%; scanned 5M compounds and found 7 hits; paper in submission
- Built SOTA DL model (few-shot learning) to be used in extremely low data situations; used GNN to create molecular representations; reduced the cost of experiments by 95%
- Trained an LSTM-based generative model for de novo molecule design; fine-tuned a transformer-based LLM trained on 1.4B compounds to train a general transporter model for the drug discovery pipeline
- Developed a PGNN model for multivariate regression of organophosphate pesticide (OPP) metabolism; reduced unrealistic concentration values in full decay curve predictions by 100%
- Implemented DVC for data science experimentation and data versioning to the company’s ML pipeline
- Wrote one first-author and one co-author, peer-reviewed papers in top tier journals
Collaborations Pharmaceuticals May - June 2022
Data Science Intern
- Analyzed a small dataset and explored various data manipulation techniques to improve models’ performances
- Built a multivariate machine learning and deep learning model to predict dose response curves of compounds on different targets
- Gave a presentation summarizing the progress made to project collaborators and CEO
The University of North Carolina at Chapel Hill Aug 2017 - Dec 2022
Ph.D. Research Assistant
- Collected positional data on animals using computer vision systems; analyzed the positional data statistically and estimated distributions (MLE); analyzed behavior from the evolutionary perspective; paper in submission
- Collected kinematics data on animals; ran CFD simulations on HPC; research became a thesis chapter
- Performed fluid dynamics experiments on plankton dispersal; performed CFD; published peer-reviewed paper
- Spearheaded two collaborative research projects and mentored 9 undergraduate students

Skills

Programming: Python | SQL | PySpark | Unix shell | SLURM
MLOps: Git | Data Version Control (DVC) | Docker
ML/AI: PyTorch | scikit_learn | dgl | dgllife
Cheminformatics: RDKit | Chembl Structure Library | ADMET modeling | small and large molecule drug discovery | hit-identification | virtual screening

Certifications & Specializations

Awards

Quick Thinking Award | Collaboration Pharmaceuticals
For extinguishing fire at the workplace and saving company assets
ARPA Graduate Degree Completion Grant ($8,000) | UNC at Chapel Hill
Toward running experiments for a thesis chapter
L. I. Gilbert Grant ($1,500) | UNC at Chapel Hill
To attend “Computational Principles to Organize Complexity” Summer School
Vehbi Koc Foundation Research Grant ($2,500) | Istanbul Technical University
Toward the conceptual design of a pulsed-jet underwater vehicle inspired by squids

Publications

The Goldilocks Paradigm: Comparing Classical Machine Learning, Large Language Models, and Few-Shot Learning for Drug Discovery Applications

Snyder, S. et. al. (2024). "The Goldilocks Paradigm: Comparing Classical Machine Learning, Large Language Models, and Few-Shot Learning for Drug Discovery Applications." Nature Communications. 1(3).

Statistical analysis of Artemia trajectories suggest that superdiffusive movement starts earlier than the feeding

The hydrodynamics of metachronal paddling in brine shrimp.

Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors

Ozalp, M.K., Vignaux, P.A., Puhl, A.C., Lane, T.R., Urbina, F. and Ekins, S., 2024. Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors. Journal of Chemical Information and Modeling.

Experiments and agent-based models of zooplankton movement within complex flow environments

Ozalp, M.K. (2020). "Experiments and agent-based models of zooplankton movement within complex flow environments." Biomimetics. 5(1).

Talks

Plankton dispersion through vegetative seabed within complex flow environments

January 04, 2020

Conference Proceeding Talk at Society of Integrative and Comparative Biology (SICB) 2020, Austin, Texas

The Effect of Immersed Structures on Zooplankton Swimming

January 04, 2019

Poster Presentation at Society of Integrative and Comparative Biology (SICB) 2019, Tampa, FL

Service and leadership

Volunteer at Table NC, a non-profit organization which delivers healthy food and nutrition education to children in Orange County, NC

Kemal Ozalp, Ph.D.