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baysquire/README.md

Abiodun Sojobi

Physicist & Software Engineer | AI for Computational Medicine

Building computational tools at the intersection of physics, AI, and kidney disease research.


About Me

I'm a System Programmer at the University of Lagos and a Data Science Lecturer at Rome Business School, Nigeria. I hold a BSc and MSc in Physics from the University of Lagos.

My independent research focuses on applying AI and physics-based computation to medical problems - specifically kidney disease and urinary health. I'm working toward a PhD in Computational Biology or Health Data Science.

  • 🔬 Research focus: Scientific Machine Learning (SciML), Physics-Informed Neural Networks, Quantum-Classical hybrid methods, and Generative AI for drug discovery.
  • 🧑‍🏫 Teaching: Neural Networks, Reinforcement Learning, and applied ML to postgraduate students.
  • 🎓 Seeking: PhD/Research opportunities in Computational Biology, Biomedical Physics, or Health Data Science.
  • ☁️ Certified: AWS Solutions Architect.

Research Projects

1. Physics-Informed Neural Networks for Kidney Filtration Modeling

  • pinn-glomerular-filtration
    • A 2D PINN that models glomerular solute transport under hypertensive conditions by embedding Poiseuille flow and convection-diffusion-reaction PDEs directly into the loss function.
    • Achieved <2.5% relative L2 error against the analytical solution.
    • 📄 Preprint: Zenodo

2. Hybrid Quantum-Classical Pipeline for Molecular Feature Generation

  • hybrid-vqe-drug-discovery
    • A VQE-based pipeline using PennyLane and PyTorch - a classical MLP reduces dimensionality before embedding features into a 4-qubit hardware-efficient ansatz for ground-state energy estimation.
    • 📄 Preprint: Zenodo

3. Graph Neural Networks for Toxicity Prediction

  • Tox21-GNN-Property-Prediction
    • A Message Passing Neural Network (MPNN) built with PyTorch Geometric for multi-label toxicity prediction across 12 Tox21 assays, with custom handling for class imbalance and missing targets.

4. Generative Molecular Design

  • SMILES-VAE-Generative-Design
    • A GRU-based Variational Autoencoder for generating novel, chemically valid molecular structures from SMILES representations, with RDKit validation.

5. CKD Mendelian Randomization Pilot

  • CKD-Mendelian-Randomization-Pilot
    • An R-based Mendelian Randomization analysis exploring causal relationships in Chronic Kidney Disease using GWAS summary statistics.

Technical Skills

  • AI & SciML: PyTorch, PyTorch Geometric, TensorFlow, Scikit-Learn, PINNs.
  • Domain: RDKit (Cheminformatics), PennyLane/Qiskit (Quantum), R (Biostatistics).
  • Infrastructure: AWS, Docker, Git, Linux.

Activity

GitHub Streak


Connect

"A physics-trained approach to medical discovery."

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  1. pinn-glomerular-filtration pinn-glomerular-filtration Public

    A 2D Physics-Informed Neural Network (PINN) in PyTorch modeling glomerular fluid dynamics and solute clearance via the Convection-Diffusion-Reaction equation.

    Jupyter Notebook

  2. CKD-Mendelian-Randomization-Pilot CKD-Mendelian-Randomization-Pilot Public

    Pilot replication of proteome-wide Mendelian randomization findings for estimated glomerular filtration rate (eGFR) by using publicly available pQTL and CKDGen GWAS data.

    R

  3. hybrid-vqe-drug-discovery hybrid-vqe-drug-discovery Public

    A Hybrid PyTorch-PennyLane machine learning pipeline utilizing a Variational Quantum Eigensolver (VQE) for continuous molecular latent representation optimization.

    Jupyter Notebook

  4. SMILES-VAE-Generative-Design SMILES-VAE-Generative-Design Public

    A PyTorch-based Character-Level Variational Autoencoder (VAE) development pipeline designed for de novo molecular generation and generative drug design, featuring RDKit validation for novel chemica…

    Python

  5. Tox21-GNN-Property-Prediction Tox21-GNN-Property-Prediction Public

    A robust PyTorch Geometric implementation of Graph Neural Networks (MPNN) for classifying chemical toxicity on the highly imbalanced Tox21 dataset, featuring NaN-target masking and RDKit featurizat…

    Python

  6. ml-guided-quantum-coarsening ml-guided-quantum-coarsening Public

    ML-guided graph coarsening for hybrid classical–quantum optimization (MaxCut/QUBO).

    Python