# coding=utf-8 # Copyright 2022 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. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. from __future__ import annotations import unittest from transformers import EsmConfig, is_tf_available from transformers.testing_utils import require_tf, slow from ...test_configuration_common import ConfigTester from ...test_modeling_tf_common import TFModelTesterMixin, floats_tensor, ids_tensor, random_attention_mask from ...test_pipeline_mixin import PipelineTesterMixin if is_tf_available(): import numpy import tensorflow as tf from transformers.models.esm.modeling_tf_esm import ( TF_ESM_PRETRAINED_MODEL_ARCHIVE_LIST, TFEsmForMaskedLM, TFEsmForSequenceClassification, TFEsmForTokenClassification, TFEsmModel, ) # copied from tests.test_modeling_tf_roberta class TFEsmModelTester: def __init__( self, parent, ): self.parent = parent self.batch_size = 13 self.seq_length = 7 self.is_training = True self.use_input_mask = True self.use_labels = True self.vocab_size = 99 self.hidden_size = 32 self.num_hidden_layers = 2 self.num_attention_heads = 4 self.intermediate_size = 37 self.hidden_act = "gelu" self.hidden_dropout_prob = 0.1 self.attention_probs_dropout_prob = 0.1 self.max_position_embeddings = 512 self.type_vocab_size = 16 self.type_sequence_label_size = 2 self.initializer_range = 0.02 self.num_labels = 3 self.num_choices = 4 self.scope = None def prepare_config_and_inputs(self): input_ids = ids_tensor([self.batch_size, self.seq_length], self.vocab_size) input_mask = None if self.use_input_mask: input_mask = random_attention_mask([self.batch_size, self.seq_length]) sequence_labels = None token_labels = None choice_labels = None if self.use_labels: sequence_labels = ids_tensor([self.batch_size], self.type_sequence_label_size) token_labels = ids_tensor([self.batch_size, self.seq_length], self.num_labels) choice_labels = ids_tensor([self.batch_size], self.num_choices) config = EsmConfig( vocab_size=self.vocab_size, hidden_size=self.hidden_size, num_hidden_layers=self.num_hidden_layers, pad_token_id=1, num_attention_heads=self.num_attention_heads, intermediate_size=self.intermediate_size, hidden_act=self.hidden_act, hidden_dropout_prob=self.hidden_dropout_prob, attention_probs_dropout_prob=self.attention_probs_dropout_prob, max_position_embeddings=self.max_position_embeddings, type_vocab_size=self.type_vocab_size, initializer_range=self.initializer_range, ) return config, input_ids, input_mask, sequence_labels, token_labels, choice_labels def prepare_config_and_inputs_for_decoder(self): ( config, input_ids, input_mask, sequence_labels, token_labels, choice_labels, ) = self.prepare_config_and_inputs() config.is_decoder = True encoder_hidden_states = floats_tensor([self.batch_size, self.seq_length, self.hidden_size]) encoder_attention_mask = ids_tensor([self.batch_size, self.seq_length], vocab_size=2) return ( config, input_ids, input_mask, sequence_labels, token_labels, choice_labels, encoder_hidden_states, encoder_attention_mask, ) def create_and_check_model(self, config, input_ids, input_mask, sequence_labels, token_labels, choice_labels): model = TFEsmModel(config=config) inputs = {"input_ids": input_ids, "attention_mask": input_mask} result = model(inputs) inputs = [input_ids, input_mask] result = model(inputs) result = model(input_ids) self.parent.assertEqual(result.last_hidden_state.shape, (self.batch_size, self.seq_length, self.hidden_size)) def create_and_check_model_as_decoder( self, config, input_ids, input_mask, sequence_labels, token_labels, choice_labels, encoder_hidden_states, encoder_attention_mask, ): config.add_cross_attention = True model = TFEsmModel(config=config) inputs = { "input_ids": input_ids, "attention_mask": input_mask, "encoder_hidden_states": encoder_hidden_states, "encoder_attention_mask": encoder_attention_mask, } result = model(inputs) inputs = [input_ids, input_mask] result = model(inputs, encoder_hidden_states=encoder_hidden_states) # Also check the case where encoder outputs are not passed result = model(input_ids, attention_mask=input_mask) self.parent.assertEqual(result.last_hidden_state.shape, (self.batch_size, self.seq_length, self.hidden_size)) def create_and_check_for_masked_lm( self, config, input_ids, input_mask, sequence_labels, token_labels, choice_labels ): model = TFEsmForMaskedLM(config=config) result = model([input_ids, input_mask]) self.parent.assertEqual(result.logits.shape, (self.batch_size, self.seq_length, self.vocab_size)) def