Publish bundled DST-GNN inputs and formal reproducibility outputs

README.md

@@ -30,11 +30,28 @@ The implementation was reconstructed from the original analysis notebooks and cr
 
 ## What Is In This Repository
 
+- `data/inputs/`: bundled direct DST-GNN input CSV for the lung fibrosis cohort
+- `data/outputs/formal_release/`: bundled formal release outputs generated by the cleaned public pipeline
+- `data/DATA_PROVENANCE.md`: provenance notes for the bundled input and output data
 - `src/dst_gnn/`: cleaned Python package for data loading, temporal graph construction, model definition, training, and explainability
 - `scripts/run_dst_gnn.py`: end-to-end CLI that builds stage graphs, trains DST-GNN, ranks dynamic nodes and edges, and optionally runs `GNNExplainer`
+- `scripts/verify_repro.py`: output comparison helper for checking a rerun against the bundled formal release
 - `references/RECOVERY_NOTES.md`: provenance notes describing the recovered notebooks and the manuscript-alignment corrections applied here
 - `upload_to_hf.py`: helper for synchronizing this folder to the Hugging Face Hub
 
+## Bundled Data
+
+The repository now includes the direct DST-GNN input table and a formal output release so users can rerun and verify the pipeline without searching for additional intermediate files.
+
+- Input:
+  - `data/inputs/cophenetic_distances_searcher_D_score_in_all_samples.csv`
+- Formal release outputs:
+  - `data/outputs/formal_release/`
+
+The input CSV is the recovered cohort-level COSTE/SSS table with `45` samples, `47` cell types, and stage labels mapped as `HD -> T1`, `LA -> T2`, `MA -> T3`.
+
+See `data/DATA_PROVENANCE.md` for the input lineage and the exact formal release settings.
+
 ## Public Implementation Choices
 
 The recovered notebook material contained exploratory and partially duplicated cells. This public release keeps the original analytical intent but makes several choices explicit:
@@ -77,6 +94,47 @@ python scripts/run_dst_gnn.py \
 
 The script writes stage-level matrices, training history, predicted next-stage graphs, top changing nodes, top changing edges, and optional explainer outputs.
 
+## Reproducibility
+
+The bundled formal release was generated with the cleaned public implementation using:
+
+- `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`
+
+Reproduce the public release from the bundled input:
+
+```bash
+python scripts/run_dst_gnn.py \
+  --csv data/inputs/cophenetic_distances_searcher_D_score_in_all_samples.csv \
+  --output-dir outputs/repro_check \
+  --device cpu \
+  --seed 0 \
+  --hidden-channels 32 \
+  --dropout 0.0 \
+  --lr 0.01 \
+  --weight-decay 5e-4 \
+  --epochs 400 \
+  --top-k 20 \
+  --run-explainer
+```
+
+Verify the rerun against the bundled formal release:
+
+```bash
+python scripts/verify_repro.py \
+  --expected-dir data/outputs/formal_release \
+  --actual-dir outputs/repro_check
+```
+
+The repository intentionally bundles the direct DST-GNN input and the formal output release, but it does not bundle the original raw Xenium data. Manuscript conclusions should still be cited to the associated paper.
+
 ## Recovery Notes
 
 The primary recovered sources were:

data/DATA_PROVENANCE.md

@@ -0,0 +1,75 @@
+# Data Provenance
+
+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.
+
+## Bundled input
+
+- `data/inputs/cophenetic_distances_searcher_D_score_in_all_samples.csv`
+
+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.
+
+Expected columns:
+
+- `row`
+- `column`
+- `value`
+- `sample`
+- `group`
+
+The cohort-level structure matches the manuscript description:
+
+- `45` total samples
+- `47` predefined cell types
+- `HD -> T1` (`healthy`)
+- `LA -> T2` (`less affected`)
+- `MA -> T3` (`more affected`)
+
+## Upstream origin
+
+The bundled CSV was recovered from the lung fibrosis analysis directory and traced to the manuscript-era COSTE workflow:
+
+- 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/`
+
+The generation flow is:
+
+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`.
+
+## Bundled formal output
+
+- `data/outputs/formal_release/`
+
+This directory contains the standard public output release generated with the cleaned DST-GNN implementation in this repository, not the raw historical notebook outputs.
+
+Formal release settings:
+
+- `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`
+
+The bundled output directory includes:
+
+- 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
+
+## Scope note
+
+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.

data/outputs/formal_release/checksums.sha256

@@ -0,0 +1,12 @@
+d10b46e245a331365ad634fa157d1f020ef631e7c93893d63ad4c5bf1dfeaa5c  input_csv::cophenetic_distances_searcher_D_score_in_all_samples.csv
+f26e5609c7fedae744ff057745897e2b08b60148c3feaaaf77a0f8ec8348cc71  explainer_edges_t2_to_t3.csv
+9c287b825eefc14342ec419ba79a0bde4d04e9d90488e3315257df99a2838365  observed_T1_sss.csv
+ff514a845155ac92e06901d74cac44964d49f052bd035357337160c31220cb2a  observed_T2_sss.csv
+7ede9d74de1d9ba76ca151498d721360189e7f444cc08391a38b04a64542e3a4  observed_T3_sss.csv
+e5fe3e25fc890c95a5f1bbac6f7ded2e38bd3796644bac2d89a29792a81ba7f0  predicted_T2_sss.csv
+a3429d6c97daa363c9eb38f9dc7ce4cf7a6fb22e13acb0103ff949f363604f51  predicted_T3_sss.csv
+3e5b414f45b164337d2a4f5b48eb9ca57e458a64d512efc1f5796a34ff292b2a  run_config.json
+57f872f687baff88beabc7e037e07e377a82411ec81168d4c1841697065db752  summary.json
+a4ac22345928508fce87d7050867951f3c5ec88dcc5b8ec6d12f9ba9e0a29582  top_dynamic_nodes.csv
+ab22c5ca07642f608067f354446a7155af4a4dbe2d042a33e3a13a93e11f9309  top_edge_changes.csv
+3ce48250c9a8aa02416f9d28b4d70b5e2f291315816d3866f18b2029b3f0618b  training_history.csv

data/outputs/formal_release/explainer_edges_t2_to_t3.csv

@@ -0,0 +1,21 @@
+source,target,message_passing_weight,explanation_score
+AT1,Mesothelial,0.055645645,0.21115941
+Arteriole,Plasma,0.7182237,0.20909835
+AT2,RASC,0.41794276,0.20763126
+Multiciliated,Adventitial FBs,0.38994718,0.20724377
+Mesothelial,pDCs,0.047421634,0.20485437
+SPP1+ Macrophages,Interstitial Macrophages,0.79041916,0.20361142
+Capillary,Myofibroblasts,0.5925608,0.2034361
+Mast,Macrophages - IFN-activated,0.61274993,0.20255637
+RASC,Basophils,0.4448223,0.20162909
+Activated Fibrotic FBs,Proliferating T-cells,0.64802027,0.20120777
+pDCs,CD4+ T-cells,0.75933605,0.19929327
+Activated Fibrotic FBs,Migratory DCs,0.8173625,0.1983966
+Lymphatic,Interstitial Macrophages,0.84074193,0.19820313
+Transitional AT2,PNEC,0.06825417,0.19819288
+NK/NKT,Migratory DCs,0.76829594,0.19755505
+Proliferating NK/NKT,Transitional AT2,0.06544685,0.19753557
+B cells,Adventitial FBs,0.39533263,0.19544418
+RASC,SPP1+ Macrophages,0.4106176,0.19417804
+CD4+ T-cells,Arteriole,0.72108775,0.1937703
+Proliferating FBs,pDCs,0.73390317,0.19282556

data/outputs/formal_release/observed_T1_sss.csv

@@ -0,0 +1,48 @@
+,AT1,AT2,Activated Fibrotic FBs,Adventitial FBs,Alveolar FBs,Alveolar Macrophages,Arteriole,B cells,Basal,Basophils,CD4+ T-cells,CD8+ T-cells,Capillary,Goblet,Inflammatory FBs,Interstitial Macrophages,KRT5-/KRT17+,Langerhans cells,Lymphatic,Macrophages - IFN-activated,Mast,Mesothelial,Migratory DCs,Monocytes/MDMs,Multiciliated,Myofibroblasts,NK/NKT,Neutrophils,PNEC,Plasma,Proliferating AT2,Proliferating Airway,Proliferating B cells,Proliferating FBs,Proliferating Myeloid,Proliferating NK/NKT,Proliferating T-cells,RASC,SMCs/Pericytes,SPP1+ Macrophages,Secretory,Subpleural FBs,Transitional AT2,Tregs,Venous,cDCs,pDCs
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+Inflammatory FBs,0.1084791,0.10745426,0.3944336,0.5432286,0.10155914,0.12130773,0.21448274,0.22149487,0.77269727,0.65458333,0.16660598,0.17458169,0.10160105,0.87702096,0.0,0.1266936,0.92911243,0.94556534,0.2529383,0.3637666,0.18663926,0.96178627,0.47636572,0.104592755,0.7497426,0.7340051,0.10632937,0.10978613,0.88384235,0.2868161,0.63671696,0.9605767,1.0,0.13770685,0.11581719,0.7897428,0.6804558,0.8090347,0.13143492,0.15469058,0.9382841,0.68032104,0.2312254,0.34656507,0.14319178,0.30300313,0.7174233
+Interstitial Macrophages,0.09133407,0.07859632,0.39792213,0.5432286,0.0797827,0.080305144,0.21388598,0.21397161,0.77196866,0.65458333,0.16600512,0.16286686,0.08680552,0.87702096,0.1266936,0.0,0.92911243,0.94556534,0.25851348,0.3610795,0.1751152,0.96178627,0.47636572,0.096792236,0.7497426,0.7340051,0.09072863,0.092155926,0.88384235,0.28147137,0.63671696,0.9605767,1.0,0.13102409,0.07769661,0.7897428,0.6804558,0.8090347,0.098787345,0.13673922,0.9382841,0.68032104,0.21362321,0.34656507,0.124531224,0.30300313,0.7174233
+KRT5-/KRT17+,0.92911243,0.92911243,0.7983762,0.92911243,0.92911243,0.92911243,0.92911243,0.92911243,0.9392012,0.98659074,0.92911243,0.92911243,0.92911243,0.9392012,0.92911243,0.92911243,0.0,0.94556534,0.92911243,0.92911243,0.92911243,0.96178627,0.92911243,0.92911243,0.9392012,0.9392012,0.92911243,0.92911243,0.9439627,0.8817228,0.81068116,0.91376543,1.0,0.92911243,0.92911243,0.9425216,0.8944572,0.98659074,0.92911243,0.92911243,1.0,0.891823,0.92911243,0.92911243,0.92911243,0.92911243,0.869499
+Langerhans cells,0.94556534,0.94556534,0.94556534,0.9389604,0.94556534,0.94556534,0.94556534,0.94556534,0.99339503,1.0,0.94556534,0.94556534,0.94556534,0.99339503,0.94556534,0.94556534,0.94556534,0.0,0.94556534,0.94556534,0.94556534,0.96178627,0.94556534,0.94556534,0.99339503,0.99339503,0.94556534,0.94556534,1.0,0.94556534,0.94556534,1.0,1.0,0.94556534,0.94556534,0.94556534,0.94556534,0.99339503,0.94556534,0.94556534,0.99339503,0.94556534,0.94556534,0.94556534,0.94556534,0.94556534,0.94556534
+Lymphatic,0.25851348,0.25851348,0.43501344,0.53155047,0.2469208,0.2501636,0.24645981,0.2594767,0.7855463,0.65458333,0.2301364,0.2301364,0.25851348,0.87702096,0.2529383,0.25851348,0.92911243,0.94556534,0.0,0.39478627,0.21927285,0.96178627,0.46146592,0.25851348,0.7355897,0.74792653,0.25851348,0.25851348,0.88384235,0.2972059,0.65422904,0.9605767,1.0,0.23605728,0.25851348,0.79944146,0.6951536,0.8090347,0.24276292,0.27731615,0.9382841,0.67282116,0.2866501,0.35279837,0.24416137,0.31867543,0.72239476
+Macrophages - IFN-activated,0.3610795,0.3610795,0.5377777,0.57991326,0.3637666,0.3610795,0.35903138,0.38727182,0.7612418,0.700089,0.38727182,0.38727182,0.3637666,0.83750737,0.3637666,0.3610795,0.92911243,0.94556534,0.39478627,0.0,0.38727182,0.96178627,0.5499074,0.3610795,0.7130251,0.7059847,0.3610795,0.3610795,0.88384235,0.4428896,0.68593246,0.9605767,1.0,0.3610795,0.3610795,0.78482693,0.714417,0.7695211,0.38016644,0.3802653,0.8987705,0.71428216,0.40898576,0.43894988,0.3637666,0.415231,0.71017057
+Mast,0.1762271,0.1726372,0.4038807,0.5497239,0.16041641,0.17339058,0.25633293,0.21985865,0.77196866,0.65458333,0.116185665,0.10618482,0.1726372,0.87702096,0.18663926,0.1751152,0.92911243,0.94556534,0.21927285,0.38727182,0.0,0.96178627,0.46146592,0.1816047,0.7497426,0.7340051,0.17615804,0.18404981,0.88384235,0.24180564,0.6464156,0.9605767,1.0,0.13560554,0.17358193,0.79944146,0.6951536,0.8090347,0.15552697,0.20640545,0.9382841,0.6816865,0.26818642,0.32190603,0.14224288,0.2789672,0.72239476
+Mesothelial,0.96178627,0.96178627,0.96178627,0.96178627,0.96178627,0.96178627,0.96178627,0.96178627,1.0,1.0,0.96178627,0.96178627,0.96178627,1.0,0.96178627,0.96178627,0.96178627,0.96178627,0.96178627,0.96178627,0.96178627,0.0,0.96178627,0.96178627,1.0,1.0,0.96178627,0.96178627,1.0,0.96178627,0.96178627,1.0,1.0,0.96178627,0.96178627,0.96178627,0.96178627,1.0,0.96178627,0.96178627,1.0,0.96178627,0.96178627,0.96178627,0.96178627,0.96178627,0.96178627
+Migratory DCs,0.47636572,0.47636572,0.56835026,0.60546815,0.47636572,0.47636572,0.48710543,0.4703858,0.8676696,0.7374349,0.4664034,0.4664034,0.47636572,0.9109398,0.47636572,0.47636572,0.92911243,0.94556534,0.46146592,0.5499074,0.46146592,0.96178627,0.0,0.47636572,0.7956322,0.80602646,0.47636572,0.47636572,0.88384235,0.51559734,0.670226,0.9605767,1.0,0.47142825,0.47636572,0.80175954,0.7349605,0.78053916,0.4664034,0.4574682,0.9382841,0.6936716,0.49177346,0.47129577,0.47142825,0.47165328,0.73719966
+Monocytes/MDMs,0.067713074,0.062456656,0.39792213,0.5432286,0.09396894,0.11020825,0.21685478,0.21506214,0.77196866,0.65458333,0.15435532,0.16857392,0.06688511,0.87702096,0.104592755,0.096792236,0.92911243,0.94556534,0.25851348,0.3610795,0.1816047,0.96178627,0.47636572,0.0,0.7497426,0.7340051,0.050825167,0.04730876,0.88384235,0.2868161,0.63671696,0.9605767,1.0,0.12444246,0.077472225,0.7897428,0.6804558,0.8090347,0.100205705,0.13649978,0.9382841,0.68032104,0.20744641,0.34656507,0.14128363,0.30300313,0.7174233
+Multiciliated,0.7497426,0.7497426,0.84494656,0.7226365,0.7497426,0.7497426,0.7418766,0.7497426,0.34868735,0.6531817,0.7497426,0.7497426,0.7497426,0.29739165,0.7497426,0.7497426,0.9392012,0.99339503,0.7355897,0.7130251,0.7497426,1.0,0.7956322,0.7497426,0.0,0.3580949,0.7497426,0.7497426,0.54366887,0.6916753,0.8859771,0.6824959,1.0,0.7497426,0.7497426,0.9265684,0.7316438,0.5465961,0.7497426,0.7497426,0.51063555,0.84522265,0.7418766,0.7516262,0.7497426,0.76139086,0.8329384
+Myofibroblasts,0.7340051,0.7340051,0.8310251,0.70951766,0.7340051,0.7340051,0.74792653,0.73565483,0.34499353,0.59711134,0.7340051,0.7340051,0.7340051,0.4917593,0.7340051,0.7340051,0.9392012,0.99339503,0.74792653,0.7059847,0.7340051,1.0,0.80602646,0.7340051,0.3580949,0.0,0.7340051,0.7340051,0.64502406,0.6775874,0.89921415,0.7510051,1.0,0.7340051,0.7340051,0.9265684,0.7316438,0.5835724,0.7340051,0.7340051,0.6391133,0.85170746,0.74792653,0.7586433,0.7340051,0.7474693,0.8329384
+NK/NKT,0.06474352,0.051192213,0.39792213,0.5432286,0.08820067,0.109773,0.21685478,0.21506214,0.77196866,0.65458333,0.15648362,0.16857392,0.05670954,0.87702096,0.10632937,0.09072863,0.92911243,0.94556534,0.25851348,0.3610795,0.17615804,0.96178627,0.47636572,0.050825167,0.7497426,0.7340051,0.0,0.06162407,0.88384235,0.2868161,0.63671696,0.9605767,1.0,0.12048433,0.06955588,0.7897428,0.6804558,0.8090347,0.09281392,0.1383635,0.9382841,0.68032104,0.20744641,0.34656507,0.13583699,0.30300313,0.7174233
+Neutrophils,0.060269274,0.06469284,0.39346927,0.5432286,0.09902334,0.1094533,0.21685478,0.21506214,0.77196866,0.65458333,0.16404241,0.17201813,0.06903158,0.87702096,0.10978613,0.092155926,0.92911243,0.94556534,0.25851348,0.3610795,0.18404981,0.96178627,0.47636572,0.04730876,0.7497426,0.7340051,0.06162407,0.0,0.88384235,0.2868161,0.6337965,0.9605767,1.0,0.1281956,0.07826202,0.7897428,0.6804558,0.8090347,0.10441573,0.13958393,0.9382841,0.68032104,0.20363453,0.34656507,0.13745551,0.30300313,0.7174233
+PNEC,0.88384235,0.88384235,0.9195441,0.8706261,0.88384235,0.88384235,0.88384235,0.88384235,0.6048547,0.7556968,0.88384235,0.88384235,0.88384235,0.58253837,0.88384235,0.88384235,0.9439627,1.0,0.88384235,0.88384235,0.88384235,1.0,0.88384235,0.88384235,0.54366887,0.64502406,0.88384235,0.88384235,0.0,0.8404829,0.96158874,0.62928087,1.0,0.88384235,0.88384235,0.9265684,0.7876235,0.7339813,0.88384235,0.88384235,0.6632017,0.8641413,0.88384235,0.88384235,0.88384235,0.88384235,0.861598
+Plasma,0.2868161,0.2868161,0.48358613,0.5909041,0.2868161,0.28147137,0.32554516,0.2726981,0.7174953,0.69576347,0.24815202,0.23860183,0.2868161,0.81895363,0.2868161,0.28147137,0.8817228,0.94556534,0.2972059,0.4428896,0.24180564,0.96178627,0.51559734,0.2868161,0.6916753,0.6775874,0.2868161,0.2868161,0.8404829,0.0,0.69994104,0.91721725,1.0,0.28651744,0.2868161,0.79944146,0.6604985,0.85485506,0.28022736,0.2868161,0.9382841,0.70268184,0.34913352,0.37688887,0.28117272,0.35142988,0.75176126
+Proliferating AT2,0.6337965,0.63671696,0.50511456,0.6712121,0.63671696,0.63491094,0.6445305,0.65847266,0.9608574,0.8411908,0.6464156,0.6464156,0.63671696,0.98659074,0.63671696,0.63671696,0.81068116,0.94556534,0.65422904,0.68593246,0.6464156,0.96178627,0.670226,0.63671696,0.8859771,0.89921415,0.63671696,0.6337965,0.96158874,0.69994104,0.0,0.9571249,1.0,0.63671696,0.63671696,0.8058672,0.828582,0.89840984,0.6464156,0.6263374,1.0,0.70878947,0.63255656,0.64455235,0.6337965,0.66588306,0.7400878
+Proliferating Airway,0.9605767,0.9605767,0.93111074,0.9605767,0.9605767,0.9605767,0.9605767,0.9605767,0.7157457,0.78953207,0.9605767,0.9605767,0.9605767,0.6824959,0.9605767,0.9605767,0.91376543,1.0,0.9605767,0.9605767,0.9605767,1.0,0.9605767,0.9605767,0.6824959,0.7510051,0.9605767,0.9605767,0.62928087,0.91721725,0.9571249,0.0,1.0,0.9605767,0.9605767,1.0,0.88550836,0.823932,0.9605767,0.9605767,0.7576453,0.93111074,0.9605767,0.9605767,0.9605767,0.9605767,0.9026305
+Proliferating B cells,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0
+Proliferating FBs,0.12668805,0.117420554,0.39738545,0.5432286,0.10960498,0.13558908,0.2192605,0.23365943,0.77196866,0.65458333,0.14924546,0.16007671,0.122832894,0.87702096,0.13770685,0.13102409,0.92911243,0.94556534,0.23605728,0.3610795,0.13560554,0.96178627,0.47142825,0.12444246,0.7497426,0.7340051,0.12048433,0.1281956,0.88384235,0.28651744,0.63671696,0.9605767,1.0,0.0,0.11698179,0.7897428,0.6804558,0.8090347,0.14195004,0.16412358,0.9382841,0.68032104,0.23281613,0.34025237,0.109755635,0.30300313,0.7174233
+Proliferating Myeloid,0.08055675,0.07035822,0.39792213,0.5432286,0.093821004,0.1126108,0.21685478,0.21368603,0.77196866,0.65458333,0.16144022,0.1701166,0.07748478,0.87702096,0.11581719,0.07769661,0.92911243,0.94556534,0.25851348,0.3610795,0.17358193,0.96178627,0.47636572,0.077472225,0.7497426,0.7340051,0.06955588,0.07826202,0.88384235,0.2868161,0.63671696,0.9605767,1.0,0.11698179,0.0,0.7897428,0.6804558,0.8090347,0.101998016,0.1372393,0.9382841,0.68032104,0.2144028,0.34656507,0.13753681,0.30300313,0.7174233
+Proliferating NK/NKT,0.7897428,0.7897428,0.828648,0.7665324,0.7897428,0.7897428,0.7897428,0.79944146,0.9265684,0.96429825,0.79944146,0.79944146,0.7897428,0.9523018,0.7897428,0.7897428,0.9425216,0.94556534,0.79944146,0.78482693,0.79944146,0.96178627,0.80175954,0.7897428,0.9265684,0.9265684,0.7897428,0.7897428,0.9265684,0.79944146,0.8058672,1.0,1.0,0.7897428,0.7897428,0.0,0.8181219,0.879144,0.79944146,0.786901,0.9523018,0.80971944,0.7897428,0.80074054,0.7897428,0.79944146,0.8252559
+Proliferating T-cells,0.6804558,0.6804558,0.77088666,0.6678263,0.6804558,0.6804558,0.6804558,0.6951536,0.7316438,0.801098,0.6951536,0.6951536,0.6804558,0.7821294,0.6804558,0.6804558,0.8944572,0.94556534,0.6951536,0.714417,0.6951536,0.96178627,0.7349605,0.6804558,0.7316438,0.7316438,0.6804558,0.6804558,0.7876235,0.6604985,0.828582,0.88550836,1.0,0.6804558,0.6804558,0.8181219,0.0,0.86405575,0.6951536,0.68545496,0.8767203,0.7038474,0.6780509,0.70366806,0.6804558,0.6951536,0.73721087
+RASC,0.8090347,0.8090347,0.85867155,0.6983159,0.8090347,0.8090347,0.8090347,0.8090347,0.61960804,0.7509452,0.8090347,0.8090347,0.8090347,0.5770624,0.8090347,0.8090347,0.98659074,0.99339503,0.8090347,0.7695211,0.8090347,1.0,0.78053916,0.8090347,0.5465961,0.5835724,0.8090347,0.8090347,0.7339813,0.85485506,0.89840984,0.823932,1.0,0.8090347,0.8090347,0.879144,0.86405575,0.0,0.8090347,0.7923607,0.6263081,0.8018125,0.79147846,0.8090347,0.8090347,0.8090347,0.89154166
+SMCs/Pericytes,0.09079078,0.083402075,0.40441737,0.5497239,0.09032586,0.12144587,0.23028581,0.2090822,0.77196866,0.65458333,0.13740781,0.14850186,0.083402075,0.87702096,0.13143492,0.098787345,0.92911243,0.94556534,0.24276292,0.38016644,0.15552697,0.96178627,0.4664034,0.100205705,0.7497426,0.7340051,0.09281392,0.10441573,0.88384235,0.28022736,0.6464156,0.9605767,1.0,0.14195004,0.101998016,0.79944146,0.6951536,0.8090347,0.0,0.13553122,0.9382841,0.6816865,0.22189121,0.34656507,0.14816248,0.29014754,0.72239476
+SPP1+ Macrophages,0.13860352,0.13121483,0.41672486,0.5432286,0.13001332,0.1511777,0.2419908,0.24233726,0.77196866,0.65458333,0.17706373,0.19599535,0.13121483,0.87702096,0.15469058,0.13673922,0.92911243,0.94556534,0.27731615,0.3802653,0.20640545,0.96178627,0.4574682,0.13649978,0.7497426,0.7340051,0.1383635,0.13958393,0.88384235,0.2868161,0.6263374,0.9605767,1.0,0.16412358,0.1372393,0.786901,0.68545496,0.7923607,0.13553122,0.0,0.9382841,0.68032104,0.24322648,0.35572755,0.18034752,0.30985957,0.7174233
+Secretory,0.9382841,0.9382841,0.97398585,0.8509634,0.9382841,0.9382841,0.9382841,0.9382841,0.60860074,0.7862752,0.9382841,0.9382841,0.9382841,0.5159004,0.9382841,0.9382841,1.0,0.99339503,0.9382841,0.8987705,0.9382841,1.0,0.9382841,0.9382841,0.51063555,0.6391133,0.9382841,0.9382841,0.6632017,0.9382841,1.0,0.7576453,1.0,0.9382841,0.9382841,0.9523018,0.8767203,0.6263081,0.9382841,0.9382841,0.0,0.9025525,0.9382841,0.9382841,0.9382841,0.9382841,0.92537194
+Subpleural FBs,0.68032104,0.68032104,0.67873347,0.5719005,0.68032104,0.68032104,0.68032104,0.6816865,0.8698947,0.8517312,0.6816865,0.6816865,0.68032104,0.8891433,0.68032104,0.68032104,0.891823,0.94556534,0.67282116,0.71428216,0.6816865,0.96178627,0.6936716,0.68032104,0.84522265,0.85170746,0.68032104,0.68032104,0.8641413,0.70268184,0.70878947,0.93111074,1.0,0.68032104,0.68032104,0.80971944,0.7038474,0.8018125,0.6816865,0.68032104,0.9025525,0.0,0.69553304,0.6829856,0.68032104,0.6816865,0.81373453
+Transitional AT2,0.20505261,0.2079731,0.4350347,0.5584406,0.22209564,0.22176452,0.24464746,0.27925056,0.78119105,0.64703614,0.25913695,0.25913695,0.2079731,0.87702096,0.2312254,0.21362321,0.92911243,0.94556534,0.2866501,0.40898576,0.26818642,0.96178627,0.49177346,0.20744641,0.7418766,0.74792653,0.20744641,0.20363453,0.88384235,0.34913352,0.63255656,0.9605767,1.0,0.23281613,0.2144028,0.7897428,0.6780509,0.79147846,0.22189121,0.24322648,0.9382841,0.69553304,0.0,0.33823445,0.23000748,0.35467046,0.7174233
+Tregs,0.34656507,0.34656507,0.48731008,0.55102295,0.34656507,0.34656507,0.3549439,0.33267248,0.81422824,0.66425425,0.32190603,0.32190603,0.34656507,0.87702096,0.34656507,0.34656507,0.92911243,0.94556534,0.35279837,0.43894988,0.32190603,0.96178627,0.47129577,0.34656507,0.7516262,0.7586433,0.34656507,0.34656507,0.88384235,0.37688887,0.64455235,0.9605767,1.0,0.34025237,0.34656507,0.80074054,0.70366806,0.8090347,0.34656507,0.35572755,0.9382841,0.6829856,0.33823445,0.0,0.34025237,0.37198597,0.73090935
+Venous,0.1274538,0.13537636,0.3858356,0.5432286,0.1219099,0.12211666,0.21417215,0.23394501,0.77196866,0.65458333,0.17100081,0.16290982,0.1295816,0.87702096,0.14319178,0.124531224,0.92911243,0.94556534,0.24416137,0.3637666,0.14224288,0.96178627,0.47142825,0.14128363,0.7497426,0.7340051,0.13583699,0.13745551,0.88384235,0.28117272,0.6337965,0.9605767,1.0,0.109755635,0.13753681,0.7897428,0.6804558,0.8090347,0.14816248,0.18034752,0.9382841,0.68032104,0.23000748,0.34025237,0.0,0.30300313,0.7174233
+cDCs,0.30300313,0.30300313,0.4447249,0.56409556,0.30300313,0.30300313,0.31852853,0.29760665,0.8074255,0.65458333,0.2789672,0.2789672,0.30300313,0.86828774,0.30300313,0.30300313,0.92911243,0.94556534,0.31867543,0.415231,0.2789672,0.96178627,0.47165328,0.30300313,0.76139086,0.7474693,0.30300313,0.30300313,0.88384235,0.35142988,0.66588306,0.9605767,1.0,0.30300313,0.30300313,0.79944146,0.6951536,0.8090347,0.29014754,0.30985957,0.9382841,0.6816865,0.35467046,0.37198597,0.30300313,0.0,0.72239476
+pDCs,0.7174233,0.7174233,0.66422004,0.74449366,0.7174233,0.7174233,0.7174233,0.72239476,0.8329384,0.85405767,0.72239476,0.72239476,0.7174233,0.883424,0.7174233,0.7174233,0.869499,0.94556534,0.72239476,0.71017057,0.72239476,0.96178627,0.73719966,0.7174233,0.8329384,0.8329384,0.7174233,0.7174233,0.861598,0.75176126,0.7400878,0.9026305,1.0,0.7174233,0.7174233,0.8252559,0.73721087,0.89154166,0.72239476,0.7174233,0.92537194,0.81373453,0.7174233,0.73090935,0.7174233,0.72239476,0.0

