add remote code and hf-format "pytorch_model.bin"
Browse filesModified by chuhac for a timm-free implementation
Model can be directly imported with ``from_pretrained`` and ``trust_remote_code = True`` in the huggingface format
Diff from HF CLIP Implementation:
1. pre-norm instead of post-norm in Vision Tower (the original implementation is right but the module registration order is misleading)
2. CLS Pooling with MLP in Text Tower
3. Remove pre norm in Vision Tower
4. CNN bias in Vision Tower
5. Change layer_norm eps from 1e-5 to 1e-12, which introduce a little numerical variations (1e-5 level)
- config.json +103 -0
- configuration_biomed_clip.py +60 -0
- modeling_biomed_clip.py +938 -0
- preprocessor_config.json +20 -0
- processing_biomed_clip.py +153 -0
- pytorch_model.bin +3 -0
config.json
ADDED
@@ -0,0 +1,103 @@
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|
1 |
+
{
|
2 |
+
"_name_or_path": "",
|
3 |
+
"architectures": [
|
4 |
+
"BiomedCLIPModel"
|
5 |
+
],
|
6 |
+
"auto_map": {
|
7 |
+
"AutoConfig": "configuration_biomed_clip.BiomedCLIPConfig",
|
8 |
+
"AutoProcessor": "processing_biomed_clip.BiomedCLIPProcessor",
|
9 |
+
"AutoModel": "modeling_biomed_clip.BiomedCLIPModel",
|
10 |
+
"AutoModelForImageClassification": "modeling_biomed_clip.BiomedCLIPForImageClassification"
|
11 |
+
},
|
12 |
+
"initializer_factor": 1.0,
|
13 |
+
"logit_scale_init_value": 4.4454,
|
14 |
+
"model_type": "clip",
|
15 |
+
"projection_dim": 512,
|
16 |
+
"text_config": {
|
17 |
+
"attention_probs_dropout_prob": 0.1,
|
18 |
+
"gradient_checkpointing": false,
|
19 |
+
"hidden_act": "gelu",
|
20 |
+
"hidden_dropout_prob": 0.1,
|
21 |
+
"hidden_size": 768,
|
22 |
+
"initializer_range": 0.02,
|
23 |
+
"intermediate_size": 3072,
|
24 |
+
"layer_norm_eps": 1e-12,
|
25 |
+
"max_position_embeddings": 512,
|
26 |
+
"model_type": "bert",
|
27 |
+
"num_attention_heads": 12,
|
28 |
+
"num_hidden_layers": 12,
|
29 |
+
"pad_token_id": 0,
|
30 |
+
"position_embedding_type": "absolute",
|
31 |
+
"transformers_version": "4.6.0.dev0",
|
32 |
+
"type_vocab_size": 2,
|
33 |
+
"use_cache": true,
|
34 |
+
"vocab_size": 30522
|
35 |
+
},
|
36 |
+
"text_config_dict": {
|
37 |
+
"attention_probs_dropout_prob": 0.1,
|
38 |
+
"gradient_checkpointing": false,
|
39 |
+
"hidden_act": "gelu",
|
40 |
+
"hidden_dropout_prob": 0.1,
|
41 |
+
"hidden_size": 768,
|
42 |
+
"initializer_range": 0.02,
|
43 |
+
"intermediate_size": 3072,
|
44 |
+
"layer_norm_eps": 1e-12,
|
45 |
+
"max_position_embeddings": 512,
|
46 |
+
"model_type": "bert",
|
47 |
+
"num_attention_heads": 12,
|
48 |
+
"num_hidden_layers": 12,
|
49 |
+
"pad_token_id": 0,
|
50 |
+
"position_embedding_type": "absolute",
|
51 |
+
"transformers_version": "4.6.0.dev0",
|
52 |
+
"type_vocab_size": 2,
|
53 |
+
"use_cache": true,
|
54 |
+
"vocab_size": 30522
|
55 |
+
},
|
56 |
+
"text_projection_config": {
|
57 |
+
"hidden_size": 768,
|
58 |
+
"intermediate_size": 640,
|
59 |
+
"projection_dim": 512,
|
60 |
+
"hidden_act": "gelu"
|
61 |
+
},
|
62 |
+
"text_projection_config_dict": {
|
63 |
+
"hidden_size": 768,
|
64 |
+
"intermediate_size": 640,
|
65 |
+
"projection_dim": 512,
|
66 |
+
"hidden_act": "gelu",
|
67 |
+
"num_hidden_layers": 2
|
68 |
+
},
|
69 |
+
"torch_dtype": "float32",
|
70 |
+
"transformers_version": null,
|
71 |
+
"vision_config": {
|
72 |
+
"attention_probs_dropout_prob": 0.0,
|
73 |
+
"hidden_act": "gelu",
|
74 |
+
"hidden_dropout_prob": 0.0,
|
75 |
+
"hidden_size": 768,
|
76 |
+
"image_size": 224,
|
77 |
+
"initializer_range": 0.02,
|
78 |
+
"intermediate_size": 3072,
|
79 |
+
"layer_norm_eps": 1e-12,
|
80 |
+
"model_type": "vit",
|
81 |
+
"num_attention_heads": 12,
|
82 |
+
"num_channels": 3,
|
83 |
+
"num_hidden_layers": 12,
|
84 |
+
"patch_size": 16,
|
85 |
+
"qkv_bias": true
|
86 |
+
},
|
87 |
+
"vision_config_dict": {
|
88 |
+
"attention_probs_dropout_prob": 0.0,
|
89 |
+
"hidden_act": "gelu",
|
90 |
+
"hidden_dropout_prob": 0.0,
|
91 |
+
"hidden_size": 768,
|
92 |
+
"image_size": 224,
|
93 |
+
"initializer_range": 0.02,
|
94 |
+
"intermediate_size": 3072,
|
95 |
+
"layer_norm_eps": 1e-12,
|
96 |
+
"model_type": "vit",
|
97 |
+
"num_attention_heads": 12,
|
98 |
+
"num_channels": 3,
|
99 |
+
"num_hidden_layers": 12,
|
100 |
+
"patch_size": 16,
|
101 |
+
"qkv_bias": true
|
102 |
+
}
|
103 |
+
}
|
configuration_biomed_clip.py
ADDED
@@ -0,0 +1,60 @@
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|
1 |
+
import os
|
2 |
+
from typing import *
|
3 |
+
from transformers.configuration_utils import PretrainedConfig
|
4 |
+
from transformers.models.clip.configuration_clip import CLIPConfig, CLIPTextConfig, CLIPVisionConfig
|
5 |
+
|
6 |
+
class BiomedCLIPTextProjectionConfig(PretrainedConfig):
|
7 |
+
def __init__(
|
8 |
+
self,
|
9 |
+
hidden_size=768,
|
10 |
+
intermediate_size=640,
|
11 |
+
projection_dim=512,
|
12 |
+
num_hidden_layers=2,
|
13 |
+
**kwargs,
|
14 |
+
):
|
15 |
+
super().__init__(**kwargs)
|
16 |
+
|
17 |
+
self.hidden_size = hidden_size
|
18 |
+
self.intermediate_size = intermediate_size
|
19 |
+
self.projection_dim = projection_dim
|
20 |
+
self.num_hidden_layers = num_hidden_layers
|
21 |
+
|
22 |
+
@classmethod
|
23 |
+
def from_pretrained(cls, pretrained_model_name_or_path: Union[str, os.PathLike], **kwargs) -> "PretrainedConfig":
|
24 |
+
cls._set_token_in_kwargs(kwargs)
|
25 |
+
|
26 |
+
config_dict, kwargs = cls.get_config_dict(pretrained_model_name_or_path, **kwargs)
|
27 |
+
|
28 |
+
# get the vision config dict if we are loading from CLIPConfig
|
29 |
+
if config_dict.get("model_type") == "clip":
|
30 |
+
config_dict = config_dict["text_projection_config"]
|
31 |
+
|
32 |
+
if "model_type" in config_dict and hasattr(cls, "model_type") and config_dict["model_type"] != cls.model_type:
|
33 |
+
logger.warning(
|
34 |
+
f"You are using a model of type {config_dict['model_type']} to instantiate a model of type "
|
35 |
+
f"{cls.model_type}. This is not supported for all configurations of models and can yield errors."
