bebms 0.4.0

Bayesian Event-Based Model for Disease Subtype and Stage Inference

pysubebm

Installation

pip install git+https://github.com/noxtoby/awkde
pip install git+https://github.com/hongtaoh/ucl_kde_ebm
pip install git+https://github.com/hongtaoh/pySuStaIn

pip install -e .

Changelogs

• 2025-08-21 (V 0.0.3)
  • Did the generate_data.py.
• 2025-08-22 (V 0.0.5)
  • Did the mh.py
  • Correct conjugate_priors implementation.
• 2025-08-23 (V 0.1.2)
  • Improved functions in utils.py.
• 2025-08-29 (V 0.1.3)
  • Didn't change much.
• 2025-08-30 (V 0.1.8)
  • Optimized compute_likelihood_and_posteriors such that we only calculate healthy participants' ln likelihood once every time.
  • Made sure subtype assignment accuracy does not apply to healthy participants at all.
  • Fixed a major bug in data generation. The very low subtype assignment might be due to this error.
  • Included both subtype accuracy in run.py.
• 2025-08-31 (V 0.2.5)
  • Resacle event times and disease stages for exp7-9 such that max(event_times) = max_stage -1, and max(disease_stages) = max_stage.
  • Changed the experiments and some of the implementation.
  • Forcing max(event_times) = max_stage -1, but not forcing disease stages.
• 2025-09-01 (V 0.2.9)
  • REMOVED THE Forcing max(event_times) = max_stage -1
  • Modified the run.py.
• 2025-09-02 (V 0.3.3.1)
  • Redid the staging and subtyping.
  • Integrated with labels and not.
• 2025-09-04 (V 0.3.3.2)
  • Made sure in staging with labels, the new_order indices starts from 1 instead of 0. This is because participant stages now start from 0.
• 2025-09-06 (V 0.3.5.6)
  • Added the plot function back.
• 2025-09-08 (V 0.3.5.8)
  • Added ml_subtype in output results.
  • Added all_logs to the output returned in run.py.
• 2025-09-21 (V 0.3.9)
  • Removed iteration >= burn_in when updating best_*.