Add BioGPTForSequenceClassification (#22253)

* added BioGptForSequenceClassification

* added source of copied code

* typo

* Format code with black

* Update comments for copied code

* Remove code copy comment

* Apply suggestions from code review

Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>
Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com>

* Fix failing tests

* Update code copied from comments

* Fix code quality

* Update src/transformers/models/biogpt/modeling_biogpt.py

Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com>

* Fix lint error

* Update src/transformers/models/biogpt/modeling_biogpt.py

Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com>

* Rename model to biogpt for consistency

* Add PipelineTesterMixin to test_modeling_biogpt.py

* Apply suggestions from code review

Co-authored-by: amyeroberts <22614925+amyeroberts@users.noreply.github.com>

* Resolve merge confict

---------

Co-authored-by: Guillem García Subies <37592763+GuillemGSubies@users.noreply.github.com>
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>
Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com>
Co-authored-by: amyeroberts <22614925+amyeroberts@users.noreply.github.com>

docs/source/en/model_doc/biogpt.mdx

@@ -55,7 +55,14 @@ This model was contributed by [kamalkraj](https://huggingface.co/kamalkraj). The
 [[autodoc]] BioGptForCausalLM
     - forward
 
+    
 ## BioGptForTokenClassification
 
 [[autodoc]] BioGptForTokenClassification
     - forward
+
+
+## BioGptForSequenceClassification
+
+[[autodoc]] BioGptForSequenceClassification
+    - forward

docs/source/en/tasks/sequence_classification.mdx

@@ -28,7 +28,7 @@ The task illustrated in this tutorial is supported by the following model archit
 
 <!--This tip is automatically generated by `make fix-copies`, do not fill manually!-->
 
