Add MiAge (Mitotic Age) clock (Fixes PR #134)#185
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marcbal77 merged 4 commits intobio-learn:masterfrom Dec 18, 2025
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Add MiAge (Mitotic Age) clock (Fixes PR #134)#185marcbal77 merged 4 commits intobio-learn:masterfrom
marcbal77 merged 4 commits intobio-learn:masterfrom
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- Fix syntax error in model definition (= to :) - Replace MiAgeNonlinearClock with proper MiAgeModel implementation - Implement correct optimization-based approach using scipy - Formula: minimize sum((c + b^(n-1) * d - beta)^2) for each sample - Correct MiAge_parameters.csv with actual CpG IDs (not CpG_1, CpG_2) - Remove unnecessary files (MiAge.csv, MiAge_coefficients.csv) - Add expected test outputs from MethylCIPHER reference data - Update model metadata (year: 2018, proper DOI, output label) Based on Youn & Wang (2018) and MethylCIPHER reference implementation.
- Add MiAgeModel to model_gallery.py imports and model_builders registry - Update expected_model_outputs/MiAge.csv with all 10 test samples - Fixes model registration error preventing MiAge clock usage - Tests passing Updates PR bio-learn#134
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sarudak
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Looks good just a couple issues
biolearn/model.py
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| "file": "MiAge.csv", | ||
| }, | ||
| }, | ||
| "OrganAgeChronological": { |
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These items are all duplicates of above.
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dear lord, that copy paste method was busy the other day
biolearn/model.py
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| float | ||
| Estimated mitotic age (number of cell divisions) | ||
| """ | ||
| from scipy.optimize import minimize_scalar |
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Imports should be at top of file
- Remove duplicate ModelGallery entries that were overwriting existing clocks
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removed duplicates and put imports at top |
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Summary
Fixes and closes PR #134