TF port of ESM (#19587)

* Partial TF port for ESM model * Add ESM-TF tests * Add the various imports for TF-ESM * TF weight conversion almost ready * Stop ignoring the decoder weights in PT * Add tests and lots of fixes * fix-copies * Fix imports, add model docs * Add get_vocab() to tokenizer * Fix vocab links for pretrained files * Allow multiple inputs with a sep * Use EOS as SEP token because ESM vocab lacks SEP * Correctly return special tokens mask from ESM tokenizer * make fixup * Stop testing unsupported embedding resizing * Handle TF bias correctly * Skip all models with slow tokenizers in the token classification test * Fixing the batch/unbatcher of pipelines to accomodate the `None` being passed around. * Fixing pipeline bug caused by slow tokenizer being different. * Update src/transformers/models/esm/modeling_tf_esm.py Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com> * Update src/transformers/models/esm/modeling_tf_esm.py Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com> * Update src/transformers/models/esm/modeling_tf_esm.py Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com> * Update set_input_embeddings and the copyright notices Co-authored-by: Your Name <you@example.com> Co-authored-by: Nicolas Patry <patry.nicolas@protonmail.com> Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com>
huggingface · Oct 17, 2022 · 3b3024d · 3b3024d
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diff --git a/docs/source/en/index.mdx b/docs/source/en/index.mdx
@@ -243,7 +243,7 @@ Flax), PyTorch, and/or TensorFlow.
 |           ELECTRA           |       ✅       |       ✅       |       ✅        |         ✅         |      ✅      |
 |       Encoder decoder       |       ❌       |       ❌       |       ✅        |         ✅         |      ✅      |
 |            ERNIE            |       ❌       |       ❌       |       ✅        |         ❌         |      ❌      |
-|             ESM             |       ✅       |       ❌       |       ✅        |         ❌         |      ❌      |
+|             ESM             |       ✅       |       ❌       |       ✅        |         ✅         |      ❌      |
 | FairSeq Machine-Translation |       ✅       |       ❌       |       ✅        |         ❌         |      ❌      |
 |          FlauBERT           |       ✅       |       ❌       |       ✅        |         ✅         |      ❌      |
 |            FLAVA            |       ❌       |       ❌       |       ✅        |         ❌         |      ❌      |

diff --git a/docs/source/en/model_doc/esm.mdx b/docs/source/en/model_doc/esm.mdx
@@ -107,3 +107,23 @@ and [Matt](https://huggingface.co/Rocketknight1).
 
 [[autodoc]] EsmForTokenClassification
     - forward
+
+## TFEsmModel
+
+[[autodoc]] TFEsmModel
+    - call
+
+## TFEsmForMaskedLM
+
+[[autodoc]] TFEsmForMaskedLM
+    - call
+
+## TFEsmForSequenceClassification
+
+[[autodoc]] TFEsmForSequenceClassification
+    - call
+
+## TFEsmForTokenClassification
+
+[[autodoc]] TFEsmForTokenClassification
+    - call
diff --git a/src/transformers/__init__.py b/src/transformers/__init__.py
@@ -2462,6 +2462,16 @@
         ]
     )
     _import_structure["models.encoder_decoder"].append("TFEncoderDecoderModel")
+    _import_structure["models.esm"].extend(
+        [
+            "ESM_PRETRAINED_MODEL_ARCHIVE_LIST",
+            "TFEsmForMaskedLM",
+            "TFEsmForSequenceClassification",
+            "TFEsmForTokenClassification",
+            "TFEsmModel",
+            "TFEsmPreTrainedModel",
+        ]
+    )
     _import_structure["models.flaubert"].extend(
         [
             "TF_FLAUBERT_PRETRAINED_MODEL_ARCHIVE_LIST",
@@ -5134,6 +5144,14 @@
             TFElectraPreTrainedModel,
         )
         from .models.encoder_decoder import TFEncoderDecoderModel
+        from .models.esm import (
+            ESM_PRETRAINED_MODEL_ARCHIVE_LIST,
+            TFEsmForMaskedLM,
+            TFEsmForSequenceClassification,
+            TFEsmForTokenClassification,
+            TFEsmModel,
+            TFEsmPreTrainedModel,
+        )
         from .models.flaubert import (
             TF_FLAUBERT_PRETRAINED_MODEL_ARCHIVE_LIST,
             TFFlaubertForMultipleChoice,