-[ALBERT](../model_doc/albert), [BART](../model_doc/bart), [BERT](../model_doc/bert), [BigBird](../model_doc/big_bird), [BigBird-Pegasus](../model_doc/bigbird_pegasus), [BLOOM](../model_doc/bloom), [CamemBERT](../model_doc/camembert), [CANINE](../model_doc/canine), [ConvBERT](../model_doc/convbert), [CTRL](../model_doc/ctrl), [Data2VecText](../model_doc/data2vec-text), [DeBERTa](../model_doc/deberta), [DeBERTa-v2](../model_doc/deberta-v2), [DistilBERT](../model_doc/distilbert), [ELECTRA](../model_doc/electra), [ERNIE](../model_doc/ernie), [ErnieM](../model_doc/ernie_m), [ESM](../model_doc/esm), [FlauBERT](../model_doc/flaubert), [FNet](../model_doc/fnet), [Funnel Transformer](../model_doc/funnel), [GPT-Sw3](../model_doc/gpt-sw3), [OpenAI GPT-2](../model_doc/gpt2), [GPTBigCode](../model_doc/gpt_bigcode), [GPT Neo](../model_doc/gpt_neo), [GPT NeoX](../model_doc/gpt_neox), [GPT-J](../model_doc/gptj), [I-BERT](../model_doc/ibert), [LayoutLM](../model_doc/layoutlm), [LayoutLMv2](../model_doc/layoutlmv2), [LayoutLMv3](../model_doc/layoutlmv3), [LED](../model_doc/led), [LiLT](../model_doc/lilt), [LLaMA](../model_doc/llama), [Longformer](../model_doc/longformer), [LUKE](../model_doc/luke), [MarkupLM](../model_doc/markuplm), [mBART](../model_doc/mbart), [MEGA](../model_doc/mega), [Megatron-BERT](../model_doc/megatron-bert), [MobileBERT](../model_doc/mobilebert), [MPNet](../model_doc/mpnet), [MVP](../model_doc/mvp), [Nezha](../model_doc/nezha), [Nyströmformer](../model_doc/nystromformer), [OpenLlama](../model_doc/open-llama), [OpenAI GPT](../model_doc/openai-gpt), [OPT](../model_doc/opt), [Perceiver](../model_doc/perceiver), [PLBart](../model_doc/plbart), [QDQBert](../model_doc/qdqbert), [Reformer](../model_doc/reformer), [RemBERT](../model_doc/rembert), [RoBERTa](../model_doc/roberta), [RoBERTa-PreLayerNorm](../model_doc/roberta-prelayernorm), [RoCBert](../model_doc/roc_bert), [RoFormer](../model_doc/roformer), [SqueezeBERT](../model_doc/squeezebert), [TAPAS](../model_doc/tapas), [Transformer-XL](../model_doc/transfo-xl), [XLM](../model_doc/xlm), [XLM-RoBERTa](../model_doc/xlm-roberta), [XLM-RoBERTa-XL](../model_doc/xlm-roberta-xl), [XLNet](../model_doc/xlnet), [X-MOD](../model_doc/xmod), [YOSO](../model_doc/yoso)
+[ALBERT](../model_doc/albert), [BART](../model_doc/bart), [BERT](../model_doc/bert), [BigBird](../model_doc/big_bird), [BigBird-Pegasus](../model_doc/bigbird_pegasus), [BioGpt](../model_doc/biogpt), [BLOOM](../model_doc/bloom), [CamemBERT](../model_doc/camembert), [CANINE](../model_doc/canine), [ConvBERT](../model_doc/convbert), [CTRL](../model_doc/ctrl), [Data2VecText](../model_doc/data2vec-text), [DeBERTa](../model_doc/deberta), [DeBERTa-v2](../model_doc/deberta-v2), [DistilBERT](../model_doc/distilbert), [ELECTRA](../model_doc/electra), [ERNIE](../model_doc/ernie), [ErnieM](../model_doc/ernie_m), [ESM](../model_doc/esm), [FlauBERT](../model_doc/flaubert), [FNet](../model_doc/fnet), [Funnel Transformer](../model_doc/funnel), [GPT-Sw3](../model_doc/gpt-sw3), [OpenAI GPT-2](../model_doc/gpt2), [GPTBigCode](../model_doc/gpt_bigcode), [GPT Neo](../model_doc/gpt_neo), [GPT NeoX](../model_doc/gpt_neox), [GPT-J](../model_doc/gptj), [I-BERT](../model_doc/ibert), [LayoutLM](../model_doc/layoutlm), [LayoutLMv2](../model_doc/layoutlmv2), [LayoutLMv3](../model_doc/layoutlmv3), [LED](../model_doc/led), [LiLT](../model_doc/lilt), [LLaMA](../model_doc/llama), [Longformer](../model_doc/longformer), [LUKE](../model_doc/luke), [MarkupLM](../model_doc/markuplm), [mBART](../model_doc/mbart), [MEGA](../model_doc/mega), [Megatron-BERT](../model_doc/megatron-bert), [MobileBERT](../model_doc/mobilebert), [MPNet](../model_doc/mpnet), [MVP](../model_doc/mvp), [Nezha](../model_doc/nezha), [Nyströmformer](../model_doc/nystromformer), [OpenLlama](../model_doc/open-llama), [OpenAI GPT](../model_doc/openai-gpt), [OPT](../model_doc/opt), [Perceiver](../model_doc/perceiver), [PLBart](../model_doc/plbart), [QDQBert](../model_doc/qdqbert), [Reformer](../model_doc/reformer), [RemBERT](../model_doc/rembert), [RoBERTa](../model_doc/roberta), [RoBERTa-PreLayerNorm](../model_doc/roberta-prelayernorm), [RoCBert](../model_doc/roc_bert), [RoFormer](../model_doc/roformer), [SqueezeBERT](../model_doc/squeezebert), [TAPAS](../model_doc/tapas), [Transformer-XL](../model_doc/transfo-xl), [XLM](../model_doc/xlm), [XLM-RoBERTa](../model_doc/xlm-roberta), [XLM-RoBERTa-XL](../model_doc/xlm-roberta-xl), [XLNet](../model_doc/xlnet), [X-MOD](../model_doc/xmod), [YOSO](../model_doc/yoso)
 