|
36 |
+
)
|
37 |
+
|
38 |
+
return cls.from_dict(config_dict, **kwargs)
|
39 |
+
|
40 |
+
class BiomedCLIPConfig(CLIPConfig):
|
41 |
+
def __init__(
|
42 |
+
self, text_config=None, text_projection_config=None, vision_config=None, projection_dim=512, logit_scale_init_value=2.6592, **kwargs
|
43 |
+
):
|
44 |
+
# If `_config_dict` exist, we use them for the backward compatibility.
|
45 |
+
# We pop out these 2 attributes before calling `super().__init__` to avoid them being saved (which causes a lot
|
46 |
+
# of confusion!).
|
47 |
+
super().__init__(text_config, vision_config, projection_dim, logit_scale_init_value, **kwargs)
|
48 |
+
|
49 |
+
text_projection_config_dict = kwargs.pop("text_projection_config_dict", None)
|
50 |
+
if text_projection_config is None:
|
51 |
+
if text_projection_config_dict is not None:
|
52 |
+
text_projection_config = {}
|
53 |
+
|
54 |
+
_text_projection_config_dict = BiomedCLIPTextProjectionConfig(**text_projection_config_dict)
|
55 |
+
|
56 |
+
text_projection_config.update(_text_projection_config_dict)
|
57 |
+
else:
|
58 |
+
text_projection_config = BiomedCLIPTextProjectionConfig(**text_projection_config)
|
59 |
+
|
60 |
+
self.text_projection_config = text_projection_config
|
modeling_biomed_clip.py
ADDED
@@ -0,0 +1,938 @@
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|
1 |
+
# coding=utf-8
|
2 |
+
# Modified by chuhac for a timm-free implementation
|
3 |
+
# Model can be directly imported with ``from_pretrained`` and ``trust_remote_code = True`` in the huggingface format
|
4 |
+
# Diff from HF CLIP Implementation:
|
5 |
+
# 1. pre-norm instead of post-norm in Vision Tower (the original implementation is right but the module registration order is misleading)
|
6 |
+
# 2. CLS Pooling with MLP in Text Tower
|
7 |
+
# 3. Remove pre norm in Vision Tower
|
8 |
+
# 4. CNN bias in Vision Tower
|
9 |
+
# 5. Change layer_norm eps from 1e-5 to 1e-12, which introduce a little numerical variations (1e-5 level)
|
10 |
+
## ******************************** ##
|
11 |
+
# Copyright 2021 The OpenAI Team Authors and The HuggingFace Team. All rights reserved.
|
12 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
13 |
+
# you may not use this file except in compliance with the License.
|
14 |
+
# You may obtain a copy of the License at
|
15 |
+
#
|
16 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
17 |
+
#
|
18 |
+
# Unless required by applicable law or agreed to in writing, software
|
19 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
20 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
21 |
+
# See the License for the specific language governing permissions and
|
22 |
+
# limitations under the License.
|
23 |
+
""" PyTorch BiomedCLIP model """
|
24 |
+
""" No need for timm or open-clip-torch """
|
25 |
+
|
26 |
+
|
27 |
+
from dataclasses import dataclass
|
28 |
+
from typing import Any, Optional, Tuple, Union, List
|
29 |
+
|
30 |
+
import math
|
31 |
+
import torch
|
32 |
+
import torch.utils.checkpoint
|
33 |
+
from torch import nn
|
34 |
+
from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
|
35 |
+
|
36 |
+
from transformers.activations import ACT2FN
|
37 |
+
from transformers.modeling_attn_mask_utils import _create_4d_causal_attention_mask, _prepare_4d_attention_mask
|
38 |
+
from transformers.modeling_outputs import (
|
39 |
+
BaseModelOutput,
|
40 |
+
BaseModelOutputWithPooling,
|
41 |
+
ImageClassifierOutput,
|
42 |
+
BaseModelOutputWithPoolingAndCrossAttentions,
|
43 |
+
BaseModelOutputWithPastAndCrossAttentions
|
44 |
+
)
|
45 |
+
from transformers.modeling_utils import PreTrainedModel
|
46 |
+
from transformers.utils import (
|
47 |
+
ModelOutput,
|
48 |
+
add_code_sample_docstrings,
|
49 |
+
add_start_docstrings,
|
50 |
+
add_start_docstrings_to_model_forward,
|
51 |
+
logging,
|
52 |
+
replace_return_docstrings,
|
53 |
+
)
|
54 |
+
from transformers.models.clip.configuration_clip import CLIPConfig, CLIPTextConfig, CLIPVisionConfig
|
55 |
+
from transformers.models.clip.modeling_clip import *
|
56 |
+
|
57 |
+
from .configuration_biomed_clip import BiomedCLIPTextProjectionConfig, BiomedCLIPConfig
|
58 |
+
|
59 |
+
|
60 |
+
logger = logging.get_logger(__name__)
|
61 |
+
|
62 |
+
|
63 |
+
|
64 |
+
# contrastive loss function, adapted from
|
65 |
+
# https://sachinruk.github.io/blog/2021-03-07-clip.html
|
66 |
+
def contrastive_loss(logits: torch.Tensor) -> torch.Tensor:
|
67 |
+
return nn.functional.cross_entropy(logits, torch.arange(len(logits), device=logits.device))
|
68 |
+
|
69 |
+
|
70 |
+
def clip_loss(similarity: torch.Tensor) -> torch.Tensor:
|
71 |
+
caption_loss = contrastive_loss(similarity)
|
72 |
+
image_loss = contrastive_loss(similarity.t())
|
73 |
+
return (caption_loss + image_loss) / 2.0
|
74 |
+
|
75 |
+
|
76 |
+
class BiomedCLIPVisionEmbeddings(CLIPVisionEmbeddings):
|
77 |
+
def __init__(self, config: CLIPVisionConfig):
|
78 |
+
super().__init__(config)
|
79 |
+
|
80 |
+
self.patch_embedding = nn.Conv2d(
|
81 |
+
in_channels=config.num_channels,
|
82 |
+
out_channels=self.embed_dim,
|
83 |
+
kernel_size=self.patch_size,
|
84 |
+
stride=self.patch_size,
|
85 |
+
# True in open_clip
|
86 |
+
bias=True,
|
87 |
+
)
|
88 |
+
|
89 |
+
# TODO
|
90 |
+
class BiomedCLIPTextEmbeddings(nn.Module):
|
91 |
+
def __init__(self, config: CLIPTextConfig):
|
92 |
+
super().__init__()
|
93 |
+
embed_dim = config.hidden_size
|
94 |
+
|
95 |
+
self.token_embedding = nn.Embedding(config.vocab_size, embed_dim)
|
96 |
+
self.position_embedding = nn.Embedding(config.max_position_embeddings, embed_dim)
|
97 |
+
self.token_type_embedding = nn.Embedding(config.type_vocab_size, embed_dim)
|
98 |
+
|
99 |
+
self.layer_norm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
|
100 |
+
self.dropout = nn.Dropout(config.hidden_dropout_prob)
|
101 |
+
# position_ids (1, len position emb) is contiguous in memory and exported when serialized
|
102 |
+
self.position_embedding_type = getattr(config, "position_embedding_type", "absolute")
|
103 |
+
|
104 |
+
# position_ids (1, len position emb) is contiguous in memory and exported when serialized
|
105 |
+
self.register_buffer(
|
106 |
+
"position_ids", torch.arange(config.max_position_embeddings).expand((1, -1)), persistent=False
|
107 |
+
)
|
108 |
+
self.register_buffer(
|
109 |
+
"token_type_ids", torch.zeros(self.position_ids.size(), dtype=torch.long), persistent=False
|
110 |
+
)
|
111 |
+
|
112 |
+
def forward(
|
113 |
+
self,
|
114 |
+
input_ids: Optional[torch.LongTensor] = None,
|
115 |
+
token_type_ids: Optional[torch.LongTensor] = None,
|
116 |
+
position_ids: Optional[torch.LongTensor] = None,
|
117 |
+
inputs_embeds: Optional[torch.FloatTensor] = None,
|
118 |
+
past_key_values_length: int = 0,
|
119 |
+
) -> torch.Tensor:
|
120 |
+
|
121 |
+
if input_ids is not None:
|
122 |
+
input_shape = input_ids.size()
|
123 |
+
else:
|
124 |
+
input_shape = inputs_embeds.size()[:-1]
|
125 |
+
|
126 |
+
seq_length = input_shape[1]
|
127 |
+
|
128 |
+
if position_ids is None:
|
129 |
+
position_ids = self.position_ids[:, past_key_values_length : seq_length + past_key_values_length]
|
130 |
+
|
131 |
+
# Setting the token_type_ids to the registered buffer in constructor where it is all zeros, which usually occurs
|
132 |
+
# when its auto-generated, registered buffer helps users when tracing the model without passing token_type_ids, solves
|
133 |
+
# issue #5664
|
134 |
+
if token_type_ids is None:
|
135 |
+
if hasattr(self, "token_type_ids"):
|
136 |
+
buffered_token_type_ids = self.token_type_ids[:, :seq_length]
|
137 |
+
buffered_token_type_ids_expanded = buffered_token_type_ids.expand(input_shape[0], seq_length)
|
138 |
+
token_type_ids = buffered_token_type_ids_expanded
|
139 |
+
else:
|
140 |
+
token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=self.position_ids.device)
|
141 |
+
|
142 |
+
if inputs_embeds is None:
|
143 |
+
inputs_embeds = self.token_embedding(input_ids)
|
144 |
+
token_type_embeddings = self.token_type_embedding(token_type_ids)
|
145 |
+
|
146 |
+
embeddings = inputs_embeds + token_type_embeddings
|
147 |
+
if self.position_embedding_type == "absolute":
|
148 |
+
position_embeddings = self.position_embedding(position_ids)
|
149 |
+
embeddings += position_embeddings
|
150 |
+
|
151 |
+
embeddings = self.layer_norm(embeddings)
|
152 |
+
embeddings = self.dropout(embeddings)
|
153 |
+
return embeddings
|
154 |
+
|
155 |
+
|
156 |
+
class BiomedCLIPAttention(nn.Module):
|
157 |
+
def __init__(self, config, position_embedding_type=None):
|
158 |
+
super().__init__()
|
159 |
+
super().__init__()
|
160 |
+
self.config = config
|
161 |
+
self.embed_dim = config.hidden_size
|
162 |
+
self.num_heads = config.num_attention_heads
|
163 |
+
self.head_dim = self.embed_dim // self.num_heads
|
164 |
+
if self.head_dim * self.num_heads != self.embed_dim:
|
165 |
+
raise ValueError(
|
166 |
+
f"embed_dim must be divisible by num_heads (got `embed_dim`: {self.embed_dim} and `num_heads`:"
|
167 |
+
f" {self.num_heads})."