data/outputs/formal_release/observed_T2_sss.csv

@@ -0,0 +1,48 @@
+,AT1,AT2,Activated Fibrotic FBs,Adventitial FBs,Alveolar FBs,Alveolar Macrophages,Arteriole,B cells,Basal,Basophils,CD4+ T-cells,CD8+ T-cells,Capillary,Goblet,Inflammatory FBs,Interstitial Macrophages,KRT5-/KRT17+,Langerhans cells,Lymphatic,Macrophages - IFN-activated,Mast,Mesothelial,Migratory DCs,Monocytes/MDMs,Multiciliated,Myofibroblasts,NK/NKT,Neutrophils,PNEC,Plasma,Proliferating AT2,Proliferating Airway,Proliferating B cells,Proliferating FBs,Proliferating Myeloid,Proliferating NK/NKT,Proliferating T-cells,RASC,SMCs/Pericytes,SPP1+ Macrophages,Secretory,Subpleural FBs,Transitional AT2,Tregs,Venous,cDCs,pDCs
+AT1,0.0,0.19834806,0.25747168,0.55009305,0.24321142,0.22625123,0.2825901,0.44758704,0.55284846,0.66214406,0.2573406,0.273842,0.1874258,0.7879222,0.22538486,0.24321142,0.33024412,0.89204127,0.26148066,0.37713763,0.2672593,0.94435436,0.27683163,0.20788749,0.6150211,0.41305378,0.2422184,0.23085278,0.9425024,0.28334573,0.45744833,0.92297137,0.93934256,0.23748279,0.24633548,0.9268982,0.3864221,0.58205724,0.2551139,0.3111034,0.81914365,0.6202745,0.26505676,0.280927,0.27790564,0.26401904,0.33092698
+AT2,0.19834806,0.0,0.18486404,0.5355857,0.16803606,0.20107049,0.24965629,0.41027912,0.55284846,0.66214406,0.21267988,0.23037782,0.17056361,0.78385484,0.21266909,0.17567913,0.27720302,0.87589437,0.18867661,0.4041289,0.19375059,0.94435436,0.2162652,0.14840098,0.619538,0.37992927,0.14382015,0.19374956,0.9425024,0.23303795,0.41595587,0.92297137,0.92829126,0.15928657,0.16262764,0.90997106,0.34766534,0.58205724,0.20618232,0.24279666,0.81914365,0.5975417,0.21918888,0.23819272,0.21684042,0.21953686,0.28130215
+Activated Fibrotic FBs,0.25747168,0.18486404,0.0,0.5355857,0.13828322,0.26390374,0.27555883,0.3856965,0.5506082,0.66214406,0.16436705,0.17477669,0.22054602,0.78385484,0.24426511,0.15036146,0.26590052,0.87589437,0.15899093,0.39263263,0.17029351,0.94435436,0.18263753,0.15806143,0.619538,0.38275275,0.19435991,0.221969,0.9425024,0.18801805,0.41307977,0.92297137,0.92829126,0.135225,0.18641393,0.90997106,0.35197973,0.58205724,0.17441344,0.2536759,0.81914365,0.5975417,0.22288463,0.18270129,0.20291008,0.17926112,0.25381884
+Adventitial FBs,0.55009305,0.5355857,0.5355857,0.0,0.5355857,0.55009305,0.53431714,0.60466737,0.5949485,0.7115628,0.5355857,0.5355857,0.5355857,0.781377,0.5266066,0.5355857,0.5355857,0.88053906,0.5355857,0.58701926,0.5355857,0.95257837,0.5355857,0.5355857,0.6100528,0.48112246,0.5355857,0.5355857,0.907396,0.5355857,0.588497,0.88300854,0.9469976,0.5355857,0.5355857,0.92342865,0.5288167,0.60242283,0.51355296,0.5267175,0.806159,0.5663757,0.5230077,0.5355857,0.5355857,0.5355857,0.5197935
+Alveolar FBs,0.24321142,0.16803606,0.13828322,0.5355857,0.0,0.25819507,0.2606669,0.3846661,0.5506082,0.66214406,0.13666196,0.15221013,0.24000232,0.78385484,0.21997719,0.0750924,0.29045048,0.87589437,0.12988767,0.38725007,0.10427364,0.94435436,0.19541813,0.1579612,0.619538,0.3750885,0.18792269,0.21976238,0.9425024,0.1895934,0.39811116,0.92297137,0.92829126,0.098151654,0.16806038,0.90997106,0.33899704,0.58205724,0.10869122,0.2250499,0.81914365,0.5975417,0.21212712,0.16941966,0.13778344,0.15718965,0.2714205
+Alveolar Macrophages,0.22625123,0.20107049,0.26390374,0.55009305,0.25819507,0.0,0.26550773,0.4483389,0.5734904,0.67394733,0.2740266,0.28592303,0.20714958,0.7917116,0.23530303,0.25581664,0.33608565,0.89204127,0.27232692,0.38529035,0.26633185,0.94435436,0.29065874,0.22559114,0.62739474,0.42962834,0.21382114,0.23128368,0.9425024,0.29045382,0.45770448,0.92297137,0.92829126,0.2567697,0.2491181,0.9073284,0.37573814,0.6026992,0.2790427,0.2933305,0.82700044,0.605611,0.30268133,0.29475406,0.2745587,0.27794287,0.34140566
+Arteriole,0.2825901,0.24965629,0.27555883,0.53431714,0.2606669,0.26550773,0.0,0.44255212,0.57125014,0.65816945,0.27891225,0.2849243,0.208046,0.795779,0.20276375,0.26654264,0.3501596,0.87589437,0.27984026,0.4023057,0.26595557,0.94435436,0.30002385,0.24372905,0.6192288,0.417397,0.21227315,0.20037653,0.9425024,0.28177634,0.42131406,0.92297137,0.92829126,0.27150732,0.2628513,0.9073284,0.33054748,0.6026992,0.24160595,0.3167757,0.82700044,0.5898351,0.29219282,0.28988993,0.2704236,0.27322754,0.33505756
+B cells,0.44758704,0.41027912,0.3856965,0.60466737,0.3846661,0.4483389,0.44255212,0.0,0.64207256,0.6922387,0.37610322,0.387468,0.42208236,0.80106324,0.42095974,0.37610322,0.43252614,0.8895891,0.39077464,0.49893957,0.38231656,0.9454295,0.40028474,0.4070485,0.6438043,0.50019944,0.4188517,0.4165638,0.9425024,0.37014917,0.48641312,0.92297137,0.89104545,0.38910136,0.4026763,0.9158468,0.47211152,0.6491945,0.40481177,0.37914816,0.8156733,0.57006955,0.402147,0.387468,0.3886754,0.39022115,0.4195146
+Basal,0.55284846,0.55284846,0.5506082,0.5949485,0.5506082,0.5734904,0.57125014,0.64207256,0.0,0.55989414,0.5506082,0.5506082,0.5734904,0.5044655,0.5734904,0.5506082,0.53651136,0.88302094,0.5506082,0.59446484,0.5506082,0.9818802,0.5506082,0.5506082,0.39402837,0.41326633,0.57125014,0.57125014,0.8123861,0.5421156,0.6365144,0.6840187,0.9469976,0.5506082,0.5506082,0.93822896,0.5985905,0.19444306,0.5506082,0.5622267,0.53190124,0.71125716,0.53066295,0.5506082,0.5421156,0.5474941,0.5586697
+Basophils,0.66214406,0.66214406,0.66214406,0.7115628,0.66214406,0.67394733,0.65816945,0.6922387,0.55989414,0.0,0.66214406,0.66214406,0.67394733,0.67974585,0.67394733,0.66214406,0.66214406,0.88698906,0.66214406,0.68811506,0.66214406,0.9818802,0.66214406,0.66214406,0.6408406,0.6439845,0.67394733,0.67394733,0.89383,0.66214406,0.6930223,0.81193215,0.9469976,0.66214406,0.66214406,0.9704371,0.69116694,0.5551777,0.66214406,0.6598018,0.71829975,0.7464143,0.6378803,0.66214406,0.66214406,0.66214406,0.66214406
+CD4+ T-cells,0.2573406,0.21267988,0.16436705,0.5355857,0.13666196,0.2740266,0.27891225,0.37610322,0.5506082,0.66214406,0.0,0.07757487,0.25472537,0.78385484,0.22993621,0.1207157,0.28140247,0.87589437,0.1679533,0.36976996,0.14024806,0.94435436,0.1549389,0.18591127,0.619538,0.3750885,0.22950788,0.23940659,0.9425024,0.155056,0.40538844,0.92297137,0.91972834,0.16583796,0.20078823,0.9158468,0.31502834,0.58205724,0.17736508,0.21876146,0.81914365,0.5975417,0.20511955,0.09390721,0.16750695,0.1629391,0.24066395
+CD8+ T-cells,0.273842,0.23037782,0.17477669,0.5355857,0.15221013,0.28592303,0.2849243,0.387468,0.5506082,0.66214406,0.07757487,0.0,0.27122676,0.78385484,0.24643761,0.12229049,0.28279418,0.87589437,0.18097748,0.36642516,0.14049117,0.94435436,0.12945704,0.20793088,0.619538,0.3750885,0.24133548,0.25243074,0.9425024,0.16598137,0.4105072,0.92297137,0.91972834,0.17588094,0.21441059,0.9158468,0.31842706,0.58205724,0.19171672,0.23867655,0.81914365,0.5975417,0.21656626,0.10005757,0.17874645,0.16165933,0.2422801
+Capillary,0.1874258,0.17056361,0.22054602,0.5355857,0.24000232,0.20714958,0.208046,0.42208236,0.5734904,0.67394733,0.25472537,0.27122676,0.0,0.795779,0.16211371,0.24587806,0.2995552,0.87589437,0.24215868,0.3882798,0.25690293,0.94435436,0.26296222,0.163533,0.6228779,0.40743917,0.1435898,0.13124779,0.9425024,0.268826,0.43144792,0.92297137,0.92829126,0.22082001,0.22454458,0.9073284,0.34766534,0.6026992,0.2468429,0.28923553,0.82700044,0.5911037,0.27033406,0.27150458,0.2582401,0.26113707,0.31809047
+Goblet,0.7879222,0.78385484,0.78385484,0.781377,0.78385484,0.7917116,0.795779,0.80106324,0.5044655,0.67974585,0.78385484,0.78385484,0.795779,0.0,0.795779,0.78385484,0.78385484,0.8918355,0.78385484,0.80439585,0.78385484,0.9818802,0.78385484,0.78385484,0.43523285,0.6633879,0.7917116,0.795779,0.7589204,0.78385484,0.80408597,0.6507668,0.9741129,0.78385484,0.78385484,0.9741129,0.8249087,0.5193587,0.78385484,0.78385484,0.48131666,0.812224,0.7557109,0.78385484,0.78385484,0.78385484,0.78385484
+Inflammatory FBs,0.22538486,0.21266909,0.24426511,0.5266066,0.21997719,0.23530303,0.20276375,0.42095974,0.5734904,0.67394733,0.22993621,0.24643761,0.16211371,0.795779,0.0,0.22585294,0.33323225,0.87589437,0.24494757,0.3816929,0.23135352,0.94435436,0.276462,0.19130681,0.6228779,0.40860614,0.1700032,0.14734975,0.9425024,0.2590772,0.41360328,0.92297137,0.92829126,0.23397435,0.24784778,0.9073284,0.3355486,0.6026992,0.20863748,0.29307255,0.82700044,0.5843963,0.2711889,0.25666195,0.22627528,0.24868838,0.3236988
+Interstitial Macrophages,0.24321142,0.17567913,0.15036146,0.5355857,0.0750924,0.25581664,0.26654264,0.37610322,0.5506082,0.66214406,0.1207157,0.12229049,0.24587806,0.78385484,0.22585294,0.0,0.28741342,0.87589437,0.15925808,0.36865595,0.11078616,0.94435436,0.18081556,0.15406251,0.619538,0.3750885,0.19803974,0.22979678,0.9425024,0.17433612,0.40693524,0.92297137,0.91972834,0.12554966,0.18040982,0.9158468,0.32487315,0.58205724,0.14196648,0.20958082,0.81914365,0.5975417,0.21212712,0.15065345,0.16015857,0.17392762,0.25282636
+KRT5-/KRT17+,0.33024412,0.27720302,0.26590052,0.5355857,0.29045048,0.33608565,0.3501596,0.43252614,0.53651136,0.66214406,0.28140247,0.28279418,0.2995552,0.78385484,0.33323225,0.28741342,0.0,0.87589437,0.2837595,0.42705166,0.29549402,0.94435436,0.27081007,0.2719115,0.619538,0.38120586,0.29728413,0.30432123,0.9425024,0.27571374,0.43359166,0.92297137,0.92525417,0.27846634,0.28638604,0.9158468,0.39704165,0.5625604,0.312409,0.29661745,0.81914365,0.5975417,0.3126187,0.27935246,0.2870015,0.27671656,0.30819926
+Langerhans cells,0.89204127,0.87589437,0.87589437,0.88053906,0.87589437,0.89204127,0.87589437,0.8895891,0.88302094,0.88698906,0.87589437,0.87589437,0.87589437,0.8918355,0.87589437,0.87589437,0.87589437,0.0,0.87589437,0.87322724,0.87589437,0.9818802,0.87589437,0.87589437,0.88302094,0.87589437,0.87589437,0.87589437,0.9645747,0.87589437,0.8877489,0.95619303,1.0,0.87589437,0.87589437,1.0,0.87589437,0.88302094,0.87589437,0.87589437,0.9108266,0.8912286,0.87589437,0.87589437,0.87589437,0.87589437,0.87589437
+Lymphatic,0.26148066,0.18867661,0.15899093,0.5355857,0.12988767,0.27232692,0.27984026,0.39077464,0.5506082,0.66214406,0.1679533,0.18097748,0.24215868,0.78385484,0.24494757,0.15925808,0.2837595,0.87589437,0.0,0.3892764,0.15160471,0.94435436,0.19631882,0.17884223,0.619538,0.38275275,0.20872678,0.22620648,0.9425024,0.19813189,0.41153297,0.92297137,0.92829126,0.13421342,0.16827345,0.90997106,0.34373623,0.58205724,0.16278023,0.24531792,0.81914365,0.5975417,0.22219267,0.19361332,0.16310409,0.1875297,0.26275676
+Macrophages - IFN-activated,0.37713763,0.4041289,0.39263263,0.58701926,0.38725007,0.38529035,0.4023057,0.49893957,0.59446484,0.68811506,0.36976996,0.36642516,0.3882798,0.80439585,0.3816929,0.36865595,0.42705166,0.87322724,0.3892764,0.0,0.38725007,0.9678032,0.3718125,0.39905688,0.6441929,0.48163494,0.39075094,0.38691702,0.9425024,0.36976996,0.4975637,0.92297137,0.91972834,0.38611215,0.39905688,0.9158468,0.4342951,0.61216474,0.40113586,0.36153072,0.8356173,0.6060102,0.40588862,0.36997142,0.3890347,0.39550048,0.39468947
+Mast,0.2672593,0.19375059,0.17029351,0.5355857,0.10427364,0.26633185,0.26595557,0.38231656,0.5506082,0.66214406,0.14024806,0.14049117,0.25690293,0.78385484,0.23135352,0.11078616,0.29549402,0.87589437,0.15160471,0.38725007,0.0,0.94435436,0.19114907,0.17038356,0.619538,0.3692113,0.20378174,0.23937954,0.9425024,0.17019765,0.39656442,0.92297137,0.92829126,0.14036079,0.16349941,0.90997106,0.33493116,0.58205724,0.15367214,0.23191422,0.81914365,0.5975417,0.19557786,0.15024264,0.14030139,0.14707397,0.2680804
+Mesothelial,0.94435436,0.94435436,0.94435436,0.95257837,0.94435436,0.94435436,0.94435436,0.9454295,0.9818802,0.9818802,0.94435436,0.94435436,0.94435436,0.9818802,0.94435436,0.94435436,0.94435436,0.9818802,0.94435436,0.9678032,0.94435436,0.0,0.94435436,0.94435436,0.9818802,0.95257837,0.94435436,0.94435436,0.9936422,0.94435436,0.94435436,1.0,1.0,0.94435436,0.94435436,1.0,0.95257837,0.9818802,0.94435436,0.94435436,1.0,0.9688783,0.94435436,0.94435436,0.94435436,0.94435436,0.95257837
+Migratory DCs,0.27683163,0.2162652,0.18263753,0.5355857,0.19541813,0.29065874,0.30002385,0.40028474,0.5506082,0.66214406,0.1549389,0.12945704,0.26296222,0.78385484,0.276462,0.18081556,0.27081007,0.87589437,0.19631882,0.3718125,0.19114907,0.94435436,0.0,0.20009153,0.619538,0.38275275,0.23170404,0.2526163,0.9425024,0.18426739,0.4254758,0.92297137,0.91972834,0.18079777,0.21023642,0.9158468,0.33222583,0.58205724,0.23749024,0.25589094,0.81914365,0.5975417,0.24342267,0.13382079,0.2028691,0.17210913,0.2376372
+Monocytes/MDMs,0.20788749,0.14840098,0.15806143,0.5355857,0.1579612,0.22559114,0.24372905,0.4070485,0.5506082,0.66214406,0.18591127,0.20793088,0.163533,0.78385484,0.19130681,0.15406251,0.2719115,0.87589437,0.17884223,0.39905688,0.17038356,0.94435436,0.20009153,0.0,0.619538,0.38555327,0.13905935,0.15391438,0.9425024,0.22137378,0.41676858,0.92297137,0.92829126,0.15044007,0.15468056,0.9073284,0.3435457,0.58205724,0.1900212,0.24055931,0.81914365,0.5975417,0.24202305,0.2114008,0.18703908,0.20172623,0.27624407
+Multiciliated,0.6150211,0.619538,0.619538,0.6100528,0.619538,0.62739474,0.6192288,0.6438043,0.39402837,0.6408406,0.619538,0.619538,0.6228779,0.43523285,0.6228779,0.619538,0.619538,0.88302094,0.619538,0.6441929,0.619538,0.9818802,0.619538,0.619538,0.0,0.5168392,0.62739474,0.6228779,0.7589204,0.619538,0.67989343,0.6596415,0.93306214,0.619538,0.619538,0.93822896,0.6447304,0.41094005,0.619538,0.619538,0.47345877,0.72277707,0.60695994,0.619538,0.619538,0.619538,0.619538
+Myofibroblasts,0.41305378,0.37992927,0.38275275,0.48112246,0.3750885,0.42962834,0.417397,0.50019944,0.41326633,0.6439845,0.3750885,0.3750885,0.40743917,0.6633879,0.40860614,0.3750885,0.38120586,0.87589437,0.38275275,0.48163494,0.3692113,0.95257837,0.38275275,0.38555327,0.5168392,0.0,0.40619525,0.4102626,0.8959112,0.3541868,0.49458063,0.8285942,0.9469976,0.38275275,0.3768755,0.93455315,0.4389984,0.46069396,0.3867202,0.38572946,0.7220962,0.64696527,0.33662397,0.3750885,0.36182073,0.38222972,0.39695132
+NK/NKT,0.2422184,0.14382015,0.19435991,0.5355857,0.18792269,0.21382114,0.21227315,0.4188517,0.57125014,0.67394733,0.22950788,0.24133548,0.1435898,0.7917116,0.1700032,0.19803974,0.29728413,0.87589437,0.20872678,0.39075094,0.20378174,0.94435436,0.23170404,0.13905935,0.62739474,0.40619525,0.0,0.12634741,0.9425024,0.24684212,0.4284996,0.92297137,0.92829126,0.16487207,0.17541787,0.90997106,0.34029946,0.6026992,0.20414628,0.25946066,0.82700044,0.5911037,0.27354577,0.24952072,0.21779256,0.21908236,0.30650377
+Neutrophils,0.23085278,0.19374956,0.221969,0.5355857,0.21976238,0.23128368,0.20037653,0.4165638,0.57125014,0.67394733,0.23940659,0.25243074,0.13124779,0.795779,0.14734975,0.22979678,0.30432123,0.87589437,0.22620648,0.38691702,0.23937954,0.94435436,0.2526163,0.15391438,0.6228779,0.4102626,0.12634741,0.0,0.9425024,0.25921,0.4269274,0.92297137,0.92829126,0.2167394,0.19552472,0.9073284,0.3387527,0.6026992,0.24694566,0.28480834,0.82700044,0.5911037,0.2762753,0.26115865,0.23391166,0.24288374,0.31322208
+PNEC,0.9425024,0.9425024,0.9425024,0.907396,0.9425024,0.9425024,0.9425024,0.9425024,0.8123861,0.89383,0.9425024,0.9425024,0.9425024,0.7589204,0.9425024,0.9425024,0.9425024,0.9645747,0.9425024,0.9425024,0.9425024,0.9936422,0.9425024,0.9425024,0.7589204,0.8959112,0.9425024,0.9425024,0.0,0.9425024,0.9425024,0.7584695,0.9741129,0.9425024,0.9425024,0.9741129,0.9287581,0.8123861,0.9425024,0.9425024,0.7796533,0.9425024,0.9317458,0.9425024,0.9425024,0.9425024,0.9425024
+Plasma,0.28334573,0.23303795,0.18801805,0.5355857,0.1895934,0.29045382,0.28177634,0.37014917,0.5421156,0.66214406,0.155056,0.16598137,0.268826,0.78385484,0.2590772,0.17433612,0.27571374,0.87589437,0.19813189,0.36976996,0.17019765,0.94435436,0.18426739,0.22137378,0.619538,0.3541868,0.24684212,0.25921,0.9425024,0.0,0.41269284,0.92297137,0.91972834,0.20003152,0.21298955,0.9158468,0.32007584,0.5735647,0.22210312,0.23490152,0.81914365,0.5975417,0.20275278,0.17442614,0.17324105,0.19535917,0.24641486
+Proliferating AT2,0.45744833,0.41595587,0.41307977,0.588497,0.39811116,0.45770448,0.42131406,0.48641312,0.6365144,0.6930223,0.40538844,0.4105072,0.43144792,0.80408597,0.41360328,0.40693524,0.43359166,0.8877489,0.41153297,0.4975637,0.39656442,0.94435436,0.4254758,0.41676858,0.67989343,0.49458063,0.4284996,0.4269274,0.9425024,0.41269284,0.0,0.92297137,0.92829126,0.41307977,0.4114353,0.9020145,0.44653416,0.6392524,0.39885172,0.41386077,0.8376731,0.62788504,0.41010132,0.4105072,0.39853832,0.39914164,0.440215
+Proliferating Airway,0.92297137,0.92297137,0.92297137,0.88300854,0.92297137,0.92297137,0.92297137,0.92297137,0.6840187,0.81193215,0.92297137,0.92297137,0.92297137,0.6507668,0.92297137,0.92297137,0.92297137,0.95619303,0.92297137,0.92297137,0.92297137,1.0,0.92297137,0.92297137,0.6596415,0.8285942,0.92297137,0.92297137,0.7584695,0.92297137,0.92297137,0.0,0.9741129,0.92297137,0.92297137,0.96368504,0.9001932,0.69224656,0.92297137,0.92297137,0.6883425,0.92297137,0.9030262,0.92297137,0.92297137,0.92297137,0.92297137
+Proliferating B cells,0.93934256,0.92829126,0.92829126,0.9469976,0.92829126,0.92829126,0.92829126,0.89104545,0.9469976,0.9469976,0.91972834,0.91972834,0.92829126,0.9741129,0.92829126,0.91972834,0.92525417,1.0,0.92829126,0.91972834,0.92829126,1.0,0.91972834,0.92829126,0.93306214,0.9469976,0.92829126,0.92829126,0.9741129,0.91972834,0.92829126,0.9741129,0.0,0.92829126,0.92829126,0.9554066,0.91972834,0.9469976,0.92829126,0.91972834,0.9741129,0.9311172,0.9469976,0.91972834,0.92829126,0.92829126,0.91972834
+Proliferating FBs,0.23748279,0.15928657,0.135225,0.5355857,0.098151654,0.2567697,0.27150732,0.38910136,0.5506082,0.66214406,0.16583796,0.17588094,0.22082001,0.78385484,0.23397435,0.12554966,0.27846634,0.87589437,0.13421342,0.38611215,0.14036079,0.94435436,0.18079777,0.15044007,0.619538,0.38275275,0.16487207,0.2167394,0.9425024,0.20003152,0.41307977,0.92297137,0.92829126,0.0,0.15657322,0.90997106,0.35018235,0.58205724,0.1313764,0.23786035,0.81914365,0.5975417,0.2246429,0.19338788,0.16344506,0.1766027,0.2660968
+Proliferating Myeloid,0.24633548,0.16262764,0.18641393,0.5355857,0.16806038,0.2491181,0.2628513,0.4026763,0.5506082,0.66214406,0.20078823,0.21441059,0.22454458,0.78385484,0.24784778,0.18040982,0.28638604,0.87589437,0.16827345,0.39905688,0.16349941,0.94435436,0.21023642,0.15468056,0.619538,0.3768755,0.17541787,0.19552472,0.9425024,0.21298955,0.4114353,0.92297137,0.92829126,0.15657322,0.0,0.90997106,0.3387527,0.58205724,0.20300983,0.2409557,0.81914365,0.5975417,0.23262326,0.22543894,0.1886151,0.19701974,0.27967796
+Proliferating NK/NKT,0.9268982,0.90997106,0.90997106,0.92342865,0.90997106,0.9073284,0.9073284,0.9158468,0.93822896,0.9704371,0.9158468,0.9158468,0.9073284,0.9741129,0.9073284,0.9158468,0.9158468,1.0,0.90997106,0.9158468,0.90997106,1.0,0.9158468,0.9073284,0.93822896,0.93455315,0.90997106,0.9073284,0.9741129,0.9158468,0.9020145,0.96368504,0.9554066,0.90997106,0.90997106,0.0,0.9158468,0.93822896,0.90997106,0.9158468,0.9741129,0.9290974,0.93455315,0.9158468,0.90997106,0.90997106,0.9158468
+Proliferating T-cells,0.3864221,0.34766534,0.35197973,0.5288167,0.33899704,0.37573814,0.33054748,0.47211152,0.5985905,0.69116694,0.31502834,0.31842706,0.34766534,0.8249087,0.3355486,0.32487315,0.39704165,0.87589437,0.34373623,0.4342951,0.33493116,0.95257837,0.33222583,0.3435457,0.6447304,0.4389984,0.34029946,0.3387527,0.9287581,0.32007584,0.44653416,0.9001932,0.91972834,0.35018235,0.3387527,0.9158468,0.0,0.62356794,0.34185362,0.35633126,0.8478691,0.62107384,0.3555737,0.32071063,0.3299489,0.33194894,0.33374864
+RASC,0.58205724,0.58205724,0.58205724,0.60242283,0.58205724,0.6026992,0.6026992,0.6491945,0.19444306,0.5551777,0.58205724,0.58205724,0.6026992,0.5193587,0.6026992,0.58205724,0.5625604,0.88302094,0.58205724,0.61216474,0.58205724,0.9818802,0.58205724,0.58205724,0.41094005,0.46069396,0.6026992,0.6026992,0.8123861,0.5735647,0.6392524,0.69224656,0.9469976,0.58205724,0.58205724,0.93822896,0.62356794,0.0,0.58205724,0.5893824,0.5425101,0.71125716,0.55779356,0.58205724,0.5735647,0.58205724,0.58205724
+SMCs/Pericytes,0.2551139,0.20618232,0.17441344,0.51355296,0.10869122,0.2790427,0.24160595,0.40481177,0.5506082,0.66214406,0.17736508,0.19171672,0.2468429,0.78385484,0.20863748,0.14196648,0.312409,0.87589437,0.16278023,0.40113586,0.15367214,0.94435436,0.23749024,0.1900212,0.619538,0.3867202,0.20414628,0.24694566,0.9425024,0.22210312,0.39885172,0.92297137,0.92829126,0.1313764,0.20300983,0.90997106,0.34185362,0.58205724,0.0,0.2553198,0.81914365,0.5835983,0.22938983,0.20081966,0.16977103,0.19479561,0.2804181
+SPP1+ Macrophages,0.3111034,0.24279666,0.2536759,0.5267175,0.2250499,0.2933305,0.3167757,0.37914816,0.5622267,0.6598018,0.21876146,0.23867655,0.28923553,0.78385484,0.29307255,0.20958082,0.29661745,0.87589437,0.24531792,0.36153072,0.23191422,0.94435436,0.25589094,0.24055931,0.619538,0.38572946,0.25946066,0.28480834,0.9425024,0.23490152,0.41386077,0.92297137,0.91972834,0.23786035,0.2409557,0.9158468,0.35633126,0.5893824,0.2553198,0.0,0.81914365,0.5886735,0.27372602,0.23894052,0.23381351,0.2437871,0.29583848
+Secretory,0.81914365,0.81914365,0.81914365,0.806159,0.81914365,0.82700044,0.82700044,0.8156733,0.53190124,0.71829975,0.81914365,0.81914365,0.82700044,0.48131666,0.82700044,0.81914365,0.81914365,0.9108266,0.81914365,0.8356173,0.81914365,1.0,0.81914365,0.81914365,0.47345877,0.7220962,0.82700044,0.82700044,0.7796533,0.81914365,0.8376731,0.6883425,0.9741129,0.81914365,0.81914365,0.9741129,0.8478691,0.5425101,0.81914365,0.81914365,0.0,0.7892955,0.8083871,0.81914365,0.81914365,0.81914365,0.81914365
+Subpleural FBs,0.6202745,0.5975417,0.5975417,0.5663757,0.5975417,0.605611,0.5898351,0.57006955,0.71125716,0.7464143,0.5975417,0.5975417,0.5911037,0.812224,0.5843963,0.5975417,0.5975417,0.8912286,0.5975417,0.6060102,0.5975417,0.9688783,0.5975417,0.5975417,0.72277707,0.64696527,0.5911037,0.5911037,0.9425024,0.5975417,0.62788504,0.92297137,0.9311172,0.5975417,0.5975417,0.9290974,0.62107384,0.71125716,0.5835983,0.5886735,0.7892955,0.0,0.6134221,0.5975417,0.5975417,0.5975417,0.5975417
+Transitional AT2,0.26505676,0.21918888,0.22288463,0.5230077,0.21212712,0.30268133,0.29219282,0.402147,0.53066295,0.6378803,0.20511955,0.21656626,0.27033406,0.7557109,0.2711889,0.21212712,0.3126187,0.87589437,0.22219267,0.40588862,0.19557786,0.94435436,0.24342267,0.24202305,0.60695994,0.33662397,0.27354577,0.2762753,0.9317458,0.20275278,0.41010132,0.9030262,0.9469976,0.2246429,0.23262326,0.93455315,0.3555737,0.55779356,0.22938983,0.27372602,0.8083871,0.6134221,0.0,0.2196435,0.21822284,0.22413714,0.28354228
+Tregs,0.280927,0.23819272,0.18270129,0.5355857,0.16941966,0.29475406,0.28988993,0.387468,0.5506082,0.66214406,0.09390721,0.10005757,0.27150458,0.78385484,0.25666195,0.15065345,0.27935246,0.87589437,0.19361332,0.36997142,0.15024264,0.94435436,0.13382079,0.2114008,0.619538,0.3750885,0.24952072,0.26115865,0.9425024,0.17442614,0.4105072,0.92297137,0.91972834,0.19338788,0.22543894,0.9158468,0.32071063,0.58205724,0.20081966,0.23894052,0.81914365,0.5975417,0.2196435,0.0,0.19494183,0.17475383,0.23731916
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+cDCs,0.26401904,0.21953686,0.17926112,0.5355857,0.15718965,0.27794287,0.27322754,0.39022115,0.5474941,0.66214406,0.1629391,0.16165933,0.26113707,0.78385484,0.24868838,0.17392762,0.27671656,0.87589437,0.1875297,0.39550048,0.14707397,0.94435436,0.17210913,0.20172623,0.619538,0.38222972,0.21908236,0.24288374,0.9425024,0.19535917,0.39914164,0.92297137,0.92829126,0.1766027,0.19701974,0.90997106,0.33194894,0.58205724,0.19479561,0.2437871,0.81914365,0.5975417,0.22413714,0.17475383,0.15736765,0.0,0.260795
+pDCs,0.33092698,0.28130215,0.25381884,0.5197935,0.2714205,0.34140566,0.33505756,0.4195146,0.5586697,0.66214406,0.24066395,0.2422801,0.31809047,0.78385484,0.3236988,0.25282636,0.30819926,0.87589437,0.26275676,0.39468947,0.2680804,0.95257837,0.2376372,0.27624407,0.619538,0.39695132,0.30650377,0.31322208,0.9425024,0.24641486,0.440215,0.92297137,0.91972834,0.2660968,0.27967796,0.9158468,0.33374864,0.58205724,0.2804181,0.29583848,0.81914365,0.5975417,0.28354228,0.23731916,0.27540362,0.260795,0.0