create_and_check_for_token_classification( self, config, input_ids, input_mask, sequence_labels, token_labels, choice_labels ): config.num_labels = self.num_labels model = TFEsmForTokenClassification(config=config) inputs = {"input_ids": input_ids, "attention_mask": input_mask} result = model(inputs) self.parent.assertEqual(result.logits.shape, (self.batch_size, self.seq_length, self.num_labels)) def prepare_config_and_inputs_for_common(self): config_and_inputs = self.prepare_config_and_inputs() ( config, input_ids, input_mask, sequence_labels, token_labels, choice_labels, ) = config_and_inputs inputs_dict = {"input_ids": input_ids, "attention_mask": input_mask} return config, inputs_dict @require_tf class TFEsmModelTest(TFModelTesterMixin, PipelineTesterMixin, unittest.TestCase): all_model_classes = ( ( TFEsmModel, TFEsmForMaskedLM, TFEsmForSequenceClassification, TFEsmForTokenClassification, ) if is_tf_available() else () ) pipeline_model_mapping = ( { "feature-extraction": TFEsmModel, "fill-mask": TFEsmForMaskedLM, "text-classification": TFEsmForSequenceClassification, "token-classification": TFEsmForTokenClassification, "zero-shot": TFEsmForSequenceClassification, } if is_tf_available() else {} ) test_head_masking = False test_onnx = False def setUp(self): self.model_tester = TFEsmModelTester(self) self.config_tester = ConfigTester(self, config_class=EsmConfig, hidden_size=37) def test_config(self): self.config_tester.run_common_tests() def test_model(self): """Test the base model""" config_and_inputs = self.model_tester.prepare_config_and_inputs() self.model_tester.create_and_check_model(*config_and_inputs) def test_model_as_decoder(self): """Test the base model as a decoder (of an encoder-decoder architecture) is_deocder=True + cross_attention + pass encoder outputs """ config_and_inputs = self.model_tester.prepare_config_and_inputs_for_decoder() self.model_tester.create_and_check_model_as_decoder(*config_and_inputs) def test_for_masked_lm(self): config_and_inputs = self.model_tester.prepare_config_and_inputs() self.model_tester.create_and_check_for_masked_lm(*config_and_inputs) def test_for_token_classification(self): config_and_inputs = self.model_tester.prepare_config_and_inputs() self.model_tester.create_and_check_for_token_classification(*config_and_inputs) @slow def test_model_from_pretrained(self): for model_name in TF_ESM_PRETRAINED_MODEL_ARCHIVE_LIST[:1]: model = TFEsmModel.from_pretrained(model_name) self.assertIsNotNone(model) @unittest.skip("Protein models do not support embedding resizing.") def test_resize_token_embeddings(self): pass @unittest.skip("Protein models do not support embedding resizing.") def test_save_load_after_resize_token_embeddings(self): pass def test_model_common_attributes(self): config, inputs_dict = self.model_tester.prepare_config_and_inputs_for_common() for model_class in self.all_model_classes: model = model_class(config) assert isinstance(model.get_input_embeddings(), tf.keras.layers.Layer) if model_class is TFEsmForMaskedLM: # Output embedding test differs from the main test because they're a matrix, not a layer name = model.get_bias() assert isinstance(name, dict) for k, v in name.items(): assert isinstance(v, tf.Variable) else: x = model.get_output_embeddings() assert x is None name = model.get_bias() assert name is None @require_tf class TFEsmModelIntegrationTest(unittest.TestCase): @slow def test_inference_masked_lm(self): model = TFEsmForMaskedLM.from_pretrained("facebook/esm2_t6_8M_UR50D") input_ids = tf.constant([[0, 1, 2, 3, 4, 5]]) output = model(input_ids)[0] expected_shape = [1, 6, 33] self.assertEqual(list(output.numpy().shape), expected_shape) # compare the actual values for a slice. expected_slice = tf.constant( [ [ [8.921518, -10.589814, -6.4671307], [-6.3967156, -13.911377, -1.1211915], [-7.781247, -13.951557, -3.740592], ] ] ) self.assertTrue(numpy.allclose(output[:, :3, :3].numpy(), expected_slice.numpy(), atol=1e-2)) @slow def test_inference_no_head(self): model = TFEsmModel.from_pretrained("facebook/esm2_t6_8M_UR50D") input_ids = tf.constant([[0, 6, 4, 13, 5, 4, 16, 12, 11, 7, 2]]) output = model(input_ids)[0] # compare the actual values for a slice. expected_slice = tf.constant( [ [ [0.14443092, 0.54125327, 0.3247739], [0.30340484, 0.00526676, 0.31077722], [0.32278043, -0.24987096, 0.3414628], ] ] ) self.assertTrue(numpy.allclose(output[:, :3, :3].numpy(), expected_slice.numpy(), atol=1e-4))