rsh-osteoarthritis-classification

This repository contains notebook-driven work for osteoarthritis-related gait classification, feature engineering, cohort analysis, and model experimentation.

The project is organized as a research workspace and includes both exploratory work and more structured/final reporting workflows.

Repository Layout

• ML/: classifier development, condition classification, and final reporting notebooks
• explore/: exploratory data inspection and metadata analysis
• features/: feature generation, augmentation, and supporting functions
• load/: data loading utilities and notebooks
• stats/: cohort, distribution, trend, and comparison notebooks
• dataset/: dataset notes and quick-start material
• downloaded_data/: local data staging area

Notebooks under ML/master/Final/ contain the most structured final-stage reporting workflows, while other notebook directories include broader experimental and intermediate work.

Final Results Location

The main final-stage reporting area is:

• ML/master/Final/

Key locations inside that tree:

• ML/master/Final/results/: final results output directory
• ML/master/Final/HOA/: HOA-focused final reporting notebooks
• ML/master/Final/KOA/: KOA-focused final reporting notebooks
• ML/master/Final/KOA/feature_experiment/: KOA feature-experiment reporting notebooks
• ML/master/Final/lasso/: lasso-based feature/model notebooks
• ML/master/Final/all_ml_experiments.ipynb: consolidated ML experiment notebook
• ML/master/Final/all_ml_experiments_population.ipynb: population-level experiment notebook
• ML/master/Final/KOA_HOA.ipynb: combined KOA/HOA analysis notebook
• ML/master/Final/ml_with_confounders.ipynb: confounder-adjusted analysis notebook
• ML/master/Final/table4.ipynb: final table-generation notebook

Python Environment

Create and activate a virtual environment in the project root:

python3 -m venv .venv
source .venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
python -m ipykernel install --user --name rsh-osteoarthritis-classification --display-name "rsh-osteoarthritis-classification"

Start JupyterLab from the repository root:

source .venv/bin/activate
jupyter lab

Running JupyterLab from the project root is the safest default for this repository because many notebooks use relative paths across directories such as features/, load/, dataset/, and ML/.

Notes

• This repository is primarily notebook-oriented.
• Some workflows depend on local data artifacts that may not all be committed in this checkout.
• requirements.txt is scoped to the Python notebook workflow and does not attempt to manage non-Python tooling.