|
168 |
+
)
|
169 |
+
self.scale = self.head_dim**-0.5
|
170 |
+
self.dropout = nn.Dropout(config.attention_dropout)
|
171 |
+
|
172 |
+
self.k_proj = nn.Linear(self.embed_dim, self.embed_dim)
|
173 |
+
self.v_proj = nn.Linear(self.embed_dim, self.embed_dim)
|
174 |
+
self.q_proj = nn.Linear(self.embed_dim, self.embed_dim)
|
175 |
+
self.out_proj = nn.Linear(self.embed_dim, self.embed_dim)
|
176 |
+
|
177 |
+
def transpose_for_scores(self, x: torch.Tensor) -> torch.Tensor:
|
178 |
+
new_x_shape = x.size()[:-1] + (self.num_heads, self.head_dim)
|
179 |
+
x = x.view(new_x_shape)
|
180 |
+
return x.permute(0, 2, 1, 3)
|
181 |
+
|
182 |
+
def forward(
|
183 |
+
self,
|
184 |
+
hidden_states: torch.Tensor,
|
185 |
+
attention_mask: Optional[torch.FloatTensor] = None,
|
186 |
+
encoder_hidden_states: Optional[torch.FloatTensor] = None,
|
187 |
+
encoder_attention_mask: Optional[torch.FloatTensor] = None,
|
188 |
+
past_key_value: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
|
189 |
+
output_attentions: Optional[bool] = False,
|
190 |
+
) -> Tuple[torch.Tensor]:
|
191 |
+
|
192 |
+
mixed_query_layer = self.q_proj(hidden_states)
|
193 |
+
|
194 |
+
# If this is instantiated as a cross-attention module, the keys
|
195 |
+
# and values come from an encoder; the attention mask needs to be
|
196 |
+
# such that the encoder's padding tokens are not attended to.
|
197 |
+
is_cross_attention = encoder_hidden_states is not None
|
198 |
+
|
199 |
+
key_layer = self.transpose_for_scores(self.k_proj(hidden_states))
|
200 |
+
value_layer = self.transpose_for_scores(self.v_proj(hidden_states))
|
201 |
+
|
202 |
+
query_layer = self.transpose_for_scores(mixed_query_layer)
|
203 |
+
|
204 |
+
|
205 |
+
# Take the dot product between "query" and "key" to get the raw attention scores.
|
206 |
+
attention_scores = torch.matmul(query_layer, key_layer.transpose(-1, -2))
|
207 |
+
|
208 |
+
|
209 |
+
attention_scores = attention_scores / math.sqrt(self.head_dim)
|
210 |
+
if attention_mask is not None:
|
211 |
+
# Apply the attention mask is (precomputed for all layers in BertModel forward() function)
|
212 |
+
attention_scores = attention_scores + attention_mask
|
213 |
+
|
214 |
+
# Normalize the attention scores to probabilities.
|
215 |
+
attention_probs = nn.functional.softmax(attention_scores, dim=-1)
|
216 |
+
|
217 |
+
# This is actually dropping out entire tokens to attend to, which might
|
218 |
+
# seem a bit unusual, but is taken from the original Transformer paper.
|
219 |
+
attention_probs = self.dropout(attention_probs)
|
220 |
+
|
221 |
+
|
222 |
+
context_layer = torch.matmul(attention_probs, value_layer)
|
223 |
+
|
224 |
+
context_layer = context_layer.permute(0, 2, 1, 3).contiguous()
|
225 |
+
new_context_layer_shape = context_layer.size()[:-2] + (self.embed_dim,)
|
226 |
+
context_layer = context_layer.view(new_context_layer_shape).contiguous()
|
227 |
+
|
228 |
+
outputs = self.out_proj(context_layer)
|
229 |
+
return outputs, attention_probs
|
230 |
+
|
231 |
+
|
232 |
+
|
233 |
+
|
234 |
+
class BiomedCLIPEncoderLayer(nn.Module):
|
235 |
+
def __init__(self, config: BiomedCLIPConfig, norm='pre'):
|
236 |
+
super().__init__()
|
237 |
+
self.embed_dim = config.hidden_size
|
238 |
+
# pre-norm
|
239 |
+
self.layer_norm1 = nn.LayerNorm(self.embed_dim, eps=config.layer_norm_eps)
|
240 |
+
self.self_attn = BiomedCLIPAttention(config)
|
241 |
+
self.layer_norm2 = nn.LayerNorm(self.embed_dim, eps=config.layer_norm_eps)
|
242 |
+
self.mlp = CLIPMLP(config)
|
243 |
+
self.norm = norm
|
244 |
+
|
245 |
+
if self.norm == 'pre':
|
246 |
+
self.forward = self.pre_norm_forward
|
247 |
+
elif self.norm == 'post':
|
248 |
+
self.forward = self.post_norm_forward
|
249 |
+
|
250 |
+
|
251 |
+
def pre_norm_forward(
|
252 |
+
self,
|
253 |
+
hidden_states: torch.Tensor,
|
254 |
+
attention_mask: torch.Tensor,
|
255 |
+
output_attentions: Optional[bool] = False,
|
256 |
+
) -> Tuple[torch.FloatTensor]:
|
257 |
+
"""
|
258 |
+
Args:
|
259 |
+
hidden_states (`torch.FloatTensor`): input to the layer of shape `(batch, seq_len, embed_dim)`
|
260 |
+
attention_mask (`torch.FloatTensor`): attention mask of size
|
261 |
+
`(batch, 1, tgt_len, src_len)` where padding elements are indicated by very large negative values.
|
262 |
+
`(config.encoder_attention_heads,)`.
|
263 |
+
output_attentions (`bool`, *optional*):
|
264 |
+
Whether or not to return the attentions tensors of all attention layers. See `attentions` under
|
265 |
+
returned tensors for more detail.
|
266 |
+
"""
|
267 |
+
residual = hidden_states
|
268 |
+
|
269 |
+
hidden_states = self.layer_norm1(hidden_states)
|
270 |
+
hidden_states, attn_weights = self.self_attn(
|
271 |
+
hidden_states=hidden_states,
|
272 |
+
attention_mask=attention_mask,
|
273 |
+
output_attentions=output_attentions,
|
274 |
+
)
|
275 |
+
hidden_states = residual + hidden_states
|
276 |
+
|
277 |
+
residual = hidden_states
|
278 |
+
hidden_states = self.layer_norm2(hidden_states)
|
279 |
+
hidden_states = self.mlp(hidden_states)
|
280 |
+
hidden_states = residual + hidden_states
|
281 |
+
|
282 |
+
outputs = (hidden_states,)
|
283 |
+
|
284 |
+
if output_attentions:
|
285 |
+
outputs += (attn_weights,)
|
286 |
+
|
287 |
+
return outputs
|
288 |
+
|
289 |
+
def post_norm_forward(
|
290 |
+
self,
|
291 |
+
hidden_states: torch.Tensor,
|
292 |
+
attention_mask: torch.Tensor,
|
293 |
+
output_attentions: Optional[bool] = False,
|
294 |
+
) -> Tuple[torch.FloatTensor]:
|
295 |
+
"""
|
296 |
+
Args:
|
297 |
+
hidden_states (`torch.FloatTensor`): input to the layer of shape `(batch, seq_len, embed_dim)`
|
298 |
+
attention_mask (`torch.FloatTensor`): attention mask of size
|
299 |
+
`(batch, 1, tgt_len, src_len)` where padding elements are indicated by very large negative values.