data/outputs/formal_release/observed_T3_sss.csv

@@ -0,0 +1,48 @@
+,AT1,AT2,Activated Fibrotic FBs,Adventitial FBs,Alveolar FBs,Alveolar Macrophages,Arteriole,B cells,Basal,Basophils,CD4+ T-cells,CD8+ T-cells,Capillary,Goblet,Inflammatory FBs,Interstitial Macrophages,KRT5-/KRT17+,Langerhans cells,Lymphatic,Macrophages - IFN-activated,Mast,Mesothelial,Migratory DCs,Monocytes/MDMs,Multiciliated,Myofibroblasts,NK/NKT,Neutrophils,PNEC,Plasma,Proliferating AT2,Proliferating Airway,Proliferating B cells,Proliferating FBs,Proliferating Myeloid,Proliferating NK/NKT,Proliferating T-cells,RASC,SMCs/Pericytes,SPP1+ Macrophages,Secretory,Subpleural FBs,Transitional AT2,Tregs,Venous,cDCs,pDCs
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+Alveolar Macrophages,0.3329764,0.30325204,0.3089826,0.49138767,0.360946,0.0,0.3728002,0.39710492,0.5307201,0.59691995,0.32980886,0.33955097,0.31984445,0.6424047,0.38003057,0.33232513,0.35960668,0.7809543,0.37164736,0.36832282,0.3566665,0.9638704,0.34871492,0.3630268,0.60981774,0.43261224,0.33479786,0.38389733,0.68897265,0.33079466,0.4708116,0.7034184,0.8669922,0.360946,0.31025466,0.9564276,0.39365435,0.53730494,0.38269225,0.32542402,0.69309205,0.679069,0.38615173,0.34119204,0.35951108,0.32883415,0.38717505
+Arteriole,0.39387137,0.38891488,0.30714586,0.42189884,0.26473027,0.3728002,0.0,0.39943585,0.5204648,0.603919,0.29400986,0.267891,0.25155705,0.64684033,0.3072695,0.26120692,0.3991524,0.7809543,0.3120759,0.42099684,0.26473027,0.96104735,0.31173486,0.30168885,0.60049427,0.45116776,0.28745982,0.33633533,0.70631576,0.29273286,0.48671293,0.7183113,0.8669922,0.25390005,0.30742052,0.9564276,0.3447643,0.5495628,0.2690727,0.40843335,0.6841989,0.6506076,0.45324373,0.28522944,0.26473027,0.3305445,0.32235894
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+Basophils,0.59778637,0.5756921,0.58398354,0.64815533,0.61304593,0.59691995,0.603919,0.6131943,0.46509394,0.0,0.58927655,0.6036397,0.61304593,0.5375138,0.63368595,0.6172892,0.5977922,0.8223814,0.6138192,0.62186986,0.61304593,0.9638704,0.60363805,0.62763894,0.503241,0.58260727,0.6036397,0.6097822,0.6415304,0.5850333,0.597433,0.5734476,0.9499421,0.61304593,0.5943876,0.97066724,0.6268896,0.4840819,0.61304593,0.56147784,0.58061564,0.7992854,0.5293611,0.6063541,0.61304593,0.5932217,0.61765087
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+CD8+ T-cells,0.37142733,0.34014064,0.19648881,0.4216128,0.14422964,0.33955097,0.267891,0.33897084,0.5264935,0.6036397,0.13217537,0.0,0.1673713,0.64639896,0.24008915,0.13180618,0.37359247,0.7809543,0.27525356,0.4039138,0.14678468,0.96104735,0.23185296,0.22976463,0.58596545,0.4398437,0.11176614,0.29090387,0.7128972,0.13742897,0.48118153,0.7089051,0.8669922,0.16032454,0.19685288,0.9564276,0.30032113,0.5240248,0.20356007,0.35916597,0.6907803,0.65206516,0.40857506,0.14469436,0.15428528,0.261549,0.26647842
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+Inflammatory FBs,0.41459662,0.37408525,0.26087323,0.40247566,0.17327788,0.38003057,0.3072695,0.39927772,0.53337544,0.63368595,0.2820627,0.24008915,0.23503125,0.66045755,0.0,0.22234955,0.4206821,0.7809543,0.2734057,0.4071208,0.17042191,0.96104735,0.30530804,0.23378368,0.5918984,0.4516448,0.25663632,0.29896745,0.70858216,0.23900506,0.49944472,0.72294796,0.8697138,0.1975149,0.2913987,0.9564276,0.3424641,0.55407107,0.2298379,0.41654724,0.68883556,0.63951695,0.43264952,0.2650233,0.17848724,0.3192007,0.33507848
+Interstitial Macrophages,0.38097188,0.32348588,0.19467142,0.41857067,0.11817422,0.33232513,0.26120692,0.35427684,0.5113902,0.6172892,0.19820414,0.13180618,0.13652073,0.64406085,0.22234955,0.0,0.3741631,0.7809543,0.27652216,0.40597257,0.14614756,0.96104735,0.2605824,0.16322057,0.579384,0.42118353,0.14325866,0.27413207,0.70631576,0.1879268,0.4874692,0.7183113,0.8669922,0.15099382,0.17704162,0.9564276,0.31120217,0.5376743,0.19477418,0.355513,0.6841989,0.64902306,0.3973617,0.1948834,0.1470943,0.2141707,0.28705484
+KRT5-/KRT17+,0.32162955,0.3602209,0.34635454,0.5187985,0.39405784,0.35960668,0.3991524,0.43831182,0.52962124,0.5977922,0.36545646,0.37359247,0.3759731,0.66277295,0.4206821,0.3741631,0.0,0.7654862,0.40301043,0.4109099,0.39466602,0.9638704,0.35724422,0.40090293,0.60243785,0.42689165,0.3696638,0.4167966,0.7107102,0.36491925,0.41423059,0.68944865,0.8669922,0.39405784,0.34482765,0.9626473,0.4135929,0.5162398,0.41306606,0.33286697,0.68205345,0.71119916,0.39748052,0.36489812,0.39466602,0.3278299,0.3951028
+Langerhans cells,0.7654862,0.75081086,0.7809543,0.81905806,0.7809543,0.7809543,0.7809543,0.8038931,0.8203576,0.8223814,0.7809543,0.7809543,0.7809543,0.8713597,0.7809543,0.7809543,0.7654862,0.0,0.7809543,0.7809543,0.7809543,0.9888916,0.7809543,0.79289544,0.82938254,0.81584835,0.7809543,0.79628646,0.8715081,0.7809543,0.74129575,0.88171613,0.91207665,0.7809543,0.7809543,0.9837845,0.79289544,0.7702117,0.7902985,0.78378356,0.8555481,0.86694396,0.766811,0.7809543,0.7809543,0.7654862,0.7809543
+Lymphatic,0.41112074,0.3924914,0.3037976,0.38359886,0.24984296,0.37164736,0.3120759,0.3643034,0.53085935,0.6138192,0.27634788,0.27525356,0.29413718,0.6507648,0.2734057,0.27652216,0.40301043,0.7809543,0.0,0.39433587,0.24390331,0.96104735,0.32904738,0.2957993,0.60026354,0.45491976,0.28331643,0.3287639,0.7127262,0.27518904,0.50539464,0.7183113,0.8697138,0.24885936,0.29816797,0.9564276,0.33431154,0.540839,0.24774607,0.40386733,0.694373,0.62326294,0.4428575,0.2771756,0.2376322,0.34173885,0.34752518
+Macrophages - IFN-activated,0.42756242,0.43411398,0.36956355,0.48164326,0.39916196,0.36832282,0.42099684,0.45537224,0.5622839,0.62186986,0.3915377,0.4039138,0.40090474,0.6397401,0.4071208,0.40597257,0.4109099,0.7809543,0.39433587,0.0,0.39916196,0.9638704,0.3869086,0.4224804,0.6226978,0.46784768,0.3980788,0.4262851,0.7055784,0.3915377,0.51950556,0.6940962,0.8697138,0.39916196,0.38000852,0.93884945,0.42633814,0.5285403,0.41197723,0.40461916,0.6856963,0.67800677,0.4748726,0.39174023,0.39916196,0.40585405,0.4214228
+Mast,0.39189273,0.35657793,0.23825331,0.4090646,0.06325318,0.3566665,0.26473027,0.37394622,0.50714695,0.61304593,0.218782,0.14678468,0.17039517,0.6398176,0.17042191,0.14614756,0.39466602,0.7809543,0.24390331,0.39916196,0.0,0.96104735,0.2787511,0.20998354,0.5789611,0.44141954,0.18345936,0.2868634,0.70631576,0.17371048,0.49543366,0.7183113,0.8697138,0.10539226,0.23770681,0.9564276,0.32004625,0.53343105,0.14034261,0.38426286,0.6841989,0.63951695,0.42301998,0.2018229,0.081102565,0.2799519,0.29551077
+Mesothelial,0.9638704,0.9638704,0.9638704,0.96104735,0.96104735,0.9638704,0.96104735,0.9638704,0.9638704,0.9638704,0.9638704,0.96104735,0.96104735,0.9638704,0.96104735,0.96104735,0.9638704,0.9888916,0.96104735,0.9638704,0.96104735,0.0,0.9638704,0.96104735,0.9638704,0.9638704,0.96104735,0.96104735,0.9638704,0.9638704,0.9638704,0.9638704,0.9888916,0.96104735,0.96104735,1.0,0.9638704,0.9638704,0.96104735,0.9638704,0.9638704,0.96814424,0.9638704,0.96104735,0.96104735,0.9638704,0.9638704
+Migratory DCs,0.3615933,0.34537023,0.22784385,0.43634754,0.2718136,0.34871492,0.31173486,0.3515181,0.5244977,0.60363805,0.20785765,0.23185296,0.26691958,0.6491983,0.30530804,0.2605824,0.35724422,0.7809543,0.32904738,0.3869086,0.2787511,0.9638704,0.0,0.29576683,0.58042264,0.41717553,0.25303787,0.34165424,0.7005211,0.23516238,0.4569722,0.696529,0.8669922,0.27206486,0.26670057,0.9564276,0.29316798,0.5216826,0.29762703,0.35936102,0.6784042,0.6548167,0.39988935,0.25987515,0.28226468,0.26456663,0.25367263
+Monocytes/MDMs,0.40072012,0.3564827,0.2589088,0.38512683,0.20738776,0.3630268,0.30168885,0.38760954,0.52253336,0.62763894,0.27122113,0.22976463,0.19934915,0.65441066,0.23378368,0.16322057,0.40090293,0.79289544,0.2957993,0.4224804,0.20998354,0.96104735,0.29576683,0.0,0.59138983,0.44494075,0.20398071,0.2130507,0.71666557,0.23474936,0.50433034,0.72866106,0.8669922,0.22886989,0.24302296,0.9564276,0.32332116,0.54389596,0.25936818,0.38401735,0.6945487,0.6415874,0.41767794,0.26308566,0.21750584,0.27334148,0.32011753
+Multiciliated,0.60922444,0.532164,0.5757566,0.5907598,0.579384,0.60981774,0.60049427,0.62186897,0.33119816,0.503241,0.58022404,0.58596545,0.5817822,0.30463043,0.5918984,0.579384,0.60243785,0.82938254,0.60026354,0.6226978,0.5789611,0.9638704,0.58042264,0.59138983,0.0,0.4043591,0.58596545,0.56394535,0.52861315,0.57784975,0.61121404,0.5661279,0.9468239,0.579384,0.5772871,0.959492,0.6096358,0.39856428,0.58364445,0.5381235,0.27229935,0.76392263,0.5395553,0.60879844,0.5817822,0.54065335,0.60384065
+Myofibroblasts,0.4260357,0.40598089,0.40501136,0.51248074,0.44141954,0.43261224,0.45116776,0.48425484,0.38352585,0.58260727,0.427872,0.4398437,0.40758997,0.5325865,0.4516448,0.42118353,0.42689165,0.81584835,0.45491976,0.46784768,0.44141954,0.9638704,0.41717553,0.44494075,0.4043591,0.0,0.42906094,0.44440788,0.6586471,0.42667294,0.5015713,0.63818014,0.9039959,0.44141954,0.41272807,0.9564276,0.46243834,0.45421165,0.44141954,0.34062535,0.50266254,0.7044272,0.3822312,0.4342948,0.44141954,0.35866988,0.45403567
+NK/NKT,0.3602125,0.31917053,0.21749182,0.4216128,0.17759435,0.33479786,0.28745982,0.3382211,0.5264935,0.6036397,0.19404832,0.11176614,0.16132908,0.64639896,0.25663632,0.14325866,0.3696638,0.7809543,0.28331643,0.3980788,0.18345936,0.96104735,0.25303787,0.20398071,0.58596545,0.42906094,0.0,0.28446695,0.7128972,0.1675706,0.4820198,0.7089051,0.8669922,0.19193214,0.18044224,0.9564276,0.31961268,0.5240248,0.23129115,0.35740566,0.6907803,0.65206516,0.3986286,0.1890217,0.18612266,0.25842032,0.2903394
+Neutrophils,0.39290157,0.3743045,0.30746254,0.3620121,0.28627566,0.38389733,0.33633533,0.41931757,0.48207998,0.6097822,0.32934108,0.29090387,0.2625448,0.61484927,0.29896745,0.27413207,0.4167966,0.79628646,0.3287639,0.4262851,0.2868634,0.96104735,0.34165424,0.2130507,0.56394535,0.44440788,0.28446695,0.0,0.7135601,0.29213125,0.50619245,0.72129756,0.8669922,0.2902196,0.2801145,0.9564276,0.35858715,0.51802385,0.31853408,0.3930071,0.6717771,0.6194812,0.42670316,0.31407726,0.2868634,0.31378642,0.36189032
+PNEC,0.7184898,0.6702106,0.7005211,0.7062138,0.70631576,0.68897265,0.70631576,0.7099194,0.58232105,0.6415304,0.70339215,0.7128972,0.70631576,0.5369489,0.70858216,0.70631576,0.7107102,0.8715081,0.7127262,0.7055784,0.70631576,0.9638704,0.7005211,0.71666557,0.52861315,0.6586471,0.7128972,0.7135601,0.0,0.7005211,0.70079875,0.6325674,0.9369091,0.70631576,0.7128972,0.96853083,0.72489256,0.59882104,0.70631576,0.67963874,0.5343295,0.85955524,0.6798583,0.7157682,0.70631576,0.6908342,0.7130452
+Plasma,0.35934493,0.33568868,0.18735583,0.42784628,0.16409895,0.33079466,0.29273286,0.31135267,0.51411736,0.5850333,0.16404781,0.13742897,0.20578495,0.63402283,0.23900506,0.1879268,0.36491925,0.7809543,0.27518904,0.3915377,0.17371048,0.9638704,0.23516238,0.23474936,0.57784975,0.42667294,0.1675706,0.29213125,0.7005211,0.0,0.46600443,0.696529,0.8669922,0.18870635,0.23807025,0.9564276,0.29170522,0.51164865,0.20538607,0.3553496,0.6784042,0.65206516,0.39883357,0.19425435,0.17648178,0.25919992,0.2656843
+Proliferating AT2,0.43687314,0.37895826,0.45369586,0.5792118,0.49543366,0.4708116,0.48671293,0.52347916,0.58122694,0.597433,0.47263914,0.48118153,0.4842124,0.6658331,0.49944472,0.4874692,0.41423059,0.74129575,0.50539464,0.51950556,0.49543366,0.9638704,0.4569722,0.50433034,0.61121404,0.5015713,0.4820198,0.50619245,0.70079875,0.46600443,0.0,0.6826865,0.8698621,0.49543366,0.47387806,0.9657118,0.5038999,0.54181594,0.51068544,0.46388453,0.66431063,0.7536241,0.41762143,0.48044333,0.49543366,0.4430333,0.4850068
+Proliferating Airway,0.71080816,0.7053723,0.69269836,0.72497624,0.7183113,0.7034184,0.7183113,0.71003985,0.53023154,0.5734476,0.696529,0.7089051,0.7183113,0.5702702,0.72294796,0.7183113,0.68944865,0.88171613,0.7183113,0.6940962,0.7183113,0.9638704,0.696529,0.72866106,0.5661279,0.63818014,0.7089051,0.72129756,0.6325674,0.696529,0.6826865,0.0,0.9468239,0.7183113,0.6996689,0.985956,0.7259067,0.58152014,0.7183113,0.6668714,0.56093276,0.86014795,0.6849378,0.7073762,0.7183113,0.70047414,0.7184593
+Proliferating B cells,0.8669922,0.8669922,0.8669922,0.8505049,0.8697138,0.8669922,0.8669922,0.789923,0.9468239,0.9499421,0.8669922,0.8669922,0.8669922,0.9468239,0.8697138,0.8669922,0.8669922,0.91207665,0.8697138,0.8697138,0.8697138,0.9888916,0.8669922,0.8669922,0.9468239,0.9039959,0.8669922,0.8669922,0.9369091,0.8669922,0.8698621,0.9468239,0.0,0.8697138,0.8669922,0.99908555,0.85737514,0.90895236,0.8711279,0.88292426,0.9468239,0.89275026,0.8735806,0.8669922,0.8697138,0.8669922,0.8669922
+Proliferating FBs,0.39371544,0.35869446,0.22636592,0.4090646,0.08748649,0.360946,0.25390005,0.36868078,0.5104748,0.61304593,0.2228101,0.16032454,0.19373818,0.6398176,0.1975149,0.15099382,0.39405784,0.7809543,0.24885936,0.39916196,0.10539226,0.96104735,0.27206486,0.22886989,0.579384,0.44141954,0.19193214,0.2902196,0.70631576,0.18870635,0.49543366,0.7183113,0.8697138,0.0,0.22633561,0.9564276,0.31946898,0.53343105,0.14443444,0.3811387,0.6841989,0.63951695,0.42301998,0.22134407,0.12040216,0.27377328,0.29598144
+Proliferating Myeloid,0.37026566,0.3193439,0.18242711,0.4301487,0.22502375,0.31025466,0.30742052,0.3500638,0.5172342,0.5943876,0.24894783,0.19685288,0.20832984,0.6371397,0.2913987,0.17704162,0.34482765,0.7809543,0.29816797,0.38000852,0.23770681,0.96104735,0.26670057,0.24302296,0.5772871,0.41272807,0.18044224,0.2801145,0.7128972,0.23807025,0.47387806,0.6996689,0.8669922,0.22633561,0.0,0.9564276,0.321758,0.51728785,0.27045324,0.33185634,0.6821019,0.65206516,0.39192125,0.23119156,0.24094574,0.26726133,0.31852418
+Proliferating NK/NKT,0.97577685,0.959492,0.9564276,0.9605234,0.9564276,0.9564276,0.9564276,0.9605234,0.9564276,0.97066724,0.9564276,0.9564276,0.9564276,0.9308487,0.9564276,0.9564276,0.9626473,0.9837845,0.9564276,0.93884945,0.9564276,1.0,0.9564276,0.9564276,0.959492,0.9564276,0.9564276,0.9564276,0.96853083,0.9564276,0.9657118,0.985956,0.99908555,0.9564276,0.9564276,0.0,0.9564276,0.9644352,0.9564276,0.9564276,0.9644352,0.97570765,0.97066724,0.9564276,0.9564276,0.9564276,0.9564276
+Proliferating T-cells,0.4328704,0.41181907,0.29345304,0.45239252,0.3176864,0.39365435,0.3447643,0.35539597,0.5523865,0.6268896,0.24846128,0.30032113,0.33944452,0.67229205,0.3424641,0.31120217,0.4135929,0.79289544,0.33431154,0.42633814,0.32004625,0.9638704,0.29316798,0.32332116,0.6096358,0.46243834,0.31961268,0.35858715,0.72489256,0.29170522,0.5038999,0.7259067,0.85737514,0.31946898,0.321758,0.9564276,0.0,0.55932415,0.34700269,0.41223067,0.70501053,0.6557802,0.46321553,0.30351532,0.32270402,0.35548225,0.3090694
+RASC,0.51798224,0.46061864,0.5120613,0.5725516,0.53343105,0.53730494,0.5495628,0.5364047,0.30595306,0.4840819,0.5225266,0.5240248,0.53343105,0.4705935,0.55407107,0.5376743,0.5162398,0.7702117,0.540839,0.5285403,0.53343105,0.9638704,0.5216826,0.54389596,0.39856428,0.45421165,0.5240248,0.51802385,0.59882104,0.51164865,0.54181594,0.58152014,0.90895236,0.53343105,0.51728785,0.9644352,0.55932415,0.0,0.53343105,0.44315785,0.44053832,0.74706584,0.45013088,0.52404636,0.53343105,0.4799497,0.53500354
+SMCs/Pericytes,0.4102928,0.3882329,0.26515406,0.38833556,0.13670456,0.38269225,0.2690727,0.39061075,0.5104748,0.61304593,0.26094782,0.20356007,0.21945438,0.6398176,0.2298379,0.19477418,0.41306606,0.7902985,0.24774607,0.41197723,0.14034261,0.96104735,0.29762703,0.25936818,0.58364445,0.44141954,0.23129115,0.31853408,0.70631576,0.20538607,0.51068544,0.7183113,0.8711279,0.14443444,0.27045324,0.9564276,0.34700269,0.53343105,0.0,0.39219218,0.6841989,0.63314587,0.43231806,0.25547436,0.12448976,0.30899924,0.32809898
+SPP1+ Macrophages,0.356567,0.34352905,0.32622164,0.49665546,0.3811387,0.32542402,0.40843335,0.4177526,0.4481687,0.56147784,0.35618463,0.35916597,0.36857724,0.59800446,0.41654724,0.355513,0.33286697,0.78378356,0.40386733,0.40461916,0.38426286,0.9638704,0.35936102,0.38401735,0.5381235,0.34062535,0.35740566,0.3930071,0.67963874,0.3553496,0.46388453,0.6668714,0.88292426,0.3811387,0.33185634,0.9564276,0.41223067,0.44315785,0.39219218,0.0,0.6274239,0.69216585,0.351904,0.3440683,0.38426286,0.31264016,0.39479464
+Secretory,0.6939527,0.6369789,0.67687535,0.6912832,0.6841989,0.69309205,0.6841989,0.70895666,0.42109996,0.58061564,0.685039,0.6907803,0.6841989,0.37053818,0.68883556,0.6841989,0.68205345,0.8555481,0.694373,0.6856963,0.6841989,0.9638704,0.6784042,0.6945487,0.27229935,0.50266254,0.6907803,0.6717771,0.5343295,0.6784042,0.66431063,0.56093276,0.9468239,0.6841989,0.6821019,0.9644352,0.70501053,0.44053832,0.6841989,0.6274239,0.0,0.85955524,0.63424313,0.69588614,0.6841989,0.6370934,0.69092834
+Subpleural FBs,0.7180578,0.67817825,0.65206516,0.5078581,0.63951695,0.679069,0.6506076,0.65297675,0.75521505,0.7992854,0.65206516,0.65206516,0.65061635,0.8311771,0.63951695,0.64902306,0.71119916,0.86694396,0.62326294,0.67800677,0.63951695,0.96814424,0.6548167,0.6415874,0.76392263,0.7044272,0.65206516,0.6194812,0.85955524,0.65206516,0.7536241,0.86014795,0.89275026,0.63951695,0.65206516,0.97570765,0.6557802,0.74706584,0.63314587,0.69216585,0.85955524,0.0,0.7016609,0.6590868,0.63951695,0.68015784,0.6743625
+Transitional AT2,0.34798542,0.22382315,0.3837089,0.53001064,0.42301998,0.38615173,0.45324373,0.47659382,0.49840364,0.5293611,0.4040354,0.40857506,0.40751523,0.6103222,0.43264952,0.3973617,0.39748052,0.766811,0.4428575,0.4748726,0.42301998,0.9638704,0.39988935,0.41767794,0.5395553,0.3822312,0.3986286,0.42670316,0.6798583,0.39883357,0.41762143,0.6849378,0.8735806,0.42301998,0.39192125,0.97066724,0.46321553,0.45013088,0.43231806,0.351904,0.63424313,0.7016609,0.0,0.41516566,0.42301998,0.35008833,0.443537
+Tregs,0.3807527,0.3671727,0.22003028,0.44099393,0.21397528,0.34119204,0.28522944,0.33087716,0.5258482,0.6063541,0.15795574,0.14469436,0.23106833,0.65574807,0.2650233,0.1948834,0.36489812,0.7809543,0.2771756,0.39174023,0.2018229,0.96104735,0.25987515,0.26308566,0.60879844,0.4342948,0.1890217,0.31407726,0.7157682,0.19425435,0.48044333,0.7073762,0.8669922,0.22134407,0.23119156,0.9564276,0.30351532,0.52404636,0.25547436,0.3440683,0.69588614,0.6590868,0.41516566,0.0,0.21236905,0.29967147,0.295906
+Venous,0.39189273,0.3618208,0.23211327,0.4090646,0.08440635,0.35951108,0.26473027,0.37394622,0.50714695,0.61304593,0.23326907,0.15428528,0.16288763,0.6398176,0.17848724,0.1470943,0.39466602,0.7809543,0.2376322,0.39916196,0.081102565,0.96104735,0.28226468,0.21750584,0.5817822,0.44141954,0.18612266,0.2868634,0.70631576,0.17648178,0.49543366,0.7183113,0.8697138,0.12040216,0.24094574,0.9564276,0.32270402,0.53343105,0.12448976,0.38426286,0.6841989,0.63951695,0.42301998,0.21236905,0.0,0.28113222,0.2972223
+cDCs,0.33943394,0.2792706,0.24912076,0.45274988,0.26850706,0.32883415,0.3305445,0.37565702,0.44645,0.5932217,0.26064965,0.261549,0.23516569,0.60991657,0.3192007,0.2141707,0.3278299,0.7654862,0.34173885,0.40585405,0.2799519,0.9638704,0.26456663,0.27334148,0.54065335,0.35866988,0.25842032,0.31378642,0.6908342,0.25919992,0.4430333,0.70047414,0.8669922,0.27377328,0.26726133,0.9564276,0.35548225,0.4799497,0.30899924,0.31264016,0.6370934,0.68015784,0.35008833,0.29967147,0.28113222,0.0,0.2995622
+pDCs,0.40772948,0.40079054,0.29079193,0.4550963,0.2935473,0.38717505,0.32235894,0.37580192,0.5290793,0.61765087,0.2597492,0.26647842,0.30723235,0.6572342,0.33507848,0.28705484,0.3951028,0.7809543,0.34752518,0.4214228,0.29551077,0.9638704,0.25367263,0.32011753,0.60384065,0.45403567,0.2903394,0.36189032,0.7130452,0.2656843,0.4850068,0.7184593,0.8669922,0.29598144,0.31852418,0.9564276,0.3090694,0.53500354,0.32809898,0.39479464,0.69092834,0.6743625,0.443537,0.295906,0.2972223,0.2995622,0.0

