SubcellPert / manifest.json
king159's picture
init
a57b684
Raw History Blame
12.4 kB
{
"benchmark_inputs": {
"baseline_count": 8,
"descriptor_pairs": 3,
"formal_fits": 608,
"intervention_descriptors": "benchmark/intervention_descriptors",
"root_path_base": "release_root",
"schema": "portable_frozen_benchmark_v1",
"setting_count": 2,
"shard_path_base": "containing_view_directory",
"shared_array_references": 4940,
"split_instances": 38,
"split_views": "benchmark/split_views",
"view_count": 112
},
"canonical_payload_included": false,
"cell_filter_policy": {
"cell_filter_stage": "after_eligible_RNA_filtering_before_population_indexing",
"minimum_eligible_rna_per_cell": 1,
"population_support": {
"aggregation": "Across eligible units in the same dataset; anatomy encoded in condition labels is preserved.",
"context_note": "UC-VDZ uses the native cellular-context annotations already used in frozen task views; patient identity is retained separately. Cells without a recoverable cellular-context annotation are excluded.",
"grouping": [
"dataset",
"benchmark_cellular_context",
"condition"
],
"minimum_cells": 50,
"policy": "dataset_context_condition_min50_v1",
"response_rule": "Prediction responses additionally require >=50 matched source and >=50 target cells.",
"stage": "after_nonempty_RNA_reconstruction_before_release_and_split_access"
},
"zero_rna_cells_retained": false
},
"checksums_file": "checksums.sha256",
"code_snapshot": {
"git_commit": "5267b4ed426d9b5f0d1dcd3cea4eb723f39ae2cc",
"source_sha256": {
"src/subcellpert/__init__.py": "d0da531ac594926c2653c5e08509f8958c77755ceef6e34fe7877e04b0b2bfa4",
"src/subcellpert/data.py": "259c5ba7a03563159e7cfe612fbaa469cf5b9024b42e39e96770b35bd059b4c6",
"src/subcellpert/data/arrays.py": "8487a3c2997063bc4d7f073b101313f379b866ae192c062a7613b1488fd0736a",
"src/subcellpert/data/batching.py": "ffd0cd802567a82208c70326a6090b74c4c9d3075e48fd70a843a564ea7c4702",
"src/subcellpert/data/context.py": "83a92d3a631c05620bfd6dc3a66ec0ec166ca976654eaedbb902f49069020e49",
"src/subcellpert/data/features.py": "27d6ac6daf80566fdb980bb02c4aa4944e582be056ad78aad338b346cb53986c",
"src/subcellpert/data/intervention.py": "775192f6b4056400e1ba16db781f0999c79a1d02c8374c0459d7e8cef54760f3",
"src/subcellpert/data/populations.py": "5df2d4589d97456c0d23cbf8e47ad87df18b582c4732b41fb72f82e6b8e3fbb6",
"src/subcellpert/data/records.py": "b9a5dca083109306d6311067cef9b4ddbe532a3098a5faed2ec74da25447414f",
"src/subcellpert/data/registry.py": "59a6652f16917acb50e41a80b7c40f854da19b934ac311643c29d0c257efd3c9",
"src/subcellpert/data/release.py": "2e6acf5e196626a5824594d57994aa09eef46860cca8449a5e09fa677633efd1",
"src/subcellpert/data/sampling.py": "a99a396a4df1f596c7526400dd44cd546698562fb28feb08d67e48889db6c60d",
"src/subcellpert/data/splits.py": "9f601f24c8b78a1c550df99acd19c7b4090321eb62e8c6f4b4edcb3b0d49a347",
"src/subcellpert/data/storage.py": "143e565b82d22a495f0c0bc2199f5ed59484d3658b6a6429449292491362a03b",
"src/subcellpert/distributed.py": "a1921dd606b694a51692d8c640629ed8fae71f329eaed37fdab05c9bfe073005",
"src/subcellpert/evaluate/__init__.py": "708c3cdc81ea291725d41d8b384660dd1f387c56fe158e7d8c98101c56a8ca3d",
"src/subcellpert/evaluate/metrics.py": "162ecd65894ad79ef882279b8d3066150b0fdac39b6f953b4eb40e4f0c0c3066",
"src/subcellpert/evaluate/reporting.py": "bba4db1bb3698bae70053d68130318c662a40e9a9cd192f31ae108652732a1ea",
"src/subcellpert/evaluate_one_step.py": "6206f15f1d4435168f69ad36de1e2cc98571b209552dcc5a07c367d8ba180be4",
"src/subcellpert/main.py": "ede610ce28379a23fe646d8135aa114b54f6cc4549c86fb2c1a1143a3cf5fcb6",
"src/subcellpert/models/count_matched_resampling.py": "096cef4f0706818a8d82c5d911b64d67f0344793b74bbdc3e1c59d4bae8c4aa6",
"src/subcellpert/models/gaussian_affine_transport.py": "bf154042054142be5d60f98ae980bc2243fb6243e5c26440c3c5b933da72d76b",
