ovarian_xenium/heldout_split/config.yaml

# InterScale -- 10x Xenium human ovarian adenocarcinoma, held-out-split model.
# Full resolved config the weights in model.pt were trained with (interscale main c98a307).
# Only dataset.h5ad_data / model.save were blanked. Load with
#   interscale.config.load_config('config.yaml')
dataset:
  batch_size: 2
  description: ''
  h5ad_data: ''
  layer_key: log1p_norm
  mask_percentage: 0.3
  mask_strategy: node
  name: ovarian_xenium
  num_classes: -1
  num_features: -1
  prediction_level: node
  prediction_obs: null
  prediction_task: regression
  sample_key:
  - sliding_window
  segmentation_robustness: null
  spatial_neigbors_kwargs:
    coord_type: generic
    library_key: sliding_window
    n_neighs: 6
    radius: 30
  split_key: split
  test_size: 0.1
  train_size: 0.7
  val_size: 0.2
model:
  decoder:
    dropout_decoder: 0.1
    dual_decoder: true
    hidden_dims:
    - 256
    - 128
    type: linear
  global_component:
    latent_obsm_key: null
    name: self-attn-transformer
    parameters:
      activation_func: relu
      dim_feedforward: 512
      dropout_global: 0.0
      long_range_attention: false
      max_seq_len: 3167
      n_heads: 4
      num_layers: 2
      type_gex_embedding: null
  local_component:
    name: GCN
    parameters:
      dropout_local: 0.1
      hidden_dim: 512
      num_layers: 2
  loss: null
  n_embed: 256
  save: ''
optim:
  accelerator: auto
  cross_corr: cell
  early_stopping: true
  loss: SmoothL1
  lr: 0.003
  lr_max_epochs: 100
  lr_scheduler: CosineWarmupScheduler
  lr_warmup: 10
  min_delta: 0.0
  min_epochs: 40
  monitor: auto
  n_epochs: 600
  patience: 20
  seed: 44
  wd: 0.001
wandb:
  project_name: InterScale_OvarianXenium
  use: false