| schema_version: 2 |
| id: intervention_ood_compositional |
| generalization_axis: perturbation_identity |
| protocols: |
| - intervention_ood_oracle |
| - intervention_ood_joint |
| split_semantics: |
| unit: intervention_component |
| gears_interface: |
| - set2conditions |
| - test_perts |
| - test_subgroup |
| refit_on_train_plus_val: true |
| biological_unit_role: leakage_block_and_clustered_uncertainty |
| prohibited: |
| - test_target_cells_in_fit |
| - test_target_rna_in_fit |
| - random_cell_split |
| - random_molecule_split |
| selection: |
| perturbation_support_filter: none |
| gene_support_filter: none |
| cell_type_support_filter: none |
| undefined_metric_policy: NA_with_coverage |
| model_fitting: |
| dataset_scope: independent |
| fold_scope: independent |
| cell_type_scope: stratified |
| learned_gene_scope: complete_G_input_and_output_in_one_forward |
| learned_record_sampling: transition_then_context_then_biological_unit; full gene |
| axis |
| classical_scope: one_closed_form_map_per_gene_using_development_conditions_only |
| classical_coordinate_weighting: equal_total_mass_per_nonempty_cell |
| final_fit: train_plus_validation_after_hyperparameters_are_frozen |
| datasets: |
| gse246584_atm_radiation_xenium: |
| track: compositional |
| cache_dir: datasets/gse246584_atm_radiation_xenium |
| split_manifest: benchmark/splits/gse246584_atm_radiation_compositional.yaml |
| default_source_condition: ATM_intact |
| source_pool: pooled_reference |
| cell_type_mode: constant |
| constant_cell_type: all_cells |
| intervention_descriptor: |
| provider: component_multihot |
| dimension: 2 |
| artifact: benchmark/intervention_descriptors/intervention_ood_compositional/gse246584_atm_radiation_xenium.npz |
| metadata: benchmark/intervention_descriptors/intervention_ood_compositional/gse246584_atm_radiation_xenium.json |
| component_normalization: l2 |
| condition_composition: additive_sum |
| target_response_data_used: false |
| component_prompt_template: '{component}' |
| gse285341_ddx54_pd1_xenium: |
| track: compositional |
| cache_dir: datasets/gse285341_ddx54_pd1_xenium |
| split_manifest: benchmark/splits/gse285341_ddx54_pd1_compositional.yaml |
| default_source_condition: WT+isotype |
| source_pool: pooled_reference |
| cell_type_mode: constant |
| constant_cell_type: all_cells |
| intervention_descriptor: |
| provider: component_multihot |
| dimension: 2 |
| artifact: benchmark/intervention_descriptors/intervention_ood_compositional/gse285341_ddx54_pd1_xenium.npz |
| metadata: benchmark/intervention_descriptors/intervention_ood_compositional/gse285341_ddx54_pd1_xenium.json |
| component_normalization: l2 |
| condition_composition: additive_sum |
| target_response_data_used: false |
| component_prompt_template: '{component}' |
| execution_protocol: scperturbench_scfoundation_cell_oracle |
| execution_note: Complete-cell Oracle uses scripts/run_cell_oracle.py; other modes |
| have no current runner. |
|
|
