init

transformers/tests/models/esm/test_modeling_esmfold.py

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+# 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, is_flaky, 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 ()
+    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)
+
+    @is_flaky(
+        description="The computed `s = s / norm_denom` in `EsmFoldAngleResnet` is numerically instable if `norm_denom` is very small."
+    )
+    def test_batching_equivalence(self):
+        super().test_batching_equivalence()
+
+    @unittest.skip(reason="Does not support attention outputs")
+    def test_attention_outputs(self):
+        pass
+
+    @unittest.skip
+    def test_correct_missing_keys(self):
+        pass
+
+    @unittest.skip(reason="Esm does not support embedding resizing")
+    def test_resize_embeddings_untied(self):
+        pass
+
+    @unittest.skip(reason="Esm does not support embedding resizing")
+    def test_resize_tokens_embeddings(self):
+        pass
+
+    @unittest.skip(reason="ESMFold does not support passing input embeds!")
+    def test_inputs_embeds(self):
+        pass
+
+    @unittest.skip(reason="ESMFold does not support head pruning.")
+    def test_head_pruning(self):
+        pass
+
+    @unittest.skip(reason="ESMFold does not support head pruning.")
+    def test_head_pruning_integration(self):
+        pass
+
+    @unittest.skip(reason="ESMFold does not support head pruning.")
+    def test_head_pruning_save_load_from_config_init(self):
+        pass
+
+    @unittest.skip(reason="ESMFold does not support head pruning.")
+    def test_head_pruning_save_load_from_pretrained(self):
+        pass
+
+    @unittest.skip(reason="ESMFold does not support head pruning.")
+    def test_headmasking(self):
+        pass
+
+    @unittest.skip(reason="ESMFold does not output hidden states in the normal way.")
+    def test_hidden_states_output(self):
+        pass
+
+    @unittest.skip(reason="ESMfold does not output hidden states in the normal way.")
+    def test_retain_grad_hidden_states_attentions(self):
+        pass
+
+    @unittest.skip(reason="ESMFold only has one output format.")
+    def test_model_outputs_equivalence(self):
+        pass
+
+    @unittest.skip(reason="ESMFold does not support input chunking.")
+    def test_feed_forward_chunking(self):
+        pass
+
+    @unittest.skip(
+        reason="ESMFold doesn't respect you and it certainly doesn't respect your initialization arguments."
+    )
+    def test_initialization(self):
+        pass
+
+    @unittest.skip(reason="ESMFold doesn't support torchscript compilation.")
+    def test_torchscript_output_attentions(self):
+        pass
+
+    @unittest.skip(reason="ESMFold doesn't support torchscript compilation.")
+    def test_torchscript_output_hidden_state(self):
+        pass
+
+    @unittest.skip(reason="ESMFold doesn't support torchscript compilation.")
+    def test_torchscript_simple(self):
+        pass
+
+    @unittest.skip(reason="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)
+        torch.testing.assert_close(position_outputs[0, 0, 0, 0], expected_slice, rtol=1e-4, atol=1e-4)