| # Data Provenance |
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| This repository bundles the direct DST-GNN input table and a formal release of the cleaned public DST-GNN outputs so the analysis can be rerun end-to-end from the repository contents alone. |
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| ## Bundled input |
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| - `data/inputs/cophenetic_distances_searcher_D_score_in_all_samples.csv` |
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| This table is the direct input to the public DST-GNN pipeline. It contains the flattened COSTE/SSS-style pairwise spatial relationship values used to build temporal cell-type graphs. |
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| Expected columns: |
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| - `row` |
| - `column` |
| - `value` |
| - `sample` |
| - `group` |
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| The cohort-level structure matches the manuscript description: |
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| - `45` total samples |
| - `47` predefined cell types |
| - `HD -> T1` (`healthy`) |
| - `LA -> T2` (`less affected`) |
| - `MA -> T3` (`more affected`) |
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| ## Upstream origin |
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| The bundled CSV was recovered from the lung fibrosis analysis directory and traced to the manuscript-era COSTE workflow: |
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| - recovered notebook using the CSV: |
| - `Y:/long/publication_datasets/Vannan_2023_Lung_Fibrosis/notebook/GNN modelling.ipynb` |
| - recovered notebook generating the CSV: |
| - `Y:/long/publication_datasets/Vannan_2023_Lung_Fibrosis/notebook/Expression Distance Similarity.ipynb` |
| - mirrored A100 location: |
| - `/mnt/taobo.hu/long/publication_datasets/Vannan_2023_Lung_Fibrosis/` |
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| The generation flow is: |
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| 1. For each sample, COSTE-style cophenetic / Searcher's D matrices were computed from annotated spatial data. |
| 2. Each per-sample matrix was flattened into `(row, column, value)` records. |
| 3. Sample identifiers and stage labels were attached. |
| 4. The concatenated table was saved as `cophenetic_distances_searcher_D_score_in_all_samples.csv`. |
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| ## Bundled formal output |
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| - `data/outputs/formal_release/` |
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| This directory contains the standard public output release generated with the cleaned DST-GNN implementation in this repository, not the raw historical notebook outputs. |
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| Formal release settings: |
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| - `device=cpu` |
| - `seed=0` |
| - `hidden_channels=32` |
| - `dropout=0.0` |
| - `lr=0.01` |
| - `weight_decay=5e-4` |
| - `epochs=400` |
| - `top_k=20` |
| - `run_explainer=true` |
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| The bundled output directory includes: |
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| - observed stage-level SSS matrices |
| - predicted later-stage SSS matrices |
| - ranked dynamic nodes |
| - ranked changing edges |
| - explainer edge scores for the `T2 -> T3` transition |
| - structured metadata in `summary.json` and `run_config.json` |
| - `checksums.sha256` covering the input CSV and generated release files |
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| ## Scope note |
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| This repository does not redistribute the raw Xenium data or the original full spatial omics study inputs. It only provides the direct DST-GNN input table needed for the public cleaned pipeline plus the corresponding formal release outputs. |
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