Archive 4 checkpoints (1-4)
Browse files- paper-releases/20260928/diffusion/data/panel/floor01_6k_20260923/full_gene_statistics.csv +0 -0
- paper-releases/20260928/diffusion/data/panel/floor01_6k_20260923/leakage_audit.json +40 -0
- paper-releases/20260928/diffusion/data/panel/floor01_6k_20260923/manifest.json +244 -0
- paper-releases/20260928/diffusion/data/panel/floor01_6k_20260923/ordered_train_recipes.csv +0 -0
paper-releases/20260928/diffusion/data/panel/floor01_6k_20260923/full_gene_statistics.csv
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paper-releases/20260928/diffusion/data/panel/floor01_6k_20260923/leakage_audit.json
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{
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"allowed_expression_splits": [
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"train"
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| 4 |
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],
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| 5 |
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"evidence": {
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| 6 |
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"collector": "pbisc_sdd.panel_ladder.collect_train_panel_statistics",
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| 7 |
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"heldout_recipe_rows": 0,
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| 8 |
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"note": "statistics reused verbatim from the 1,048,576-cell pass; only the detection floor differs, and the floor enters after the statistics",
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| 9 |
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"reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_1m_20260922/sample_8192x128",
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"sampling_passes": 1,
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"split_manifest_requests": [
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"train"
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],
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| 14 |
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"stable_sample_order": "recipe order then RNG-chosen order within recipe"
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},
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| 16 |
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"exact_model7_implementation_bound": true,
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| 17 |
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"exact_ordered_recipe_ids_persisted": true,
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| 18 |
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"exact_sample_refs_persisted": true,
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| 19 |
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"exact_sufficient_statistics_bound": true,
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"expression_splits_accessed": [
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"train"
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],
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"held_out_expression_accessed": false,
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"held_out_splits": [
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"val",
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"test",
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"diagnostic",
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"evaluation"
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],
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"model7_implementation_sha256": "604e6d84cf813473a88ee8ad92c00998378091e8132029cf1ef670f19c9395ce",
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| 31 |
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"ordered_recipe_ids_sha256": "7c3aadcc409c685605f0f610a0dcc48b1ee5e126dcd80b427e835d1e598e5a3a",
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| 32 |
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"production_ready": true,
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| 33 |
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"provenance_limitation": null,
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| 34 |
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"provenance_statistics_binding_sha256": "d8a75dd300e6917d4393570976f95d3764c23d4305dfd0eb78ae4ee68105048e",
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| 35 |
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"sampled_cell_refs_sha256": "ed038c6a9f6da650616631a1b7db5505f6e125933e629a5a0e3125dc879b9fc1",
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| 36 |
+
"schema_version": "pbisc_sdd.panel_ladder.leakage_audit.v1",
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| 37 |
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"selection_scope": "train_split_only",
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| 38 |
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"status": "pass",
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| 39 |
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"sufficient_statistics_sha256": "b3e4b95f2f0dcaa08ea93cd8b52bb9138a961444d7ca009475cc2740c3fd53ea"
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| 40 |
+
}
