CV

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Last updated: August 2025

Education

Ph.D. in Pharmaceutical Sciences (Cheminformatics)

University of Vienna | Vienna, Austria | 2022 - Present
CD-Lab MIB Industry Partnership
Thesis: Machine learning models for domain generalization in chemical space

M.Sc. in Biomedical Engineering

Sharif University of Technology | Tehran, Iran | 2017
🏆 Best Master’s Student Award

B.Sc. in Mechanical Engineering

Amirkabir University of Technology (Tehran Polytechnic) | Tehran, Iran | 2014

Work Experience

Chief Data Scientist (CDS)

Celeris Therapeutics | Graz, Austria | Feb 2021 - Feb 2022

Developed machine learning models for targeted protein degradation
Built ML pipelines to identify targets susceptible to degradation
Created ternary complex prediction models (protein-protein-degrader complexes)

Senior Data Scientist - Cheminformatics/ML Expert

AI VIVO | Cambridge, UK | Apr 2019 - Dec 2020

Led machine learning initiatives for drug repositioning and de novo design
Predicted small molecule perturbation effects on different cell lines
Developed ML tools for drug combination synergy prediction

Chief Scientific Officer (CSO)

Shenakht Pajouh | Tehran, Iran | May 2018 - Dec 2019

Integrated psychological knowledge with machine learning for automated mental health assistance
Led scientific strategy and research development

Machine Learning Researcher

Cambridge Systems Biology Centre | Cambridge, UK | Feb 2017 - Jan 2018

Applied deep learning methods to drug discovery challenges
Developed novel computational approaches for pharmaceutical research

Bioinformatics Researcher

Royan Institute | Tehran, Iran | Jan 2017 - Aug 2017

Reconstructed context-specific metabolic networks from gene expression data
Applied computational methods to systems biology problems

Teaching Assistant

Sharif University of Technology | Tehran, Iran | Spring 2017

Advanced Bioinformatics course
Systems Biology course

Technical Skills

Programming & Development

Python (Advanced): NumPy, Pandas, SciPy, Matplotlib, Seaborn
R (Advanced): Statistical modeling, data visualization, Bioconductor
C++ (Intermediate): Performance optimization, algorithm implementation
Rust (Intermediate): Systems programming

Machine Learning & AI

Deep Learning: PyTorch, TensorFlow, JAX
Classical ML: scikit-learn, XGBoost, LightGBM
Specialized Methods: Bayesian inference, causal inference, reinforcement learning
Model Development: Feature engineering, hyperparameter optimization, cross-validation

Computational Chemistry & Bioinformatics

Cheminformatics: RDKit, Open Babel, DeepChem, Schrödinger Suite
Molecular Modeling: Protein-ligand docking, molecular dynamics simulations
Bioinformatics: Sequence analysis, pathway analysis, network biology
Data Integration: Multi-omics analysis, systems biology approaches

Research Expertise

Drug Discovery Automation: End-to-end ML pipelines for pharmaceutical research
Targeted Protein Degradation: PROTAC design and ternary complex prediction
Out-of-Distribution Generalization: Robust model development for chemical space
Multi-omics Data Integration: Combining genomics, proteomics, and metabolomics data
Network Pharmacology: Systems-level drug mechanism analysis
Causal Inference: Understanding cause-effect relationships in biological systems

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)

Peer Review Activities

Journal Reviewing

Nature Machine Intelligence - Premier AI/ML journal
Journal of Chemical Information and Modeling - Leading cheminformatics publication
Artificial Intelligence in the Life Sciences - Interdisciplinary AI applications

Expertise Areas

Machine learning model evaluation and validation
Computational chemistry and cheminformatics methods
Drug discovery and pharmaceutical applications

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