|
300 |
+
`(config.encoder_attention_heads,)`.
|
301 |
+
output_attentions (`bool`, *optional*):
|
302 |
+
Whether or not to return the attentions tensors of all attention layers. See `attentions` under
|
303 |
+
returned tensors for more detail.
|
304 |
+
"""
|
305 |
+
residual = hidden_states
|
306 |
+
|
307 |
+
hidden_states, attn_weights = self.self_attn(
|
308 |
+
hidden_states=hidden_states,
|
309 |
+
attention_mask=attention_mask,
|
310 |
+
output_attentions=output_attentions,
|
311 |
+
)
|
312 |
+
hidden_states = residual + hidden_states
|
313 |
+
|
314 |
+
hidden_states = self.layer_norm1(hidden_states)
|
315 |
+
|
316 |
+
residual = hidden_states
|
317 |
+
hidden_states = self.mlp(hidden_states)
|
318 |
+
hidden_states = residual + hidden_states
|
319 |
+
hidden_states = self.layer_norm2(hidden_states)
|
320 |
+
outputs = (hidden_states,)
|
321 |
+
|
322 |
+
if output_attentions:
|
323 |
+
outputs += (attn_weights,)
|
324 |
+
|
325 |
+
return outputs
|
326 |
+
|
327 |
+
|
328 |
+
class BiomedCLIPTextProjection(nn.Module):
|
329 |
+
def __init__(self, config):
|
330 |
+
super().__init__()
|
331 |
+
self.config = config
|
332 |
+
self.fc1 = nn.Linear(config.hidden_size, config.intermediate_size, bias=False)
|
333 |
+
self.activation_fn = ACT2FN[config.hidden_act]
|
334 |
+
self.fc2 = nn.Linear(config.intermediate_size, config.projection_dim, bias=False)
|
335 |
+
|
336 |
+
def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
|
337 |
+
hidden_states = self.fc1(hidden_states)
|
338 |
+
hidden_states = self.activation_fn(hidden_states)
|
339 |
+
hidden_states = self.fc2(hidden_states)
|
340 |
+
return hidden_states
|
341 |
+
|
342 |
+
|
343 |
+
class BiomedCLIPEncoder(nn.Module):
|
344 |
+
"""
|
345 |
+
Transformer encoder consisting of `config.num_hidden_layers` self attention layers. Each layer is a
|
346 |
+
[`BiomedCLIPEncoderLayer`].
|
347 |
+
|
348 |
+
Args:
|
349 |
+
config: BiomedCLIPConfig
|
350 |
+
"""
|
351 |
+
def __init__(self, config, norm='pre'):
|
352 |
+
super().__init__()
|
353 |
+
self.config = config
|
354 |
+
self.norm = norm
|
355 |
+
self.layers = nn.ModuleList([BiomedCLIPEncoderLayer(config, norm) for _ in range(config.num_hidden_layers)])
|
356 |
+
self.gradient_checkpointing = False
|
357 |
+
|
358 |
+
def forward(
|
359 |
+
self,
|
360 |
+
hidden_states: torch.Tensor,
|
361 |
+
attention_mask: Optional[torch.FloatTensor] = None,
|
362 |
+
head_mask: Optional[torch.FloatTensor] = None,
|
363 |
+
encoder_hidden_states: Optional[torch.FloatTensor] = None,
|
364 |
+
encoder_attention_mask: Optional[torch.FloatTensor] = None,
|
365 |
+
past_key_values: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
|
366 |
+
use_cache: Optional[bool] = None,
|
367 |
+
output_attentions: Optional[bool] = False,
|
368 |
+
output_hidden_states: Optional[bool] = False,
|
369 |
+
return_dict: Optional[bool] = True,
|
370 |
+
) :
|
371 |
+
all_hidden_states = () if output_hidden_states else None
|
372 |
+
all_self_attentions = () if output_attentions else None
|
373 |
+
all_cross_attentions = () if output_attentions and self.config.add_cross_attention else None
|
374 |
+
|
375 |
+
if self.gradient_checkpointing and self.training:
|
376 |
+
if use_cache:
|
377 |
+
logger.warning_once(
|
378 |
+
"`use_cache=True` is incompatible with gradient checkpointing. Setting `use_cache=False`..."
|
379 |
+
)
|
380 |
+
use_cache = False
|
381 |
+
|
382 |
+
next_decoder_cache = () if use_cache else None
|
383 |
+
for i, layer_module in enumerate(self.layers):
|
384 |
+
if output_hidden_states:
|
385 |
+
all_hidden_states = all_hidden_states + (hidden_states,)
|
386 |
+
|
387 |
+
layer_head_mask = head_mask[i] if head_mask is not None else None
|
388 |
+
past_key_value = past_key_values[i] if past_key_values is not None else None
|
389 |
+
|
390 |
+
if self.gradient_checkpointing and self.training:
|
391 |
+
layer_outputs = self._gradient_checkpointing_func(
|
392 |
+
layer_module.__call__,
|
393 |
+
hidden_states,
|
394 |
+
attention_mask,
|
395 |
+
output_attentions,
|
396 |
+
)
|
397 |
+
else:
|
398 |
+
layer_outputs = layer_module(
|
399 |
+
hidden_states,
|
400 |
+
attention_mask,
|
401 |
+
output_attentions,
|
402 |
+
)
|
403 |
+
|
404 |
+
hidden_states = layer_outputs[0]
|
405 |
+
if use_cache:
|
406 |
+
next_decoder_cache += (layer_outputs[-1],)
|
407 |
+
if output_attentions:
|
408 |
+
all_self_attentions = all_self_attentions + (layer_outputs[1],)
|
409 |
+
if self.config.add_cross_attention:
|
410 |
+
all_cross_attentions = all_cross_attentions + (layer_outputs[2],)
|
411 |
+
|
412 |
+
if output_hidden_states:
|
413 |
+
all_hidden_states = all_hidden_states + (hidden_states,)
|
414 |
+
|
415 |
+
if not return_dict:
|
416 |
+
return tuple(
|
417 |
+
v
|
418 |
+
for v in [
|
419 |
+
hidden_states,
|
420 |
+
next_decoder_cache,
|
421 |
+
all_hidden_states,
|
422 |
+
all_self_attentions,
|
423 |
+
all_cross_attentions,
|
424 |
+
]
|
425 |
+
if v is not None
|
426 |
+
)
|
427 |
+
return BaseModelOutputWithPastAndCrossAttentions(
|
428 |
+
last_hidden_state=hidden_states,
|
429 |
+
past_key_values=next_decoder_cache,
|
430 |
+
hidden_states=all_hidden_states,
|
431 |
+
attentions=all_self_attentions,
|
432 |
+
cross_attentions=all_cross_attentions,
|
433 |
+
)
|
434 |
+
|
435 |
+
|
436 |
+
|
437 |
+
class BiomedCLIPTextTransformer(CLIPPreTrainedModel):
|
438 |
+
def __init__(self, config: CLIPTextConfig):
|
439 |
+
super().__init__(config)
|
440 |
+
self.config = config
|
441 |
+
embed_dim = config.hidden_size
|
442 |
+
self.embeddings = BiomedCLIPTextEmbeddings(config)
|
443 |
+
self.encoder = BiomedCLIPEncoder(config, norm='post')
|
444 |
+
# no final_ln
|
445 |
+
# self.final_layer_norm = nn.LayerNorm(embed_dim, eps=config.layer_norm_eps)
|
446 |
+
|
447 |
+
# For `pooled_output` computation
|
448 |
+
|
449 |
+
def forward(
|
450 |
+
self,
|
451 |
+
input_ids: Optional[torch.Tensor] = None,
|
452 |
+
attention_mask: Optional[torch.Tensor] = None,
|
453 |
+
token_type_ids: Optional[torch.Tensor] = None,
|
454 |
+
position_ids: Optional[torch.Tensor] = None,
|
455 |
+
inputs_embeds: Optional[torch.Tensor] = None,
|
456 |
+
encoder_hidden_states: Optional[torch.Tensor] = None,
|
457 |
+
encoder_attention_mask: Optional[torch.Tensor] = None,
|
458 |
+
past_key_values: Optional[List[torch.FloatTensor]] = None,
|
459 |
+
use_cache: Optional[bool] = None,
|
460 |
+
output_attentions: Optional[bool] = None,
|
461 |
+
output_hidden_states: Optional[bool] = None,
|
462 |
+
return_dict: Optional[bool] = None,
|
463 |
+
) -> Union[Tuple[torch.Tensor], BaseModelOutputWithPoolingAndCrossAttentions]:
|
464 |
+
r"""
|
465 |
+
encoder_hidden_states (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
|
466 |
+
Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
|
467 |
+
the model is configured as a decoder.
