suinleelab / cxr_covid Goto Github PK
View Code? Open in Web Editor NEWCode for paper "AI for radiographic COVID-19 detection selects shortcuts over signal"
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jhnhum
python train_covid.py --dataset 1 returns a ROC AUC ValueError
Ran on environment provided.
-------- Epoch 000 --------
Traceback (most recent call last):
File "train_covid.py", line 202, in <module>
main()
File "train_covid.py", line 193, in main
train_githubcxr14(args.seed,
File "train_covid.py", line 52, in train_githubcxr14
classifier.train(trainds,
File "/uss/xrai/nick_folder/cxr_covid/models/cxrclassifier.py", line 178, in train
valloss, valauroc = self._val_epoch(val_dataloader)
File "/uss/xrai/nick_folder/cxr_covid/models/cxrclassifier.py", line 261, in _val_epoch
auroc = sklearn.metrics.roc_auc_score(true[:,-1], probs[:,-1])
File "/datasets/home/00/300/nil021/.conda/envs/cxr_covid/lib/python3.8/site-packages/sklearn/metrics/_ranking.py", line 387, in roc_auc_score
return _average_binary_score(partial(_binary_roc_auc_score,
File "/datasets/home/00/300/nil021/.conda/envs/cxr_covid/lib/python3.8/site-packages/sklearn/metrics/_base.py", line 77, in _average_binary_score
return binary_metric(y_true, y_score, sample_weight=sample_weight)
File "/datasets/home/00/300/nil021/.conda/envs/cxr_covid/lib/python3.8/site-packages/sklearn/metrics/_ranking.py", line 221, in _binary_roc_auc_score
raise ValueError("Only one class present in y_true. ROC AUC score "
ValueError: Only one class present in y_true. ROC AUC score is not defined in that case.
compile error: make_csv.py
(1)
Replicate Error: run make_csv.py
Error Message:
File "make_csv.py", line 109
contains_CR_DX = lambda x: return ('CR' in x) or ('DX' in x)
^
SyntaxError: invalid syntax
Problem:
lambda statement doesn't allow return statement
FIX:
Before: contains_CR_DX = lambda x: return ('CR' in x) or ('DX' in x)
After: contains_CR_DX = lambda x: ('CR' in x) or ('DX' in x)
(2)
Replicate Error: run make_csv.py
Error Message:
File "make_csv.py", line 113
is_dir = os.path.isdir(os.path.join(datapath, subject, sessionfile))
^
SyntaxError: invalid syntax
Problem:
Missing closing parentheses
FIX:
Before: image_candidates_dir = os.listdir(os.path.join(datapath, subject, sessionfile, 'mod-rx')
After: image_candidates_dir = os.listdir(os.path.join(datapath, subject, sessionfile, 'mod-rx'))
Update make_csv.py
include these into series_description_map:
'TORAX AP': 'AP',
'TÓRAX AP': 'AP',
'TORAX BIPE AP': 'AP',
'W034 TÓRAX LAT': 'LAT',
'W033 TÓRAX P.A.': 'PA',
Add another exception to series_description:
try:
series_description = metadata['0008103E']['Value'][0]
except Exception as e:
try:
series_description = metadata['00081032']['Value'][0]['00080104']['Value'][0]
except Exception as e:
try:
series_description = metadata["00185101"]["Value"][0]
except Exception as e:
raise e
Update githubcovid.py
Error Replication
Running python train_models.py --dataset 1 gives the following Error
Traceback (most recent call last):
File "train_covid.py", line 202, in <module>
main()
File "train_covid.py", line 193, in main
train_githubcxr14(args.seed,
File "train_covid.py", line 52, in train_githubcxr14
classifier.train(trainds,
File "/uss/xrai/nick_folder/cxr_covid/models/cxrclassifier.py", line 178, in train
valloss, valauroc = self._val_epoch(val_dataloader)
File "/uss/xrai/nick_folder/cxr_covid/models/cxrclassifier.py", line 262, in _val_epoch
auroc = sklearn.metrics.roc_auc_score(true[:,-1], probs[:,-1])
File "/datasets/home/00/300/nil021/.conda/envs/cxr_covid/lib/python3.8/site-packages/sklearn/metrics/_ranking.py", line 387, in roc_auc_score
return _average_binary_score(partial(_binary_roc_auc_score,
File "/datasets/home/00/300/nil021/.conda/envs/cxr_covid/lib/python3.8/site-packages/sklearn/metrics/_base.py", line 77, in _average_binary_score
return binary_metric(y_true, y_score, sample_weight=sample_weight)
File "/datasets/home/00/300/nil021/.conda/envs/cxr_covid/lib/python3.8/site-packages/sklearn/metrics/_ranking.py", line 221, in _binary_roc_auc_score
raise ValueError("Only one class present in y_true. ROC AUC score "
ValueError: Only one class present in y_true. ROC AUC score is not defined in that case.
Problem Identification
Looking at the metadata, we see that values in finding columns may have been updated to new values.
Github-COVID feature engineering datasets/githubcovid.py needs to be updated
Current solution gives false for every datapoint, because of line 71: covid_set = ['COVID-19','COVID-19, ARDS']
Solution
Patients w/ COVID now have the following string 'Pneumonia/Viral/COVID-19' instead of 'COVID-19','COVID-19, ARDS']
Pneumonia patients and healthy set must also be updated to correspond with the new changes
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