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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 BioGPT model. """
import math
import unittest
from transformers import BioGptConfig, is_torch_available
from transformers.testing_utils import require_torch, slow, torch_device
from ...generation.test_utils import GenerationTesterMixin
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 import BioGptForCausalLM, BioGptModel, BioGptTokenizer
from transformers.models.biogpt.modeling_biogpt import BIOGPT_PRETRAINED_MODEL_ARCHIVE_LIST
class BioGptModelTester:
def __init__(
self,
parent,
batch_size=13,
seq_length=7,
is_training=True,
use_input_mask=True,
use_token_type_ids=False,
use_labels=True,
vocab_size=99,
hidden_size=32,
num_hidden_layers=5,
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])
token_type_ids = None
if self.use_token_type_ids:
token_type_ids = ids_tensor([self.batch_size, self.seq_length], self.type_vocab_size)
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, token_type_ids, input_mask, sequence_labels, token_labels, choice_labels
def get_config(self):
return BioGptConfig(
vocab_size=self.vocab_size,
hidden_size=self.hidden_size,
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,
is_decoder=False,
initializer_range=self.initializer_range,
)
def create_and_check_model(
self, config, input_ids, token_type_ids, input_mask, sequence_labels, token_labels, choice_labels
):
model = BioGptModel(config=config)
model.to(torch_device)
model.eval()
result = model(input_ids, attention_mask=input_mask)
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_for_causal_lm(
self,
config,
input_ids,
token_type_ids,
input_mask,
sequence_labels,
token_labels,
choice_labels,
encoder_hidden_states,
encoder_attention_mask,
):
model = BioGptForCausalLM(config=config)
model.to(torch_device)
model.eval()
result = model(input_ids, attention_mask=input_mask, token_type_ids=token_type_ids, labels=token_labels)
self.parent.assertEqual(result.logits.shape, (self.batch_size, self.seq_length, self.vocab_size))
def create_and_check_biogpt_model_attention_mask_past(
self, config, input_ids, input_mask, head_mask, token_type_ids, *args
):
model = BioGptModel(config=config)
model.to(torch_device)
model.eval()
# create attention mask
attn_mask = torch.ones(input_ids.shape, dtype=torch.long, device=torch_device)
half_seq_length = self.seq_length // 2
attn_mask[:, half_seq_length:] = 0
# first forward pass
output, past = model(input_ids, attention_mask=attn_mask).to_tuple()
# create hypothetical next token and extent to next_input_ids
next_tokens = ids_tensor((self.batch_size, 1), config.vocab_size)
# change a random masked slice from input_ids
random_seq_idx_to_change = ids_tensor((1,), half_seq_length).item() + 1
random_other_next_tokens = ids_tensor((self.batch_size, 1), config.vocab_size).squeeze(-1)
input_ids[:, -random_seq_idx_to_change] = random_other_next_tokens
# append to next input_ids and attn_mask
next_input_ids = torch.cat([input_ids, next_tokens], dim=-1)
attn_mask = torch.cat(
[attn_mask, torch.ones((attn_mask.shape[0], 1), dtype=torch.long, device=torch_device)],
dim=1,
)
# get two different outputs
output_from_no_past = model(next_input_ids, attention_mask=attn_mask)["last_hidden_state"]
output_from_past = model(next_tokens, past_key_values=past, attention_mask=attn_mask)["last_hidden_state"]
# select random slice
random_slice_idx = ids_tensor((1,), output_from_past.shape[-1]).item()
output_from_no_past_slice = output_from_no_past[:, -1, random_slice_idx].detach()
output_from_past_slice = output_from_past[:, 0, random_slice_idx].detach()
# test that outputs are equal for slice
self.parent.assertTrue(torch.allclose(output_from_past_slice, output_from_no_past_slice, atol=1e-3))
def create_and_check_biogpt_model_past_large_inputs(
