Spaces:
Runtime error
Runtime error
File size: 9,923 Bytes
96e9536 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 |
# 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))
|