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                                            njan-creative

Running CheXpert labeler on Google Colab?

I am also trying to setup on Google colab without success.. Were you able to get it to work ?

"pip install negbio" doesn't work

pip install is not working for me too.

MIMIC-CXR JPG dataset resize

Happy new year.. Alistair Johnson.. @alistairewj

File missing lesion_dict.json

Can you upload this file to google drive and share link here.

classifier_sample_known - IndexError: index 1 is out of bounds for dimension 1 with size 1

I commented out the viz part, as visualization was not working for me, I saved it as npy instead by changing the below code. ``` gathered_samples = [th.zeros_like(sample) for _...

Error - ValueError: Parser model has not been loaded.

Please find the output below. ``` Model directory: /home/user/.local/share/bllipparser/GENIA+PubMed Model directory already exists, not reinstalling ``` `RerankingParser(unified_model_dir='/home/user/.local/share/bllipparser/GENIA+PubMed')`

Error - ValueError: Parser model has not been loaded.

`Traceback (most recent call last): File "label.py", line 53, in label(parser.parse_args()) File "label.py", line 44, in label classifier.classify(loader.collection) File "/DATA/njan/medical/chexpert/chexpert-labeler/stages/classify.py", line 100, in classify self.parser.parse_doc(document) File "/home/user/.local/lib/python3.7/site-packages/negbio/pipeline/parse.py", line 55, in...

Error - ValueError: Parser model has not been loaded.

Traceback (most recent call last): File "label.py", line 53, in label(parser.parse_args()) File "label.py", line 44, in label classifier.classify(loader.collection) File "/DATA/njan/medical/chexpert/chexpert-labeler/stages/classify.py", line 100, in classify self.parser.parse_doc(document) File "/home/user/.local/lib/python3.7/site-packages/negbio/pipeline/parse.py", line 55, in...