CV

Download PDF version of my CV from here.

Education

Ph.D. Student, Pharmaceutical Sciences (Cheminformatics), University of Vienna - CD-Lab MIB Industry Partnership, Vienna, Austria, Present
M.Sc., Electrical Engineering (Biomedical Engineering), Sharif University of Technology, Tehran, Iran, 2017
B.Sc., Mechanical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran, 2014

Work experience

Feb 2021 - Feb 2022: Chief Data Scientist (CDS)
- Celeris Therapeutics, Graz, Austria
- Duties included: Machine learning for targeted protein degradation
  - Machine learning to identify targets that are susceptible to degradation.
  - Machine learning for ternary complex prediction (complex formed by two proteins and degrader).
Apr 2019 - Dec 2020: Senior Data Scientist - Chemoinformatics / Machine learning expert
- AI VIVO, Cambridge, UK
- Duties included: Machine learning for drug repositioning, drug combination, and de novo drug design.
  - Predicting the effect of different perturbations (mostly small molecules) on different cell lines.
  - Developing machine learning tools for predicting synergy of drug combinations.
May 2018 - Dec 2019: Chief Scientific Officer (CSO)
- Shenakht Pajouh, Tehran, Iran
- Duties included: Reconciling Psychological knowledge with machine learning in order to build automated mental health assistant.
Feb 2017 - Jan 2018: Machine learning reasearcher
- Cambridge system biology centre
- Duties included: Deep learning in drug discovery
Jan 2017 - Aug 2017: Bioinformatics researcher
- Royan Institute, Tehran, Iran
- Duties included: Reconstructing context-specific metabolic networks from gene expression data.
Spring 2017: Teaching assistant
- Sharif University of Technology, Tehran, Iran
- Duties included: Advanced bioinformatics course, system biology course

Technical Skills

Machine Learning: Advanced (Bayesian methods, causal inference, deep learning, reinforcement learning)
Programming: Python (advanced), R (advanced), C++ (intermediate), Rust (intermediate)
ML Frameworks: PyTorch, TensorFlow, scikit-learn, XGBoost, Jax
Cheminformatics Tools: RDKit, Open Babel, DeepChem, Schrödinger Suite
Bioinformatics: Sequence analysis, pathway analysis, network biology

Research Expertise

Drug discovery automation
Targeted protein degradation
Multi-omics data integration
Network pharmacology
Systems biology

Publications

Optimum Design, Manufacturing and Experiment of a Passive Walking Biped: Effects of Structural Parameters on Efficiency, Stability and Robustness on Uneven Trains

Hadi, Sadati et al. (2013). "Optimum Design, Manufacturing and Experiment of a Passive Walking Biped: Effects of Structural Parameters on Efficiency, Stability and Robustness on Uneven Trains." Applied Mechanics and Materials.

Enhanced Waddington Landscape Model with Cell-Cell Communication Can Explain Molecular Mechanisms of Self-Organization

Hosein, Fooladi. (2019). "Enhanced Waddington Landscape Model with Cell-Cell Communication Can Explain Molecular Mechanisms of Self-Organization." Bioinformatics 1. 1(3).

Recognizing Arrow Of Time In The Short Stories

Hosseini, Fahimeh, Hosein Fooladi, and Mohammad Reza Samsami. "Recognizing Arrow Of Time In The Short Stories." arXiv preprint arXiv:1903.10548 (2019).

Bayesian optimization for ternary complex prediction (BOTCP)

Rao, Arjun, et al. "Bayesian optimization for ternary complex prediction (BOTCP)." Artificial Intelligence in the Life Sciences 3 (2023): 100072.

Encoding Protein-Ligand Interactions: Binding Affinity Prediction with Multigraph-based Modeling and Graph Convolutional Network

Mekni, Nedra, et al. "Encoding Protein-Ligand Interactions: Binding Affinity Prediction with Multigraph-based Modeling and Graph Convolutional Network" ChemRxiv (2023)

Quantifying the hardness of bioactivity prediction tasks for transfer learning

Fooladi, Hosein, et al. "Quantifying the hardness of bioactivity prediction tasks for transfer learning" Journal of Chemical Information and Modeling (2024)

Evaluating Machine Learning Models for Molecular Property Prediction: Performance and Robustness on Out-of-Distribution Data

Fooladi, Hosein, et al. "Evaluating Machine Learning Models for Molecular Property Prediction: Performance and Robustness on Out-of-Distribution Data" ChemRxiv (2025)

Reviewer

Talks

System biology and waddington landscape

October 01, 2019

Talk at Sharif University of Technology, Department of Computer Engineering, Tehran

Causal learning and inference

November 10, 2019