self, config, input_ids, input_mask, head_mask, token_type_ids, *args
):
model = BioGptModel(config=config).to(torch_device).eval()
attention_mask = torch.ones(input_ids.shape, dtype=torch.long, device=torch_device)
# first forward pass
outputs = model(input_ids, attention_mask=attention_mask, use_cache=True)
output, past_key_values = outputs.to_tuple()
# create hypothetical multiple next token and extent to next_input_ids
next_tokens = ids_tensor((self.batch_size, 3), config.vocab_size)
next_attn_mask = ids_tensor((self.batch_size, 3), 2)
# append to next input_ids and
next_input_ids = torch.cat([input_ids, next_tokens], dim=-1)
next_attention_mask = torch.cat([attention_mask, next_attn_mask], dim=-1)
output_from_no_past = model(next_input_ids, attention_mask=next_attention_mask)["last_hidden_state"]
output_from_past = model(next_tokens, attention_mask=next_attention_mask, past_key_values=past_key_values)[
"last_hidden_state"
]
# select random slice
random_slice_idx = ids_tensor((1,), output_from_past.shape[-1]).item()
output_from_no_past_slice = output_from_no_past[:, -3:, random_slice_idx].detach()
output_from_past_slice = output_from_past[:, :, random_slice_idx].detach()
self.parent.assertTrue(output_from_past_slice.shape[1] == next_tokens.shape[1])
# test that outputs are equal for slice
self.parent.assertTrue(torch.allclose(output_from_past_slice, output_from_no_past_slice, atol=1e-3))
def create_and_check_forward_and_backwards(
self, config, input_ids, input_mask, head_mask, token_type_ids, *args, gradient_checkpointing=False
):
model = BioGptForCausalLM(config)
model.to(torch_device)
if gradient_checkpointing:
model.gradient_checkpointing_enable()
result = model(input_ids, labels=input_ids)
self.parent.assertEqual(result.loss.shape, ())
self.parent.assertEqual(result.logits.shape, (self.batch_size, self.seq_length, self.vocab_size))
result.loss.backward()
def create_and_check_biogpt_weight_initialization(self, config, *args):
model = BioGptModel(config)
model_std = model.config.initializer_range / math.sqrt(2 * model.config.num_hidden_layers)
for key in model.state_dict().keys():
if "c_proj" in key and "weight" in key:
self.parent.assertLessEqual(abs(torch.std(model.state_dict()[key]) - model_std), 0.001)
self.parent.assertLessEqual(abs(torch.mean(model.state_dict()[key]) - 0.0), 0.01)
def prepare_config_and_inputs_for_common(self):
config_and_inputs = self.prepare_config_and_inputs()
(
config,
input_ids,
token_type_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 BioGptModelTest(ModelTesterMixin, GenerationTesterMixin, PipelineTesterMixin, unittest.TestCase):
all_model_classes = (BioGptModel, BioGptForCausalLM) if is_torch_available() else ()
all_generative_model_classes = (BioGptForCausalLM,) if is_torch_available() else ()
pipeline_model_mapping = (
{"feature-extraction": BioGptModel, "text-generation": BioGptForCausalLM} if is_torch_available() else {}
)
test_pruning = False
def setUp(self):
self.model_tester = BioGptModelTester(self)
self.config_tester = ConfigTester(self, config_class=BioGptConfig, 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)
def test_model_various_embeddings(self):
config_and_inputs = self.model_tester.prepare_config_and_inputs()
for type in ["absolute", "relative_key", "relative_key_query"]:
config_and_inputs[0].position_embedding_type = type
self.model_tester.create_and_check_model(*config_and_inputs)
def test_biogpt_model_att_mask_past(self):
config_and_inputs = self.model_tester.prepare_config_and_inputs()
self.model_tester.create_and_check_biogpt_model_attention_mask_past(*config_and_inputs)
def test_biogpt_gradient_checkpointing(self):
config_and_inputs = self.model_tester.prepare_config_and_inputs()
self.model_tester.create_and_check_forward_and_backwards(*config_and_inputs, gradient_checkpointing=True)
