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train_cellvit_sweep.yaml
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train_cellvit_sweep.yaml
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# Example configuration for HoverNet-Cell-Segmentation
# comment and project setup for wandb
logging:
mode: # "online" or "offline" [str]
project: # Name of project to use [str]
notes: # Notes about the run, verbose description [str]
log_comment: # Comment to add to name the local logging folder [str]
tags: # List of tags, e.g., ["baseline", "run1"] [str]
- "tag1"
- "tag2"
- "..."
wandb_dir: # Direcotry to store the wandb file. CAREFUL: Directory must exists [str]
log_dir: # Direcotry to store all logging related files and outputs [str]
level: # Level of logging must be either ["critical", "error", "warning", "info", "debug"] [str]
log_images: # If images should be logged to WandB for this run. [bool] [Optional, defaults to False]
group: # WandB group tag [str] [Optional, defaults to None]
# sweep options -> compare https://docs.wandb.ai/guides/sweeps and https://docs.wandb.ai/guides/sweeps/define-sweep-configuration
# use the same keys as shown below
# Keys are defined here: https://docs.wandb.ai/guides/sweeps/define-sweep-configuration#configuration-keys
sweep:
method: # Sweep Method [str]
name: # Sweep Name [str]
metric: # Sweep Metric [str] (https://docs.wandb.ai/guides/sweeps/define-sweep-configuration#metric)
name: # This metric must be logged, e.g. use AUC/Validation [str]
goal: # Optimization goal. Either "maximize" or "minimize" [str]
early_terminate: # Just applies for bayes method (https://docs.wandb.ai/guides/sweeps/define-sweep-configuration#early_terminate)
type: hyperband # Currently: just hyperband
#... # Other options
run_cap: # Number of trials for the sweep [int]
# Sweep parameters are defined on the according configuration section. Please be carefull to have only on "parameters" key on every level to avoid doubled key conflicts
# Examples are given below
# Documentation on parameters: https://docs.wandb.ai/guides/sweeps/define-sweep-configuration#parameters
# seeding
random_seed: 19 # Seed for numpy, pytorch etc. [int]
# hardware
gpu: # Number of GPU to run experiment on [int]
# setting paths and dataset
data:
dataset: # Name of dataset, currently supported: PanNuke [str]
dataset_path: # Path to dataset, compare ./docs/readmes/pannuke.md for further details [str]
train_folds: [...] # List of fold Numbers to use for training [list[int]]
val_split: # Percentage of training set that should be used for validation. Either val_split or val_fold must be provided, not both. [float]
val_folds: # List of fold Numbers to use for validation [list[int]]
test_folds: # List of fold Numbers to use for final testing [list[int]]
num_nuclei_classes: # Number of different nuclei classes (including background!, e.g. 5 nuclei classes + background = 6) [int]
# model options
model:
backbone: # Backbone Type: Options are: default, ViT256, SAM-B, SAM-L, SAM-H
pretrained_encoder: # Set path to a pretrained encoder [str]
pretrained: # Path to a pretrained model (.pt file) [str, default None]
embed_dim: # Embedding dimension for ViT - typical values are 384 (ViT-S), 768 (ViT-B), 1024 (ViT-L), 1280 (ViT-H) [int]
input_channels: # Number of input channels, usually 3 for RGB [int, default 3]
depth: # Number of Transformer Blocks to use - typical values are 12 (ViT-S), 12 (ViT-B), 24 (ViT-L), 32 (ViT-H) [int]
num_heads: # Number of attention heads for MHA - typical values are 6 (ViT-S), 12 (ViT-B), 16 (ViT-L), 16 (ViT-H) [int]
extract_layers: # List of layers to extract for skip connections - starting from 1 with a maximum value equals the depth [int]
shared_skip_connections: # If skip connections should be share accross all upsampling branches [bool] [Optional, defaults to False]
# loss function settings (best shown by an example). See all implemented loss functions in base_ml.base_loss module
loss:
