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scheduler/scheduler_config.json

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+{
+  "_class_name": "PNDMScheduler",
+  "_diffusers_version": "0.6.0",
+  "beta_end": 0.012,
+  "beta_schedule": "scaled_linear",
+  "beta_start": 0.00085,
+  "num_train_timesteps": 1000,
+  "set_alpha_to_one": false,
+  "skip_prk_steps": true,
+  "steps_offset": 1,
+  "trained_betas": null,
+  "clip_sample": false
+}

text_encoder_BiomedCLIP/config.json

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+{
+  "_name_or_path": "",
+  "architectures": [
+    "BiomedCLIPModel"
+  ],
+  "auto_map": {
+    "AutoConfig": "configuration_biomed_clip.BiomedCLIPConfig",
+    "AutoProcessor": "processing_biomed_clip.BiomedCLIPProcessor",
+    "AutoModel": "modeling_biomed_clip.BiomedCLIPModel",
+    "AutoModelForImageClassification": "modeling_biomed_clip.BiomedCLIPForImageClassification"
+  },
+  "initializer_factor": 1.0,
+  "logit_scale_init_value": 4.4454,
+  "model_type": "clip",
+  "projection_dim": 512,
+  "text_config": {
+    "attention_probs_dropout_prob": 0.1,
+    "gradient_checkpointing": false,
+    "hidden_act": "gelu",
+    "hidden_dropout_prob": 0.1,
+    "hidden_size": 768,
+    "initializer_range": 0.02,
+    "intermediate_size": 3072,
+    "layer_norm_eps": 1e-12,
+    "max_position_embeddings": 512,
+    "model_type": "bert",
+    "num_attention_heads": 12,
+    "num_hidden_layers": 12,
+    "pad_token_id": 0,
+    "position_embedding_type": "absolute",
+    "transformers_version": "4.6.0.dev0",
+    "type_vocab_size": 2,
+    "use_cache": true,
+    "vocab_size": 30522
+  },
+  "text_config_dict": {
+    "attention_probs_dropout_prob": 0.1,
+    "gradient_checkpointing": false,
+    "hidden_act": "gelu",
+    "hidden_dropout_prob": 0.1,
+    "hidden_size": 768,
+    "initializer_range": 0.02,
+    "intermediate_size": 3072,
+    "layer_norm_eps": 1e-12,
+    "max_position_embeddings": 512,
+    "model_type": "bert",
+    "num_attention_heads": 12,
+    "num_hidden_layers": 12,
+    "pad_token_id": 0,
+    "position_embedding_type": "absolute",
+    "transformers_version": "4.6.0.dev0",
+    "type_vocab_size": 2,
+    "use_cache": true,
+    "vocab_size": 30522
+  },
+  "text_projection_config": {
+    "hidden_size": 768,
+    "intermediate_size": 640,
+    "projection_dim": 512,
+    "hidden_act": "gelu"
+  },
+  "text_projection_config_dict": {
+    "hidden_size": 768,
+    "intermediate_size": 640,
+    "projection_dim": 512,
+    "hidden_act": "gelu",
+    "num_hidden_layers": 2
+  },
+  "torch_dtype": "float32",
+  "transformers_version": null,
+  "vision_config": {
+    "attention_probs_dropout_prob": 0.0,
+    "hidden_act": "gelu",
+    "hidden_dropout_prob": 0.0,
+    "hidden_size": 768,
+    "image_size": 224,
+    "initializer_range": 0.02,
+    "intermediate_size": 3072,
+    "layer_norm_eps": 1e-12,
+    "model_type": "vit",
+    "num_attention_heads": 12,
+    "num_channels": 3,
+    "num_hidden_layers": 12,
+    "patch_size": 16,
+    "qkv_bias": true
+  },
+  "vision_config_dict": {
+    "attention_probs_dropout_prob": 0.0,
+    "hidden_act": "gelu",
+    "hidden_dropout_prob": 0.0,
+    "hidden_size": 768,
+    "image_size": 224,
+    "initializer_range": 0.02,
+    "intermediate_size": 3072,
+    "layer_norm_eps": 1e-12,
+    "model_type": "vit",
+    "num_attention_heads": 12,
+    "num_channels": 3,
+    "num_hidden_layers": 12,
+    "patch_size": 16,
+    "qkv_bias": true
+  }
+}