data/outputs/formal_release/predicted_T2_sss.csv

@@ -0,0 +1,48 @@
+,AT1,AT2,Activated Fibrotic FBs,Adventitial FBs,Alveolar FBs,Alveolar Macrophages,Arteriole,B cells,Basal,Basophils,CD4+ T-cells,CD8+ T-cells,Capillary,Goblet,Inflammatory FBs,Interstitial Macrophages,KRT5-/KRT17+,Langerhans cells,Lymphatic,Macrophages - IFN-activated,Mast,Mesothelial,Migratory DCs,Monocytes/MDMs,Multiciliated,Myofibroblasts,NK/NKT,Neutrophils,PNEC,Plasma,Proliferating AT2,Proliferating Airway,Proliferating B cells,Proliferating FBs,Proliferating Myeloid,Proliferating NK/NKT,Proliferating T-cells,RASC,SMCs/Pericytes,SPP1+ Macrophages,Secretory,Subpleural FBs,Transitional AT2,Tregs,Venous,cDCs,pDCs
+AT1,0.0,0.2125075,0.28208277,0.37499964,0.2132236,0.2145766,0.22596872,0.22502056,0.58319944,0.49458998,0.21724275,0.21782224,0.21263635,0.6941774,0.21535489,0.21379697,0.57479167,0.8226021,0.23017141,0.28041497,0.21844077,0.89611983,0.33606526,0.21328954,0.5410782,0.5369148,0.21306951,0.21339893,0.7086801,0.23860317,0.44139367,0.7957892,0.91333735,0.21547271,0.21363336,0.6617729,0.49342722,0.6446253,0.21435899,0.21781568,0.79899085,0.4914454,0.2273068,0.26446933,0.21604617,0.24859893,0.5217509
+AT2,0.2124995,0.0,0.28196156,0.37479138,0.21288387,0.2142353,0.22568278,0.22473544,0.5829834,0.49436787,0.2168931,0.21743627,0.21230322,0.6939887,0.21501268,0.21345656,0.5745744,0.82257336,0.22986695,0.28029633,0.21805403,0.8961014,0.33587635,0.21294971,0.5408575,0.5366938,0.21272996,0.21305896,0.7084966,0.23850965,0.44117457,0.7957571,0.91332185,0.21513037,0.2132931,0.6615739,0.4932051,0.6444217,0.21401793,0.21742976,0.79895926,0.49122328,0.22701964,0.26436606,0.21570316,0.24849981,0.5215292
+Activated Fibrotic FBs,0.28064513,0.28051248,0.0,0.3949866,0.28079903,0.28133896,0.28579983,0.28549626,0.60356694,0.5156917,0.28239512,0.2826031,0.28056407,0.70800394,0.28164864,0.28102806,0.5952849,0.8253443,0.28713423,0.29947144,0.28282732,0.8978666,0.35510805,0.28082535,0.56195796,0.5578292,0.2807374,0.2808691,0.7204199,0.28887802,0.46230176,0.79884446,0.9148222,0.28169557,0.28096268,0.6803582,0.5145298,0.663722,0.2812518,0.28260127,0.8020102,0.51254904,0.2862271,0.29400584,0.28192332,0.2908966,0.54276705
+Adventitial FBs,0.37235796,0.37213925,0.39335793,0.0,0.3726117,0.3735018,0.37995327,0.3795734,0.6170017,0.53304577,0.37524265,0.37558532,0.37222427,0.71127945,0.37401232,0.37298933,0.60986334,0.82762396,0.3816,0.3930236,0.3759456,0.8993152,0.4039925,0.3726551,0.57900757,0.57491803,0.37251014,0.37272725,0.72361046,0.3836735,0.47963858,0.80138683,0.9160528,0.37408966,0.3728816,0.68380535,0.53188777,0.66924477,0.37335834,0.3755821,0.80452234,0.529913,0.38048714,0.38956225,0.37446505,0.38599494,0.5599787
+Alveolar FBs,0.21323295,0.21290122,0.28222337,0.3752413,0.0,0.21497309,0.22630085,0.22535168,0.58345,0.4948477,0.21768247,0.2182706,0.21303023,0.6943962,0.21575241,0.21419242,0.5750436,0.8226355,0.23052499,0.28055507,0.21889012,0.89614105,0.33628452,0.21368428,0.54133415,0.5371712,0.21346399,0.21379383,0.70889294,0.23871167,0.44164786,0.79582626,0.9133554,0.21587044,0.21402857,0.66200364,0.49368498,0.64486146,0.21475518,0.21826407,0.7990276,0.4917031,0.22764549,0.2645891,0.21644464,0.248714,0.5220082
+Alveolar Macrophages,0.21461877,0.21428548,0.28271666,0.37608895,0.21500593,0.0,0.22749853,0.22680348,0.58432806,0.49575108,0.2192564,0.2198476,0.21441507,0.69516253,0.21715124,0.21558276,0.5759265,0.8227525,0.2317674,0.28104657,0.22047026,0.8962156,0.33705541,0.21507221,0.5422313,0.5380695,0.21485089,0.21518227,0.7096381,0.2390923,0.44253927,0.7959565,0.9134189,0.21727727,0.21541813,0.66281176,0.49458835,0.6456887,0.21614815,0.21984103,0.7991563,0.49260634,0.22887701,0.26500934,0.21791744,0.24911758,0.5229099
+Arteriole,0.22573493,0.22534896,0.28674656,0.38223127,0.22618327,0.22780873,0.0,0.23915763,0.59065163,0.5022744,0.23102364,0.23165931,0.22549908,0.7006638,0.2287488,0.2268673,0.5822865,0.8235986,0.24302915,0.2850079,0.2323288,0.89675516,0.3429106,0.22626007,0.54870075,0.5445483,0.22600374,0.22638756,0.7149852,0.24702094,0.4489858,0.79689914,0.91387755,0.22889115,0.22666973,0.6686185,0.5011115,0.65163535,0.22754587,0.23165224,0.80008775,0.49912927,0.24089842,0.26833218,0.229584,0.25299424,0.5294153
+B cells,0.22505362,0.2246685,0.28647363,0.38186967,0.22550102,0.22709785,0.23913819,0.0,0.5902813,0.50189155,0.23030573,0.23094001,0.22481826,0.7003425,0.22803582,0.2261676,0.58191395,0.82354873,0.24228062,0.28473598,0.23160806,0.8967234,0.34256554,0.22557764,0.5483214,0.5441684,0.22532184,0.2257048,0.7146729,0.24626417,0.44860694,0.7968435,0.91385055,0.22817788,0.22597735,0.66827905,0.5007286,0.65128756,0.22683562,0.23093298,0.8000329,0.49874634,0.24015439,0.26812962,0.2288692,0.25240803,0.5290338
+Basal,0.579379,0.5791577,0.6002351,0.6137551,0.5796356,0.58053476,0.58701026,0.58663106,0.0,0.62924325,0.58228934,0.58263403,0.57924384,0.7325912,0.5810499,0.5800172,0.6709519,0.8320676,0.5886514,0.5999083,0.58299637,0.8960649,0.61051166,0.5796795,0.65365064,0.6514783,0.57953286,0.5797524,0.74022585,0.5907111,0.61648893,0.8063485,0.90984607,0.5811278,0.5799084,0.7156671,0.62862253,0.70685565,0.58039004,0.5826308,0.8094243,0.62756026,0.5875428,0.596521,0.5815063,0.59300864,0.6435356
+Basophils,0.49025488,0.49002096,0.51247483,0.53075093,0.4905262,0.49147728,0.4983455,0.49794236,0.632265,0.0,0.49333498,0.4937003,0.4901119,0.7149791,0.4920224,0.4909297,0.6275968,0.83018863,0.5000916,0.5121248,0.49408427,0.90024066,0.5235505,0.49057254,0.60934323,0.60706,0.49041757,0.4906496,0.72721267,0.50228596,0.55395174,0.8042496,0.9143111,0.49210495,0.49081457,0.68770236,0.5831551,0.67323554,0.4913241,0.4936968,0.8073508,0.5820493,0.49891198,0.50849324,0.49250564,0.5047373,0.5987286
+CD4+ T-cells,0.21736316,0.21700835,0.28368145,0.37774658,0.21779953,0.21933423,0.23079282,0.23009385,0.5860414,0.49751556,0.0,0.22295164,0.21714161,0.6966563,0.22021739,0.21844979,0.5776495,0.8229809,0.23420776,0.2820079,0.2235806,0.8963614,0.33863434,0.21787426,0.5439828,0.53982335,0.21762477,0.21799836,0.7110903,0.23985127,0.4442812,0.79621094,0.9135428,0.22035113,0.21826419,0.66438735,0.49635276,0.6473018,0.21908732,0.222945,0.7994078,0.49437055,0.23177795,0.26583123,0.22100201,0.24990693,0.5246704
+CD8+ T-cells,0.21796586,0.21758948,0.28387144,0.37807286,0.21840313,0.21994087,0.23144487,0.23074457,0.58637804,0.49786258,0.22296712,0.0,0.21773584,0.6969494,0.2208258,0.21905471,0.57798797,0.8230259,0.23468955,0.2821972,0.22419564,0.89639,0.33894524,0.21847802,0.544327,0.5401681,0.21822804,0.21860234,0.71137536,0.24019237,0.44462386,0.79626113,0.9135672,0.22095983,0.21886873,0.66469675,0.4966997,0.64761853,0.21969345,0.22355881,0.7994573,0.4947175,0.232432,0.26600504,0.22161199,0.25006238,0.52501655
+Capillary,0.21263143,0.21230575,0.28200868,0.3748724,0.21301597,0.21436799,0.22579399,0.2248463,0.5830674,0.49445423,0.21702701,0.21758634,0.0,0.69406205,0.21514574,0.2135889,0.5746589,0.8225845,0.22998536,0.28034118,0.2182044,0.8961085,0.33594984,0.21308185,0.5409433,0.5367798,0.212862,0.21319115,0.708568,0.23854604,0.44125977,0.7957696,0.9133279,0.21526349,0.21342538,0.66165125,0.49329153,0.6445009,0.21415053,0.21757981,0.79897153,0.49130964,0.2271313,0.2644062,0.21583654,0.24853839,0.52161545
+Goblet,0.6929505,0.6927573,0.706643,0.710352,0.6931745,0.6939591,0.6995896,0.6992608,0.73167056,0.71453536,0.69548804,0.69578815,0.6928324,0.0,0.6944082,0.6935075,0.72776484,0.84218204,0.7010113,0.7065771,0.69610345,0.8889814,0.70888597,0.69321275,0.7161527,0.716001,0.69308484,0.69327635,0.78833294,0.70279247,0.71268755,0.8302657,0.90348804,0.6944761,0.69341254,0.76709294,0.7144931,0.7594069,0.6938328,0.6957853,0.8318584,0.71441853,0.7000511,0.7058432,0.694806,0.7047753,0.7154506
+Inflammatory FBs,0.21541603,0.21508184,0.28299958,0.37657505,0.21580425,0.217172,0.2284594,0.22776553,0.584831,0.4962689,0.22016226,0.22075516,0.2152118,0.6956013,0.0,0.21638262,0.5764323,0.8228194,0.23248158,0.28132847,0.2213797,0.8962585,0.33751836,0.21587074,0.5427454,0.5385843,0.21564882,0.2159811,0.7100647,0.23931062,0.4430503,0.7960311,0.9134553,0.21817307,0.21621755,0.6632745,0.49510607,0.6461624,0.21694954,0.22074857,0.7992301,0.49312404,0.22958498,0.26525036,0.2188193,0.24934903,0.5234266
+Interstitial Macrophages,0.21382019,0.21348776,0.28243262,0.37560087,0.2142063,0.21556377,0.22679546,0.22586758,0.5838226,0.495231,0.21834934,0.21893874,0.21361704,0.69472146,0.2163447,0.0,0.5754183,0.82268506,0.23105161,0.28076357,0.2195596,0.89617276,0.3366107,0.21427242,0.54171485,0.53755236,0.2140517,0.21438217,0.70920926,0.23887311,0.44202608,0.7958815,0.9133824,0.21646291,0.21461739,0.6623466,0.49406826,0.6452126,0.21534546,0.21893223,0.79908216,0.4920863,0.22816747,0.26476738,0.21703829,0.24888514,0.5223908
+KRT5-/KRT17+,0.57079387,0.5705715,0.5917757,0.6064562,0.57105184,0.57195586,0.57846755,0.57808614,0.6712388,0.6248643,0.5737199,0.5740665,0.57065797,0.7289069,0.5724737,0.5714355,0.0,0.83183455,0.5801185,0.5914467,0.5744309,0.8965121,0.6021256,0.571096,0.6493993,0.6472146,0.57094854,0.57116926,0.736609,0.5821905,0.60947454,0.8060881,0.91024,0.5725521,0.5713261,0.7118414,0.6242405,0.7029606,0.57181025,0.57406324,0.809167,0.6231733,0.5790033,0.58803695,0.5729326,0.5845022,0.63922864
+Langerhans cells,0.82340384,0.82337135,0.82649815,0.82905835,0.8234415,0.82357377,0.82452965,0.8244734,0.83403176,0.8319329,0.82383204,0.8238829,0.823384,0.84197676,0.8236496,0.82349765,0.8337813,0.0,0.82477295,0.82645255,0.8239363,0.9020897,0.82804775,0.823448,0.83304054,0.8329367,0.8234265,0.8234587,0.84561056,0.8250793,0.8306649,0.8680786,0.9095095,0.823661,0.8234816,0.8348892,0.83190393,0.8348981,0.82355237,0.8238825,0.86904985,0.83185285,0.8246085,0.8259446,0.82371676,0.82542056,0.8325599
+Lymphatic,0.22934984,0.2292476,0.28798229,0.38379875,0.22946835,0.2309084,0.24311423,0.24238513,0.5922545,0.50393265,0.23415378,0.23479575,0.2292874,0.7020531,0.23185734,0.22995798,0.583899,0.82381415,0.0,0.28622702,0.23547588,0.89689255,0.34440672,0.22948869,0.5503428,0.54619294,0.2294209,0.22952236,0.716335,0.2503587,0.45062742,0.7971392,0.9139943,0.23200108,0.2297585,0.6700865,0.50276977,0.65313965,0.23064306,0.23478858,0.80032516,0.5007875,0.24414189,0.26933533,0.23270053,0.25554544,0.53106755
+Macrophages - IFN-activated,0.27900654,0.27887434,0.29976618,0.39466906,0.27915987,0.27969787,0.28407413,0.28378427,0.6032489,0.51535976,0.28075027,0.28095752,0.27892575,0.70794743,0.28000647,0.27938807,0.5949646,0.8253049,0.2853931,0.0,0.28117543,0.89784163,0.35480374,0.2791861,0.5616308,0.55750144,0.27909845,0.27922967,0.7203648,0.28711712,0.4619714,0.7988005,0.914801,0.28005323,0.27932292,0.6801158,0.5141978,0.66342527,0.27961102,0.2809557,0.8019668,0.512217,0.28449985,0.29222658,0.28028017,0.28912842,0.5424372
+Mast,0.21860075,0.21822359,0.2840712,0.37841597,0.21903895,0.2205799,0.23213169,0.23142995,0.58673185,0.49822724,0.22361244,0.224212,0.21837026,0.69725746,0.22146666,0.21969189,0.5783438,0.8230732,0.2351968,0.28239626,0.0,0.89642024,0.3392722,0.219114,0.54468894,0.54053044,0.21886346,0.21923858,0.7116748,0.24071258,0.44498414,0.79631376,0.91359276,0.22160096,0.21950552,0.66502184,0.4970644,0.6479514,0.22033201,0.22420532,0.79950935,0.49508217,0.23312089,0.26619694,0.22225448,0.25022587,0.5253803
+Mesothelial,0.89789873,0.89787817,0.89984643,0.9014534,0.89792246,0.8980059,0.8986081,0.8985727,0.8977773,0.9019799,0.8981687,0.8982007,0.8978862,0.8909608,0.8980536,0.8979578,0.8981911,0.9019223,0.8987613,0.89981776,0.89823437,0.0,0.9008196,0.89792657,0.90009075,0.9002682,0.8979129,0.8979333,0.88994217,0.89895415,0.90245956,0.89522696,0.9288308,0.89806086,0.8979477,0.8930601,0.9020109,0.894159,0.8979923,0.8982005,0.8960224,0.90206236,0.89865786,0.8994985,0.89809597,0.89916885,0.90091115
+Migratory DCs,0.33396885,0.33376607,0.35402492,0.40510085,0.33421037,0.3350577,0.34120676,0.34084433,0.6136053,0.5262085,0.33671567,0.33704212,0.33384353,0.7099833,0.33554384,0.33456975,0.60539585,0.82672286,0.34277838,0.3537046,0.33738542,0.89874303,0.0,0.33425167,0.57230335,0.5681972,0.33411363,0.33432028,0.722348,0.34475857,0.4727927,0.8003816,0.9155668,0.33561742,0.33446723,0.6824409,0.5250487,0.667848,0.33492115,0.33703905,0.80352914,0.523071,0.3417162,0.35038957,0.33597496,0.3469771,0.5532053
