seed: 42
data:
  mode: rna_he
  processed_h5: ./sami/Xenium_Human_Breast_Cancer_Rep1/processed_breast_cancer_rep1.h5
  tile_manifest: ./sami/Xenium_Human_Breast_Cancer_Rep1/tiles/manifest.json
  num_workers: 0
  pin_memory: false
model:
  branch_mode: multimodal_fusion
  hidden_dim: 64
  omics1_in_dim: 50
  omics2_in_dim: 1024
  omics1_target_dim: 50
  omics2_target_dim: 1024
  omics1_encoder:
    feature_adapter:
      adapter_type: mlp_bottleneck
      adapter_dim: 64
      dropout: 0.1
      force_linear: false
  omics2_encoder:
    adapter_type: mlp_bottleneck
    adapter_dim: 512
    dropout: 0.1
    force_linear: false
  omics1_augmentation:
    enabled: false
    alpha: 0.5
  graph:
    top_k: 6
    symmetrize: true
    add_self_loops: false
    chunk_size: 512
  graph_backbone:
    omics1:
      type: pointnext
      use_layer_transformer: true
    omics2:
      type: pointnext
      use_layer_transformer: true
    pointnext:
      expansion: 4
      dropout: 0.1
      max_neighbors: 6
      pooling: mean
  cross_modal_attention:
    num_heads: 4
    dropout: 0.1
  gat:
    num_layers: 3
    omics1_num_layers: 3
    omics2_num_layers: 3
    num_heads: 4
    dropout: 0.1
    leaky_relu_negative_slope: 0.2
  layer_transformer:
    num_heads: 4
    ff_dim: 256
    dropout: 0.1
    pooling: mean
  fusion:
    mlp_hidden_dim: 256
    dropout: 0.1
train:
  device: cuda
  epochs: 50
  lr: 0.001
  weight_decay: 0.0001
  grad_clip_norm: 5.0
  amp: false
  gradient_accumulation: 4
  early_stopping_patience: 10
  log_interval: 10
  output_dir: ./outputs
loss:
  lambda_omics1: 10.0
  lambda_omics2: 10.0
  lambda_contrastive: 0.5
  lambda_consistency: 1.0
  contrastive:
    use_symmetric_loss: false
  consistency:
    temperature: 0.1
    projector_hidden_dim: 128
    projector_out_dim: 64