|
468 |
+
encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
|
469 |
+
Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
|
470 |
+
the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:
|
471 |
+
|
472 |
+
- 1 for tokens that are **not masked**,
|
473 |
+
- 0 for tokens that are **masked**.
|
474 |
+
past_key_values (`tuple(tuple(torch.FloatTensor))` of length `config.n_layers` with each tuple having 4 tensors of shape `(batch_size, num_heads, sequence_length - 1, embed_size_per_head)`):
|
475 |
+
Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.
|
476 |
+
|
477 |
+
If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
|
478 |
+
don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
|
479 |
+
`decoder_input_ids` of shape `(batch_size, sequence_length)`.
|
480 |
+
use_cache (`bool`, *optional*):
|
481 |
+
If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
|
482 |
+
`past_key_values`).
|
483 |
+
"""
|
484 |
+
output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
|
485 |
+
output_hidden_states = (
|
486 |
+
output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
|
487 |
+
)
|
488 |
+
return_dict = return_dict if return_dict is not None else self.config.use_return_dict
|
489 |
+
|
490 |
+
if self.config.is_decoder:
|
491 |
+
use_cache = use_cache if use_cache is not None else self.config.use_cache
|
492 |
+
else:
|
493 |
+
use_cache = False
|
494 |
+
|
495 |
+
if input_ids is not None and inputs_embeds is not None:
|
496 |
+
raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
|
497 |
+
elif input_ids is not None:
|
498 |
+
input_shape = input_ids.size()
|
499 |
+
elif inputs_embeds is not None:
|
500 |
+
input_shape = inputs_embeds.size()[:-1]
|
501 |
+
else:
|
502 |
+
raise ValueError("You have to specify either input_ids or inputs_embeds")
|
503 |
+
|
504 |
+
batch_size, seq_length = input_shape
|
505 |
+
device = input_ids.device if input_ids is not None else inputs_embeds.device
|
506 |
+
|
507 |
+
# past_key_values_length
|
508 |
+
past_key_values_length = past_key_values[0][0].shape[2] if past_key_values is not None else 0
|
509 |
+
|
510 |
+
if token_type_ids is None:
|
511 |
+
if hasattr(self.embeddings, "token_type_ids"):
|
512 |
+
buffered_token_type_ids = self.embeddings.token_type_ids[:, :seq_length]
|
513 |
+
buffered_token_type_ids_expanded = buffered_token_type_ids.expand(batch_size, seq_length)
|
514 |
+
token_type_ids = buffered_token_type_ids_expanded
|
515 |
+
else:
|
516 |
+
token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=device)
|
517 |
+
|
518 |
+
embedding_output = self.embeddings(
|
519 |
+
input_ids=input_ids,
|
520 |
+
position_ids=position_ids,
|
521 |
+
token_type_ids=token_type_ids,
|
522 |
+
inputs_embeds=inputs_embeds,
|
523 |
+
past_key_values_length=past_key_values_length,
|
524 |
+
)
|
525 |
+
|
526 |
+
if attention_mask is None:
|
527 |
+
attention_mask = torch.ones((batch_size, seq_length + past_key_values_length), device=device)
|
528 |
+
|
529 |
+
# We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length]
|
530 |
+
# ourselves in which case we just need to make it broadcastable to all heads.
|
531 |
+
extended_attention_mask = self.get_extended_attention_mask(attention_mask, input_shape)
|
532 |
+
|
533 |
+
# If a 2D or 3D attention mask is provided for the cross-attention
|
534 |
+
# we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length]
|
535 |
+
if self.config.is_decoder and encoder_hidden_states is not None:
|
536 |
+
encoder_batch_size, encoder_sequence_length, _ = encoder_hidden_states.size()
|
537 |
+
encoder_hidden_shape = (encoder_batch_size, encoder_sequence_length)
|
538 |
+
if encoder_attention_mask is None:
|
539 |
+
encoder_attention_mask = torch.ones(encoder_hidden_shape, device=device)
|
540 |
+
|
541 |
+
if use_sdpa_attention_masks:
|
542 |
+
# Expand the attention mask for SDPA.
|
543 |
+
# [bsz, seq_len] -> [bsz, 1, seq_len, seq_len]
|
544 |
+
encoder_extended_attention_mask = _prepare_4d_attention_mask_for_sdpa(
|
545 |
+
encoder_attention_mask, embedding_output.dtype, tgt_len=seq_length
|
546 |
+
)
|
547 |
+
else:
|
548 |
+
encoder_extended_attention_mask = self.invert_attention_mask(encoder_attention_mask)
|
549 |
+
else:
|
550 |
+
encoder_extended_attention_mask = None
|
551 |
+
|
552 |
+
|
553 |
+
encoder_outputs = self.encoder(
|
554 |
+
embedding_output,
|
555 |
+
attention_mask=extended_attention_mask,
|
556 |
+
output_attentions=output_attentions,
|
557 |
+
output_hidden_states=output_hidden_states,
|
558 |
+
return_dict=return_dict,
|
559 |
+
)
|
560 |
+
sequence_output = encoder_outputs[0]
|
561 |
+
|
562 |
+
return (sequence_output, sequence_output[:, 0, :])
|
563 |
+
|
564 |
+
|
565 |
+
|
566 |
+
class BiomedCLIPVisionTransformer(nn.Module):
|
567 |
+
def __init__(self, config: CLIPVisionConfig):
|
568 |
+
super().__init__()
|
569 |
+
self.config = config
|
570 |
+
embed_dim = config.hidden_size
|
571 |
+
|
572 |
+
self.embeddings = BiomedCLIPVisionEmbeddings(config)
|
573 |
+
# No pre_norm in open_clip Vision Tower
|
574 |
+
# self.pre_layrnorm = nn.LayerNorm(embed_dim, eps=config.layer_norm_eps)
|
575 |
+
self.encoder = BiomedCLIPEncoder(config)
|
576 |
+
self.post_layernorm = nn.LayerNorm(embed_dim, eps=config.layer_norm_eps)
|
577 |
+
|
578 |
+
def forward(
|
579 |
+
self,
|
580 |
+
pixel_values: Optional[torch.FloatTensor] = None,
|
581 |
+
output_attentions: Optional[bool] = None,
|
582 |
+
output_hidden_states: Optional[bool] = None,
|
583 |
+
return_dict: Optional[bool] = None,
|
584 |
+
) -> Union[Tuple, BaseModelOutputWithPooling]:
|
585 |
+
r"""
|
586 |
+
Returns:
|
587 |
+
|
588 |
+
"""
|
589 |
+
output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
|
590 |
+
output_hidden_states = (
|
591 |
+
output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
|
592 |
+
)
|
593 |
+
return_dict = return_dict if return_dict is not None else self.config.use_return_dict
|
594 |
+
|
595 |
+
if pixel_values is None:
|
596 |
+
raise ValueError("You have to specify pixel_values")
|
597 |
+
|
598 |
+
hidden_states = self.embeddings(pixel_values)
|
599 |
+
# hidden_states = self.pre_layrnorm(hidden_states)
|
600 |
+
|
601 |
+
encoder_outputs = self.encoder(
|
602 |
+
hidden_states=hidden_states,
|
603 |
+
output_attentions=output_attentions,
|
604 |
+
output_hidden_states=output_hidden_states,
|
605 |
+
return_dict=return_dict,
|
606 |
+
)
|
607 |
+
|
608 |
+
last_hidden_state = encoder_outputs[0]
|
609 |
+
pooled_output = last_hidden_state[:, 0, :]
|
610 |
+
pooled_output = self.post_layernorm(pooled_output)
|
611 |
+
|
612 |
+
if not return_dict:
|
613 |
+
return (last_hidden_state, pooled_output) + encoder_outputs[1:]
|
614 |
+
|
615 |
+
return BaseModelOutputWithPooling(
|
616 |
+
last_hidden_state=last_hidden_state,
|
617 |
+
pooler_output=pooled_output,
|
618 |
+
hidden_states=encoder_outputs.hidden_states,
|
619 |
+
attentions=encoder_outputs.attentions,
|
620 |
+
)
|
621 |
+
|
622 |
+
|
623 |
+
class BiomedCLIPModel(CLIPPreTrainedModel):
|
624 |
+
config_class = BiomedCLIPConfig
|
625 |
+
_no_split_modules = ["BiomedCLIPTextEmbeddings", "BiomedCLIPEncoderLayer"]
|
626 |
+
|
627 |
+
def __init__(self, config: BiomedCLIPConfig):
|
628 |
+
super().__init__(config)
|
629 |
+
|
630 |
+
if not isinstance(config.text_config, CLIPTextConfig):
|
631 |
+
raise ValueError(
|
632 |
+
"config.text_config is expected to be of type CLIPTextConfig but is of type"
|
633 |
+
f" {type(config.text_config)}."
