card Config

This is the config for card.

examples/tuning/deconv_card/hcc_liver/pipeline_params_tuning_config.yaml

---
type: preprocessor
tune_mode: pipeline_params
pipeline_tuning_top_k: 3
parameter_tuning_freq_n: 20
pipeline:
  - type: pseudobulk
    target: CellTopicProfile
    params:
      split_name: ref
      method: mean
  - type: filter.gene
    include: [FilterGenesMatch]
    default_params:
      FilterGenesMatch:
        prefixes: [mt-]
  - type: filter.gene
    target: FilterGenesCommon
    params:
      split_keys: [ref, test]
  - type: filter.gene
    target: FilterGenesMarker
  - type: filter.gene
    include:
      - FilterGenesPercentile
      - FilterGenesScanpyOrder
      - FilterGenesPlaceHolder
    default_params:
      FilterGenesScanpyOrder:
        order: [min_counts, max_counts, min_cells, max_cells]
        min_counts: 100
        max_counts: 0.99
        min_cells: 0.01
        max_cells: 0.99
  - type: normalize
    include:
      - ColumnSumNormalize
      - ScTransform
      - Log1P
      - NormalizeTotal
      - NormalizePlaceHolder
      - NormalizeTotalLog1P
    default_params:
      ScTransform:
        processes_num: 8
      # NormalizeTotalLog1P:
      #   target_sum: 1e4
  - type: filter.gene
    include:
      - HighlyVariableGenesLogarithmizedByMeanAndDisp
      - HighlyVariableGenesRawCount
      - FilterGenesNumberPlaceHolder
      - HighlyVariableGenesLogarithmizedByTopGenes
      - FilterGenesTopK
      - FilterGenesRegression
    default_params:
      FilterGenesTopK:
        num_genes: 3000
      FilterGenesRegression:
        num_genes: 3000
      HighlyVariableGenesRawCount:
        n_top_genes: 3000
      HighlyVariableGenesLogarithmizedByTopGenes:
        n_top_genes: 3000
  # - type: feature.cell
  #   include:
  #     - CellPCA
  #     - CellSVD
  #     - WeightedFeaturePCA
  #     - WeightedFeatureSVD
  #     - GaussRandProjFeature
  #     - FeatureCellPlaceHolder
  #   params:
  #     out: feature.cell
  #     log_level: INFO
  #   default_params:
  #     CellPCA:
  #       n_components: 400
  #     CellSVD:
  #       n_components: 400
  #     GaussRandProjFeature:
  #       n_components: 400
  #     WeightedFeaturePCA:
  #       n_components: 400
  #     WeightedFeatureSVD:
  #        n_components: 400  # TODO 修改降维
  - type: misc
    target: SetConfig
    params:
      config_dict:
        feature_channel: [null, spatial]
        feature_channel_type: [X, obsm]
        label_channel: cell_type_portion
wandb:
  entity: xzy11632
  project: dance-dev
  method: grid  # try grid to provide a comprehensive search
  metric:
    name: MSE
    goal: minimize