 
 <!--End of the generated tip-->

src/transformers/__init__.py

@@ -1147,6 +1147,7 @@ else:
         [
             "BIOGPT_PRETRAINED_MODEL_ARCHIVE_LIST",
             "BioGptForCausalLM",
+            "BioGptForSequenceClassification",
             "BioGptForTokenClassification",
             "BioGptModel",
             "BioGptPreTrainedModel",
@@ -4792,6 +4793,7 @@ if TYPE_CHECKING:
         from .models.biogpt import (
             BIOGPT_PRETRAINED_MODEL_ARCHIVE_LIST,
             BioGptForCausalLM,
+            BioGptForSequenceClassification,
             BioGptForTokenClassification,
             BioGptModel,
             BioGptPreTrainedModel,

src/transformers/models/auto/modeling_auto.py

@@ -648,6 +648,7 @@ MODEL_FOR_SEQUENCE_CLASSIFICATION_MAPPING_NAMES = OrderedDict(
         ("bert", "BertForSequenceClassification"),
         ("big_bird", "BigBirdForSequenceClassification"),
         ("bigbird_pegasus", "BigBirdPegasusForSequenceClassification"),
+        ("biogpt", "BioGptForSequenceClassification"),
         ("bloom", "BloomForSequenceClassification"),
         ("camembert", "CamembertForSequenceClassification"),
         ("canine", "CanineForSequenceClassification"),

src/transformers/models/biogpt/__init__.py

@@ -31,6 +31,7 @@ else:
         "BIOGPT_PRETRAINED_MODEL_ARCHIVE_LIST",
         "BioGptForCausalLM",
         "BioGptForTokenClassification",
+        "BioGptForSequenceClassification",
         "BioGptModel",
         "BioGptPreTrainedModel",
     ]
@@ -49,6 +50,7 @@ if TYPE_CHECKING:
         from .modeling_biogpt import (
             BIOGPT_PRETRAINED_MODEL_ARCHIVE_LIST,
             BioGptForCausalLM,
+            BioGptForSequenceClassification,
             BioGptForTokenClassification,
             BioGptModel,
             BioGptPreTrainedModel,

src/transformers/models/biogpt/modeling_biogpt.py

@@ -22,16 +22,22 @@ from typing import Optional, Tuple, Union
 import torch
 import torch.utils.checkpoint
 from torch import nn
-from torch.nn import CrossEntropyLoss
+from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
 
 from ...activations import ACT2FN
 from ...modeling_outputs import (
     BaseModelOutputWithPastAndCrossAttentions,
     CausalLMOutputWithCrossAttentions,
+    SequenceClassifierOutputWithPast,
     TokenClassifierOutput,
 )
 from ...modeling_utils import PreTrainedModel
-from ...utils import add_code_sample_docstrings, add_start_docstrings, add_start_docstrings_to_model_forward, logging
+from ...utils import (
+    add_code_sample_docstrings,
+    add_start_docstrings,
+    add_start_docstrings_to_model_forward,
+    logging,
+)
 from .configuration_biogpt import BioGptConfig
 
 
@@ -40,8 +46,10 @@ logger = logging.get_logger(__name__)
 _CHECKPOINT_FOR_DOC = "microsoft/biogpt"
 _CONFIG_FOR_DOC = "BioGptConfig"
 
+
 BIOGPT_PRETRAINED_MODEL_ARCHIVE_LIST = [
     "microsoft/biogpt",
+    "microsoft/BioGPT-Large",
     # See all BioGPT models at https://huggingface.co/models?filter=biogpt
 ]
 