+Monocytes/MDMs,0.21330044,0.21296862,0.28224745,0.37528268,0.21368587,0.215041,0.22635774,0.22540838,0.5834929,0.4948918,0.21775913,0.21834739,0.21309766,0.6944336,0.2158205,0.21426013,0.5750867,0.82264113,0.23058552,0.28057906,0.21896704,0.8961447,0.33632204,0.0,0.54137796,0.537215,0.21353152,0.21386147,0.7089293,0.23873024,0.44169137,0.7958327,0.9133585,0.21593855,0.21409625,0.66204304,0.49372903,0.6449019,0.21482301,0.21834086,0.7990338,0.4917471,0.22770551,0.2646096,0.21651286,0.24873368,0.5220522
+Multiciliated,0.53630286,0.5360771,0.55820787,0.5761874,0.5365647,0.5374825,0.5442253,0.5438252,0.655054,0.6077306,0.5392742,0.5396264,0.53616494,0.7164161,0.53800845,0.5369542,0.6505152,0.831182,0.5459571,0.55786234,0.53999656,0.89841443,0.56911814,0.5366096,0.0,0.6304982,0.53645986,0.5366839,0.7286114,0.548132,0.5809579,0.805359,0.9120559,0.538088,0.53684306,0.6967524,0.6070963,0.6876107,0.53733474,0.539623,0.8084469,0.6060111,0.54478717,0.5542749,0.5384745,0.55055964,0.62235457
+Myofibroblasts,0.5320699,0.53183687,0.55412495,0.5721432,0.5323402,0.5332875,0.5401195,0.5397189,0.6530246,0.6055905,0.535137,0.5355005,0.5319275,0.71628004,0.53383034,0.5327422,0.64847356,0.83108807,0.54185385,0.5537787,0.5358826,0.8986076,0.56505746,0.5323864,0.63064104,0.0,0.532232,0.5324632,0.728479,0.544032,0.5774368,0.8052541,0.91226244,0.5339125,0.5326275,0.69485414,0.604955,0.685681,0.53313494,0.53549707,0.8083432,0.60386777,0.5406822,0.55018485,0.5343114,0.54646343,0.6202444
+NK/NKT,0.21307512,0.21274358,0.28216708,0.37514457,0.21346028,0.21481434,0.22616787,0.2252191,0.5833497,0.4947445,0.21750328,0.21809107,0.2128725,0.6943086,0.21559325,0.21403408,0.57494277,0.82262206,0.2303834,0.28049895,0.21871015,0.8961325,0.33619675,0.21352622,0.5412317,0.5370685,0.0,0.21363571,0.7088077,0.23866823,0.4415461,0.79581136,0.91334826,0.21571119,0.21387032,0.6619112,0.49358177,0.6447669,0.21459654,0.21808454,0.7990129,0.49159992,0.2275068,0.26454112,0.21628508,0.24866794,0.52190524
+Neutrophils,0.21341248,0.21308056,0.2822874,0.3753513,0.21379806,0.21515368,0.2264521,0.22550248,0.58356404,0.494965,0.21788633,0.21847488,0.21320961,0.6944957,0.2159335,0.21437255,0.57515824,0.8226506,0.23068604,0.28061885,0.21909475,0.8961507,0.33638433,0.21386412,0.5414507,0.5372878,0.21364366,0.0,0.70898974,0.23876111,0.44176358,0.7958432,0.9133637,0.21605161,0.21420862,0.66210854,0.49380225,0.6449689,0.21493565,0.21846832,0.79904425,0.49182037,0.22780511,0.26464364,0.21662614,0.24876638,0.52212524
+PNEC,0.7077835,0.7075957,0.7193629,0.7229741,0.70800126,0.70876384,0.71423423,0.7139149,0.7392817,0.7270453,0.7102498,0.71054137,0.7076687,0.7883559,0.7092003,0.708325,0.73544675,0.8457934,0.71561474,0.7192988,0.71084774,0.8881081,0.721547,0.7080385,0.72861874,0.72847104,0.7079141,0.7081003,0.0,0.7173439,0.72524726,0.8348874,0.90271634,0.7092664,0.70823264,0.7740097,0.7270042,0.7664825,0.7086411,0.71053857,0.83627,0.7269316,0.71468246,0.71858406,0.709587,0.7178471,0.7279356
+Plasma,0.2378786,0.23777373,0.2896198,0.38577232,0.23800014,0.23842894,0.247215,0.24647757,0.5942662,0.5060166,0.23928493,0.23945351,0.23781456,0.70379406,0.23867995,0.23818113,0.58592314,0.824086,0.2504738,0.28784147,0.2396308,0.89706564,0.34629154,0.23802102,0.55240494,0.54825854,0.23795147,0.23805554,0.7180259,0.0,0.45269212,0.79744214,0.91414154,0.23871796,0.23812953,0.6719269,0.50485384,0.65502584,0.23835823,0.23945211,0.80062443,0.5028717,0.2482543,0.2707675,0.23890257,0.2594171,0.53314316
+Proliferating AT2,0.43777847,0.4375482,0.4597653,0.47800472,0.4380457,0.43898278,0.4457605,0.44536215,0.61937547,0.5558663,0.44081408,0.4411743,0.43763772,0.7133404,0.43951997,0.4384432,0.61225355,0.829054,0.44748664,0.45941734,0.4415531,0.9002222,0.4708019,0.43809143,0.5833502,0.579776,0.43793875,0.43816736,0.72561735,0.4496578,0.0,0.80298275,0.91619647,0.43960133,0.43832988,0.68597573,0.5552095,0.6714672,0.4388318,0.44117096,0.8060992,0.55408627,0.4463203,0.45581037,0.4399963,0.45208564,0.5710591
+Proliferating Airway,0.79606,0.7960237,0.79951674,0.8023799,0.7961021,0.79624975,0.7973172,0.7972543,0.8079497,0.8055979,0.7965381,0.79659486,0.7960378,0.83029556,0.7963343,0.7961647,0.8076689,0.86814064,0.79758894,0.79946584,0.7966545,0.8954553,0.8012493,0.79610926,0.8068388,0.8067224,0.79608524,0.7961212,0.83481884,0.79793125,0.8041779,0.0,0.903324,0.79634714,0.79614687,0.81900907,0.8055654,0.8126685,0.79622585,0.79659444,0.86052275,0.8055081,0.7974053,0.7988981,0.79640937,0.7983125,0.8063003
+Proliferating B cells,0.91517985,0.91516244,0.91682845,0.91818774,0.91519994,0.9152705,0.9157804,0.9157504,0.91160953,0.9158004,0.9154084,0.9154355,0.91516924,0.90561837,0.915311,0.91522986,0.91197276,0.90929997,0.91591007,0.9168042,0.915464,0.9287878,0.91765165,0.9152034,0.9136513,0.9138422,0.9151918,0.9152091,0.9047219,0.9160733,0.9178109,0.9030541,0.0,0.9153172,0.9152214,0.9074647,0.9158522,0.9084309,0.9152591,0.9154353,0.9037964,0.9159387,0.9158225,0.916534,0.9153468,0.91625506,0.9145333
+Proliferating FBs,0.21553676,0.21520244,0.28304246,0.3766487,0.21592513,0.21730119,0.22860546,0.22791122,0.5849072,0.49634725,0.22029942,0.22089264,0.21533245,0.6956677,0.21817653,0.21650374,0.5765088,0.8228296,0.23258975,0.28137118,0.22151744,0.89626485,0.3375885,0.21599166,0.54282326,0.5386622,0.2157696,0.21610203,0.71012926,0.23934375,0.44312766,0.79604244,0.9134608,0.0,0.2163386,0.6633445,0.49518445,0.64623404,0.2170709,0.22088602,0.7992413,0.49320245,0.22969218,0.2652869,0.21895593,0.24938414,0.5235048
+Proliferating Myeloid,0.21365261,0.2133204,0.28237292,0.3754983,0.2140385,0.21539521,0.22665432,0.22570407,0.5837164,0.4951217,0.218159,0.2187481,0.21344958,0.6946287,0.21617565,0.21461342,0.5753114,0.8226709,0.23090132,0.28070405,0.21936853,0.89616364,0.33651766,0.21410461,0.54160625,0.53744364,0.21388397,0.2142143,0.70911896,0.23882708,0.4419182,0.7958658,0.9133747,0.21629387,0.0,0.66224873,0.49395892,0.64511245,0.215177,0.21874152,0.79906666,0.49197698,0.22801852,0.2647165,0.21686886,0.24883635,0.52228165
+Proliferating NK/NKT,0.6598047,0.6596009,0.67832005,0.6822261,0.6600411,0.6608689,0.66681594,0.6664684,0.71481717,0.6866366,0.6624828,0.66279966,0.6596802,0.7670452,0.66134286,0.6603925,0.71076316,0.83363706,0.6683192,0.67825073,0.66313267,0.8909661,0.68068177,0.66008157,0.694741,0.6927247,0.6599465,0.6601487,0.77393883,0.67020345,0.6846878,0.81880546,0.905352,0.6614146,0.6602922,0.0,0.686592,0.7436853,0.6607356,0.6627967,0.820695,0.6865133,0.667304,0.6755048,0.6617628,0.6723023,0.6876021
+Proliferating T-cells,0.48910725,0.4888734,0.51132745,0.52960706,0.48937854,0.49032956,0.4971975,0.4967944,0.6316858,0.58319646,0.49218717,0.49255243,0.48896435,0.7149412,0.49087465,0.48978207,0.6270147,0.8301625,0.49894354,0.5109773,0.49293637,0.90025127,0.52240485,0.4894249,0.6087504,0.60646594,0.48926997,0.48950204,0.7271758,0.50113785,0.55333644,0.8042203,0.9143572,0.49095717,0.48966697,0.6876624,0.0,0.67319465,0.49017638,0.492549,0.8073219,0.58144355,0.4977639,0.50734544,0.4913578,0.50358933,0.5981302
+RASC,0.64224803,0.64203936,0.6618064,0.66730124,0.6424899,0.6433374,0.6494288,0.6490726,0.70603466,0.67181927,0.64498985,0.6453144,0.6421205,0.75932944,0.64382267,0.6428496,0.7019078,0.83298725,0.6509694,0.6615016,0.6456554,0.8921548,0.6657199,0.64253134,0.6856121,0.68356293,0.64239305,0.6426,0.7663819,0.65290105,0.66982263,0.8123848,0.9064004,0.64389616,0.6427471,0.74365556,0.67177355,0.0,0.643201,0.6453113,0.8143292,0.6716929,0.64992887,0.6583388,0.64425254,0.6550534,0.67606056
+SMCs/Pericytes,0.21439585,0.21406281,0.28263703,0.37595233,0.21478271,0.21614286,0.22730123,0.22653742,0.5841866,0.49560556,0.21900317,0.21959385,0.21419233,0.6950392,0.21692528,0.21535912,0.57578427,0.8227334,0.2315675,0.2809672,0.22021602,0.8962036,0.3369296,0.214849,0.54208684,0.5379248,0.21462782,0.21495898,0.7095182,0.2390308,0.4423956,0.7959354,0.91340864,0.21704373,0.21519464,0.6626816,0.49444282,0.6455555,0.0,0.21958727,0.79913545,0.49246082,0.22867888,0.26494145,0.21766534,0.24905235,0.5227646
+SPP1+ Macrophages,0.2179592,0.21758278,0.2838698,0.3780698,0.21839641,0.21993415,0.23143761,0.23073736,0.58637494,0.49785927,0.2229603,0.22355865,0.21772914,0.6969467,0.22081904,0.21904801,0.5779848,0.82302564,0.23468435,0.2821956,0.22418883,0.89638984,0.33894232,0.21847133,0.5443238,0.5401649,0.21822134,0.21859565,0.71137273,0.240187,0.44462064,0.79626083,0.913567,0.22095305,0.21886201,0.66469383,0.49669638,0.6476156,0.21968673,0.0,0.799457,0.49471423,0.23242472,0.26600346,0.22160521,0.2500611,0.52501327
+Secretory,0.7993262,0.7992904,0.8027413,0.80556965,0.79936785,0.7995137,0.80056834,0.8005063,0.81107074,0.80874807,0.7997986,0.7998547,0.79930437,0.83188874,0.7995972,0.7994297,0.81079346,0.869104,0.8008368,0.80269104,0.79991364,0.8962429,0.80445296,0.7993749,0.8099736,0.8098587,0.7993512,0.7993867,0.8361983,0.80117506,0.8073457,0.8605148,0.90405864,0.79961,0.7994121,0.82090294,0.808716,0.8149982,0.7994901,0.7998543,0.0,0.8086595,0.80065536,0.80213016,0.7996715,0.8015517,0.8094418
+Subpleural FBs,0.48715168,0.4869179,0.50937164,0.52765685,0.4874229,0.4883738,0.495241,0.49483785,0.63069516,0.5821616,0.49023116,0.4905963,0.4870088,0.7148739,0.48891875,0.48782638,0.6260189,0.8301159,0.4969869,0.50902146,0.49098027,0.9002677,0.52045184,0.48746932,0.6077363,0.60544974,0.48731437,0.48754638,0.7271103,0.49918118,0.55228436,0.80416834,0.91443384,0.4890013,0.48771137,0.68759155,0.5815144,0.67312205,0.48822063,0.49059287,0.8072705,0.0,0.49580735,0.5053891,0.48940197,0.50163275,0.5971068
+Transitional AT2,0.22670624,0.22630826,0.28714135,0.38273942,0.2271722,0.22881089,0.24092585,0.2402012,0.59117174,0.5028123,0.23203571,0.2326733,0.22646114,0.7011149,0.22975382,0.22786655,0.58280975,0.82366854,0.24408421,0.28539008,0.23334484,0.8967997,0.34339556,0.22725204,0.5492335,0.5450819,0.22698563,0.22738452,0.7154234,0.24808772,0.44951817,0.7969769,0.91391546,0.22989663,0.22766834,0.66909504,0.50164944,0.65212363,0.22854722,0.23266618,0.80016476,0.49966708,0.0,0.26864317,0.23059161,0.25381985,0.52995133
+Tregs,0.26329175,0.2631767,0.29449633,0.39137587,0.26342514,0.26389328,0.26760638,0.26737183,0.59994024,0.5119112,0.2648446,0.26504445,0.26322147,0.70730036,0.2641618,0.26362368,0.5916337,0.8248535,0.2687262,0.2926944,0.2652546,0.8975544,0.35164994,0.263448,0.5582292,0.55409324,0.26337168,0.26348588,0.7197344,0.27025715,0.4585421,0.7982974,0.9145569,0.26420248,0.26356703,0.677105,0.51074886,0.66033584,0.26381764,0.2650427,0.8014696,0.5087673,0.26794696,0.0,0.26439995,0.2729568,0.5390089
+Venous,0.21612424,0.21578923,0.28325054,0.3770062,0.21651338,0.21796037,0.22931609,0.22862034,0.5852767,0.4967278,0.22096708,0.22156157,0.21591952,0.6959899,0.21883954,0.21709312,0.57688046,0.82287896,0.23311578,0.28157854,0.22218776,0.8962964,0.33792895,0.21658003,0.543201,0.53904045,0.21635754,0.21669063,0.7104425,0.23950836,0.44350332,0.7960974,0.91348755,0.21897271,0.21692765,0.66368437,0.495565,0.646582,0.21771461,0.22155496,0.7992955,0.49358287,0.23029682,0.2654642,0.0,0.24955438,0.5238845
+cDCs,0.24770941,0.24759887,0.2915397,0.3879815,0.24783757,0.24828734,0.25195256,0.25142634,0.5965098,0.50834453,0.24916713,0.24934043,0.2476419,0.7057319,0.24854533,0.24802834,0.5881809,0.8243884,0.25529775,0.28974843,0.24952264,0.8972582,0.3484029,0.24785952,0.55470663,0.55056417,0.24778621,0.24789593,0.7190852,0.25955296,0.4550006,0.7977791,0.91430527,0.2485844,0.2479739,0.6739767,0.5071819,0.6571274,0.24821466,0.24933898,0.80095744,0.5051999,0.25303438,0.27376157,0.24877413,0.0,0.5354606
+pDCs,0.5170846,0.5168509,0.5392343,0.55737364,0.5173557,0.5183059,0.5251619,0.52475977,0.6456076,0.59778404,0.5201613,0.52052605,0.5169418,0.71578705,0.51885045,0.51775885,0.64101267,0.83074737,0.5269033,0.53888613,0.5209094,0.8993073,0.5502355,0.51740205,0.6230217,0.62076867,0.51724714,0.51747906,0.7279992,0.5290907,0.56819534,0.8048736,0.91301,0.5189329,0.51764387,0.688554,0.5971443,0.67861843,0.5181529,0.52052265,0.8079672,0.59604996,0.52572685,0.535273,0.51933306,0.53153324,0.0