|
634 |
+
)
|
635 |
+
|
636 |
+
if not isinstance(config.vision_config, CLIPVisionConfig):
|
637 |
+
raise ValueError(
|
638 |
+
"config.vision_config is expected to be of type CLIPVisionConfig but is of type"
|
639 |
+
f" {type(config.vision_config)}."
|
640 |
+
)
|
641 |
+
|
642 |
+
text_config = config.text_config
|
643 |
+
text_projection_config = config.text_projection_config
|
644 |
+
vision_config = config.vision_config
|
645 |
+
|
646 |
+
|
647 |
+
self.projection_dim = config.projection_dim
|
648 |
+
self.text_embed_dim = text_config.hidden_size
|
649 |
+
self.vision_embed_dim = vision_config.hidden_size
|
650 |
+
|
651 |
+
self.text_model = BiomedCLIPTextTransformer(text_config)
|
652 |
+
self.vision_model = BiomedCLIPVisionTransformer(vision_config)
|
653 |
+
|
654 |
+
self.visual_projection = nn.Linear(self.vision_embed_dim, self.projection_dim, bias=False)
|
655 |
+
|
656 |
+
self.text_projection = BiomedCLIPTextProjection(text_projection_config)
|
657 |
+
|
658 |
+
self.logit_scale = nn.Parameter(torch.tensor(self.config.logit_scale_init_value))
|
659 |
+
|
660 |
+
# Initialize weights and apply final processing
|
661 |
+
self.post_init()
|
662 |
+
|
663 |
+
def get_text_features(
|
664 |
+
self,
|
665 |
+
input_ids: Optional[torch.Tensor] = None,
|
666 |
+
attention_mask: Optional[torch.Tensor] = None,
|
667 |
+
token_type_ids: Optional[torch.Tensor] = None,
|
668 |
+
position_ids: Optional[torch.Tensor] = None,
|
669 |
+
output_attentions: Optional[bool] = None,
|
670 |
+
output_hidden_states: Optional[bool] = None,
|
671 |
+
return_dict: Optional[bool] = None,
|
672 |
+
) -> torch.FloatTensor:
|
673 |
+
r"""
|
674 |
+
Returns:
|
675 |
+
text_features (`torch.FloatTensor` of shape `(batch_size, output_dim`): The text embeddings obtained by
|
676 |
+
applying the projection layer to the pooled output of [`CLIPTextModel`].
|
677 |
+
|
678 |
+
Examples:
|
679 |
+
|
680 |
+
```python
|
681 |
+
>>> from transformers import AutoTokenizer, CLIPModel
|
682 |
+
|
683 |
+
>>> model = CLIPModel.from_pretrained("openai/clip-vit-base-patch32")
|
684 |
+
>>> tokenizer = AutoTokenizer.from_pretrained("openai/clip-vit-base-patch32")
|
685 |
+
|
686 |
+
>>> inputs = tokenizer(["a photo of a cat", "a photo of a dog"], padding=True, return_tensors="pt")
|
687 |
+
>>> text_features = model.get_text_features(**inputs)
|
688 |
+
```"""
|
689 |
+
# Use CLIP model's config for some fields (if specified) instead of those of vision & text components.
|
690 |
+
output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
|
691 |
+
output_hidden_states = (
|
692 |
+
output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
|
693 |
+
)
|
694 |
+
return_dict = return_dict if return_dict is not None else self.config.use_return_dict
|
695 |
+
|
696 |
+
text_outputs = self.text_model(
|
697 |
+
input_ids=input_ids,
|
698 |
+
attention_mask=attention_mask,
|
699 |
+
token_type_ids=token_type_ids,
|
700 |
+
position_ids=position_ids,
|
701 |
+
output_attentions=output_attentions,
|
702 |
+
output_hidden_states=output_hidden_states,
|
703 |
+
return_dict=return_dict,
|
704 |
+
)
|
705 |
+
|
706 |
+
pooled_output = text_outputs[1]
|
707 |
+
text_features = self.text_projection(pooled_output)
|
708 |
+
|
709 |
+
return text_features
|
710 |
+
|
711 |
+
def get_image_features(
|
712 |
+
self,
|
713 |
+
pixel_values: Optional[torch.FloatTensor] = None,
|
714 |
+
output_attentions: Optional[bool] = None,
|
715 |
+
output_hidden_states: Optional[bool] = None,
|
716 |
+
return_dict: Optional[bool] = None,
|
717 |
+
) -> torch.FloatTensor:
|
718 |
+
r"""
|
719 |
+
Returns:
|
720 |
+
image_features (`torch.FloatTensor` of shape `(batch_size, output_dim`): The image embeddings obtained by
|
721 |
+
applying the projection layer to the pooled output of [`CLIPVisionModel`].
|
722 |
+
|
723 |
+
Examples:
|
724 |
+
|
725 |
+
```python
|
726 |
+
>>> from PIL import Image
|
727 |
+
>>> import requests
|
728 |
+
>>> from transformers import AutoProcessor, CLIPModel
|
729 |
+
|
730 |
+
>>> model = CLIPModel.from_pretrained("openai/clip-vit-base-patch32")
|
731 |
+
>>> processor = AutoProcessor.from_pretrained("openai/clip-vit-base-patch32")
|
732 |
+
|
733 |
+
>>> url = "http://images.cocodataset.org/val2017/000000039769.jpg"
|
734 |
+
>>> image = Image.open(requests.get(url, stream=True).raw)
|
735 |
+
|
736 |
+
>>> inputs = processor(images=image, return_tensors="pt")
|
737 |
+
|
738 |
+
>>> image_features = model.get_image_features(**inputs)
|
739 |
+
```"""
|
740 |
+
# Use CLIP model's config for some fields (if specified) instead of those of vision & text components.
|
741 |
+
output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
|
742 |
+
output_hidden_states = (
|
743 |
+
output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
|
744 |
+
)
|
745 |
+
return_dict = return_dict if return_dict is not None else self.config.use_return_dict
|
746 |
+
|
747 |
+
vision_outputs = self.vision_model(
|
748 |
+
pixel_values=pixel_values,
|
749 |
+
output_attentions=output_attentions,
|
750 |
+
output_hidden_states=output_hidden_states,
|
751 |
+
return_dict=return_dict,
|
752 |
+
)
|
753 |
+
|
754 |
+
pooled_output = vision_outputs[1] # pooled_output
|
755 |
+
image_features = self.visual_projection(pooled_output)
|
756 |
+
|
757 |
+
return image_features
|
758 |
+
|
759 |
+
def forward(
|
760 |
+
self,
|
761 |
+
input_ids: Optional[torch.LongTensor] = None,
|
762 |
+
pixel_values: Optional[torch.FloatTensor] = None,
|
763 |
+
attention_mask: Optional[torch.Tensor] = None,
|
764 |
+
token_type_ids: Optional[torch.LongTensor] = None,
|
765 |
+
position_ids: Optional[torch.LongTensor] = None,
|
766 |
+
return_loss: Optional[bool] = None,
|
767 |
+
output_attentions: Optional[bool] = None,
|
768 |
+
output_hidden_states: Optional[bool] = None,
|
769 |
+
return_dict: Optional[bool] = None,
|
770 |
+
) -> Union[Tuple, CLIPOutput]:
|
771 |
+
r"""
|
772 |
+
Returns:
|
773 |
+
|
774 |
+
Examples:
|
775 |
+
|
776 |
+
```python
|
777 |
+
>>> from PIL import Image
|
778 |
+
>>> import requests
|
779 |
+
>>> from transformers import AutoProcessor, CLIPModel
|
780 |
+
|
781 |
+
>>> model = CLIPModel.from_pretrained("openai/clip-vit-base-patch32")
|
782 |
+
>>> processor = AutoProcessor.from_pretrained("openai/clip-vit-base-patch32")
|
783 |
+
|
784 |
+
>>> url = "http://images.cocodataset.org/val2017/000000039769.jpg"
|
785 |
+
>>> image = Image.open(requests.get(url, stream=True).raw)
|
786 |
+
|
787 |
+
>>> inputs = processor(
|
788 |
+
... text=["a photo of a cat", "a photo of a dog"], images=image, return_tensors="pt", padding=True
|
789 |
+
... )
|
790 |
+
|
791 |
+
>>> outputs = model(**inputs)
|
792 |
+
>>> logits_per_image = outputs.logits_per_image # this is the image-text similarity score
|
793 |
+
>>> probs = logits_per_image.softmax(dim=1) # we can take the softmax to get the label probabilities
|
794 |
+
```"""