@@ -832,3 +840,129 @@ class BioGptForTokenClassification(BioGptPreTrainedModel):
             hidden_states=transformer_outputs.hidden_states,
             attentions=transformer_outputs.attentions,
         )
+
+
+@add_start_docstrings(
+    """
+    The BioGpt Model transformer with a sequence classification head on top (linear layer).
+
+    [`BioGptForSequenceClassification`] uses the last token in order to do the classification, as other causal models
+    (e.g. GPT-2) do.
+
+    Since it does classification on the last token, it is required to know the position of the last token. If a
+    `pad_token_id` is defined in the configuration, it finds the last token that is not a padding token in each row. If
+    no `pad_token_id` is defined, it simply takes the last value in each row of the batch. Since it cannot guess the
+    padding tokens when `inputs_embeds` are passed instead of `input_ids`, it does the same (take the last value in
+    each row of the batch).
+    """,
+    BIOGPT_START_DOCSTRING,
+)
+class BioGptForSequenceClassification(BioGptPreTrainedModel):
+    def __init__(self, config: BioGptConfig):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        self.biogpt = BioGptModel(config)
+        self.score = nn.Linear(config.hidden_size, self.num_labels, bias=False)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    @add_start_docstrings_to_model_forward(BIOGPT_INPUTS_DOCSTRING)
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=SequenceClassifierOutputWithPast,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        past_key_values: Optional[Tuple[Tuple[torch.Tensor]]] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, SequenceClassifierOutputWithPast]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the sequence classification/regression loss. Indices should be in `[0, ...,
+            config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
+            `config.num_labels > 1` a classification loss is computed (Cross-Entropy).
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        transformer_outputs = self.biogpt(
+            input_ids,
+            past_key_values=past_key_values,
+            attention_mask=attention_mask,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        hidden_states = transformer_outputs[0]
+        logits = self.score(hidden_states)
+
+        if input_ids is not None:
+            batch_size, sequence_length = input_ids.shape[:2]
+        else:
+            batch_size, sequence_length = inputs_embeds.shape[:2]
+
+        if self.config.pad_token_id is None:
+            sequence_length = -1
+        else:
+            if input_ids is not None:
+                sequence_length = (torch.ne(input_ids, self.config.pad_token_id).sum(-1) - 1).to(logits.device)
+            else:
+                sequence_length = -1
+                logger.warning(
+                    f"{self.__class__.__name__} will not detect padding tokens in `inputs_embeds`. Results may be "
+                    "unexpected if using padding tokens in conjunction with `inputs_embeds.`"
+                )
+
+        pooled_logits = logits[torch.arange(batch_size, device=logits.device), sequence_length]
+
+        loss = None
+        if labels is not None:
+            if self.config.problem_type is None:
+                if self.num_labels == 1:
+                    self.config.problem_type = "regression"
+                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
+                    self.config.problem_type = "single_label_classification"
+                else:
+                    self.config.problem_type = "multi_label_classification"
+
+            if self.config.problem_type == "regression":
+                loss_fct = MSELoss()
+                if self.num_labels == 1:
+                    loss = loss_fct(pooled_logits.squeeze(), labels.squeeze())
+                else:
+                    loss = loss_fct(pooled_logits, labels)
+            elif self.config.problem_type == "single_label_classification":
+                loss_fct = CrossEntropyLoss()
+                loss = loss_fct(pooled_logits.view(-1, self.num_labels), labels.view(-1))
+            elif self.config.problem_type == "multi_label_classification":
+                loss_fct = BCEWithLogitsLoss()
+                loss = loss_fct(pooled_logits, labels)
+        if not return_dict:
+            output = (pooled_logits,) + transformer_outputs[1:]
+            return ((loss,) + output) if loss is not None else output
+
+        return SequenceClassifierOutputWithPast(
+            loss=loss,
+            logits=pooled_logits,
+            past_key_values=transformer_outputs.past_key_values,
+            hidden_states=transformer_outputs.hidden_states,
+            attentions=transformer_outputs.attentions,
+        )
+
+    def get_input_embeddings(self):
+        return self.biogpt.embed_tokens
+
+    def set_input_embeddings(self, value):
+        self.biogpt.embed_tokens = value

src/transformers/utils/dummy_pt_objects.py

@@ -1103,6 +1103,13 @@ class BioGptForCausalLM(metaclass=DummyObject):
         requires_backends(self, ["torch"])
 