data/outputs/formal_release/predicted_T3_sss.csv

@@ -0,0 +1,48 @@
+,AT1,AT2,Activated Fibrotic FBs,Adventitial FBs,Alveolar FBs,Alveolar Macrophages,Arteriole,B cells,Basal,Basophils,CD4+ T-cells,CD8+ T-cells,Capillary,Goblet,Inflammatory FBs,Interstitial Macrophages,KRT5-/KRT17+,Langerhans cells,Lymphatic,Macrophages - IFN-activated,Mast,Mesothelial,Migratory DCs,Monocytes/MDMs,Multiciliated,Myofibroblasts,NK/NKT,Neutrophils,PNEC,Plasma,Proliferating AT2,Proliferating Airway,Proliferating B cells,Proliferating FBs,Proliferating Myeloid,Proliferating NK/NKT,Proliferating T-cells,RASC,SMCs/Pericytes,SPP1+ Macrophages,Secretory,Subpleural FBs,Transitional AT2,Tregs,Venous,cDCs,pDCs
+AT1,0.0,0.3051255,0.30727768,0.48191607,0.3035427,0.31420633,0.3171259,0.38489613,0.48391888,0.58709013,0.30434078,0.30500084,0.3072397,0.6698873,0.30751142,0.30361298,0.3775945,0.8128508,0.3060113,0.38766798,0.30448344,0.8925231,0.31331187,0.3044461,0.5216404,0.40181082,0.30582097,0.30685902,0.80014604,0.3069436,0.43029755,0.79501003,0.86429155,0.30423093,0.30535477,0.8647578,0.39323747,0.51352155,0.30532262,0.30919608,0.7153443,0.5559172,0.30801445,0.30723485,0.30521497,0.3068983,0.36382097
+AT2,0.30438036,0.0,0.2950989,0.47748336,0.28099984,0.30945566,0.3132923,0.3807,0.4794847,0.5827782,0.28226942,0.28406602,0.293558,0.668989,0.29522854,0.281067,0.37342966,0.81223243,0.2871019,0.3834605,0.2826788,0.892133,0.30888546,0.28246513,0.517207,0.3975495,0.28618452,0.29140368,0.799496,0.29254085,0.42594922,0.79434764,0.86381465,0.28193322,0.28493196,0.8642823,0.389008,0.50908375,0.2848616,0.3023312,0.714517,0.55152833,0.29853117,0.294586,0.28460726,0.29243127,0.35972026
+Activated Fibrotic FBs,0.30641997,0.29605475,0.0,0.47988266,0.29449907,0.311514,0.3153645,0.3829694,0.48188484,0.58511406,0.2952834,0.2959322,0.29813305,0.66922545,0.2984002,0.29456812,0.37568203,0.81239533,0.29692546,0.3857361,0.29542366,0.8922359,0.31094173,0.29538697,0.5196074,0.3998545,0.2967384,0.2977588,0.79966724,0.29784197,0.42830187,0.7945221,0.8639403,0.29517546,0.29628012,0.8644076,0.3912956,0.5114864,0.29624853,0.30436304,0.71473485,0.5539053,0.3005485,0.29812828,0.29614267,0.2977974,0.3619377
+Adventitial FBs,0.48098493,0.47631964,0.4788472,0.0,0.47445515,0.48198158,0.4826598,0.4952905,0.53955513,0.5978258,0.4753958,0.47617298,0.4788027,0.6753741,0.47912118,0.47453803,0.49309993,0.8166119,0.47736102,0.49561635,0.47556385,0.8948901,0.48148334,0.47551987,0.56093997,0.4975645,0.47713736,0.47835618,0.8041009,0.47845542,0.50929636,0.7990411,0.86718774,0.4752664,0.47658926,0.86764556,0.49611974,0.5560383,0.47655147,0.4805367,0.720391,0.5802908,0.4797105,0.47879696,0.47642493,0.47840223,0.4907528
+Alveolar FBs,0.3028786,0.28009355,0.2936236,0.47571155,0.0,0.3079399,0.31176624,0.37902686,0.47771236,0.58105016,0.27790895,0.27976575,0.29208714,0.6686224,0.29375285,0.27588904,0.37176925,0.8119799,0.28564554,0.38178265,0.27831444,0.89197373,0.30737126,0.27810282,0.51543325,0.39584965,0.2840312,0.28993925,0.79923064,0.29107302,0.4242134,0.7940772,0.8636199,0.2775759,0.28142413,0.8640881,0.38732114,0.50730854,0.281272,0.30083516,0.7141793,0.5497709,0.29704595,0.2931122,0.28073055,0.29096377,0.35808602
+Alveolar Macrophages,0.31416592,0.31015182,0.3123235,0.48286283,0.30855453,0.0,0.32015404,0.3857942,0.48486587,0.588009,0.3093599,0.31002605,0.3122852,0.6700654,0.31255937,0.30862543,0.37848604,0.8129733,0.31104568,0.38856846,0.3095039,0.89260036,0.3166789,0.3094662,0.52258646,0.40272257,0.3108536,0.3119011,0.8002749,0.3119864,0.43122733,0.7951413,0.86438596,0.30924907,0.31038323,0.864852,0.3941426,0.5144687,0.31035075,0.31377926,0.7155084,0.55685306,0.31306693,0.31228027,0.31024212,0.3119407,0.36469907
+Arteriole,0.31802452,0.31398365,0.31616992,0.48350608,0.3123756,0.3200539,0.0,0.38640478,0.48550934,0.58863294,0.3131864,0.31385705,0.31613135,0.6701158,0.31640732,0.31244698,0.3790922,0.81300795,0.3148835,0.38918063,0.3133314,0.8926222,0.31915054,0.31329343,0.5232291,0.40334234,0.31469017,0.31574467,0.8003113,0.31583056,0.43185923,0.7951785,0.8644127,0.31307483,0.3142166,0.8648786,0.39475787,0.51511216,0.31418392,0.3176353,0.7155548,0.5574886,0.31691825,0.31612638,0.31407455,0.3157845,0.3652961
+B cells,0.3850043,0.38058734,0.38297844,0.4955066,0.37882656,0.38595006,0.38659397,0.0,0.49751168,0.5914495,0.3797146,0.3804488,0.38293633,0.6725586,0.38323796,0.37890473,0.4095059,0.81468517,0.38157195,0.41757745,0.3798733,0.8936788,0.3854772,0.37983176,0.5341837,0.42679578,0.3813604,0.3825136,0.8020747,0.3826075,0.4469659,0.79697573,0.86570513,0.37959242,0.38084227,0.86616725,0.4208547,0.5270629,0.3808065,0.38457936,0.71780276,0.56419194,0.3837962,0.38293087,0.38068685,0.3825572,0.39985773
+Basal,0.48312548,0.4784586,0.48098707,0.53966016,0.47659335,0.48412248,0.48480085,0.49743366,0.0,0.5983964,0.47753438,0.47831184,0.48094258,0.6750474,0.48126113,0.47667626,0.49524298,0.81638867,0.47950038,0.49775958,0.4777025,0.89474994,0.48362404,0.4776585,0.5615245,0.49970788,0.47927663,0.4804959,0.80386615,0.48059517,0.5098896,0.7988018,0.86701614,0.47740492,0.47872838,0.86747444,0.49826303,0.5566243,0.4786905,0.4826772,0.7200908,0.58086884,0.48185068,0.48093683,0.4785639,0.48054197,0.4928956
+Basophils,0.58499736,0.58045155,0.58291656,0.5955647,0.5786298,0.5859662,0.586393,0.58979213,0.5957679,0.0,0.57954925,0.5803083,0.5828732,0.69964755,0.58318347,0.57871085,0.5884513,0.8187986,0.58146775,0.5897005,0.57971346,0.895631,0.58548206,0.5796704,0.615348,0.58973444,0.5812496,0.5824381,0.80640143,0.5825348,0.59125787,0.8013863,0.86886823,0.5794228,0.58071476,0.8693211,0.5894116,0.6106321,0.58067787,0.5845614,0.72757226,0.6338661,0.58375734,0.5828677,0.58055425,0.582483,0.5879253
+CD4+ T-cells,0.3036353,0.2822134,0.29436693,0.47660482,0.27797523,0.30870366,0.31253523,0.37987015,0.47860596,0.5819217,0.0,0.28199503,0.29282826,0.66877073,0.2944964,0.27817628,0.3726061,0.81208205,0.2863769,0.38262832,0.280614,0.8920382,0.30813423,0.28040126,0.5163277,0.39670643,0.28476012,0.29067713,0.7993381,0.2918126,0.42508847,0.7941867,0.8636987,0.2798717,0.28285712,0.86416674,0.38817134,0.5082037,0.2827871,0.30158898,0.71431595,0.55065715,0.29779428,0.29385477,0.28253385,0.2917032,0.35890964
+CD8+ T-cells,0.3042615,0.28406212,0.29498214,0.4773432,0.28052613,0.30933568,0.3131715,0.3805676,0.47934458,0.58264166,0.28204718,0.0,0.29344153,0.66891664,0.29511172,0.28059322,0.3732983,0.81218255,0.28698215,0.38332775,0.28245637,0.8921016,0.30876562,0.28224283,0.51706684,0.39741504,0.28596044,0.29128778,0.79944366,0.29242465,0.42581195,0.7942943,0.86377627,0.28171113,0.28470844,0.864244,0.38887453,0.50894344,0.2846381,0.30221277,0.71445036,0.55138946,0.2984136,0.29446933,0.2843839,0.2923151,0.35959095
+Capillary,0.30638593,0.29441857,0.29706946,0.4798427,0.29286793,0.3114797,0.31532997,0.38293162,0.48184487,0.58507526,0.29364973,0.29429644,0.0,0.6694678,0.29719958,0.2929368,0.37564448,0.81256217,0.29528654,0.3856982,0.29378954,0.892341,0.31090745,0.29375297,0.5195675,0.3998161,0.29510003,0.2961172,0.79984266,0.2962001,0.42826262,0.7947008,0.864069,0.29354215,0.29464325,0.86453587,0.39125752,0.5114464,0.29461175,0.3043292,0.714958,0.55386573,0.30051485,0.2966217,0.29450625,0.29615563,0.36190075
+Goblet,0.667935,0.6669168,0.6672294,0.6742182,0.6665026,0.66813934,0.66821045,0.67097473,0.6739017,0.6968829,0.6666765,0.6668426,0.6674594,0.0,0.66750705,0.66651607,0.66987175,0.82444215,0.6670326,0.67089564,0.6667049,0.8910401,0.66770196,0.66673523,0.67537516,0.67091495,0.6670912,0.6673554,0.8170184,0.66724914,0.67215437,0.8136895,0.86830527,0.6666621,0.6669666,0.8687781,0.6706535,0.6748637,0.6669525,0.66779786,0.76726145,0.68169934,0.6675591,0.6672595,0.6669113,0.6672115,0.66944504
+Inflammatory FBs,0.30664328,0.296082,0.29819775,0.48014486,0.29452625,0.31173941,0.31559142,0.38321775,0.48214713,0.58536917,0.29531065,0.29595947,0.29816043,0.66950625,0.0,0.2945953,0.3759285,0.8125886,0.29695275,0.3859851,0.29545087,0.8923577,0.3111669,0.29541415,0.5198697,0.40010664,0.29676566,0.29778615,0.7998705,0.2978693,0.42855912,0.7947292,0.86408937,0.29520264,0.29630736,0.8645562,0.39154592,0.5117489,0.2962758,0.30458558,0.7149935,0.5541649,0.30076942,0.29815564,0.29616994,0.2978247,0.3621804
+Interstitial Macrophages,0.3029452,0.28023598,0.29368904,0.47579023,0.27589512,0.30800715,0.31183395,0.37910113,0.47779104,0.581127,0.27811602,0.279924,0.2921524,0.6686336,0.29381832,0.0,0.37184298,0.81198764,0.28570992,0.38185716,0.27852172,0.89197856,0.30743843,0.27830997,0.51551205,0.39592507,0.2840954,0.29000422,0.7992388,0.29113817,0.4242905,0.7940855,0.86362576,0.27778283,0.28148797,0.8640941,0.38739604,0.5073874,0.2813358,0.30090156,0.7141896,0.549849,0.29711184,0.29317755,0.28079426,0.29102886,0.35815856
+KRT5-/KRT17+,0.3781072,0.37372127,0.3760954,0.4934315,0.3719731,0.3790464,0.37968594,0.41007927,0.4954364,0.59026676,0.37285474,0.37358367,0.3760536,0.67148024,0.37635303,0.37205073,0.0,0.81394553,0.37469885,0.41178438,0.37301233,0.893213,0.37857682,0.37297106,0.53296614,0.42096728,0.37448883,0.37563384,0.8012969,0.37572706,0.44163093,0.796183,0.8651353,0.3727334,0.37397435,0.8655991,0.41504857,0.52502686,0.37393883,0.37768516,0.7168107,0.56298864,0.3769074,0.37604818,0.37382,0.37567708,0.39414415
+Langerhans cells,0.8141012,0.813406,0.81361955,0.81837076,0.81312287,0.8142405,0.81428915,0.81617117,0.81815654,0.8208405,0.81324184,0.81335527,0.8137766,0.82543886,0.81380916,0.8131321,0.81542104,0.0,0.813485,0.8161174,0.81326115,0.9007205,0.8139422,0.81328195,0.81915313,0.8161306,0.8135252,0.81370556,0.86993504,0.81363297,0.81697226,0.8682114,0.89019996,0.81323195,0.8134401,0.8908453,0.81595284,0.81880736,0.81343037,0.8140076,0.84237653,0.82005304,0.8138446,0.81364006,0.8134023,0.8136072,0.81513053
+Lymphatic,0.30521932,0.28807697,0.29592317,0.47847122,0.28654614,0.31030235,0.3141447,0.3816339,0.48047295,0.58374053,0.28731796,0.28795642,0.2943797,0.669073,0.296053,0.28661412,0.37435648,0.8122903,0.0,0.38439697,0.28745595,0.89216954,0.3097313,0.28741986,0.51819557,0.39849812,0.2890101,0.29222187,0.7995569,0.29336095,0.42691758,0.79440963,0.86385936,0.28721175,0.2882988,0.86432683,0.38994944,0.5100732,0.28826764,0.303167,0.71459436,0.55250746,0.29936093,0.2954094,0.2881635,0.29325116,0.36063266
+Macrophages - IFN-activated,0.38782254,0.3833934,0.38579115,0.49581543,0.3816276,0.38877082,0.3894165,0.417555,0.4978205,0.5913464,0.38251817,0.38325444,0.3857489,0.6724646,0.38605136,0.381706,0.41118795,0.8146208,0.38438076,0.0,0.38267735,0.89363825,0.3882967,0.38263565,0.5340775,0.42849728,0.38416862,0.38532504,0.80200696,0.38541916,0.44868487,0.7969067,0.8656554,0.38239563,0.38364905,0.8661178,0.42254996,0.52695656,0.3836132,0.38739643,0.71771634,0.56408703,0.38661113,0.38574344,0.38349319,0.38536873,0.40152708
+Mast,0.30377057,0.2826351,0.29449984,0.47676438,0.2783931,0.3088402,0.31267267,0.38002083,0.47876555,0.5820773,0.2806263,0.28241652,0.2929607,0.66879445,0.2946293,0.27859426,0.37275565,0.81209844,0.28650764,0.38277942,0.0,0.8920485,0.3082706,0.2808213,0.5164874,0.3968595,0.28489038,0.290809,0.7993552,0.2919448,0.42524478,0.7942041,0.86371136,0.2802913,0.28327945,0.86417925,0.38832325,0.50836354,0.2832093,0.30172375,0.71433777,0.55081546,0.29792807,0.2939875,0.28295588,0.29183534,0.3590568
+Mesothelial,0.8946993,0.8942663,0.89439934,0.89735115,0.8940899,0.894786,0.8948163,0.8959864,0.8972183,0.89788634,0.89416397,0.89423466,0.89449716,0.8932123,0.8945174,0.8940957,0.89552027,0.90055746,0.89431554,0.89595306,0.89417607,0.0,0.89460033,0.894189,0.8978358,0.8959612,0.8943406,0.8944529,0.8976542,0.89440775,0.89648384,0.89625406,0.9140271,0.89415795,0.8942876,0.9145459,0.8958508,0.89762163,0.8942815,0.89464104,0.8895369,0.8982282,0.89453954,0.8944121,0.8942639,0.8943917,0.8953396
+Migratory DCs,0.31375524,0.309744,0.31191415,0.4823882,0.30814788,0.31684598,0.3194183,0.38534388,0.48439112,0.58754843,0.30895266,0.30961832,0.31187585,0.66962594,0.31214982,0.30821875,0.37803897,0.812671,0.3106372,0.38811693,0.30909654,0.8924097,0.0,0.30905887,0.52211225,0.4022654,0.3104453,0.311492,0.79995704,0.3115773,0.43076113,0.79481745,0.86415285,0.30884188,0.30997527,0.86461955,0.3936888,0.5139939,0.3099428,0.31336886,0.7151037,0.5563839,0.31265703,0.31187093,0.30983424,0.3115316,0.36425874