nuclei_binary_map: # Name of the branch. Possible branches are "nuclei_binary_map", "hv_map", "nuclei_type_map", "tissue_types". If not defined default HoverNet settings are used [str]
bce: # Name of the loss [str]
loss_fn: xentropy_loss # Loss_fn, name is defined in LOSS_DICT in base_ml.base_loss module [str]
weight: 1 # Weight parameter [int] [Optional, defaults to 1]
args: # Parameters for the loss function if necessary. Does not need to be set, can also be empty. Just given as an example here
arg1: # 1. Parameter etc. (Name must match to the initialization parameter given for the loss)
dice: # Name of the loss [str]
loss_fn: dice_loss # Loss_fn, name is defined in LOSS_DICT in base_ml.base_loss module [str]
weight: 1 # Weight parameter [int] [Optional, defaults to 1]
focaltverskyloss: # Name of the loss [str]
loss_fn: FocalTverskyLoss # Loss_fn, name is defined in LOSS_DICT in base_ml.base_loss module [str]
weight: 1 # Weight parameter [int] [Optional, defaults to 1]
# optional parameters, not implemented yet
# hv_map: another branch
# nuclei_type_map: another branch
# tissue_types: another branch
# training options
training:
############# Exemplary parameters ########################################################################################################################################
parameters:
attn_drop_rate:
min: 0.0
max: 0.15
drop_rate:
values: [0, 0.15, 0.25]
############################################################################################################################################################################
batch_size: 32
epochs: 100
unfreeze_epoch:
drop_path_rate:
############# Exemplary parameters (on a lower level) ######################################################################################################################
optimizer: AdamW
optimizer_hyperparameter:
parameters:
lr:
min: 0.00001
max: 0.01
betas:
values:
[[0.85, 0.9], [0.9, 0.999], [0.85, 0.95]]
weight_decay:
min: 0.00001
max: 0.001
############################################################################################################################################################################
early_stopping_patience:
scheduler:
scheduler_type:
# hyperparameters
sampling_strategy:
sampling_gamma:
mixed_precision:
# transformations, here all options are given. Remove transformations by removing them from this section
transformations:
randomrotate90: # RandomRotation90
p: # Probability [float, between 0 and 1]
horizontalflip: # HorizontalFlip
p: # Probability [float, between 0 and 1]
verticalflip: # VerticalFlip
p: # Probability [float, between 0 and 1]
downscale: # Downscaling
p: # Probability [float, between 0 and 1]
scale: # Scaling factor, maximum should be 0.5. Must be smaller than 1 [float, between 0 and 1]
blur: # Blur
p: # Probability [float, between 0 and 1]
blur_limit: # Bluring limit, maximum should be 10, recommended 10 [float]
gaussnoise: # GaussianNoise
p: # Probability [float, between 0 and 1]
var_limit: # Variance limit, maxmimum should be 50, recommended 10 [float]
colorjitter: # ColorJitter
p: # Probability [float, between 0 and 1]
scale_setting: # Scaling for contrast and brightness, recommended 0.25 [float]
scale_color: # Scaling for hue and saturation, recommended 0.1 [float]
superpixels: # SuperPixels
p: # Probability [float, between 0 and 1]
zoomblur: # ZoomBlur
p: # Probability [float, between 0 and 1]
randomsizedcrop: # RandomResizeCrop
p: # Probability [float, between 0 and 1]
elastictransform: # ElasticTransform
p: # Probability [float, between 0 and 1]
normalize: # Normalization
mean: # Mean for Normalizing, default to (0.5, 0.5, 0.5) [list[float], between 0 and 1 for each entry]
std: # STD for Normalizing, default to (0.5, 0.5, 0.5) [list[float], between 0 and 1 for each entry]
eval_checkpoint: # Either select "best_checkpoint.pth", "latest_checkpoint.pth" or one of the intermediate checkpoint names, e.g., "checkpoint_100.pth"