Add ProtBert model card
Author: agemagician
Pull request: yes
Labels: name: model card

This is a model card for our ProtBert:
https://huggingface.co/Rostlab/prot_bert

Comments:
Any idea why there is one failed test case ?
I have checked the code on the notebook and it runs without any issue on Colab.

This seems completely unrelated, just relaunched the failed test.

# [Codecov](https://codecov.io/gh/huggingface/transformers/pull/6764?src=pr&el=h1) Report
> Merging [#6764](https://codecov.io/gh/huggingface/transformers/pull/6764?src=pr&el=desc) into [master](https://codecov.io/gh/huggingface/transformers/commit/4bd7be9a4268221d2a0000c7e8033aaeb365c03b?el=desc) will **decrease** coverage by `0.04%`.
> The diff coverage is `n/a`.

[![Impacted file tree graph](https://codecov.io/gh/huggingface/transformers/pull/6764/graphs/tree.svg?width=650&height=150&src=pr&token=9qOlN6Hb1c)](https://codecov.io/gh/huggingface/transformers/pull/6764?src=pr&el=tree)

```diff
@@            Coverage Diff             @@
##           master    #6764      +/-   ##
==========================================
- Coverage   79.74%   79.70%   -0.05%     
==========================================
  Files         157      157              
  Lines       28479    28479              
==========================================
- Hits        22712    22698      -14     
- Misses       5767     5781      +14     
```


| [Impacted Files](https://codecov.io/gh/huggingface/transformers/pull/6764?src=pr&el=tree) | Coverage Δ | |
|---|---|---|
| [src/transformers/tokenization\_roberta.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy90b2tlbml6YXRpb25fcm9iZXJ0YS5weQ==) | `87.67% <0.00%> (-10.96%)` | :arrow_down: |
| [src/transformers/tokenization\_utils\_base.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy90b2tlbml6YXRpb25fdXRpbHNfYmFzZS5weQ==) | `86.58% <0.00%> (-7.19%)` | :arrow_down: |
| [src/transformers/tokenization\_transfo\_xl.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy90b2tlbml6YXRpb25fdHJhbnNmb194bC5weQ==) | `38.73% <0.00%> (-3.76%)` | :arrow_down: |
| [src/transformers/tokenization\_openai.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy90b2tlbml6YXRpb25fb3BlbmFpLnB5) | `82.57% <0.00%> (-1.52%)` | :arrow_down: |
| [src/transformers/tokenization\_utils\_fast.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy90b2tlbml6YXRpb25fdXRpbHNfZmFzdC5weQ==) | `92.85% <0.00%> (-1.43%)` | :arrow_down: |
| [src/transformers/tokenization\_bert.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy90b2tlbml6YXRpb25fYmVydC5weQ==) | `91.07% <0.00%> (-0.45%)` | :arrow_down: |
| [src/transformers/tokenization\_utils.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy90b2tlbml6YXRpb25fdXRpbHMucHk=) | `89.45% <0.00%> (-0.40%)` | :arrow_down: |
| [src/transformers/file\_utils.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy9maWxlX3V0aWxzLnB5) | `82.41% <0.00%> (-0.26%)` | :arrow_down: |
| [src/transformers/generation\_tf\_utils.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy9nZW5lcmF0aW9uX3RmX3V0aWxzLnB5) | `86.46% <0.00%> (-0.26%)` | :arrow_down: |
| [src/transformers/tokenization\_marian.py](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree#diff-c3JjL3RyYW5zZm9ybWVycy90b2tlbml6YXRpb25fbWFyaWFuLnB5) | `99.16% <0.00%> (+32.50%)` | :arrow_up: |
| ... and [1 more](https://codecov.io/gh/huggingface/transformers/pull/6764/diff?src=pr&el=tree-more) | |

------

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> Powered by [Codecov](https://codecov.io/gh/huggingface/transformers/pull/6764?src=pr&el=footer). Last update [4bd7be9...c7eb12c](https://codecov.io/gh/huggingface/transformers/pull/6764?src=pr&el=lastupdated). Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments).


Hi @agemagician, your model https://huggingface.co/Rostlab/prot_bert is not recognized by our Hosted inference API, probably because it doesn't have a `architectures` field in its config.json:

<img width="565" alt="Screenshot 2020-10-21 at 21 52 57" src="https://user-images.githubusercontent.com/326577/96775413-849fb700-13b5-11eb-8075-11d7792548f6.png">


Do you mind if we update the config.json on the model hub? Alternatively, do you prefer doing it yourself?

Thanks!

Hi @julien-c  , No problem.
I already have seen you updated it.

However, it doesn't work properly because we don't lower case tokens:
https://huggingface.co/Rostlab/prot_bert?text=A+T+G+%5BMASK%5D+C

I have uploaded the "tokenizer_config.json" file which should fix it, but we have to wait until the model is no longer in memory and reload it.

I have also did the same for our better bert model "prot_bert_bfd", and it is working fine:
https://huggingface.co/Rostlab/prot_bert_bfd?text=A+T+G+%5BMASK%5D+C

Thanks for your help.

Now properly loaded, and looks great!

https://huggingface.co/Rostlab/prot_bert?text=D+L+I+P+T+S+S+K+V+V+%5BMASK%5D+D+T+S+L+Q+V+K+K+A+F+F+A+L+V+T

<img width="693" alt="Screenshot 2020-10-21 at 22 56 44" src="https://user-images.githubusercontent.com/326577/96786965-ff210480-13be-11eb-9133-375bb20e60a1.png">

Thanks a lot @agemagician