+Monocytes/MDMs,0.30373567,0.2824129,0.29446554,0.47672328,0.27817294,0.30880496,0.3126372,0.37998196,0.47872445,0.5820372,0.28040507,0.28219444,0.29292655,0.6688277,0.29459503,0.27837405,0.37271708,0.8121214,0.28647393,0.38274044,0.28081277,0.89206296,0.30823544,0.0,0.51644623,0.39682007,0.2848568,0.29077497,0.7993793,0.2919107,0.42520443,0.7942287,0.86372894,0.28007022,0.2830569,0.8641969,0.38828412,0.5083223,0.28298682,0.30168897,0.71436846,0.55077463,0.29789358,0.29395327,0.28273353,0.29180127,0.35901886
+Multiciliated,0.5203466,0.5156789,0.51820856,0.55966264,0.51381147,0.52134293,0.5220207,0.5334351,0.5601435,0.617655,0.51475376,0.515532,0.5181641,0.6763616,0.5184827,0.5138945,0.5320562,0.817286,0.51672137,0.5333408,0.514922,0.8953133,0.5208449,0.514878,0.0,0.53337574,0.5164975,0.5177173,0.80481,0.5178166,0.5349434,0.7997639,0.8677061,0.5146241,0.51594883,0.8681624,0.5330436,0.5764682,0.515911,0.5198985,0.7212981,0.60040665,0.5190722,0.5181584,0.51578426,0.5177634,0.5300974
+Myofibroblasts,0.4020049,0.39751896,0.39994773,0.49767402,0.3957298,0.402965,0.4036187,0.426484,0.49967918,0.5912942,0.39663222,0.39737818,0.39990497,0.6724171,0.40021124,0.3958093,0.420079,0.8145882,0.3985192,0.42820776,0.39679348,0.8936177,0.402485,0.3967513,0.5340239,0.0,0.39830434,0.39947563,0.8019727,0.399571,0.45775643,0.7968718,0.86563045,0.39650807,0.39777792,0.86609274,0.43150663,0.5269028,0.3977416,0.4015734,0.7176726,0.564034,0.40077817,0.39989942,0.39762002,0.39951992,0.4114404
+NK/NKT,0.3050401,0.2864244,0.29574704,0.47826025,0.28489885,0.31012145,0.3139626,0.3814344,0.48026192,0.58353513,0.285668,0.28630427,0.29420418,0.6691421,0.29587686,0.2849666,0.3741585,0.812338,0.28897947,0.3841969,0.28580552,0.89219964,0.30955058,0.28576952,0.5179845,0.3982955,0.0,0.29204705,0.799607,0.2931857,0.42671075,0.7944606,0.863896,0.28556216,0.28688917,0.8643635,0.38974833,0.50986195,0.28681853,0.3029884,0.7146581,0.5522984,0.29918364,0.2952335,0.28656316,0.29307598,0.36043778
+Neutrophils,0.3060247,0.2922899,0.2967145,0.47941828,0.29074588,0.31111515,0.31496298,0.38252988,0.4814204,0.58466244,0.29152438,0.29216835,0.29516864,0.66937494,0.29684454,0.29081446,0.3752458,0.8124982,0.29315418,0.3852954,0.29166353,0.89230067,0.31054324,0.29162714,0.51914304,0.39940816,0.2929685,0.0,0.7997755,0.29454485,0.4278464,0.7946324,0.8640197,0.2914172,0.2925136,0.8644867,0.3908526,0.51102155,0.29248226,0.30396935,0.71487254,0.5534456,0.30015752,0.29619995,0.2923772,0.29450467,0.3615082
+PNEC,0.8011017,0.8003698,0.8005946,0.8055985,0.8000717,0.80124843,0.8012996,0.80328137,0.80537283,0.8082012,0.80019695,0.80031633,0.80076,0.816472,0.80079424,0.8000815,0.8024915,0.86993873,0.80045307,0.80322486,0.80021733,0.8978245,0.8009343,0.8002392,0.80642295,0.80323863,0.8004952,0.80068517,0.0,0.80060875,0.80412525,0.86448836,0.88703555,0.8001866,0.8004056,0.8876972,0.80305153,0.8060586,0.8003955,0.8010032,0.83592856,0.8073712,0.80083156,0.80061626,0.80036575,0.8005817,0.80218554
+Plasma,0.30610353,0.2934754,0.29679194,0.4795109,0.29192767,0.3111947,0.31504303,0.38261753,0.48151302,0.5847525,0.29270798,0.2933535,0.2956032,0.66926044,0.296922,0.2919964,0.37533277,0.8124193,0.2943417,0.38538328,0.2928475,0.8922511,0.31062272,0.292811,0.51923573,0.39949718,0.29415554,0.29517084,0.7996926,0.0,0.42793718,0.7945479,0.8639588,0.29260057,0.29369962,0.864426,0.39094096,0.51111424,0.2936682,0.30404782,0.71476704,0.55353725,0.3002355,0.2962773,0.2935629,0.29520923,0.36159384
+Proliferating AT2,0.4300729,0.42549658,0.42797488,0.51124066,0.4236701,0.43105173,0.43171796,0.4458359,0.5117283,0.59251624,0.4245914,0.42535287,0.42793122,0.67353046,0.4282437,0.42375126,0.44199765,0.81535107,0.42651737,0.44731867,0.42475608,0.8940977,0.43056232,0.424713,0.5352825,0.45667878,0.42629814,0.4274932,0.80277485,0.42759055,0.0,0.79768944,0.8662177,0.42446464,0.42576087,0.8666784,0.45064878,0.5283368,0.4257238,0.4296329,0.71869653,0.5652776,0.4288219,0.4279256,0.42559975,0.4275384,0.43968272
+Proliferating Airway,0.7959239,0.7951777,0.79540694,0.8005086,0.7948739,0.79607344,0.7961255,0.798146,0.8002784,0.8031628,0.79500157,0.7951233,0.79557544,0.8132021,0.79561037,0.79488385,0.7973406,0.8682448,0.7952626,0.7980883,0.7950223,0.89645046,0.7957532,0.7950446,0.80134916,0.7981024,0.79530567,0.79549927,0.86451644,0.7954213,0.7990063,0.0,0.88553494,0.79499096,0.7952143,0.88620424,0.7979116,0.80097777,0.7952039,0.79582345,0.8329343,0.80231625,0.7956485,0.79542893,0.7951737,0.7953937,0.79702866
+Proliferating B cells,0.8662968,0.8657647,0.8659282,0.86955976,0.8655479,0.8664035,0.86644065,0.8678799,0.86939627,0.87144274,0.8656389,0.8657258,0.8660484,0.8706563,0.86607325,0.8655549,0.86730653,0.89011157,0.8658252,0.8678389,0.86565375,0.9140992,0.8661752,0.8656696,0.8701566,0.8678489,0.86585593,0.865994,0.88694155,0.8659384,0.868492,0.8854135,0.0,0.8656314,0.8657907,0.90541506,0.86771315,0.86989284,0.8657833,0.8662252,0.86757666,0.8708427,0.86610043,0.8659439,0.86576176,0.86591876,0.8670844
+Proliferating FBs,0.30353126,0.28186664,0.29426473,0.47648206,0.27763173,0.30859864,0.31242952,0.37975422,0.47848317,0.581802,0.27986118,0.28164846,0.29272634,0.66876036,0.2943942,0.27783257,0.3724911,0.812075,0.28627634,0.3825121,0.28026843,0.8920337,0.30802935,0.28005588,0.5162048,0.39658865,0.2846599,0.29057565,0.79933053,0.2917109,0.42496815,0.794179,0.8636932,0.0,0.28250992,0.8641612,0.3880545,0.5080807,0.28243995,0.30148536,0.7143064,0.55053544,0.2976914,0.29375267,0.28218693,0.2916015,0.3587964
+Proliferating Myeloid,0.30459774,0.2849512,0.29531243,0.4777394,0.28232098,0.30967504,0.31351316,0.380942,0.47974095,0.5830278,0.2830859,0.28473157,0.29377088,0.6690315,0.29544216,0.2823883,0.37366983,0.81226164,0.28768346,0.38370317,0.28334242,0.89215153,0.3091046,0.28318688,0.5174633,0.39779535,0.28685305,0.29161566,0.7995268,0.2927533,0.4262002,0.79437906,0.8638373,0.28298062,0.0,0.8643048,0.38925192,0.5093403,0.28552827,0.30254772,0.71455616,0.5517822,0.29874617,0.29479933,0.2852736,0.2926437,0.3599567
+Proliferating NK/NKT,0.86663586,0.8661047,0.86626786,0.86989164,0.86588836,0.86674225,0.8667793,0.8682155,0.8697285,0.87177056,0.8659793,0.86606604,0.86638796,0.8709932,0.8664127,0.8658955,0.8676433,0.8906996,0.86616516,0.86817455,0.86599416,0.9145712,0.8665144,0.86600995,0.8704873,0.8681845,0.86619586,0.8663336,0.8875444,0.86627823,0.86882627,0.88602346,0.90536416,0.8659718,0.86613077,0.0,0.868049,0.8702241,0.86612344,0.86656433,0.86813986,0.8711719,0.8664398,0.8662836,0.866102,0.86625856,0.8674216
+Proliferating T-cells,0.3935064,0.38905355,0.39146423,0.49629897,0.38727808,0.39445958,0.39510858,0.42081603,0.49830407,0.59104913,0.38817358,0.38891384,0.39142174,0.6721937,0.39172584,0.3873569,0.41443464,0.814435,0.39004627,0.42253375,0.38833362,0.89352125,0.39398304,0.3882917,0.53377146,0.43178046,0.38983303,0.39099562,0.8018116,0.39109027,0.45200038,0.7967076,0.8655124,0.38805032,0.3893106,0.8659751,0.0,0.52664995,0.38927454,0.39307803,0.71746707,0.5637846,0.3922886,0.39141628,0.38915387,0.39103955,0.40474993
+RASC,0.51240915,0.5077373,0.51026905,0.5551381,0.50586855,0.5134065,0.51408505,0.52651536,0.5556199,0.6133146,0.5068115,0.5075903,0.5102245,0.6758825,0.51054347,0.50595164,0.5245158,0.8169591,0.50878054,0.52642095,0.5069799,0.89510816,0.512908,0.5069358,0.5768438,0.5264559,0.50855654,0.50977737,0.8044662,0.5098767,0.5280262,0.79941344,0.8674547,0.50668174,0.50800747,0.8679118,0.5261232,0.0,0.50796956,0.51196057,0.7208581,0.5959985,0.5111335,0.5102188,0.5078427,0.5098235,0.5221731
+SMCs/Pericytes,0.30456713,0.28487918,0.2952824,0.47770333,0.28217313,0.30964413,0.31348208,0.38090795,0.47970483,0.5829926,0.28293785,0.28465956,0.29374087,0.669018,0.2954121,0.28224048,0.373636,0.8122524,0.287611,0.383669,0.2832706,0.8921457,0.30907375,0.28305668,0.51742727,0.39776072,0.28678071,0.29158583,0.7995171,0.29272342,0.42616487,0.79436904,0.8638301,0.2828326,0.2855266,0.8642977,0.38921762,0.50930417,0.0,0.30251727,0.71454376,0.5517464,0.2987159,0.29476932,0.28520152,0.2926138,0.3599234
+SPP1+ Macrophages,0.30928499,0.3031177,0.3052619,0.4814896,0.3015408,0.31289634,0.31675607,0.38449174,0.48349226,0.58667594,0.30233586,0.3029935,0.3052241,0.6697599,0.3054948,0.3016108,0.3771931,0.81276315,0.3040002,0.38726252,0.30247802,0.89246786,0.31232268,0.3024408,0.5212141,0.4014003,0.30381057,0.3048448,0.80005395,0.30492908,0.42987883,0.7949162,0.86422396,0.30222645,0.30334613,0.8646904,0.39282998,0.5130948,0.30331406,0.0,0.71522707,0.5554954,0.305996,0.3052192,0.3032068,0.3048839,0.3634257
+Secretory,0.7145747,0.7136381,0.71392566,0.72034484,0.713257,0.7147625,0.7148279,0.71736807,0.72005457,0.72635126,0.71341705,0.7135699,0.7141373,0.7669746,0.71418107,0.7132695,0.71635497,0.84233856,0.71374464,0.7172954,0.7134432,0.88705975,0.71436036,0.7134711,0.7214057,0.71731323,0.7137986,0.7140416,0.8358186,0.7139438,0.7184512,0.8328042,0.86565703,0.7134039,0.713684,0.866425,0.717073,0.72093683,0.7136709,0.7144486,0.0,0.7226272,0.7142289,0.7139534,0.71363306,0.71390915,0.71596277
+Subpleural FBs,0.5541778,0.5495543,0.55206084,0.5777717,0.54770297,0.555164,0.55583465,0.56294197,0.5782476,0.6349347,0.5486373,0.54940873,0.55201674,0.68520164,0.55233234,0.54778534,0.56157863,0.8180943,0.5505874,0.56284887,0.54880416,0.8958205,0.5546711,0.5487605,0.5991704,0.5628833,0.5503657,0.55157423,0.80566037,0.5516725,0.5644328,0.80063075,0.8683272,0.54850876,0.5498219,0.86878175,0.562555,0.594387,0.54978436,0.5537342,0.7223868,0.0,0.5529161,0.552011,0.54965883,0.5516199,0.561044
+Transitional AT2,0.3071195,0.29938602,0.30151525,0.48070374,0.29782024,0.31221995,0.31607518,0.38374707,0.4827062,0.58591247,0.2986097,0.2992627,0.30147773,0.6695397,0.30174655,0.29788977,0.3764539,0.81261164,0.30026233,0.38651583,0.29875085,0.89237225,0.31164697,0.2987139,0.5204285,0.40064415,0.30007404,0.30110106,0.79989463,0.30118474,0.42910752,0.7947538,0.8641071,0.29850104,0.29961285,0.8645739,0.3920794,0.5123083,0.29958105,0.30522192,0.71502423,0.55471796,0.0,0.3014729,0.29947454,0.3011399,0.36269772
+Tregs,0.30637944,0.2955288,0.29764232,0.47983506,0.2939748,0.31147316,0.31532335,0.3829244,0.4818373,0.58506787,0.2947583,0.2954064,0.297605,0.6692591,0.29787186,0.29404375,0.37563735,0.81241846,0.29639864,0.385691,0.2948984,0.89225036,0.31090096,0.2948617,0.5195599,0.3998088,0.29621175,0.29723114,0.79969156,0.2973142,0.4282552,0.7945469,0.8639582,0.29465044,0.29575396,0.8644254,0.39125028,0.5114388,0.2957224,0.30432275,0.71476585,0.5538582,0.30050844,0.0,0.2956167,0.29726967,0.3618937
+Venous,0.30446485,0.28461826,0.29518187,0.47758284,0.2816434,0.30954087,0.31337813,0.38079405,0.47958428,0.5828752,0.2826009,0.2843988,0.2936407,0.66897947,0.29531154,0.28171068,0.37352297,0.8122259,0.28734928,0.3835548,0.2830106,0.89212894,0.30897063,0.2827968,0.5173066,0.39764503,0.28651878,0.29148605,0.79948914,0.2926234,0.4260468,0.7943407,0.8638096,0.2823021,0.28526533,0.8642773,0.3891028,0.5091834,0.2851949,0.30241534,0.71450824,0.551627,0.2986147,0.29466888,0.0,0.29251382,0.3598121
+cDCs,0.30606037,0.2933788,0.29674953,0.47946015,0.29183137,0.31115112,0.3149992,0.38256955,0.4814623,0.5847032,0.29261157,0.29325694,0.2955634,0.6692229,0.2968796,0.2919001,0.37528515,0.8123935,0.29424497,0.38533518,0.2927511,0.89223474,0.3105792,0.29271457,0.51918495,0.3994484,0.29405886,0.29507393,0.7996654,0.29515666,0.42788747,0.7945202,0.863939,0.2925042,0.293603,0.86440617,0.3908926,0.51106346,0.29357162,0.30400485,0.71473247,0.55348706,0.3001928,0.29623494,0.2934663,0.0,0.36154696
+pDCs,0.36445612,0.36013687,0.36247462,0.49120072,0.3584159,0.36538133,0.36601144,0.40087807,0.49320534,0.58987087,0.35928378,0.3600014,0.36243343,0.6711191,0.36272842,0.3584923,0.39459306,0.81369746,0.36109936,0.40257102,0.3594389,0.89305675,0.36491877,0.3593983,0.5309061,0.41169223,0.36089256,0.36202008,0.8010362,0.36211193,0.4394312,0.7959173,0.86494416,0.35916433,0.360386,0.8654085,0.40581256,0.5228006,0.36035106,0.3640404,0.7164783,0.5625859,0.36327437,0.3624281,0.36023408,0.36206272,0.0