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paper-releases/20260928/diffusion/data/panel/floor01_6k_20260923/manifest.json
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| 1 |
+
{
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| 2 |
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"bindings": {
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| 3 |
+
"binding_sha256": "4d45ba1ec9af9236f0c53d29875b903f0985eb67589a932944d5feba453bd7e2",
|
| 4 |
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"corpus_fingerprint": "eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007",
|
| 5 |
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"gene_panel_sha256": "9f6dd441e00d4e00168d69d6133ddb2802ab9e87a20c35ddfe1bcfa84f5ebcce",
|
| 6 |
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"parameters_sha256": "4cc0eac6f3638e7d60a41b6833e32c7e48fb85b76551506a5e9f9d6713e7c588",
|
| 7 |
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"provenance": {
|
| 8 |
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"leakage_audit_sha256": "9a23da8d67113ff64beff9698801aab89949e9f1f20665130e9610793c3ce0bd",
|
| 9 |
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"model7_implementation_sha256": "604e6d84cf813473a88ee8ad92c00998378091e8132029cf1ef670f19c9395ce",
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| 10 |
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"ordered_train_recipes_sha256": "7c3aadcc409c685605f0f610a0dcc48b1ee5e126dcd80b427e835d1e598e5a3a",
|
| 11 |
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"sampled_cell_references_sha256": "ed038c6a9f6da650616631a1b7db5505f6e125933e629a5a0e3125dc879b9fc1",
|
| 12 |
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"sufficient_statistics_sha256": "b3e4b95f2f0dcaa08ea93cd8b52bb9138a961444d7ca009475cc2740c3fd53ea"
|
| 13 |
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},
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| 14 |
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"selection_code_bundle_sha256": "3ac3fee6bd28571ec0cde53c0e7b07c5d6ae8a266ba49c0770b462f223bd614c"
|
| 15 |
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},
|
| 16 |
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"corpus_fingerprint": "eeb609250457248225432b6df94573b26a8cad8ac743670b5ca43134fea7e007",
|
| 17 |
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"finite_tiers": [
|
| 18 |
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"2k",
|
| 19 |
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"6k",
|
| 20 |
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"p15k"
|
| 21 |
+
],
|
| 22 |
+
"full_gene_statistics_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/full_gene_statistics.csv",
|
| 23 |
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"full_gene_statistics_sha256": "745c8b5df2d1007f31e24e8391f15421885b78ca1c1026705ced4ae8d7591288",
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| 24 |
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"gene_panel_sha256": "9f6dd441e00d4e00168d69d6133ddb2802ab9e87a20c35ddfe1bcfa84f5ebcce",
|
| 25 |
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"leakage_audit_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/leakage_audit.json",
|
| 26 |
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"leakage_audit_sha256": "9a23da8d67113ff64beff9698801aab89949e9f1f20665130e9610793c3ce0bd",
|
| 27 |
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"n_eligible_genes": 15114,
|
| 28 |
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"n_full_genes": 20097,
|
| 29 |
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"n_rejected_genes": 4983,
|
| 30 |
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"parameters": {
|
| 31 |
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"cells_per_recipe": 128,
|
| 32 |
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"detection_floor_fraction": 0.001,
|
| 33 |
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"mean_bins": 20,
|
| 34 |
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"min_detected_cells": 1048,
|
| 35 |
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"min_measured_cells": 104857,
|
| 36 |
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"model7_root": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang",
|
| 37 |
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"recipes": 8192,
|
| 38 |
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"seed": 20260627,
|
| 39 |
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"statistics_reused_from": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_1m_20260922/sample_8192x128",
|
| 40 |
+
"target_sum": 10000.0,
|
| 41 |
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"tier_sizes": {
|
| 42 |
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"2k": 2000,
|
| 43 |
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"6k": 6000,
|
| 44 |
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"p15k": 15114
|
| 45 |
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}
|
| 46 |
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},
|
| 47 |
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"parameters_sha256": "4cc0eac6f3638e7d60a41b6833e32c7e48fb85b76551506a5e9f9d6713e7c588",
|
| 48 |
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"production_ready": true,
|
| 49 |
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"provenance": {
|
| 50 |
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"ordered_train_recipes_columns": [