|
795 |
+
# Use CLIP model's config for some fields (if specified) instead of those of vision & text components.
|
796 |
+
output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
|
797 |
+
output_hidden_states = (
|
798 |
+
output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
|
799 |
+
)
|
800 |
+
return_dict = return_dict if return_dict is not None else self.config.use_return_dict
|
801 |
+
|
802 |
+
vision_outputs = self.vision_model(
|
803 |
+
pixel_values=pixel_values,
|
804 |
+
output_attentions=output_attentions,
|
805 |
+
output_hidden_states=output_hidden_states,
|
806 |
+
return_dict=return_dict,
|
807 |
+
)
|
808 |
+
|
809 |
+
text_outputs = self.text_model(
|
810 |
+
input_ids=input_ids,
|
811 |
+
token_type_ids=token_type_ids,
|
812 |
+
attention_mask=attention_mask,
|
813 |
+
position_ids=position_ids,
|
814 |
+
output_attentions=output_attentions,
|
815 |
+
output_hidden_states=output_hidden_states,
|
816 |
+
return_dict=return_dict,
|
817 |
+
)
|
818 |
+
|
819 |
+
image_embeds = vision_outputs[1]
|
820 |
+
image_embeds = self.visual_projection(image_embeds)
|
821 |
+
|
822 |
+
text_embeds = text_outputs[1]
|
823 |
+
text_embeds = self.text_projection(text_embeds)
|
824 |
+
|
825 |
+
# normalized features
|
826 |
+
image_embeds = image_embeds / image_embeds.norm(p=2, dim=-1, keepdim=True)
|
827 |
+
text_embeds = text_embeds / text_embeds.norm(p=2, dim=-1, keepdim=True)
|
828 |
+
|
829 |
+
# cosine similarity as logits
|
830 |
+
logit_scale = self.logit_scale.exp()
|
831 |
+
logits_per_text = torch.matmul(text_embeds, image_embeds.t()) * logit_scale
|
832 |
+
logits_per_image = logits_per_text.t()
|
833 |
+
|
834 |
+
loss = None
|
835 |
+
if return_loss:
|
836 |
+
loss = clip_loss(logits_per_text)
|
837 |
+
|
838 |
+
if not return_dict:
|
839 |
+
output = (logits_per_image, logits_per_text, text_embeds, image_embeds, text_outputs, vision_outputs)
|
840 |
+
return ((loss,) + output) if loss is not None else output
|
841 |
+
|
842 |
+
return CLIPOutput(
|
843 |
+
loss=loss,
|
844 |
+
logits_per_image=logits_per_image,
|
845 |
+
logits_per_text=logits_per_text,
|
846 |
+
text_embeds=text_embeds,
|
847 |
+
image_embeds=image_embeds,
|
848 |
+
text_model_output=text_outputs,
|
849 |
+
vision_model_output=vision_outputs,
|
850 |
+
)
|
851 |
+
|
852 |
+
|
853 |
+
class BiomedCLIPForImageClassification(CLIPPreTrainedModel):
|
854 |
+
main_input_name = "pixel_values"
|
855 |
+
|
856 |
+
def __init__(self, config: BiomedCLIPConfig) -> None:
|
857 |
+
super().__init__(config)
|
858 |
+
|
859 |
+
self.num_labels = config.num_labels
|
860 |
+
self.vision_model = BiomedCLIPVisionTransformer(config.vision_config)
|
861 |
+
|
862 |
+
# Classifier head
|
863 |
+
self.classifier = (
|
864 |
+
nn.Linear(config.vision_config.hidden_size, config.num_labels) if config.num_labels > 0 else nn.Identity()
|
865 |
+
)
|
866 |
+
|
867 |
+
# Initialize weights and apply final processing
|
868 |
+
self.post_init()
|
869 |
+
|
870 |
+
def forward(
|
871 |
+
self,
|
872 |
+
pixel_values: Optional[torch.Tensor] = None,
|
873 |
+
labels: Optional[torch.Tensor] = None,
|
874 |
+
output_attentions: Optional[bool] = None,
|
875 |
+
output_hidden_states: Optional[bool] = None,
|
876 |
+
return_dict: Optional[bool] = None,
|
877 |
+
) -> Union[tuple, ImageClassifierOutput]:
|
878 |
+
r"""
|
879 |
+
labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
|
880 |
+
Labels for computing the image classification/regression loss. Indices should be in `[0, ...,
|
881 |
+
config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
|
882 |
+
`config.num_labels > 1` a classification loss is computed (Cross-Entropy).
|
883 |
+
"""
|
884 |
+
output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
|
885 |
+
output_hidden_states = (
|
886 |
+
output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
|
887 |
+
)
|
888 |
+
return_dict = return_dict if return_dict is not None else self.config.use_return_dict
|
889 |
+
|
890 |
+
outputs = self.vision_model(
|
891 |
+
pixel_values,
|
892 |
+
output_attentions=output_attentions,
|
893 |
+
output_hidden_states=output_hidden_states,
|
894 |
+
return_dict=return_dict,
|
895 |
+
)
|
896 |
+
|
897 |
+
sequence_output = outputs[0]
|
898 |
+
|
899 |
+
# average pool the patch tokens
|
900 |
+
sequence_output = torch.mean(sequence_output[:, 1:, :], dim=1)
|
901 |
+
# apply classifier
|
902 |
+
logits = self.classifier(sequence_output)
|
903 |
+
|
904 |
+
loss = None
|
905 |
+
if labels is not None:
|
906 |
+
# move labels to correct device to enable model parallelism
|
907 |
+
labels = labels.to(logits.device)
|
908 |
+
if self.config.problem_type is None:
|
909 |
+
if self.num_labels == 1:
|
910 |
+
self.config.problem_type = "regression"
|
911 |
+
elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
|
912 |
+
self.config.problem_type = "single_label_classification"
|
913 |
+
else:
|
914 |
+
self.config.problem_type = "multi_label_classification"
|
915 |
+
|
916 |
+
if self.config.problem_type == "regression":
|
917 |
+
loss_fct = MSELoss()
|
918 |
+
if self.num_labels == 1:
|
919 |
+
loss = loss_fct(logits.squeeze(), labels.squeeze())
|
920 |
+
else:
|
921 |
+
loss = loss_fct(logits, labels)
|
922 |
+
elif self.config.problem_type == "single_label_classification":
|
923 |
+
loss_fct = CrossEntropyLoss()
|
924 |
+
loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
|
925 |
+
elif self.config.problem_type == "multi_label_classification":
|
926 |
+
loss_fct = BCEWithLogitsLoss()
|
927 |
+
loss = loss_fct(logits, labels)
|
928 |
+
|
929 |
+
if not return_dict:
|
930 |
+
output = (logits,) + outputs[2:]
|
931 |
+
return ((loss,) + output) if loss is not None else output
|
932 |
+
|
933 |
+
return ImageClassifierOutput(
|
934 |
+
loss=loss,
|
935 |
+
logits=logits,
|
936 |
+
hidden_states=outputs.hidden_states,
|
937 |
+
attentions=outputs.attentions,
|
938 |
+
)
|
preprocessor_config.json
ADDED
@@ -0,0 +1,20 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"crop_size": 224,
|
3 |
+
"do_center_crop": true,
|
4 |
+
"do_normalize": true,
|
5 |
+
"do_resize": true,
|
6 |
+
"image_processor_type": "CLIPImageProcessor",
|
7 |
+
"tokenizer_type": "BertTokenizer",
|
8 |
+
"image_mean": [
|
9 |
+
0.48145466,
|
10 |
+
0.4578275,
|
11 |
+
0.40821073
|
12 |
+
],
|
13 |
+
"image_std": [
|
14 |
+
0.26862954,
|
15 |
+
0.26130258,
|
16 |
+
0.27577711
|
17 |
+
],
|
18 |
+
"resample": 3,
|
19 |
+
"size": 224
|
20 |
+
}
|
processing_biomed_clip.py
ADDED
@@ -0,0 +1,153 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# coding=utf-8
|
2 |
+
# Copyright 2021 The HuggingFace Inc. team.
|
3 |
+
#
|
4 |
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
5 |
+
# you may not use this file except in compliance with the License.
|
6 |
+
# You may obtain a copy of the License at
|
7 |
+
#
|
8 |
+
# http://www.apache.org/licenses/LICENSE-2.0
|
9 |
+
#
|
10 |
+
# Unless required by applicable law or agreed to in writing, software
|
11 |
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
12 |
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
13 |
+
# See the License for the specific language governing permissions and
|
14 |
+
# limitations under the License.
|
15 |
+
"""
|
16 |
+
Image/Text processor class for CLIP
|
17 |
+
"""
|
18 |
+
|
19 |
+
import warnings
|
20 |
+
|
21 |
+
from transformers.processing_utils import ProcessorMixin
|
22 |
+
from transformers.tokenization_utils_base import BatchEncoding
|
23 |
+
|
24 |
+
|
25 |
+
class BiomedCLIPProcessor(ProcessorMixin):
|
26 |
+
r"""
|
27 |
+
Constructs a CLIP processor which wraps a CLIP image processor and a CLIP tokenizer into a single processor.
