clemsgrs
commented
1 year ago Hi @bryanwong17, happy to help:
1. As TCGA and camelyon16 datasets are different, should I initialize the checkpoints pretrained model and train DINO models again for both local and global? How many epochs do you think would be sufficient?
As long as you keep the img_size_* and patch_size_* arguments equal to what's in the default.yaml config, you can use the same pre-trained checkpoints. Otherwise, you could still use these checkpoints but it could lead to poor results (for different reasons).
2. What should I put inside of train.csv, tune.csv, and test.csv?
Sorry, I forgot to give details about this in the README.md. These file should contain the slide ids & corresponding classification labels:
slide_id,label
TRAIN_1,1
TRAIN_2,1
...3. Why is img_size_4096 equal to 3584? Is it teacher size in region level?
This has to do with how the intermediate Transformer block was pre-trained (using crops). See HIPT author explaining why here:
"To be more exact, technically the image size for VisionTransformer4K should be 3584 while the patch size is 256, as during pretraining, as the maximum global crop size is [14 x 14] in a [16 x 16 x 384] 2D grid of pre-extracted feature embeddings of 256-sized patches."
4.What is label_name in default.yaml?
label_name should correspond to the name of the column holding the labels in your train.csv & tune.csv files.
If the column name is "label", then label_name = "label".
5. Where to put actual labels for each slide?
See previous answers
6. Could you help me to solve this issue?
Just add a blank wandb.group parameter to your config file:
wandb:
project: 'hipt'
username: 'clemsg'
exp_name: 'toy_training'
dir: '/home/user'
to_log: ['loss', 'auc', 'kappa', 'roc_auc_curve']
group:Let me know if you have any further questions.
bryanwong17
Hi @clemsgrs , I'm trying to use your HIPT implementation code with the CAMELYON16 dataset and having a few questions:
wandb: Appending key for api.wandb.ai to your netrc file: /home/bryan/.netrc Error executing job with overrides: [] Traceback (most recent call last): File "extract_features.py", line 159, in
main()
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/hydra/main.py", line 90, in decorated_main
_run_hydra(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/hydra/_internal/utils.py", line 389, in _run_hydra
_run_app(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/hydra/_internal/utils.py", line 452, in _run_app
run_and_report(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/hydra/_internal/utils.py", line 216, in run_and_report
raise ex
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/hydra/_internal/utils.py", line 213, in run_and_report
return func()
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/hydra/_internal/utils.py", line 453, in
lambda: hydra.run(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/hydra/internal/hydra.py", line 132, in run
= ret.return_value
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/hydra/core/utils.py", line 260, in return_value
raise self._return_value
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/hydra/core/utils.py", line 186, in run_job
ret.return_value = task_function(task_cfg)
File "extract_features.py", line 39, in main
wandb_run = initialize_wandb(cfg, key=key)
File "/mnt/d/hipt/source/utils.py", line 67, in initialize_wandb
group=cfg.wandb.group,
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/dictconfig.py", line 359, in getattr
self._format_and_raise(key=key, value=None, cause=e)
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/base.py", line 231, in _format_and_raise
format_and_raise(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/_utils.py", line 819, in format_and_raise
_raise(ex, cause)
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/_utils.py", line 797, in _raise
raise ex.with_traceback(sys.exc_info()[2]) # set env var OC_CAUSE=1 for full trace
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/dictconfig.py", line 351, in getattr
return self._get_impl(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/dictconfig.py", line 442, in _get_impl
node = self._get_child(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/basecontainer.py", line 73, in _get_child
child = self._get_node(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/dictconfig.py", line 475, in _get_node
self._validate_get(key)
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/dictconfig.py", line 164, in _validate_get
self._format_and_raise(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/base.py", line 231, in _format_and_raise
format_and_raise(
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/_utils.py", line 899, in format_and_raise
_raise(ex, cause)
File "/home/bryan/anaconda3/envs/hipt_try/lib/python3.8/site-packages/omegaconf/_utils.py", line 797, in _raise
raise ex.with_traceback(sys.exc_info()[2]) # set env var OC_CAUSE=1 for full trace
omegaconf.errors.ConfigAttributeError: Key 'group' is not in struct
full_key: wandb.group
object_type=dict
Thank you!