|
| 51 |
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"recipe_order",
|
| 52 |
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"stream_recipe_index",
|
| 53 |
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"recipe_id",
|
| 54 |
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"block_id",
|
| 55 |
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"recipe_index",
|
| 56 |
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"schedule_slot",
|
| 57 |
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"split",
|
| 58 |
+
"platform",
|
| 59 |
+
"validation_scope",
|
| 60 |
+
"heldout",
|
| 61 |
+
"sample_key",
|
| 62 |
+
"dataset_id",
|
| 63 |
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"donor_id",
|
| 64 |
+
"sample_id",
|
| 65 |
+
"k",
|
| 66 |
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"rng_seed",
|
| 67 |
+
"sampling_policy"
|
| 68 |
+
],
|
| 69 |
+
"ordered_train_recipes_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/ordered_train_recipes.csv",
|
| 70 |
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"ordered_train_recipes_rows": 8192,
|
| 71 |
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"ordered_train_recipes_sha256": "7c3aadcc409c685605f0f610a0dcc48b1ee5e126dcd80b427e835d1e598e5a3a",
|
| 72 |
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"sampled_cell_references_columns": [
|
| 73 |
+
"sample_order",
|
| 74 |
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"recipe_order",
|
| 75 |
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"chosen_order_within_recipe",
|
| 76 |
+
"recipe_id",
|
| 77 |
+
"block_id",
|
| 78 |
+
"sample_key",
|
| 79 |
+
"ref_position_in_recipe",
|
| 80 |
+
"selection_occurrence_id",
|
| 81 |
+
"segment_index",
|
| 82 |
+
"shard_id",
|
| 83 |
+
"count_zarr",
|
| 84 |
+
"source_coordinate_id",
|
| 85 |
+
"strict_row_index",
|
| 86 |
+
"row_index"
|
| 87 |
+
],
|
| 88 |
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"sampled_cell_references_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/sampled_cell_references.csv",
|
| 89 |
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"sampled_cell_references_rows": 1048576,
|
| 90 |
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"sampled_cell_references_sha256": "ed038c6a9f6da650616631a1b7db5505f6e125933e629a5a0e3125dc879b9fc1",
|
| 91 |
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"selection_occurrence_contract": "recipe_id + ref_position_in_recipe; ordered by sample_order",
|
| 92 |
+
"source_coordinate_contract": "corpus_fingerprint + shard_id + strict_row_index",
|
| 93 |
+
"status": "complete"
|
| 94 |
+
},
|
| 95 |
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"ranked_gene_positions_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/ranked_gene_positions.npy",
|
| 96 |
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"ranked_gene_positions_sha256": "4f6ce4fa492525cf06d68119a40c27d525ab6a36a4a99e09046684ae6edd767a",
|
| 97 |
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"ranking_contract": {
|
| 98 |
+
"broad_tier_policy": "all_eligible_genes",
|
| 99 |
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"finite_tier_policy": "universal_eligible_rank_prefix",
|
| 100 |
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"min_detected_cells": 1048,
|
| 101 |
+
"min_measured_cells": 104857,
|
| 102 |
+
"rank_base": 1,
|
| 103 |
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"ranked_population": "all_canonical_genes_eligible_first",
|
| 104 |
+
"tensor_order": "canonical_gene_panel_order",
|
| 105 |
+
"tier_independent": true
|
| 106 |
+
},
|
| 107 |
+
"replay_proof_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/replay_proof.json",
|
| 108 |
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"replay_proof_sha256": "b1c847a3b308c32a1698a94e09a00a69a30a4781d4c9721572b81c7bb18aab16",
|
| 109 |
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"sampled_cells": 1048576,
|
| 110 |
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"sampled_recipes": 8192,
|
| 111 |
+
"schema_version": "pbisc_sdd.panel_ladder.v2",
|
| 112 |
+
"selection_code": {
|
| 113 |
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"bundle_sha256": "3ac3fee6bd28571ec0cde53c0e7b07c5d6ae8a266ba49c0770b462f223bd614c",
|
| 114 |
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"files": {
|
| 115 |
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"legacy_ranking_kernel": {
|
| 116 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/gene_selection.py",
|
| 117 |
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"sha256": "6818525e212b2192e40e7b9f5f879e29f644c17a099aa09a6ab2adb66f1b7e7d"
|
| 118 |
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},
|
| 119 |
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"panel_ladder": {
|
| 120 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/src/pbisc_sdd/panel_ladder.py",
|
| 121 |
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"sha256": "45116a496e1f38247dfdaa3d306ab54aa28e13736754dbe9dd75eaa5dc7d518f"
|
| 122 |
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}
|
| 123 |
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},
|
| 124 |
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"model7_data_e2": {
|
| 125 |
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"bundle_sha256": "604e6d84cf813473a88ee8ad92c00998378091e8132029cf1ef670f19c9395ce",
|
| 126 |
