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.