dmis-lab / biobert

Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining
http://doi.org/10.1093/bioinformatics/btz682
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importing biobert_v1.1_pubmed ERROR 404: Not Found to Colab notebook #184

Open JaskaranKaurGill opened 1 year ago

JaskaranKaurGill commented 1 year ago

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 commented 1 year ago

The same problem is here in issue #185 link

wonjininfo commented 1 year ago

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