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"data_module_class": "model7_no_annotation.data_e2.E2FullDataModule",
|
| 127 |
+
"methods": {
|
| 128 |
+
"_load_sparse_refs": {
|
| 129 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/data_e2.py",
|
| 130 |
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"qualified_name": "model7_no_annotation.data_e2.E2FullDataModule._load_sparse_refs",
|
| 131 |
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"sha256": "6f6db69002ae01857a0f1882b2e6e98552f3ee00aa1116e4fd4a308cbf761b71"
|
| 132 |
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},
|
| 133 |
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"_recipe_refs_and_pools": {
|
| 134 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/data_e2.py",
|
| 135 |
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"qualified_name": "model7_no_annotation.data_e2.E2FullDataModule._recipe_refs_and_pools",
|
| 136 |
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|
| 137 |
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},
|
| 138 |
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"_zarr_group": {
|
| 139 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/data_e2.py",
|
| 140 |
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"qualified_name": "model7_no_annotation.data_e2.E2FullDataModule._zarr_group",
|
| 141 |
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|
| 142 |
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|
| 143 |
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"prime_pools": {
|
| 144 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/data_e2.py",
|
| 145 |
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"qualified_name": "model7_no_annotation.data_e2.E2FullDataModule.prime_pools",
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| 146 |
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|
| 147 |
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},
|
| 148 |
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"split_manifest": {
|
| 149 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/data_e2.py",
|
| 150 |
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"qualified_name": "model7_no_annotation.data_e2.E2FullDataModule.split_manifest",
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| 151 |
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| 152 |
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|
| 153 |
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},
|
| 154 |
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"schema_version": "pbisc_sdd.panel_ladder.model7_implementation.v1"
|
| 155 |
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|
| 156 |
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},
|
| 157 |
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"selection_scope": "train_split_only",
|
| 158 |
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"sufficient_statistics": {
|
| 159 |
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"arrays": {
|
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"detected_cells": {
|
| 161 |
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"dtype": "int64",
|
| 162 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/sufficient_statistics/detected_cells.npy",
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| 163 |
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"sha256": "872a96f4e57494605c5ec08084faefec8479de7cb0dbc13e412ce7fe23a64ce5",
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| 164 |
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"shape": [
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20097
|
| 166 |
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|
| 167 |
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},
|
| 168 |
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"measured_cells": {
|
| 169 |
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"dtype": "int64",
|
| 170 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/sufficient_statistics/measured_cells.npy",
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| 171 |
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"sha256": "20f943fd9f02ad2afdfde14b205939925f19b1f33288bc8e87f91db64edc921d",
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| 172 |
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20097
|
| 174 |
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|
| 175 |
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|
| 176 |
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"value_square_sum": {
|
| 177 |
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"dtype": "float64",
|
| 178 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/sufficient_statistics/value_square_sum.npy",
|
| 179 |
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"sha256": "d509e2d53a5441686e5c98fcb58ab10e75acabf87c2bbcc6141cd61b9e211517",
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| 180 |
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|
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|
| 183 |
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|
| 184 |
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"value_sum": {
|
| 185 |
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"dtype": "float64",
|
| 186 |
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"path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/sufficient_statistics/value_sum.npy",
|
| 187 |
