Add ESM to huggingface

[liujas000]

What does this PR do?

Adding ESM-1b to huggingface following the steps in https://huggingface.co/transformers/add_new_model.html

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@sgugger

[sgugger]

Thanks a lot for your PR! I left a few comments but it's already in pretty good shape.

I have a few more general interrogations:

• The tokenizer fast is imported in the main inits and used in the doc, but it does not exist in the files, so you should either add the tokenizer fast or remove any mention of it.
• Do all the model head make sense for this new architecture? From what I understand it's linked to proteins so I don't know if the task-specific heads like multiple choice or question answering really are useful.
• There should be a file to test the tokenizer

[liujas000]

@sgugger , thanks for the feedback!
There's two common tests that I'm failing; do you have any insight into what the proper fix would be?

❯ pytest tests/test_modeling_esm.py --disable-warnings
==================================================== test session starts ====================================================
platform linux -- Python 3.7.10, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /private/home/jasonliu/work-huggingface/transformers-dev, configfile: setup.cfg
plugins: dash-1.21.0, forked-1.3.0, xdist-2.3.0, timeout-1.4.2, hydra-core-1.1.0
collected 67 items

tests/test_modeling_esm.py .....................................s..............FF.....sss..ss.                        [100%]

========================================================= FAILURES ==========================================================
______________________________________ ESMModelTest.test_save_load_fast_init_from_base ______________________________________

self = <tests.test_modeling_esm.ESMModelTest testMethod=test_save_load_fast_init_from_base>

    def test_save_load_fast_init_from_base(self):
        config, inputs_dict = self.model_tester.prepare_config_and_inputs_for_common()
>       base_class = MODEL_MAPPING[config.__class__]

tests/test_modeling_common.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = _LazyAutoMapping(), key = <class 'transformers.models.esm.configuration_esm.ESMConfig'>

    def __getitem__(self, key):
>       model_type = self._reverse_config_mapping[key.__name__]
E       KeyError: 'ESMConfig'

src/transformers/models/auto/auto_factory.py:513: KeyError
_______________________________________ ESMModelTest.test_save_load_fast_init_to_base _______________________________________

self = <tests.test_modeling_esm.ESMModelTest testMethod=test_save_load_fast_init_to_base>

    def test_save_load_fast_init_to_base(self):
        config, inputs_dict = self.model_tester.prepare_config_and_inputs_for_common()
>       base_class = MODEL_MAPPING[config.__class__]

tests/test_modeling_common.py:253:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = _LazyAutoMapping(), key = <class 'transformers.models.esm.configuration_esm.ESMConfig'>

    def __getitem__(self, key):
>       model_type = self._reverse_config_mapping[key.__name__]
E       KeyError: 'ESMConfig'

src/transformers/models/auto/auto_factory.py:513: KeyError
================================================== short test summary info ==================================================
FAILED tests/test_modeling_esm.py::ESMModelTest::test_save_load_fast_init_from_base - KeyError: 'ESMConfig'
FAILED tests/test_modeling_esm.py::ESMModelTest::test_save_load_fast_init_to_base - KeyError: 'ESMConfig'
============================== 2 failed, 59 passed, 6 skipped, 30 warnings in 99.74s (0:01:39) ==============================

[sgugger]

It doesn't look like you added your model in the configuration_auto mappings, just the modeling_auto mappings. That's why you get this error.

[liujas000]

Thanks! I think this is ready for review again (rebased to upstream)

[patrickvonplaten]

could we maybe replace those classes by the corresponding ESM... classes, e.g. ESMIntermediate, ...

[patrickvonplaten]

This would still be nice to change before merging

[patrickvonplaten]

I fixed a couple of things (corrected the config and removed dead code of ESMForQuestionAnswering) - hope that was ok!

PR is good for merge IMO. It would be nice if we could replace the BERT modules with ESM modules in the conversion script and then we should probably also flip the private model repo to public so that the integration test can run :-)

Should we upload the other checkpoitns as well: https://github.com/facebookresearch/esm#pre-trained-models-

[LysandreJik]

Nice, this looks good to me! Thank you for working on this!

[patrickvonplaten]

Hey @liujas000,

Can we help you in any way to get this PR merged? :-)

[liujas000]

@patrickvonplaten sorry for the delay; I will land this week!

[patrickvonplaten]

Test failure seems unrelated

[patrickvonplaten]

Thanks a lot for making this PR more or less mergeable @liujas000 . I think there are just some final comments from @sgugger and @patrickvonplaten to be taken care of and the PR is good to go :-)

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[gianhiltbrunner]

I'd love to use this model, what still needs to be done to get this merged?

[patrickvonplaten]

cc @liujas000 @Rocketknight1

[Rocketknight1]

@gianhiltbrunner We're still waiting on an internal review from Facebook from the contributors, I believe! I'll let you know if there's any update.

[franzigeiger]

I would also be very happy if this gets merged! Any progress?

[patrickvonplaten]

Any updates here?