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# 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))
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