def test_biogpt_model_past_with_large_inputs(self):
config_and_inputs = self.model_tester.prepare_config_and_inputs()
self.model_tester.create_and_check_biogpt_model_past_large_inputs(*config_and_inputs)
def test_biogpt_weight_initialization(self):
config_and_inputs = self.model_tester.prepare_config_and_inputs()
self.model_tester.create_and_check_biogpt_weight_initialization(*config_and_inputs)
@slow
def test_batch_generation(self):
model = BioGptForCausalLM.from_pretrained("microsoft/biogpt")
model.to(torch_device)
tokenizer = BioGptTokenizer.from_pretrained("microsoft/biogpt")
tokenizer.padding_side = "left"
# Define PAD Token = EOS Token = 50256
tokenizer.pad_token = tokenizer.eos_token
model.config.pad_token_id = model.config.eos_token_id
# use different length sentences to test batching
sentences = [
"Hello, my dog is a little",
"Today, I",
]
inputs = tokenizer(sentences, return_tensors="pt", padding=True)
input_ids = inputs["input_ids"].to(torch_device)
outputs = model.generate(
input_ids=input_ids,
attention_mask=inputs["attention_mask"].to(torch_device),
)
inputs_non_padded = tokenizer(sentences[0], return_tensors="pt").input_ids.to(torch_device)
output_non_padded = model.generate(input_ids=inputs_non_padded)
num_paddings = inputs_non_padded.shape[-1] - inputs["attention_mask"][-1].long().sum().cpu().item()
inputs_padded = tokenizer(sentences[1], return_tensors="pt").input_ids.to(torch_device)
output_padded = model.generate(input_ids=inputs_padded, max_length=model.config.max_length - num_paddings)
batch_out_sentence = tokenizer.batch_decode(outputs, skip_special_tokens=True)
non_padded_sentence = tokenizer.decode(output_non_padded[0], skip_special_tokens=True)
padded_sentence = tokenizer.decode(output_padded[0], skip_special_tokens=True)
expected_output_sentence = [
"Hello, my dog is a little bit bigger than a little bit.",
"Today, I have a good idea of how to use the information",
]
self.assertListEqual(expected_output_sentence, batch_out_sentence)
self.assertListEqual(expected_output_sentence, [non_padded_sentence, padded_sentence])
@slow
def test_model_from_pretrained(self):
for model_name in BIOGPT_PRETRAINED_MODEL_ARCHIVE_LIST[:1]:
model = BioGptModel.from_pretrained(model_name)
self.assertIsNotNone(model)
@require_torch
class BioGptModelIntegrationTest(unittest.TestCase):
@slow
def test_inference_lm_head_model(self):
model = BioGptForCausalLM.from_pretrained("microsoft/biogpt")
input_ids = torch.tensor([[2, 4805, 9, 656, 21]])
output = model(input_ids)[0]
vocab_size = 42384
expected_shape = torch.Size((1, 5, vocab_size))
self.assertEqual(output.shape, expected_shape)
expected_slice = torch.tensor(
[[[-9.5236, -9.8918, 10.4557], [-11.0469, -9.6423, 8.1022], [-8.8664, -7.8826, 5.5325]]]
)
self.assertTrue(torch.allclose(output[:, :3, :3], expected_slice, atol=1e-4))
@slow
def test_biogpt_generation(self):
tokenizer = BioGptTokenizer.from_pretrained("microsoft/biogpt")
model = BioGptForCausalLM.from_pretrained("microsoft/biogpt")
model.to(torch_device)
torch.manual_seed(0)
tokenized = tokenizer("COVID-19 is", return_tensors="pt").to(torch_device)
output_ids = model.generate(
**tokenized,
min_length=100,
max_length=1024,
num_beams=5,
early_stopping=True,
)
output_str = tokenizer.decode(output_ids[0], skip_special_tokens=True)
EXPECTED_OUTPUT_STR = (
"COVID-19 is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the"
" causative agent of coronavirus disease 2019 (COVID-19), which has spread to more than 200 countries and"
" territories, including the United States (US), Canada, Australia, New Zealand, the United Kingdom (UK),"
" and the United States of America (USA), as of March 11, 2020, with more than 800,000 confirmed cases and"
" more than 800,000 deaths."
)
self.assertEqual(output_str, EXPECTED_OUTPUT_STR)
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