"src/subcellpert/models/radial_quantile_transport.py": "8b77d707baa7091ce1b051f6559e4b48719b5a7c5c83cff49c226f3a5f581b29",
"src/subcellpert/models/scfoundation.py": "3aa05fca424b6167d234cda62b43ae0c22f766c0319fea99dfdc55200d9e6959",
"src/subcellpert/models/scgpt.py": "0d8fe75ff8092eca0d40c7db527d930abeffbfdc5a1e066e4773daf19490223b",
"src/subcellpert/models/scgpt_spatial.py": "a594078e1a24eba07285139cfc7a36df8aad134d79b8cbe7885dde00b0083473",
"src/subcellpert/models/shared.py": "e0fd61a3bb866bf81b1434da5e519c74018d2bd7062ebb16291052c3283e7403",
"src/subcellpert/models/spatialformer.py": "1809a29f4a5980b74ca9b6573643002e177d2a39e55d0212f2df4d034aef0f6a",
"src/subcellpert/models/state_se.py": "96d224d0c1bcb2f7cce1a3cf38af4ccd93cd2b35b4f320848261b9197a224052",
"src/subcellpert/train_one_step.py": "3fe464027eb7d09c51262c8c309265fd8ee8e6d1ba28948e1312cfcab1086d17",
"src/subcellpert/utils.py": "6391b68ac1e4f4f5fc8d8e0b27dab8c9c1edd808a300377a0b1107f7644eb9cb"
},
"working_tree_modified": true
},
"datasets": [
{
"id": "dss_colitis_merfish",
"metadata_manifest": "datasets/dss_colitis_merfish/manifest.json",
"population": "datasets/dss_colitis_merfish/population",
"size_bytes": 1349393560
},
{
"id": "gse246584_atm_radiation_xenium",
"metadata_manifest": "datasets/gse246584_atm_radiation_xenium/manifest.json",
"population": "datasets/gse246584_atm_radiation_xenium/population",
"size_bytes": 1415821380
},
{
"id": "gse269719_kidney_iri_xenium",
"metadata_manifest": "datasets/gse269719_kidney_iri_xenium/manifest.json",
"population": "datasets/gse269719_kidney_iri_xenium/population",
"size_bytes": 1613306511
},
{
"id": "gse280376_cardiac_repair_xenium",
"metadata_manifest": "datasets/gse280376_cardiac_repair_xenium/manifest.json",
"population": "datasets/gse280376_cardiac_repair_xenium/population",
"size_bytes": 541108205
},
{
"id": "gse285341_ddx54_pd1_xenium",
"metadata_manifest": "datasets/gse285341_ddx54_pd1_xenium/manifest.json",
"population": "datasets/gse285341_ddx54_pd1_xenium/population",
"size_bytes": 5370118948
},
{
"id": "gse291460_spinal_ko_xenium",
"metadata_manifest": "datasets/gse291460_spinal_ko_xenium/manifest.json",
"population": "datasets/gse291460_spinal_ko_xenium/population",
"size_bytes": 340366320
},
{
"id": "gse295862_adipose_weightloss_xenium",
"metadata_manifest": "datasets/gse295862_adipose_weightloss_xenium/manifest.json",
"population": "datasets/gse295862_adipose_weightloss_xenium/population",
"size_bytes": 19323287
},
{
"id": "gse296517_breast_fus_cosmx",
"metadata_manifest": "datasets/gse296517_breast_fus_cosmx/manifest.json",
"population": "datasets/gse296517_breast_fus_cosmx/population",
"size_bytes": 1101850507
},
{
"id": "gse296577_gbm_ohsv_xenium",
"metadata_manifest": "datasets/gse296577_gbm_ohsv_xenium/manifest.json",
"population": "datasets/gse296577_gbm_ohsv_xenium/population",
"size_bytes": 4954316263
},
{
"id": "gse325253_lung_drug_xenium",
"metadata_manifest": "datasets/gse325253_lung_drug_xenium/manifest.json",
"population": "datasets/gse325253_lung_drug_xenium/population",
"size_bytes": 7440009880
},
{
"id": "gut_microbiota_merfish",
"metadata_manifest": "datasets/gut_microbiota_merfish/manifest.json",
"population": "datasets/gut_microbiota_merfish/population",
"size_bytes": 1940872101
},
{
"id": "merfish_sickness",
"metadata_manifest": "datasets/merfish_sickness/manifest.json",
"population": "datasets/merfish_sickness/population",
"size_bytes": 9939052479
},
{
"id": "perturbfish_astrocytes",
"metadata_manifest": "datasets/perturbfish_astrocytes/manifest.json",
"population": "datasets/perturbfish_astrocytes/population",
"size_bytes": 96425798
},
{
"id": "uc_vedolizumab_cosmx",
"metadata_manifest": "datasets/uc_vedolizumab_cosmx/manifest.json",
