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importing biobert_v1.1_pubmed ERROR 404: Not Found to Colab notebook #184

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JaskaranKaurGill opened this issue Dec 3, 2022 · 2 comments

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@JaskaranKaurGill
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I am trying to import BioBERT from the original https://github.com/dmis-lab/biobert and transfer the files to our Colab notebook.

!pip install transformers !wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1R84voFKHfWV9xjzeLzWBbmY1uOMYpnyD' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1R84voFKHfWV9xjzeLzWBbmY1uOMYpnyD" -O biobert_weights && rm -rf /tmp/cookies.txt !tar -xzf biobert_weights !transformers-cli convert --model_type bert --tf_checkpoint biobert_v1.1_pubmed/model.ckpt-1000000 --config biobert_v1.1_pubmed/bert_config.json --pytorch_dump_output biobert_v1.1_pubmed/pytorch_model.bin !mv biobert_v1.1_pubmed/bert_config.json biobert_v1.1_pubmed/config.json

I am getting the following error:
ERROR 404: Not Found
image

Has the link changed

@vahab-mspour
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The same problem is here in issue #185 link

@wonjininfo
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Hi
As mentioned in above comment (thanks Vahab Mostafapour!), my school has ceased to provide google drive access.

We have made a mirror at the following URLs:
http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/biobert_v1.1_pubmed.tar.gz
http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/NERdata.zip
http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/REdata.zip
http://nlp.dmis.korea.edu/projects/biobert-2020-checkpoints/QA.zip

Thank you.
Best,
Wonjin

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