|
28 |
+
|
29 |
+
[`CLIPProcessor`] offers all the functionalities of [`CLIPImageProcessor`] and [`CLIPTokenizerFast`]. See the
|
30 |
+
[`~CLIPProcessor.__call__`] and [`~CLIPProcessor.decode`] for more information.
|
31 |
+
|
32 |
+
Args:
|
33 |
+
image_processor ([`CLIPImageProcessor`], *optional*):
|
34 |
+
The image processor is a required input.
|
35 |
+
tokenizer ([`CLIPTokenizerFast`], *optional*):
|
36 |
+
The tokenizer is a required input.
|
37 |
+
"""
|
38 |
+
|
39 |
+
attributes = ["image_processor", "tokenizer"]
|
40 |
+
image_processor_class = "CLIPImageProcessor"
|
41 |
+
tokenizer_class = ("BertTokenizer", "BertTokenizerFast")
|
42 |
+
|
43 |
+
def __init__(self, image_processor=None, tokenizer=None, **kwargs):
|
44 |
+
feature_extractor = None
|
45 |
+
if "feature_extractor" in kwargs:
|
46 |
+
warnings.warn(
|
47 |
+
"The `feature_extractor` argument is deprecated and will be removed in v5, use `image_processor`"
|
48 |
+
" instead.",
|
49 |
+
FutureWarning,
|
50 |
+
)
|
51 |
+
feature_extractor = kwargs.pop("feature_extractor")
|
52 |
+
|
53 |
+
image_processor = image_processor if image_processor is not None else feature_extractor
|
54 |
+
if image_processor is None:
|
55 |
+
raise ValueError("You need to specify an `image_processor`.")
|
56 |
+
if tokenizer is None:
|
57 |
+
raise ValueError("You need to specify a `tokenizer`.")
|
58 |
+
|
59 |
+
super().__init__(image_processor, tokenizer)
|
60 |
+
|
61 |
+
def __call__(self, text=None, images=None, return_tensors=None, **kwargs):
|
62 |
+
"""
|
63 |
+
Main method to prepare for the model one or several sequences(s) and image(s). This method forwards the `text`
|
64 |
+
and `kwargs` arguments to CLIPTokenizerFast's [`~CLIPTokenizerFast.__call__`] if `text` is not `None` to encode
|
65 |
+
the text. To prepare the image(s), this method forwards the `images` and `kwrags` arguments to
|
66 |
+
CLIPImageProcessor's [`~CLIPImageProcessor.__call__`] if `images` is not `None`. Please refer to the doctsring
|
67 |
+
of the above two methods for more information.
|
68 |
+
|
69 |
+
Args:
|
70 |
+
text (`str`, `List[str]`, `List[List[str]]`):
|
71 |
+
The sequence or batch of sequences to be encoded. Each sequence can be a string or a list of strings
|
72 |
+
(pretokenized string). If the sequences are provided as list of strings (pretokenized), you must set
|
73 |
+
`is_split_into_words=True` (to lift the ambiguity with a batch of sequences).
|
74 |
+
images (`PIL.Image.Image`, `np.ndarray`, `torch.Tensor`, `List[PIL.Image.Image]`, `List[np.ndarray]`, `List[torch.Tensor]`):
|
75 |
+
The image or batch of images to be prepared. Each image can be a PIL image, NumPy array or PyTorch
|
76 |
+
tensor. Both channels-first and channels-last formats are supported.
|
77 |
+
|
78 |
+
return_tensors (`str` or [`~utils.TensorType`], *optional*):
|
79 |
+
If set, will return tensors of a particular framework. Acceptable values are:
|
80 |
+
|
81 |
+
- `'tf'`: Return TensorFlow `tf.constant` objects.
|
82 |
+
- `'pt'`: Return PyTorch `torch.Tensor` objects.
|
83 |
+
- `'np'`: Return NumPy `np.ndarray` objects.
|
84 |
+
- `'jax'`: Return JAX `jnp.ndarray` objects.
|
85 |
+
|
86 |
+
Returns:
|
87 |
+
[`BatchEncoding`]: A [`BatchEncoding`] with the following fields:
|
88 |
+
|
89 |
+
- **input_ids** -- List of token ids to be fed to a model. Returned when `text` is not `None`.
|
90 |
+
- **attention_mask** -- List of indices specifying which tokens should be attended to by the model (when
|
91 |
+
`return_attention_mask=True` or if *"attention_mask"* is in `self.model_input_names` and if `text` is not
|
92 |
+
`None`).
|
93 |
+
- **pixel_values** -- Pixel values to be fed to a model. Returned when `images` is not `None`.
|
94 |
+
"""
|
95 |
+
tokenizer_kwargs, image_processor_kwargs = {}, {}
|
96 |
+
if kwargs:
|
97 |
+
tokenizer_kwargs = {k: v for k, v in kwargs.items() if k not in self.image_processor._valid_processor_keys}
|
98 |
+
image_processor_kwargs = {
|
99 |
+
k: v for k, v in kwargs.items() if k in self.image_processor._valid_processor_keys
|
100 |
+
}
|
101 |
+
|
102 |
+
if text is None and images is None:
|
103 |
+
raise ValueError("You have to specify either text or images. Both cannot be none.")
|
104 |
+
|
105 |
+
if text is not None:
|
106 |
+
encoding = self.tokenizer(text, return_tensors=return_tensors, **tokenizer_kwargs)
|
107 |
+
|
108 |
+
if images is not None:
|
109 |
+
image_features = self.image_processor(images, return_tensors=return_tensors, **image_processor_kwargs)
|
110 |
+
|
111 |
+
if text is not None and images is not None:
|
112 |
+
encoding["pixel_values"] = image_features.pixel_values
|
113 |
+
return encoding
|
114 |
+
elif text is not None:
|
115 |
+
return encoding
|
116 |
+
else:
|
117 |
+
return BatchEncoding(data=dict(**image_features), tensor_type=return_tensors)
|
118 |
+
|
119 |
+
def batch_decode(self, *args, **kwargs):
|
120 |
+
"""
|
121 |
+
This method forwards all its arguments to CLIPTokenizerFast's [`~PreTrainedTokenizer.batch_decode`]. Please
|
122 |
+
refer to the docstring of this method for more information.
|
123 |
+
"""
|
124 |
+
return self.tokenizer.batch_decode(*args, **kwargs)
|
125 |
+
|
126 |
+
def decode(self, *args, **kwargs):
|
127 |
+
"""
|
128 |
+
This method forwards all its arguments to CLIPTokenizerFast's [`~PreTrainedTokenizer.decode`]. Please refer to
|
129 |
+
the docstring of this method for more information.
|
130 |
+
"""
|
131 |
+
return self.tokenizer.decode(*args, **kwargs)
|
132 |
+
|
133 |
+
@property
|
134 |
+
def model_input_names(self):
|
135 |
+
tokenizer_input_names = self.tokenizer.model_input_names
|
136 |
+
image_processor_input_names = self.image_processor.model_input_names
|
137 |
+
return list(dict.fromkeys(tokenizer_input_names + image_processor_input_names))
|
138 |
+
|
139 |
+
@property
|
140 |
+
def feature_extractor_class(self):
|
141 |
+
warnings.warn(
|
142 |
+
"`feature_extractor_class` is deprecated and will be removed in v5. Use `image_processor_class` instead.",
|
143 |
+
FutureWarning,
|
144 |
+
)
|
145 |
+
return self.image_processor_class
|
146 |
+
|
147 |
+
@property
|
148 |
+
def feature_extractor(self):
|
149 |
+
warnings.warn(
|
150 |
+
"`feature_extractor` is deprecated and will be removed in v5. Use `image_processor` instead.",
|
151 |
+
FutureWarning,
|
152 |
+
)
|
153 |
+
return self.image_processor
|
pytorch_model.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:5bdc400de59a85620ddc7584d06913dc901c47f22647899c6addec71b9a5c9a2
|
3 |
+
size 783733062
|