"population": "datasets/uc_vedolizumab_cosmx/population",
"size_bytes": 203967001
}
],
"distribution": {
"repo_type": "dataset",
"repository": "king159/SubcellPert"
},
"excluded_datasets": [
"axolotl_brain_regeneration_stereoseq",
"fn03_ra_treatment_xenium",
"gse318507_dmd_exon_skipping_xenium",
"l109_uv_microbiota_xenium"
],
"file_hash_algorithm": "sha256",
"layout": "population_only_public_release",
"normalization_parameters_included": true,
"population_format": "cell_major_rna_csr_numpy_parquet_v3",
"population_support_filter": {
"aggregation": "Across eligible units in the same dataset; anatomy encoded in condition labels is preserved.",
"context_note": "UC-VDZ uses the native cellular-context annotations already used in frozen task views; patient identity is retained separately. Cells without a recoverable cellular-context annotation are excluded.",
"grouping": [
"dataset",
"benchmark_cellular_context",
"condition"
],
"minimum_cells": 50,
"policy": "dataset_context_condition_min50_v1",
"response_rule": "Prediction responses additionally require >=50 matched source and >=50 target cells.",
"stage": "after_nonempty_RNA_reconstruction_before_release_and_split_access"
},
"publication_files": [
"README.md",
"assets/teaser.png",
"benchmark/protocols/context_ood_joint.yaml",
"benchmark/protocols/context_ood_oracle.yaml",
"benchmark/protocols/intervention_ood_joint.yaml",
"benchmark/protocols/intervention_ood_oracle.yaml",
"benchmark/protocols/temporal_stage_ood_joint.yaml",
"benchmark/protocols/temporal_stage_ood_oracle.yaml",
"benchmark/registry/baselines.yaml",
"benchmark/registry/datasets.yaml",
"benchmark/registry/metrics.yaml",
"benchmark/schedules/cell_current.json",
"benchmark/splits/cell_seed_schedule_dual_min50.json",
"benchmark/splits/cell_validation_dual_min50.json",
"benchmark/splits/dss_colitis_context_ood.yaml",
"benchmark/splits/dss_colitis_temporal_stage_ood.yaml",
"benchmark/splits/gse246584_atm_radiation_compositional.yaml",
"benchmark/splits/gse269719_kidney_iri_context_ood.yaml",
"benchmark/splits/gse280376_cardiac_repair_context_ood.yaml",
"benchmark/splits/gse285341_ddx54_pd1_compositional.yaml",
"benchmark/splits/gse291460_spinal_ko_context_ood.yaml",
"benchmark/splits/gse295862_adipose_context_ood.yaml",
"benchmark/splits/gse296517_breast_fus_context_ood.yaml",
"benchmark/splits/gse296577_gbm_ohsv_context_ood.yaml",
"benchmark/splits/gse325253_lung_context_ood.yaml",
"benchmark/splits/gut_microbiota_context_ood.yaml",
"benchmark/splits/merfish_sickness_context_ood.yaml",
"benchmark/splits/perturbfish_astrocytes_intervention_ood.yaml",
"benchmark/splits/uc_vedolizumab_patient_context_ood.yaml",
"benchmark/tasks/context_ood_biological_unit.yaml",
"benchmark/tasks/context_ood_expansion.yaml",
"benchmark/tasks/context_ood_lung.yaml",
"benchmark/tasks/context_ood_reaudited.yaml",
"benchmark/tasks/intervention_ood_compositional.yaml",
"benchmark/tasks/intervention_ood_main.yaml",
"benchmark/tasks/temporal_stage_ood_dss.yaml",
"checksums.sha256",
"manifest.json"
],
"publication_trees": [
"datasets",
"catalog",
"benchmark/split_views",
"benchmark/intervention_descriptors"
],
"raw_payload_included": false,
"release_filter_code": {
"path": "scripts/filter_release_population.py",
"sha256": "455a01b47caf1946f867a86172c15bb459a00fba9806ae31f4d9ee5e0acab471"
},
"release_id": "subcellpert_14datasets_population_min50_20260924",
"repository_only_roots": [
"configs",
"docs",
"experiments",
"paper",
"results",
"scripts",
"src",
"tests",
"visualization"
],
"schema_version": 1,
"source_release": {
"manifest_sha256": "7146b88cdd1dffd66ef7c0611153f8c35141214c44afc3e424f92e39bbd41e01",
"release_id": "subcellpert_14datasets_20260914"
},
"status": "pre_release",
"total_size_bytes": 36325932240,
"tree_hash_algorithm": ""
}