Sync pac

README.md

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+---
+library_name: pyaging
+tags:
+- pyaging
+- aging-clock
+- biology
+- proteomics
+---
+
+# pac
+
+Mortality-equivalent proteomic age from the original Kuo et al. R release, using all 128 Olink Explore 3072 plasma protein NPX values plus chronological age in years. Supply original lowercase identifiers, including fut3_fut5 and ntprobnp; there is no sex covariate. NPX is assay-normalized log2 relative abundance, not raw counts, concentrations, linear abundances or z-scores. NPX labeling alone does not establish comparability across panels, batches, plasma and serum. No cohort scaling, normalization, or imputation is applied during scoring. Every predictor column is required; supplied NaNs propagate. The paper used k-nearest-neighbor imputation (k=10) before model fitting; any upstream imputation is a separate caller decision. The full-precision original Gompertz constants are retained, without the later Insilico wrapper's rounding or optional distribution matching. Output is mortality-equivalent age in years, not a clinical diagnosis or an age-acceleration residual. Development cohort: UK Biobank adults aged 39-70. The original repository specifies no code license; the publication is CC BY 4.0. No author approval of this conversion is claimed.
+
+Model weights retain the original authors' terms; the pyaging software license does not relicense them. These weights are restricted to research use under the authors' terms.
+
+| | |
+|---|---|
+| **Predicts** | biological age |
+| **Species** | Homo sapiens |
+| **Tissue** | plasma |
+| **Data type** | proteomics |
+| **Model type** | Gompertz proportional hazards model |
+| **Year** | 2024 |
+
+## Use with pyaging
+
+```python
+import pyaging as pya
+
+pya.pred.predict_age(adata, ["pac"])
+```
+
+Browse every clock in the [pyaging Clock Catalogue](https://pyaging.readthedocs.io).
+
+## Citation
+
+Kuo, C.-L., et al. "Proteomic aging clock (PAC) predicts age-related outcomes in middle-aged and older adults." Aging Cell 23, e14195 (2024).
+
+https://doi.org/10.1111/acel.14195

config.json

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+{
+ "approved_by_author": "\u231b",
+ "citation": "Kuo, C.-L., et al. \"Proteomic aging clock (PAC) predicts age-related outcomes in middle-aged and older adults.\" Aging Cell 23, e14195 (2024).",
+ "citations": 68,
+ "citations_date": "2026-10-02",
+ "clock_name": "pac",
+ "data_type": "proteomics",
+ "doi": "https://doi.org/10.1111/acel.14195",
+ "journal": "Aging Cell",
+ "last_author": "Breno S. Diniz",
+ "model_type": "Gompertz proportional hazards model",
+ "n_features": 129,
+ "notes": "Mortality-equivalent proteomic age from the original Kuo et al. R release, using all 128 Olink Explore 3072 plasma protein NPX values plus chronological age in years. Supply original lowercase identifiers, including fut3_fut5 and ntprobnp; there is no sex covariate. NPX is assay-normalized log2 relative abundance, not raw counts, concentrations, linear abundances or z-scores. NPX labeling alone does not establish comparability across panels, batches, plasma and serum. No cohort scaling, normalization, or imputation is applied during scoring. Every predictor column is required; supplied NaNs propagate. The paper used k-nearest-neighbor imputation (k=10) before model fitting; any upstream imputation is a separate caller decision. The full-precision original Gompertz constants are retained, without the later Insilico wrapper's rounding or optional distribution matching. Output is mortality-equivalent age in years, not a clinical diagnosis or an age-acceleration residual. Development cohort: UK Biobank adults aged 39-70. The original repository specifies no code license; the publication is CC BY 4.0. No author approval of this conversion is claimed.",
+ "platform": [
+  "Olink Explore 3072"
+ ],
+ "population": "adults",
+ "predicts": [
+  "biological age"
+ ],
+ "research_only": true,
+ "species": "Homo sapiens",
+ "tissue": [
+  "plasma"
+ ],
+ "training_target": [
+  "mortality"
+ ],
+ "unit": [
+  "years"
+ ],
+ "year": 2024
+}

pac.provenance.json

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+{
+  "repository": "https://github.com/kuo-lab-uchc/PAC",
+  "commit": "e15edb66800f876a928cec9c8856500048c46fea",
+  "coefficient_path": "pac_proteomic_age.R",
+  "coefficient_sha256": "b87edc70f11e34740f0323e4b7c677eb1d53c5008d631ecf87a35cd22be1d2ff",
+  "prediction_code_path": "pac_proteomic_age.R",
+  "prediction_code_sha256": "b87edc70f11e34740f0323e4b7c677eb1d53c5008d631ecf87a35cd22be1d2ff",
+  "paper": "https://doi.org/10.1111/acel.14195",
+  "input_scale": "Olink NPX, with chronological age in years; no scoring-time scaling",
+  "missingness": "All predictor columns required; supplied NaNs propagate; no reference-value imputation",
+  "original_repository_license": "unspecified",
+  "publication_license": "CC BY 4.0"
+}

pac.pt

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