diff --git a/src/transformers/models/auto/modeling_tf_auto.py b/src/transformers/models/auto/modeling_tf_auto.py
@@ -47,6 +47,7 @@
         ("distilbert", "TFDistilBertModel"),
         ("dpr", "TFDPRQuestionEncoder"),
         ("electra", "TFElectraModel"),
+        ("esm", "TFEsmModel"),
         ("flaubert", "TFFlaubertModel"),
         ("funnel", ("TFFunnelModel", "TFFunnelBaseModel")),
         ("gpt2", "TFGPT2Model"),
@@ -129,6 +130,7 @@
         ("ctrl", "TFCTRLLMHeadModel"),
         ("distilbert", "TFDistilBertForMaskedLM"),
         ("electra", "TFElectraForMaskedLM"),
+        ("esm", "TFEsmForMaskedLM"),
         ("flaubert", "TFFlaubertWithLMHeadModel"),
         ("funnel", "TFFunnelForMaskedLM"),
         ("gpt2", "TFGPT2LMHeadModel"),
@@ -223,6 +225,7 @@
         ("deberta-v2", "TFDebertaV2ForMaskedLM"),
         ("distilbert", "TFDistilBertForMaskedLM"),
         ("electra", "TFElectraForMaskedLM"),
+        ("esm", "TFEsmForMaskedLM"),
         ("flaubert", "TFFlaubertWithLMHeadModel"),
         ("funnel", "TFFunnelForMaskedLM"),
         ("layoutlm", "TFLayoutLMForMaskedLM"),
@@ -273,6 +276,7 @@
         ("deberta-v2", "TFDebertaV2ForSequenceClassification"),
         ("distilbert", "TFDistilBertForSequenceClassification"),
         ("electra", "TFElectraForSequenceClassification"),
+        ("esm", "TFEsmForSequenceClassification"),
         ("flaubert", "TFFlaubertForSequenceClassification"),
         ("funnel", "TFFunnelForSequenceClassification"),
         ("gpt2", "TFGPT2ForSequenceClassification"),
@@ -346,6 +350,7 @@
         ("deberta-v2", "TFDebertaV2ForTokenClassification"),
         ("distilbert", "TFDistilBertForTokenClassification"),
         ("electra", "TFElectraForTokenClassification"),
+        ("esm", "TFEsmForTokenClassification"),
         ("flaubert", "TFFlaubertForTokenClassification"),
         ("funnel", "TFFunnelForTokenClassification"),
         ("layoutlm", "TFLayoutLMForTokenClassification"),

diff --git a/src/transformers/models/auto/tokenization_auto.py b/src/transformers/models/auto/tokenization_auto.py
@@ -122,6 +122,7 @@
             ),
             ("electra", ("ElectraTokenizer", "ElectraTokenizerFast" if is_tokenizers_available() else None)),
             ("ernie", ("BertTokenizer", "BertTokenizerFast" if is_tokenizers_available() else None)),
+            ("esm", ("EsmTokenizer", None)),
             ("flaubert", ("FlaubertTokenizer", None)),
             ("fnet", ("FNetTokenizer", "FNetTokenizerFast" if is_tokenizers_available() else None)),
             ("fsmt", ("FSMTTokenizer", None)),

diff --git a/src/transformers/models/esm/__init__.py b/src/transformers/models/esm/__init__.py
@@ -17,7 +17,7 @@
 # limitations under the License.
 from typing import TYPE_CHECKING
 
-from ...utils import OptionalDependencyNotAvailable, _LazyModule, is_torch_available
+from ...utils import OptionalDependencyNotAvailable, _LazyModule, is_tf_available, is_torch_available
 
 
 _import_structure = {
@@ -40,6 +40,21 @@
         "EsmPreTrainedModel",
     ]
 
+try:
+    if not is_tf_available():
+        raise OptionalDependencyNotAvailable()
+except OptionalDependencyNotAvailable:
+    pass
+else:
+    _import_structure["modeling_tf_esm"] = [
+        "TF_ESM_PRETRAINED_MODEL_ARCHIVE_LIST",
+        "TFEsmForMaskedLM",
+        "TFEsmForSequenceClassification",
+        "TFEsmForTokenClassification",
+        "TFEsmModel",
+        "TFEsmPreTrainedModel",
+    ]
+
 
 if TYPE_CHECKING:
     from .configuration_esm import ESM_PRETRAINED_CONFIG_ARCHIVE_MAP, EsmConfig
@@ -60,6 +75,21 @@
             EsmPreTrainedModel,
         )
 
+    try:
+        if not is_tf_available():
+            raise OptionalDependencyNotAvailable()
+    except OptionalDependencyNotAvailable:
+        pass
+    else:
+        from .modeling_tf_esm import (
+            TF_ESM_PRETRAINED_MODEL_ARCHIVE_LIST,
+            TFEsmForMaskedLM,
+            TFEsmForSequenceClassification,
+            TFEsmForTokenClassification,
+            TFEsmModel,
+            TFEsmPreTrainedModel,
+        )
+
 
 else:
     import sys

diff --git a/src/transformers/models/esm/modeling_esm.py b/src/transformers/models/esm/modeling_esm.py
@@ -1,5 +1,5 @@
 # coding=utf-8
-# Copyright 2022 Facebook and The HuggingFace Inc. team. All rights reserved.
+# Copyright 2022 Meta and The HuggingFace Inc. team. All rights reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -42,12 +42,14 @@
 
 logger = logging.get_logger(__name__)
 
