stdgcn Config

This is the config for stdgcn.

examples/tuning/deconv_stdgcn/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: misc
    target: CelltypeTransform
  - type: pseudobulk
    target: pseudoSpotGen
    params:
      spot_num: 30000
      min_cell_number_in_spot: 8
      max_cell_number_in_spot: 12
      max_cell_types_in_spot: 4
      generation_method: celltype
      n_jobs: -1
  - type: misc
    target: RemoveSplit
    params:
      split_name: ref
      log_level: INFO
  - type: filter.gene
    target: FilterGenesCommon
    params:
      split_keys: [pseudo, test]
  - 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: misc
    target: SaveRaw
  - type: normalize
    include:
      - ColumnSumNormalize
      - ScTransform
      - Log1P
      - NormalizeTotal
      - NormalizePlaceHolder
      - NormalizeTotalLog1P
    default_params:
      ScTransform:
        processes_num: 8
  - 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: misc
    target: updateAnndataObsTransform
    params:
      split: test
  - type: misc
    target: CellTypeNum
  - 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
  - type: data.interagration
    target: DataInteragraionTransform
    params:
      batch_removal_method:
      min_dim: 30
      dimensionality_reduction_method:
      scale: false
      cpu_num: 1
      AE_device: cpu
  - type: graph.cell
    target: stdgcnGraph
    params:
      inter_find_neighbor_method: MNN
      inter_dist_method: cosine
      inter_corr_dist_neighbors: 20
      spatial_link_method: soft
      space_dist_threshold: 2.0
      real_intra_find_neighbor_method: MNN
      real_intra_dist_method: cosine
      real_intra_pca_dimensionality_reduction: false
      real_intra_corr_dist_neighbors: 10
      real_intra_dim: 50
      pseudo_intra_find_neighbor_method: MNN
      pseudo_intra_dist_method: cosine
      pseudo_intra_corr_dist_neighbors: 20
      pseudo_intra_pca_dimensionality_reduction: false
      pseudo_intra_dim: 50
  - type: data.interagration
    target: DataInteragraionTransform
    params:
      batch_removal_method:
      min_dim: 80
      dimensionality_reduction_method:
      scale: false
      cpu_num: 1
      AE_device: cpu
  - type: misc
    target: SetConfig
    params:
      config_dict:
        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