only_downstream_analyses.yaml

meta:
  name_of_run: "name_of_run"
  output_dir: "outputdir"
  dataset_dir: "datasetdir"
  folder_depth_for_labels: 0 # 0 is the folder where the images are, 1 is the folder above, etc.
  test_datasetsplit_fraction: 0.1
  seed: 40 #should match scDINO seed if you want to use the same train/test split
  images_are_RGB: False
  channel_dict: { 0: "APC", 1: "BF", 2: "DAPI", 3: "GREEN", 4: "PE" } #do not use underscore or slash in channel name
  selected_channel_combination_per_run: ["01234", "0", "1", "2", "3", "4"] #01234 is all 5 channels, 0 is only APC, 1 is only BF, etc.
  center_crop: 0 #0 is no center crop
compute_cls_features:
  use_weighted_sampler: False # if False, valdataset is used defined in meta
  class_weights: "[0.1, 0.1, 0.1, 0.1, 0.1]" # only used if use_weighted_sampler is True, length of list must be equal to number of classes
  num_samples: 5000 # only used if use_weighted_sampler is True
  normalize: True
  parse_mean_std_from_file: True
  mean_std_file_location: "dir/mean_and_std_of_dataset.txt"
  norm_per_channel: "[(x,x,x,x,x)(x,x,x,x,x)]" #only used if parse_mean_std_from_file is False
  use_cuda: True
  num_gpus: 1
  batch_size_per_gpu: 24
  num_workers: 8
  pretrained_weights: "dir_to_pretrained_weights"
  read_model_arch_dynamically: False
  arch: "vit_small" #only used if read_model_arch_dynamically is False
  patch_size: 8 #only used if read_model_arch_dynamically is False
  use_mean_patch_embedding: False
  use_custom_embedding_map: False # if True, the embedding map is defined by the user below
  custom_embedding_map: "{0:2, 1:2, 2:2, 3:2, 4:2}" #first is the channel of the input image and the second is the channel of the embedding
  images_are_RGB: False
  resize: True
  resize_length: 224 #only used if resize is True
attention_visualisation:
  num_images_per_class: 1
kNN:
  global:
    n_neighbors: [5, 10, 50, 100, 200, 500]
    temperature: 0.1
umap_eval:
  n_neighbors: 30
  min_dist: 0.4
  n_components: 2
  metric: euclidean
  spread: 1.1
  epochs: 100
  topometry_plots: False