all.yaml

data:
  img_size: 112
  batch_size: 4
  num_workers: 8
  volume_threshold: 100
  cache_dir: null
  training_sets:
    # - CTStroke_Tr
    # - ADNI_Tr
    - AMOS_Tr
    - CTOrgan_Tr
    - AbdomenCT_Tr
    # - ISLES_Tr
    - WORD_Tr
    - StanfordKnee_Tr
    - PancreasCt_Tr
    - MedSamDecathlon_Tr
    - Kits_Tr
    - SegThoracicOrgans_Tr
    - MultiModalWholeHeart_Tr
    - CovidCT_Tr
    - ONDRI_Tr
    - TotalSegmentator_Tr
    - LUNA_Tr
    - ProstateMRI_Tr
    - LiTS_Tr
    - MRIGlioblastoma_Tr
    - HealthyTotalBody_Tr
  validation_sets:
    - BRATS_Tr
    - WORD_Val
    - AMOS_Val
    - ONDRI_Val
    - ProstateMRI_Ts


model:
  model_type: vit_l
  work_dir: ./work_dir
  task_name: train-neurosam-scratch
  lr: 1e-03
  weight_decay: 0.005
  lr_scheduler: steplr
  step_size: 
    - 2000
  gamma: 0.9
  largest_first: true
  click_type: random
  multi_click: true
  bbox_first: false
  num_clicks: 11
  logging_batches_idx:
    - 1
    - 2
    - 3
    - 4
    - 5
  checkpoint: null
  model_cfg: null
  pretrained_weights: null

trainer:
  default_root_dir: ${model.work_dir}/${model.task_name}
  accelerator: auto
  devices: auto
  accumulate_grad_batches: 2 # TODO
  check_val_every_n_epoch: 1
  callbacks:
    - class_path: lightning.pytorch.callbacks.ModelCheckpoint
      init_args:
        monitor: train_loss
        verbose: true
        dirpath: ${trainer.default_root_dir}
        filename: 'best-train-loss-{epoch}-{train_loss:.4f}'
    - class_path: lightning.pytorch.callbacks.ModelCheckpoint
      init_args:
        monitor: train_dice
        verbose: true
        mode: max
        dirpath: ${trainer.default_root_dir}
        filename: 'best-train-dice-{epoch}-{train_dice:.4f}'
    - class_path: lightning.pytorch.callbacks.ModelCheckpoint
      init_args:
        monitor: val_loss
        verbose: true
        dirpath: ${trainer.default_root_dir}
        filename: 'best-val-loss-{epoch}-{train_loss:.4f}'
    - class_path: lightning.pytorch.callbacks.ModelCheckpoint
      init_args:
        monitor: val_dice
        verbose: true
        mode: max
        dirpath: ${trainer.default_root_dir}
        filename: 'best-val-dice-{epoch}-{train_dice:.4f}'
    - class_path: lightning.pytorch.callbacks.LearningRateMonitor
      init_args:
        logging_interval: step

  max_epochs: 200
  precision: bf16-mixed
  num_nodes: 1
  gradient_clip_val: null
  gradient_clip_algorithm: null
  logger:
    class_path: lightning.pytorch.loggers.WandbLogger
    init_args:
      name: ${model.task_name}
      project: NeuroSam
      entity: aiconslab
      log_model: all
      save_dir: ${model.work_dir}/${model.task_name}

  benchmark: true
  enable_progress_bar: true
  use_distributed_sampler: true
  strategy: ddp_find_unused_parameters_true
  log_every_n_steps: 1
  val_check_interval: 0.2