-_CHECKPOINT_FOR_DOC = "facebook/esm-1b"
+_CHECKPOINT_FOR_DOC = "Rocketknight1/esm2_t6_8M_UR50D"
 _CONFIG_FOR_DOC = "EsmConfig"
 _TOKENIZER_FOR_DOC = "EsmTokenizer"
 
 ESM_PRETRAINED_MODEL_ARCHIVE_LIST = [
-    "facebook/esm-1b",
+    "Rocketknight1/esm2_t6_8M_UR50D",
+    "Rocketknight1/esm2_t12_35M_UR50D",
+    # This is not a complete list of all ESM models!
     # See all ESM models at https://huggingface.co/models?filter=esm
 ]
 
@@ -115,7 +117,6 @@ class EsmEmbeddings(nn.Module):
     def __init__(self, config):
         super().__init__()
         self.word_embeddings = nn.Embedding(config.vocab_size, config.hidden_size, padding_idx=config.pad_token_id)
-        self.position_embeddings = nn.Embedding(config.max_position_embeddings, config.hidden_size)
 
         if config.emb_layer_norm_before:
             self.layer_norm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
@@ -658,15 +659,6 @@ def _init_weights(self, module):
             module.bias.data.zero_()
             module.weight.data.fill_(1.0)
 
-    def update_keys_to_ignore(self, config, del_keys_to_ignore):
-        """Remove some keys from ignore list"""
-        if not config.tie_word_embeddings:
-            # must make a new list, or the class variable gets modified!
-            self._keys_to_ignore_on_save = [k for k in self._keys_to_ignore_on_save if k not in del_keys_to_ignore]
-            self._keys_to_ignore_on_load_missing = [
-                k for k in self._keys_to_ignore_on_load_missing if k not in del_keys_to_ignore
-            ]
-
 
 ESM_START_DOCSTRING = r"""
 
@@ -907,8 +899,7 @@ def forward(
 
 @add_start_docstrings("""ESM Model with a `language modeling` head on top.""", ESM_START_DOCSTRING)
 class EsmForMaskedLM(EsmPreTrainedModel):
-    _keys_to_ignore_on_save = [r"lm_head.decoder.weight", r"lm_head.decoder.bias"]
-    _keys_to_ignore_on_load_missing = [r"position_ids", r"lm_head.decoder.weight", r"lm_head.decoder.bias"]
+    _keys_to_ignore_on_load_missing = [r"position_ids"]
     _keys_to_ignore_on_load_unexpected = [r"pooler"]
 
     def __init__(self, config):
@@ -923,9 +914,6 @@ def __init__(self, config):
         self.esm = EsmModel(config, add_pooling_layer=False)
         self.lm_head = EsmLMHead(config)
 
-        # The LM head weights require special treatment only when they are tied with the word embeddings
-        self.update_keys_to_ignore(config, ["lm_head.decoder.weight"])
-
         self.init_weights()
 
     def get_output_embeddings(self):
@@ -944,17 +932,17 @@ def set_output_embeddings(self, new_embeddings):
     )
     def forward(
         self,
-        input_ids=None,
-        attention_mask=None,
-        position_ids=None,
-        head_mask=None,
-        inputs_embeds=None,
-        encoder_hidden_states=None,
-        encoder_attention_mask=None,
-        labels=None,
-        output_attentions=None,
-        output_hidden_states=None,
-        return_dict=None,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.Tensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
     ):
         r"""
         labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
@@ -1009,17 +997,13 @@ def __init__(self, config):
         self.decoder = nn.Linear(config.hidden_size, config.vocab_size, bias=False)
         self.bias = nn.Parameter(torch.zeros(config.vocab_size))
 
-        # Need a link between the two variables so that the bias is correctly resized with `resize_token_embeddings`
-        self.decoder.bias = self.bias
-
     def forward(self, features, **kwargs):
         x = self.dense(features)
         x = gelu(x)
         x = self.layer_norm(x)
 
         # project back to size of vocabulary with bias
-        x = self.decoder(x)
-
+        x = self.decoder(x) + self.bias
         return x
 
 
@@ -1052,15 +1036,15 @@ def __init__(self, config):
     )
     def forward(
         self,
-        input_ids=None,
-        attention_mask=None,
-        position_ids=None,
-        head_mask=None,
-        inputs_embeds=None,
-        labels=None,
-        output_attentions=None,
-        output_hidden_states=None,
-        return_dict=None,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
     ):
         r"""
         labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
@@ -1148,15 +1132,15 @@ def __init__(self, config):
     )
     def forward(
         self,
-        input_ids=None,
-        attention_mask=None,
-        position_ids=None,
-        head_mask=None,
-        inputs_embeds=None,
-        labels=None,
-        output_attentions=None,
-        output_hidden_states=None,
-        return_dict=None,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
     ):
         r"""
         labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):