data/outputs/formal_release/run_config.json

@@ -0,0 +1,56 @@
+{
+  "analysis": {
+    "node_count": 47,
+    "sample_counts": {
+      "T1": 10,
+      "T2": 15,
+      "T3": 20
+    },
+    "stage_order": [
+      "T1",
+      "T2",
+      "T3"
+    ]
+  },
+  "device": "cpu",
+  "environment": {
+    "matplotlib": null,
+    "numpy": "2.1.2",
+    "pandas": "2.3.2",
+    "python": "3.12.11",
+    "torch": "2.5.1+cu121",
+    "torch_geometric": "2.6.1"
+  },
+  "generated_files": [
+    "checksums.sha256",
+    "explainer_edges_t2_to_t3.csv",
+    "observed_T1_sss.csv",
+    "observed_T2_sss.csv",
+    "observed_T3_sss.csv",
+    "predicted_T2_sss.csv",
+    "predicted_T3_sss.csv",
+    "run_config.json",
+    "summary.json",
+    "top_dynamic_nodes.csv",
+    "top_edge_changes.csv",
+    "training_history.csv"
+  ],
+  "input_csv": {
+    "filename": "cophenetic_distances_searcher_D_score_in_all_samples.csv",
+    "path": "data/inputs/cophenetic_distances_searcher_D_score_in_all_samples.csv",
+    "resolved_path": "/data/taobo.hu/tmp/dst_gnn_release_repo/data/inputs/cophenetic_distances_searcher_D_score_in_all_samples.csv",
+    "sha256": "d10b46e245a331365ad634fa157d1f020ef631e7c93893d63ad4c5bf1dfeaa5c"
+  },
+  "model": {
+    "dropout": 0.0,
+    "epochs": 400,
+    "hidden_channels": 32,
+    "lr": 0.01,
+    "run_explainer": true,
+    "top_k": 20,
+    "weight_decay": 0.0005
+  },
+  "output_dir": "data/outputs/formal_release",
+  "resolved_output_dir": "/data/taobo.hu/tmp/dst_gnn_release_repo/data/outputs/formal_release",
+  "seed": 0
+}

data/outputs/formal_release/summary.json

@@ -0,0 +1,47 @@
+{
+  "csv_path": "data/inputs/cophenetic_distances_searcher_D_score_in_all_samples.csv",
+  "resolved_csv_path": "/data/taobo.hu/tmp/dst_gnn_release_repo/data/inputs/cophenetic_distances_searcher_D_score_in_all_samples.csv",
+  "csv_sha256": "d10b46e245a331365ad634fa157d1f020ef631e7c93893d63ad4c5bf1dfeaa5c",
+  "device": "cpu",
+  "seed": 0,
+  "node_count": 47,
+  "stage_order": [
+    "T1",
+    "T2",
+    "T3"
+  ],
+  "sample_counts": {
+    "T1": 10,
+    "T2": 15,
+    "T3": 20
+  },
+  "top_dynamic_nodes": [
+    "Secretory",
+    "KRT5-/KRT17+",
+    "Proliferating NK/NKT",
+    "RASC",
+    "pDCs"
+  ],
+  "top_edge_change_pairs": [
+    {
+      "source": "KRT5-/KRT17+",
+      "target": "AT1"
+    },
+    {
+      "source": "AT1",
+      "target": "KRT5-/KRT17+"
+    },
+    {
+      "source": "cDCs",
+      "target": "KRT5-/KRT17+"
+    },
+    {
+      "source": "KRT5-/KRT17+",
+      "target": "cDCs"
+    },
+    {
+      "source": "KRT5-/KRT17+",
+      "target": "SPP1+ Macrophages"
+    }
+  ]
+}

data/outputs/formal_release/top_dynamic_nodes.csv

@@ -0,0 +1,21 @@
+node,drift_score
+Secretory,0.66684085
+KRT5-/KRT17+,0.63817286
+Proliferating NK/NKT,0.6206382
+RASC,0.6157724
+pDCs,0.60553324
+Proliferating Airway,0.567926
+Myofibroblasts,0.5598956
+Proliferating T-cells,0.546863
+Basal,0.5465807
+Proliferating B cells,0.53555185
+Goblet,0.52530444
+Langerhans cells,0.44658872
+Multiciliated,0.4255937
+PNEC,0.41318658
+Migratory DCs,0.40672618
+Proliferating AT2,0.3757535
+Activated Fibrotic FBs,0.35773247
+Tregs,0.3274673
+Adventitial FBs,0.3191264
+Basophils,0.31525227

data/outputs/formal_release/top_edge_changes.csv

@@ -0,0 +1,21 @@
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+374.0,0.011693323962390423
+375.0,0.011687489226460457
+376.0,0.011620733886957169
+377.0,0.011575442738831043
+378.0,0.011538020335137844
+379.0,0.011527602560818195
+380.0,0.011442109011113644
+381.0,0.01145379338413477
+382.0,0.01137448288500309
+383.0,0.011374224908649921
+384.0,0.011346443556249142
+385.0,0.011324610561132431
+386.0,0.011312553659081459
+387.0,0.011286530643701553
+388.0,0.011272173374891281
+389.0,0.011227942071855068
+390.0,0.011189186945557594
+391.0,0.011134150438010693
+392.0,0.01109320018440485
+393.0,0.01103812362998724
+394.0,0.011001260951161385
+395.0,0.01095337513834238
+396.0,0.010926294140517712
+397.0,0.010883156210184097
+398.0,0.010856426320970058
+399.0,0.01082596741616726
+400.0,0.01079186424612999

scripts/run_dst_gnn.py

@@ -4,7 +4,10 @@
 from __future__ import annotations
 
 import argparse
+import hashlib
 import json
+import platform
+import random
 import sys
 from pathlib import Path
 
@@ -38,6 +41,7 @@ def parse_args() -> argparse.Namespace:
     parser = argparse.ArgumentParser(description="Run DST-GNN on temporal COSTE/SSS graphs.")
     parser.add_argument("--csv", type=Path, required=True, help="Path to the flattened COSTE/SSS CSV.")
     parser.add_argument("--output-dir", type=Path, required=True, help="Directory for outputs.")
+    parser.add_argument("--seed", type=int, default=0, help="Random seed for reproducible training.")
     parser.add_argument("--hidden-channels", type=int, default=32, help="Hidden channel dimension.")
     parser.add_argument("--dropout", type=float, default=0.0, help="Dropout probability.")
     parser.add_argument("--epochs", type=int, default=400, help="Training epochs.")
@@ -57,6 +61,52 @@ def parse_args() -> argparse.Namespace:
     return parser.parse_args()
 
 
+def set_reproducibility(seed: int) -> None:
+    """Set deterministic seeds for the current process."""
+
+    random.seed(seed)
+    np.random.seed(seed)
+    torch.manual_seed(seed)
+    if torch.cuda.is_available():
+        torch.cuda.manual_seed_all(seed)
+    torch.use_deterministic_algorithms(True, warn_only=True)
+    if hasattr(torch.backends, "cudnn"):
+        torch.backends.cudnn.deterministic = True
+        torch.backends.cudnn.benchmark = False
+
+
+def sha256_file(path: Path) -> str:
+    """Return the SHA256 digest of a file."""
+
+    digest = hashlib.sha256()
+    with path.open("rb") as handle:
+        while True:
+            chunk = handle.read(1024 * 1024)
+            if not chunk:
+                break
+            digest.update(chunk)
+    return digest.hexdigest()
+
+
+def get_runtime_versions() -> dict[str, str | None]:
+    """Collect runtime version information for reproducibility metadata."""
+
+    versions: dict[str, str | None] = {
+        "python": platform.python_version(),
+        "torch": torch.__version__,
+        "pandas": pd.__version__,
+        "numpy": np.__version__,
+        "matplotlib": getattr(plt, "__version__", None) if plt is not None else None,
+    }
+    try:
+        import torch_geometric
+
+        versions["torch_geometric"] = torch_geometric.__version__
+    except ModuleNotFoundError:
+        versions["torch_geometric"] = None
+    return versions
+
+
 def save_matrix(matrix: torch.Tensor | pd.DataFrame | np.ndarray, output_path: Path, node_names: list[str]) -> None:
     if isinstance(matrix, torch.Tensor):
         values = matrix.detach().cpu().numpy()
@@ -95,9 +145,69 @@ def plot_top_nodes(nodes: pd.DataFrame, output_path: Path) -> None:
     plt.close()
 
 
+def write_checksums(csv_path: Path, output_dir: Path) -> None:
+    """Write SHA256 checksums for the input CSV and generated output files."""
+
+    checksum_path = output_dir / "checksums.sha256"
+    entries: list[tuple[str, str]] = [
+        (sha256_file(csv_path), f"input_csv::{csv_path.name}"),
+    ]
+    for path in sorted(output_dir.iterdir()):
+        if path.is_file() and path.name != checksum_path.name:
+            entries.append((sha256_file(path), path.name))
+
+    lines = [f"{digest}  {label}" for digest, label in entries]
+    checksum_path.write_text("\n".join(lines) + "\n", encoding="utf-8")
+
+
+def build_run_config(
+    args: argparse.Namespace,
+    bundle,
+    output_dir: Path,
+    generated_files: list[str],
+    csv_argument: str,
+    output_argument: str,
+) -> dict[str, object]:
+    """Build the structured run configuration metadata."""
+
+    return {
+        "input_csv": {
+            "path": csv_argument,
+            "resolved_path": str(args.csv),
+            "filename": args.csv.name,
+            "sha256": sha256_file(args.csv),
+        },
+        "output_dir": output_argument,
+        "resolved_output_dir": str(output_dir),
+        "seed": args.seed,
+        "device": args.device,
+        "model": {
+            "hidden_channels": args.hidden_channels,
+            "dropout": args.dropout,
+            "epochs": args.epochs,
+            "lr": args.lr,
+            "weight_decay": args.weight_decay,
+            "top_k": args.top_k,
+            "run_explainer": args.run_explainer,
+        },
+        "analysis": {
+            "node_count": len(bundle.node_names),
+            "stage_order": list(STAGE_ORDER),
+            "sample_counts": bundle.sample_counts,
+        },
+        "environment": get_runtime_versions(),
+        "generated_files": generated_files,
+    }
+
+
 def main() -> None:
     args = parse_args()
+    csv_argument = str(args.csv)
+    output_argument = str(args.output_dir)
+    args.csv = args.csv.resolve()
+    args.output_dir = args.output_dir.resolve()
     args.output_dir.mkdir(parents=True, exist_ok=True)
+    set_reproducibility(args.seed)
 
     bundle = build_temporal_graphs(args.csv)
     node_names = bundle.node_names
@@ -144,8 +254,11 @@ def main() -> None:
         save_matrix(predictions[index], args.output_dir / f"predicted_{stage}_sss.csv", node_names)
 
     summary = {
-        "csv_path": str(args.csv),
+        "csv_path": csv_argument,
+        "resolved_csv_path": str(args.csv),
+        "csv_sha256": sha256_file(args.csv),
         "device": args.device,
+        "seed": args.seed,
         "node_count": len(node_names),
         "stage_order": list(STAGE_ORDER),
         "sample_counts": bundle.sample_counts,
@@ -168,6 +281,29 @@ def main() -> None:
             edge_frame = edge_mask_to_frame(graphs[1], node_names, explanation.edge_mask)
             edge_frame.head(args.top_k).to_csv(args.output_dir / "explainer_edges_t2_to_t3.csv", index=False)
 
+    generated_files = sorted(
+        path.name
+        for path in args.output_dir.iterdir()
+        if path.is_file()
+    )
+    for name in ("run_config.json", "checksums.sha256"):
+        if name not in generated_files:
+            generated_files.append(name)
+    generated_files = sorted(generated_files)
+    run_config = build_run_config(
+        args,
+        bundle,
+        args.output_dir,
+        generated_files,
+        csv_argument,
+        output_argument,
+    )
+    (args.output_dir / "run_config.json").write_text(
+        json.dumps(run_config, indent=2, sort_keys=True),
+        encoding="utf-8",
+    )
+    write_checksums(args.csv, args.output_dir)
+
     print(f"Finished. Outputs written to {args.output_dir}")
 
 

scripts/verify_repro.py

@@ -0,0 +1,192 @@
+#!/usr/bin/env python
+"""Compare rerun outputs against the bundled formal DST-GNN release."""
+
+from __future__ import annotations
+
+import argparse
+import json
+import re
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+
+
+NUMERIC_CSV_FILES = {
+    "observed_T1_sss.csv",
+    "observed_T2_sss.csv",
+    "observed_T3_sss.csv",
+    "predicted_T2_sss.csv",
+    "predicted_T3_sss.csv",
+    "top_dynamic_nodes.csv",
+    "top_edge_changes.csv",
+    "training_history.csv",
+    "explainer_edges_t2_to_t3.csv",
+}
+JSON_FILES = {"summary.json", "run_config.json"}
+TEXT_FILES = {"checksums.sha256"}
+
+
+def parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser(description="Verify DST-GNN outputs against the bundled release.")
+    parser.add_argument("--expected-dir", type=Path, required=True, help="Directory containing the bundled release.")
+    parser.add_argument("--actual-dir", type=Path, required=True, help="Directory containing rerun outputs.")
+    parser.add_argument("--atol", type=float, default=1e-5, help="Absolute tolerance for numeric comparisons.")
+    parser.add_argument("--rtol", type=float, default=1e-5, help="Relative tolerance for numeric comparisons.")
+    return parser.parse_args()
+
+
+def load_csv(path: Path) -> pd.DataFrame:
+    """Load a CSV and normalize unnamed index columns."""
+
+    frame = pd.read_csv(path)
+    unnamed = [column for column in frame.columns if str(column).startswith("Unnamed:")]
+    if unnamed:
+        frame = frame.set_index(unnamed[0])
+        frame.index.name = None
+    return frame
+
+
+def compare_numeric_csv(expected_path: Path, actual_path: Path, atol: float, rtol: float) -> list[str]:
+    """Compare two CSV files with mixed numeric and non-numeric columns."""
+
+    errors: list[str] = []
+    expected = load_csv(expected_path)
+    actual = load_csv(actual_path)
+
+    if list(expected.columns) != list(actual.columns):
+        return [f"{expected_path.name}: columns differ"]
+    if list(expected.index) != list(actual.index):
+        return [f"{expected_path.name}: row order/index differs"]
+
+    for column in expected.columns:
+        left = expected[column]
+        right = actual[column]
+        if pd.api.types.is_numeric_dtype(left) and pd.api.types.is_numeric_dtype(right):
+            if not np.allclose(left.to_numpy(), right.to_numpy(), atol=atol, rtol=rtol, equal_nan=True):
+                max_delta = float(np.nanmax(np.abs(left.to_numpy() - right.to_numpy())))
+                errors.append(f"{expected_path.name}:{column} numeric mismatch (max_abs_delta={max_delta:.6g})")
+        else:
+            if not left.fillna("<NA>").equals(right.fillna("<NA>")):
+                errors.append(f"{expected_path.name}:{column} text mismatch")
+    return errors
+
+
+def compare_summary(expected: dict[str, object], actual: dict[str, object]) -> list[str]:
+    """Compare the stable fields in summary.json."""
+
+    errors: list[str] = []
+    for key in ("device", "seed", "node_count", "stage_order", "sample_counts"):
+        if expected.get(key) != actual.get(key):
+            errors.append(f"summary.json:{key} differs")
+    return errors
+
+
+def compare_run_config(expected: dict[str, object], actual: dict[str, object]) -> list[str]:
+    """Compare the stable fields in run_config.json."""
+
+    errors: list[str] = []
+
+    for key in ("seed", "device"):
+        if expected.get(key) != actual.get(key):
+            errors.append(f"run_config.json:{key} differs")
+
+    expected_model = expected.get("model", {})
+    actual_model = actual.get("model", {})
+    for key in ("hidden_channels", "dropout", "epochs", "lr", "weight_decay", "top_k", "run_explainer"):
+        if expected_model.get(key) != actual_model.get(key):
+            errors.append(f"run_config.json:model.{key} differs")
+
+    expected_analysis = expected.get("analysis", {})
+    actual_analysis = actual.get("analysis", {})
+    for key in ("node_count", "stage_order", "sample_counts"):
+        if expected_analysis.get(key) != actual_analysis.get(key):
+            errors.append(f"run_config.json:analysis.{key} differs")
+
+    expected_input = expected.get("input_csv", {})
+    actual_input = actual.get("input_csv", {})
+    if expected_input.get("sha256") != actual_input.get("sha256"):
+        errors.append("run_config.json:input_csv.sha256 differs")
+
+    expected_env = expected.get("environment", {})
+    actual_env = actual.get("environment", {})
+    for key in ("python", "torch", "torch_geometric", "pandas", "numpy"):
+        if key not in actual_env:
+            errors.append(f"run_config.json:environment.{key} missing in actual output")
+        if key not in expected_env:
+            errors.append(f"run_config.json:environment.{key} missing in expected output")
+
+    return errors
+
+
+def compare_json(expected_path: Path, actual_path: Path) -> list[str]:
+    """Compare structured JSON outputs."""
+
+    expected = json.loads(expected_path.read_text(encoding="utf-8"))
+    actual = json.loads(actual_path.read_text(encoding="utf-8"))
+    if expected_path.name == "summary.json":
+        return compare_summary(expected, actual)
+    if expected_path.name == "run_config.json":
+        return compare_run_config(expected, actual)
+    return [] if expected == actual else [f"{expected_path.name}: JSON differs"]
+
+
+def parse_checksums(path: Path) -> dict[str, str]:
+    """Parse a checksums.sha256 file."""
+
+    entries: dict[str, str] = {}
+    pattern = re.compile(r"^([0-9a-f]{64})\s{2}(.+)$")
+    for line in path.read_text(encoding="utf-8").splitlines():
+        match = pattern.match(line.strip())
+        if not match:
+            raise ValueError(f"{path} contains an invalid checksum line: {line!r}")
+        entries[match.group(2)] = match.group(1)
+    return entries
+
+
+def compare_text(expected_path: Path, actual_path: Path) -> list[str]:
+    """Compare non-CSV plain-text files."""
+
+    if expected_path.name == "checksums.sha256":
+        expected = parse_checksums(expected_path)
+        actual = parse_checksums(actual_path)
+        if set(expected) != set(actual):
+            return ["checksums.sha256 labels differ"]
+        return []
+    return [] if expected_path.read_text(encoding="utf-8") == actual_path.read_text(encoding="utf-8") else [
+        f"{expected_path.name}: text differs"
+    ]
+
+
+def main() -> None:
+    args = parse_args()
+    args.expected_dir = args.expected_dir.resolve()
+    args.actual_dir = args.actual_dir.resolve()
+
+    expected_files = sorted(path.name for path in args.expected_dir.iterdir() if path.is_file())
+    missing_files = [name for name in expected_files if not (args.actual_dir / name).exists()]
+    if missing_files:
+        raise SystemExit("Missing files in actual output: " + ", ".join(missing_files))
+
+    errors: list[str] = []
+    for name in expected_files:
+        expected_path = args.expected_dir / name
+        actual_path = args.actual_dir / name
+        if name in NUMERIC_CSV_FILES:
+            errors.extend(compare_numeric_csv(expected_path, actual_path, args.atol, args.rtol))
+        elif name in JSON_FILES:
+            errors.extend(compare_json(expected_path, actual_path))
+        elif name in TEXT_FILES:
+            errors.extend(compare_text(expected_path, actual_path))
+        else:
+            if expected_path.read_bytes() != actual_path.read_bytes():
+                errors.append(f"{name}: binary/text content differs")
+
+    if errors:
+        raise SystemExit("Verification failed:\n- " + "\n- ".join(errors))
+
+    print(f"Verification passed for {args.actual_dir} against {args.expected_dir}")
+
+
+if __name__ == "__main__":
+    main()

upload_to_hf.py

@@ -31,7 +31,7 @@ def parse_args() -> argparse.Namespace:
     )
     parser.add_argument(
         "--commit-message",
-        default="Upload cleaned DST-GNN manuscript code",
+        default="Publish bundled DST-GNN inputs and formal reproducibility outputs",
         help="Commit message used for the Hub upload.",
     )
     return parser.parse_args()