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View Code? Open in Web Editor NEWA clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework
License: MIT License
A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework
License: MIT License
Hi,
Could you please share 170 annotated publications? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6852618/
Best regards,
Elena
Hi, I've used BERT Parser as you said and tried to get a prediction on test data you provided but I got nothing except, exceptionlist.txt
in the output directory.
I replaced downloadedbluebert_pretrained_ori.tar.gz
with the same folder in the directory and put the NCBI_BERT's files
in the bert_init_models
folder and just modified bluebert_dir = "bluebert_pretrained_ori"
am I right?
I would be grateful if you could help me.
Hi!
I've already installed the requirements but if I try to run the example I have the next error:
'tensorflow' has no attribute 'flags'
Loading customized config and text tokenizer...
2020-11-10 21:26:21.042753: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory
2020-11-10 21:26:21.042783: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
ln: failed to create symbolic link 'QuickUMLS': File exists
Traceback (most recent call last):
File "run_bluebert_ner_predict.py", line 34, in
flags = tf.flags
AttributeError: module 'tensorflow' has no attribute 'flags'
How can I solve that problem?
In your documentation for LSTM parser you mention that LSTM_Parser/cluster/model/download.txt
contains a link for the context vector download. This download link is broken:
https://drive.google.com/open?id=1Qs0--7eX9dMq4ngQQRpG_VnYGygGdIaF
Is there another download link that would work? Thanks!
Hi Tian,
I'm interested in your work and have some questions.
Thanks a lot in advance.
Hi, I've tried to evaluate your model with scibert pico data set, but the tokenization wasn't the same, could you please share the F1 score you get?
Hi Tian,
Would you be able to share pubmed_util_batch.py script please?It's currently a soft link to your local dir. Thank you in advance!
https://github.com/Tian312/PICO_Parser/blob/master/BERT_Parser/text_processing/pubmed_util_batch.py
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