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"sha256": "cbd548e302ca1f1c499ec123efc08a62707b85ca13c135e33683fcade30e2cb5",
|
| 188 |
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"shape": [
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| 189 |
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|
| 190 |
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|
| 191 |
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|
| 192 |
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|
| 193 |
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"binding_file_sha256": "771ad39bb88322bb837934b265f36f5258e3f23975c267ffc76cacabaede1a26",
|
| 194 |
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"binding_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/sufficient_statistics/binding.json",
|
| 195 |
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"binding_sha256": "b3e4b95f2f0dcaa08ea93cd8b52bb9138a961444d7ca009475cc2740c3fd53ea",
|
| 196 |
+
"status": "complete"
|
| 197 |
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},
|
| 198 |
+
"tiers": {
|
| 199 |
+
"2k": {
|
| 200 |
+
"gene_positions_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/2k/gene_positions.npy",
|
| 201 |
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"gene_positions_sha256": "5d3868ca43fa6d5565fa2a90f9c6aa07edc7d1f29a52b3673e1e4277542c9cb6",
|
| 202 |
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"legacy_selection_manifest_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/2k/legacy_selection_manifest.v1.json",
|
| 203 |
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"legacy_selection_manifest_sha256": "7ed9c935075207d0133f981856f6dcd4f3be24aef2028e0031e6d6be1d8fcda1",
|
| 204 |
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"n_genes": 2000,
|
| 205 |
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"rank_prefix_length": 2000,
|
| 206 |
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"selected_genes_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/2k/selected_genes.csv",
|
| 207 |
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"selected_genes_sha256": "4d7d5cfdd56872cf07a211864fc5e6b2aa9f696f650a26add4036e8bafb436a0",
|
| 208 |
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"tensor_order": "canonical_gene_panel_order"
|
| 209 |
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},
|
| 210 |
+
"6k": {
|
| 211 |
+
"gene_positions_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/6k/gene_positions.npy",
|
| 212 |
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"gene_positions_sha256": "653ffa45ac519000baa41086c52408009391d6e68cfb218bc6a50d34163fcb24",
|
| 213 |
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"legacy_selection_manifest_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/6k/legacy_selection_manifest.v1.json",
|
| 214 |
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"legacy_selection_manifest_sha256": "1a6090d312df7d0071b3adaa59bb686a915b996a6c555a9aef9cab151905900a",
|
| 215 |
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"n_genes": 6000,
|
| 216 |
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"rank_prefix_length": 6000,
|
| 217 |
+
"selected_genes_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/6k/selected_genes.csv",
|
| 218 |
+
"selected_genes_sha256": "09248a3930e3fdefe1dbcd5d60cae4be81028526dcf097dd78169f5a415edfb6",
|
| 219 |
+
"tensor_order": "canonical_gene_panel_order"
|
| 220 |
+
},
|
| 221 |
+
"broad": {
|
| 222 |
+
"gene_positions_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/broad/gene_positions.npy",
|
| 223 |
+
"gene_positions_sha256": "ad9e135e70181fff9b9daab945fe8411dec4f8c4a139870e13f6d8763d6ed0c6",
|
| 224 |
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"n_genes": 15114,
|
| 225 |
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"policy": "all_eligible_genes",
|
| 226 |
+
"rank_prefix_length": 15114,
|
| 227 |
+
"selected_genes_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/broad/selected_genes.csv",
|
| 228 |
+
"selected_genes_sha256": "d9def4c24f8a7cea6e41be9e12c814b5ce6927d640cd879131d1047d30a005ef",
|
| 229 |
+
"tensor_order": "canonical_gene_panel_order"
|
| 230 |
+
},
|
| 231 |
+
"p15k": {
|
| 232 |
+
"gene_positions_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/p15k/gene_positions.npy",
|
| 233 |
+
"gene_positions_sha256": "ad9e135e70181fff9b9daab945fe8411dec4f8c4a139870e13f6d8763d6ed0c6",
|
| 234 |
+
"legacy_selection_manifest_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/p15k/legacy_selection_manifest.v1.json",
|
| 235 |
+
"legacy_selection_manifest_sha256": "7daea586bb48fd1276dba5b894628aa873ba5b69329bf174c42e27f9045506c0",
|
| 236 |
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"n_genes": 15114,
|
| 237 |
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"rank_prefix_length": 15114,
|
| 238 |
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"selected_genes_path": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/artifacts/panel_ladder_floor01_1m_20260923/tiers/p15k/selected_genes.csv",
|
| 239 |
+
"selected_genes_sha256": "d9def4c24f8a7cea6e41be9e12c814b5ce6927d640cd879131d1047d30a005ef",
|
| 240 |
+
"tensor_order": "canonical_gene_panel_order"
|
| 241 |
+
}
|
| 242 |
+
},
|
| 243 |
+
"tiers_are_nested": true
|
| 244 |
+
}
|
paper-releases/20260928/diffusion/data/panel/floor01_6k_20260923/ordered_train_recipes.csv
ADDED
|
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|
|