 
+class BioGptForSequenceClassification(metaclass=DummyObject):
+    _backends = ["torch"]
+
+    def __init__(self, *args, **kwargs):
+        requires_backends(self, ["torch"])
+
+
 class BioGptForTokenClassification(metaclass=DummyObject):
     _backends = ["torch"]
 

tests/models/biogpt/test_modeling_biogpt.py

@@ -29,7 +29,13 @@ from ...test_pipeline_mixin import PipelineTesterMixin
 if is_torch_available():
     import torch
 
-    from transformers import BioGptForCausalLM, BioGptForTokenClassification, BioGptModel, BioGptTokenizer
+    from transformers import (
+        BioGptForCausalLM,
+        BioGptForSequenceClassification,
+        BioGptForTokenClassification,
+        BioGptModel,
+        BioGptTokenizer,
+    )
     from transformers.models.biogpt.modeling_biogpt import BIOGPT_PRETRAINED_MODEL_ARCHIVE_LIST
 
 
@@ -274,13 +280,18 @@ class BioGptModelTester:
 
 @require_torch
 class BioGptModelTest(ModelTesterMixin, GenerationTesterMixin, PipelineTesterMixin, unittest.TestCase):
-    all_model_classes = (BioGptModel, BioGptForCausalLM, BioGptForTokenClassification) if is_torch_available() else ()
+    all_model_classes = (
+        (BioGptModel, BioGptForCausalLM, BioGptForSequenceClassification, BioGptForTokenClassification)
+        if is_torch_available()
+        else ()
+    )
     all_generative_model_classes = (BioGptForCausalLM,) if is_torch_available() else ()
     pipeline_model_mapping = (
         {
             "feature-extraction": BioGptModel,
             "text-generation": BioGptForCausalLM,
             "token-classification": BioGptForTokenClassification,
+            "text-classification": BioGptForSequenceClassification,
         }
         if is_torch_available()
         else {}
@@ -374,6 +385,35 @@ class BioGptModelTest(ModelTesterMixin, GenerationTesterMixin, PipelineTesterMix
             model = BioGptModel.from_pretrained(model_name)
             self.assertIsNotNone(model)
 
+    # Copied from tests.models.opt.test_modeling_opt.OPTModelTest with OPT->BioGpt, prepare_config_and_inputs-> prepare_config_and_inputs_for_common
+    def test_biogpt_sequence_classification_model(self):
+        config, input_dict = self.model_tester.prepare_config_and_inputs_for_common()
+        config.num_labels = 3
+        input_ids = input_dict["input_ids"]
+        attention_mask = input_ids.ne(1).to(torch_device)
+        sequence_labels = ids_tensor([self.model_tester.batch_size], self.model_tester.type_sequence_label_size)
+        model = BioGptForSequenceClassification(config)
+        model.to(torch_device)
+        model.eval()
+        result = model(input_ids, attention_mask=attention_mask, labels=sequence_labels)
+        self.assertEqual(result.logits.shape, (self.model_tester.batch_size, self.model_tester.num_labels))
+
+    # Copied from tests.models.opt.test_modeling_opt.OPTModelTest with OPT->BioGpt, prepare_config_and_inputs-> prepare_config_and_inputs_for_common
+    def test_biogpt_sequence_classification_model_for_multi_label(self):
+        config, input_dict = self.model_tester.prepare_config_and_inputs_for_common()
+        config.num_labels = 3
+        config.problem_type = "multi_label_classification"
+        input_ids = input_dict["input_ids"]
+        attention_mask = input_ids.ne(1).to(torch_device)
+        sequence_labels = ids_tensor(
+            [self.model_tester.batch_size, config.num_labels], self.model_tester.type_sequence_label_size
+        ).to(torch.float)
+        model = BioGptForSequenceClassification(config)
+        model.to(torch_device)
+        model.eval()
+        result = model(input_ids, attention_mask=attention_mask, labels=sequence_labels)
+        self.assertEqual(result.logits.shape, (self.model_tester.batch_size, self.model_tester.num_labels))
+
 
 @require_torch
 class BioGptModelIntegrationTest(unittest.TestCase):