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bolak92/README.md

Bola Khalil

AI/ML for Drug Discovery • Cheminformatics • Uncertainty Quantification • Representation Learning • Knowledge Graphs

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🚀 About Me

I build reliable ML systems for molecular design and bioactivity prediction. I focus on uncertainty-aware modeling, scalable benchmarking, peptide and small-molecule design, and knowledge graphs for target discovery. I translate complex data into simple, actionable decisions for chemists and discovery teams.

  • 🎓 PhD researcher in In Silico Discovery at Johnson & Johnson and Leiden University
  • 🧪 10+ years across pharma sciences, medicinal chemistry, and computational methods
  • 📏 Focus on UQ, calibration, OOD robustness, and representation learning for chemical and biological data
  • 🤝 Experienced leading cross-functional work with chemists, discovery scientists, and IT partners

What I do

  • 🔍 Uncertainty-aware prediction: ensembles, MC dropout, evidential DL, Bayesian and hybrid models
  • 🧬 Generative & optimization workflows: enumeration, sequence/graph models, multi-objective design
  • 🧫 Proteochemometrics & peptides: sequence–graph fusion, permeability modeling, PCM with assay descriptors
  • 🕸️ Knowledge graphs: multi-omics integration, link prediction, graph evidence propagation for repositioning
  • ⚙️ Production-ready pipelines: scalable training, calibration, selection, and reporting on HPC and cloud

💻 Tech Stack

Languages, Machine Learning and AI

Cheminformatics and Computational Chemistry

RDKit OpenEye Schrödinger MOE KNIME PyMOL

Data Engineering and Scientific Computing

DevOps, HPC and Infrastructure

Linux SLURM Docker GNU Bash AWS

Databases and Knowledge Graphs

Neo4j Cypher SQL PostgreSQL MySQL

Version Control and IDEs

Git GitHub Jupyter PyCharm IntelliJ IDEA VS Code Sublime Text

AI & Development Tools

GitHub Copilot OpenAI GPT Anthropic Claude Google Gemini NotebookLM Google AntiGravity Cursor

📊 GitHub Stats

GitHub Streak


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  1. CDDLeiden/uqdd CDDLeiden/uqdd Public

    Hybrid Uncertainty Quantification for Bioactivity Assessment

    Python 1