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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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BioBERT with bert-as-service #96

Closed Manajit89 closed 4 years ago

Manajit89 commented 4 years ago

Hi!

First of all let me begin by thanking you for the pre-trained BERT model which is a life saver. For my latest project, I would like to get to ELMo like contextual embeddings from BioBERT. To reduce the complexity barrier, I resorted to using bert-as-service (https://github.com/hanxiao/bert-as-service), which admittedly accepts pre-trained models. However, when I try to run it I encounter strange errors. I am wondering if it is due to the Tensorflow version or something. According to the documentation of bert-as-service, (https://bert-as-service.readthedocs.io/en/latest/section/faq.html#can-i-use-my-own-fine-tuned-bert-model), one needs to provide just the checkpoint, vocab and bert_config.json, which are all present in the BioBert directory. Despite that, I see the following errors: Issue_1 Issue_2

Am I missing something? Is there an easier alternative to get the embeddings without having to set-up the code ecosystem?

Thanks in advance, Manajit

jhyuklee commented 4 years ago

Not familiar with bert-as-service but this (https://github.com/naver/biobert-pretrained/issues/7) might help.

Manajit89 commented 4 years ago

Thank you very much for this. Not sure how I missed that.

Best, Manajit

Manajit Chakraborty PhD Student, Faculty of Informatics, Università della Svizzera italiana (USI), Lugano 6900, CH

On 26 Feb 2020, at 12:54 PM, Jinhyuk Lee notifications@github.com<mailto:notifications@github.com> wrote:

Not familiar with bert-as-service but this (naver/biobert-pretrained#7https://github.com/naver/biobert-pretrained/issues/7) might help.

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