exp_name: bag-base-lr3e-3-mse-ema999
data:
  patch_size: 4096
  oversample: 2
  val_oversample: 1
  target_cells_per_subslide: 50000
  target_partial_keep_ratio: 0.1
vocab:
  gene_vocab_size: 19228
  organ_vocab_size: 12
  platform_vocab_size: 4
  gene_pad_id: 0
model:
  embed_dim: 384
  encoder_depth: 8
  encoder_heads: 6
  predictor_depth: 3
  predictor_heads: 3
  predictor_dim: 192
  mlp_ratio: 2.0
  dropout: 0.1
  gene_encoder:
    max_len: 512
  spatial_encoding:
    normalize: center_scale
    alibi_scale: 1.0
masking:
  mask_ratio: 0.6
training:
  epochs: 100
  total_steps: 10000
  batch_size: 32
  gradient_accumulation_steps: 1
  learning_rate: 3e-3
  weight_decay: 0.05
  warmup_epochs: 10
  warmup_steps: 1000
  ema_start: 0.999
  ema_end: 0.9999
  num_workers: 2
  grad_clip: 1.0
  seed: 0
  precision: bf16
logging:
  group: bag-scale
output:
  save_every: 500
  val_every: 50