Sync paopac

README.md

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+---
+license: other
+license_name: original-author-license
+license_link: https://huggingface.co/pyaging/paopac/blob/main/paopac.LICENSE.txt
+library_name: pyaging
+tags:
+- pyaging
+- aging-clock
+- biology
+- proteomics
+---
+
+# paopac
+
+Conventional PAOPAC from the authors' MIT v1.0.0 release: 800 LightGBM trees with 189 Olink protein predictors and TDI, plus chronological age for cohort correction. Supply plasma Olink Explore 3072 NPX (assay-normalized log2 relative abundance), not linear abundance, concentrations, counts or pre-standardized values. NPX labeling alone does not establish equivalence across assays, panels, batches or plasma and serum. Exact duplicate protein columns are averaged on the NPX scale, then names uppercased; newly colliding names are rejected. The original interface applies 2**NPX, fills missing or absent values with zero on that linear scale, and fits StandardScaler over the complete supplied cohort. TDI is optional and read only from the protein matrix; it is exponentiated and standardized like the other inputs. TDI in sample metadata is ignored; absent TDI becomes zero. Required chronological age is supplied as an age column in years. Final output is raw predicted age minus LOWESS(raw predicted age minus chronological age, chronological age), with frac=0.75 and the original statsmodels defaults. Predictions depend on cohort composition, including cohort ages; this is not a fixed per-sample age or a portable age-acceleration residual. Very small or age-degenerate cohorts can produce trivial corrections. No fixed UKB scaler or LOWESS curve is supplied by the original release. Preserve NaNs when preparing AnnData to reproduce the author's missing-value rule. Nature Biotechnology trial supplement S2 identifies the Conventional endpoint; exact identity of that trial's private model artifact with this later public release has not been verified. MIT source; preprint 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. See the [original author license](paopac.LICENSE.txt). These weights are restricted to research use under the authors' terms.
+
+| | |
+|---|---|
+| **Predicts** | chronological age |
+| **Species** | Homo sapiens |
+| **Tissue** | plasma |
+| **Data type** | proteomics |
+| **Model type** | LightGBM with cohort standardization and LOWESS correction |
+| **Year** | 2026 |
+
+## Use with pyaging
+
+```python
+import pyaging as pya
+
+pya.pred.predict_age(adata, ["paopac"])
+```
+
+Browse every clock in the [pyaging Clock Catalogue](https://pyaging.readthedocs.io).
+
+## Citation
+
+Xu, H., et al. Proteome-aware organ proxy aging clocks. bioRxiv (2026).
+
+https://doi.org/10.64898/2026.04.24.720503

config.json

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+{
+ "approved_by_author": "\u231b",
+ "citation": "Xu, H., et al. Proteome-aware organ proxy aging clocks. bioRxiv (2026).",
+ "citations": 1,
+ "citations_date": "2026-10-02",
+ "clock_name": "paopac",
+ "data_type": "proteomics",
+ "doi": "https://doi.org/10.64898/2026.04.24.720503",
+ "journal": "bioRxiv",
+ "last_author": "Jing-Dong J. Han",
+ "model_type": "LightGBM with cohort standardization and LOWESS correction",
+ "n_features": 191,
+ "notes": "Conventional PAOPAC from the authors' MIT v1.0.0 release: 800 LightGBM trees with 189 Olink protein predictors and TDI, plus chronological age for cohort correction. Supply plasma Olink Explore 3072 NPX (assay-normalized log2 relative abundance), not linear abundance, concentrations, counts or pre-standardized values. NPX labeling alone does not establish equivalence across assays, panels, batches or plasma and serum. Exact duplicate protein columns are averaged on the NPX scale, then names uppercased; newly colliding names are rejected. The original interface applies 2**NPX, fills missing or absent values with zero on that linear scale, and fits StandardScaler over the complete supplied cohort. TDI is optional and read only from the protein matrix; it is exponentiated and standardized like the other inputs. TDI in sample metadata is ignored; absent TDI becomes zero. Required chronological age is supplied as an age column in years. Final output is raw predicted age minus LOWESS(raw predicted age minus chronological age, chronological age), with frac=0.75 and the original statsmodels defaults. Predictions depend on cohort composition, including cohort ages; this is not a fixed per-sample age or a portable age-acceleration residual. Very small or age-degenerate cohorts can produce trivial corrections. No fixed UKB scaler or LOWESS curve is supplied by the original release. Preserve NaNs when preparing AnnData to reproduce the author's missing-value rule. Nature Biotechnology trial supplement S2 identifies the Conventional endpoint; exact identity of that trial's private model artifact with this later public release has not been verified. MIT source; preprint CC BY 4.0. No author approval of this conversion is claimed.",
+ "platform": [
+  "Olink Explore 3072"
+ ],
+ "population": "adults",
+ "predicts": [
+  "chronological age"
+ ],
+ "research_only": true,
+ "species": "Homo sapiens",
+ "tissue": [
+  "plasma"
+ ],
+ "training_target": [
+  "chronological age"
+ ],
+ "unit": [
+  "years"
+ ],
+ "year": 2026
+}

paopac.LICENSE.txt

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+MIT License
+
+Copyright (c) 2026 JackieHanLab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

paopac.provenance.json

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+{
+  "repository": "https://github.com/JackieHanLab/PAOPAC",
+  "commit": "a166bc763ffd1395a96c6557db889706fcc9ef85",
+  "release": "v1.0.0",
+  "release_commit": "d65afe8610063d6d5ec02decb501c90ef70030c2",
+  "source_sha256": {
+    "model.bin": "5b0c5dadbac0fc382c51151a8845ff6a7ac1da31f89c0579731b02338c10c3f1",
+    "pre.cp39-win_amd64.pyd": "c8ecb6f06d0830f3c88dc18e05f5e838042762b3f9f186e125963e089015e85c",
+    "LICENSE": "52b3413ff0be04732237f3ec067fb994d51139ddfa61594160ca7b445e7ff3fe"
+  },
+  "model_text_sha256": "10eb9c389ff5fe8fc9adb9c0c27430fcc43dcf628c43ecf42b70e4f8dbfb31d5",
+  "model_key": "Conventional",
+  "trees": 800,
+  "tree_input_count": 190,
+  "protein_count": 189,
+  "cohort_age_dependency_count": 1,
+  "preprocessing_oracle": "Unmodified pre.cp39-win_amd64.pyd predict() under CPython 3.9.13 / Wine 8.0",
+  "packaging": "Public MIT loader key; Fernet then zlib; restricted inert-record pickle reader",
+  "retained_state": "Fitted numeric split features, thresholds, children, leaf values only",
+  "training_participant_records_retained": false,
+  "citation_count_source": "https://api.openalex.org/works/https://doi.org/10.64898/2026.04.24.720503"
+}

paopac.pt

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