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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.
""" Testing suite for the PyTorch ESM model. """
import unittest
from transformers import EsmConfig, is_torch_available
from transformers.testing_utils import TestCasePlus, require_torch, slow, torch_device
from ...test_configuration_common import ConfigTester
from ...test_modeling_common import ModelTesterMixin, ids_tensor, random_attention_mask
from ...test_pipeline_mixin import PipelineTesterMixin
if is_torch_available():
import torch
from transformers.models.esm.modeling_esmfold import EsmForProteinFolding
class EsmFoldModelTester:
def __init__(
self,
parent,
batch_size=13,
seq_length=7,
is_training=False,
use_input_mask=True,
use_token_type_ids=False,
use_labels=False,
vocab_size=19,
hidden_size=32,
num_hidden_layers=2,
num_attention_heads=4,
intermediate_size=37,
hidden_act="gelu",
hidden_dropout_prob=0.1,
attention_probs_dropout_prob=0.1,
max_position_embeddings=512,
type_vocab_size=16,
type_sequence_label_size=2,
initializer_range=0.02,
num_labels=3,
num_choices=4,
scope=None,
):
self.parent = parent
self.batch_size = batch_size
self.seq_length = seq_length
self.is_training = is_training
self.use_input_mask = use_input_mask
self.use_token_type_ids = use_token_type_ids
self.use_labels = use_labels
self.vocab_size = vocab_size
self.hidden_size = hidden_size
self.num_hidden_layers = num_hidden_layers
self.num_attention_heads = num_attention_heads
self.intermediate_size = intermediate_size
self.hidden_act = hidden_act
self.hidden_dropout_prob = hidden_dropout_prob
self.attention_probs_dropout_prob = attention_probs_dropout_prob
self.max_position_embeddings = max_position_embeddings
self.type_vocab_size = type_vocab_size
self.type_sequence_label_size = type_sequence_label_size
self.initializer_range = initializer_range
self.num_labels = num_labels
self.num_choices = num_choices
self.scope = scope
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 = self.get_config()
return config, input_ids, input_mask, sequence_labels, token_labels, choice_labels
def get_config(self):
esmfold_config = {
"trunk": {
"num_blocks": 2,
"sequence_state_dim": 64,
"pairwise_state_dim": 16,
"sequence_head_width": 4,
"pairwise_head_width": 4,
"position_bins": 4,
"chunk_size": 16,
"structure_module": {
"ipa_dim": 16,
"num_angles": 7,
"num_blocks": 2,
"num_heads_ipa": 4,
"pairwise_dim": 16,
"resnet_dim": 16,
"sequence_dim": 48,
},
},
"fp16_esm": False,
"lddt_head_hid_dim": 16,
}
config = EsmConfig(
vocab_size=33,
hidden_size=self.hidden_size,
pad_token_id=1,
num_hidden_layers=self.num_hidden_layers,
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,
is_folding_model=True,
esmfold_config=esmfold_config,
)
return config
def create_and_check_model(self, config, input_ids, input_mask, sequence_labels, token_labels, choice_labels):
model = EsmForProteinFolding(config=config).float()
model.to(torch_device)
model.eval()
result = model(input_ids, attention_mask=input_mask)
result = model(input_ids)
result = model(input_ids)
self.parent.assertEqual(result.positions.shape, (2, self.batch_size, self.seq_length, 14, 3))
self.parent.assertEqual(result.angles.shape, (2, self.batch_size, self.seq_length, 7, 2))
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_torch
class EsmFoldModelTest(ModelTesterMixin, PipelineTesterMixin, unittest.TestCase):
test_mismatched_shapes = False
all_model_classes = (EsmForProteinFolding,) if is_torch_available() else ()
all_generative_model_classes = ()
pipeline_model_mapping = {} if is_torch_available() else {}
test_sequence_classification_problem_types = False
def setUp(self):
self.model_tester = EsmFoldModelTester(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):
config_and_inputs = self.model_tester.prepare_config_and_inputs()
self.model_tester.create_and_check_model(*config_and_inputs)
@unittest.skip("Does not support attention outputs")
def test_attention_outputs(self):
pass
@unittest.skip
def test_correct_missing_keys(self):
pass
@unittest.skip("Esm does not support embedding resizing")
def test_resize_embeddings_untied(self):
pass
@unittest.skip("Esm does not support embedding resizing")
def test_resize_tokens_embeddings(self):
pass
@unittest.skip("ESMFold does not support passing input embeds!")
def test_inputs_embeds(self):
pass
@unittest.skip("ESMFold does not support head pruning.")
def test_head_pruning(self):
pass
@unittest.skip("ESMFold does not support head pruning.")
def test_head_pruning_integration(self):
pass
@unittest.skip("ESMFold does not support head pruning.")
def test_head_pruning_save_load_from_config_init(self):
pass
@unittest.skip("ESMFold does not support head pruning.")
def test_head_pruning_save_load_from_pretrained(self):
pass
@unittest.skip("ESMFold does not support head pruning.")
def test_headmasking(self):
pass
@unittest.skip("ESMFold does not output hidden states in the normal way.")
def test_hidden_states_output(self):
pass
@unittest.skip("ESMfold does not output hidden states in the normal way.")
def test_retain_grad_hidden_states_attentions(self):
pass
@unittest.skip("ESMFold only has one output format.")
def test_model_outputs_equivalence(self):
pass
@unittest.skip("This test doesn't work for ESMFold and doesn't test core functionality")
def test_save_load_fast_init_from_base(self):
pass
@unittest.skip("ESMFold does not support input chunking.")
def test_feed_forward_chunking(self):
pass
@unittest.skip("ESMFold doesn't respect you and it certainly doesn't respect your initialization arguments.")
def test_initialization(self):
pass
@unittest.skip("ESMFold doesn't support torchscript compilation.")
def test_torchscript_output_attentions(self):
pass
@unittest.skip("ESMFold doesn't support torchscript compilation.")
def test_torchscript_output_hidden_state(self):
pass
@unittest.skip("ESMFold doesn't support torchscript compilation.")
def test_torchscript_simple(self):
pass
@unittest.skip("ESMFold doesn't support data parallel.")
def test_multi_gpu_data_parallel_forward(self):
pass
@require_torch
class EsmModelIntegrationTest(TestCasePlus):
@slow
def test_inference_protein_folding(self):
model = EsmForProteinFolding.from_pretrained("facebook/esmfold_v1").float()
model.eval()
input_ids = torch.tensor([[0, 6, 4, 13, 5, 4, 16, 12, 11, 7, 2]])
position_outputs = model(input_ids)["positions"]
expected_slice = torch.tensor([2.5828, 0.7993, -10.9334], dtype=torch.float32)
self.assertTrue(torch.allclose(position_outputs[0, 0, 0, 0], expected_slice, atol=1e-4))
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