text_encoder_BiomedCLIP/configuration_biomed_clip.py

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+import os
+from typing import *
+from transformers.configuration_utils import PretrainedConfig
+from transformers.models.clip.configuration_clip import CLIPConfig, CLIPTextConfig, CLIPVisionConfig
+
+class BiomedCLIPTextProjectionConfig(PretrainedConfig):
+    def __init__(
+        self,
+        hidden_size=768,
+        intermediate_size=640,
+        projection_dim=512,
+        num_hidden_layers=2,
+        **kwargs,
+    ):
+        super().__init__(**kwargs)
+
+        self.hidden_size = hidden_size
+        self.intermediate_size = intermediate_size
+        self.projection_dim = projection_dim
+        self.num_hidden_layers = num_hidden_layers
+
+    @classmethod
+    def from_pretrained(cls, pretrained_model_name_or_path: Union[str, os.PathLike], **kwargs) -> "PretrainedConfig":
+        cls._set_token_in_kwargs(kwargs)
+
+        config_dict, kwargs = cls.get_config_dict(pretrained_model_name_or_path, **kwargs)
+
+        # get the vision config dict if we are loading from CLIPConfig
+        if config_dict.get("model_type") == "clip":
+            config_dict = config_dict["text_projection_config"]
+
+        if "model_type" in config_dict and hasattr(cls, "model_type") and config_dict["model_type"] != cls.model_type:
+            logger.warning(
+                f"You are using a model of type {config_dict['model_type']} to instantiate a model of type "
+                f"{cls.model_type}. This is not supported for all configurations of models and can yield errors."
+            )
+
+        return cls.from_dict(config_dict, **kwargs)
+
+class BiomedCLIPConfig(CLIPConfig):
+    def __init__(
+        self, text_config=None, text_projection_config=None, vision_config=None, projection_dim=512, logit_scale_init_value=2.6592, **kwargs
+    ):
+        # If `_config_dict` exist, we use them for the backward compatibility.
+        # We pop out these 2 attributes before calling `super().__init__` to avoid them being saved (which causes a lot
+        # of confusion!).
+        super().__init__(text_config, vision_config, projection_dim, logit_scale_init_value, **kwargs)
+        
+        text_projection_config_dict = kwargs.pop("text_projection_config_dict", None)
+        if text_projection_config is None:
+            if text_projection_config_dict is not None:
+                text_projection_config = {}
+    
+                _text_projection_config_dict = BiomedCLIPTextProjectionConfig(**text_projection_config_dict)
+                
+                text_projection_config.update(_text_projection_config_dict)
+        else:
+            text_projection_config = BiomedCLIPTextProjectionConfig(**text_projection_config)
+            
+        self.text_projection_config = text_projection_config

text_encoder_BiomedCLIP/model.safetensors

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+version https://git-lfs.github.com/spec/v1
+oid sha256:8d6e9edd227566b056eef0c682bb13f9e501364c1c29b8ccb06986a9ffb5cfbb
+size 783658420

text_encoder_BiomedCLIP/modeling_biomed_clip.py

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+# coding=utf-8
+# Modified 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)
+## ******************************** ##
+# Copyright 2021 The OpenAI Team Authors and The HuggingFace 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.
+""" PyTorch BiomedCLIP model """
+""" No need for timm or open-clip-torch """
+
+
+from dataclasses import dataclass
+from typing import Any, Optional, Tuple, Union, List
+
+import math
+import torch
+import torch.utils.checkpoint
+from torch import nn
+from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
+
+from transformers.activations import ACT2FN
+from transformers.modeling_attn_mask_utils import _create_4d_causal_attention_mask, _prepare_4d_attention_mask
+from transformers.modeling_outputs import (
+    BaseModelOutput, 
+    BaseModelOutputWithPooling, 
+    ImageClassifierOutput,
+    BaseModelOutputWithPoolingAndCrossAttentions,
+    BaseModelOutputWithPastAndCrossAttentions
+)
+from transformers.modeling_utils import PreTrainedModel
+from transformers.utils import (
+    ModelOutput,
+    add_code_sample_docstrings,
+    add_start_docstrings,
+    add_start_docstrings_to_model_forward,
+    logging,
+    replace_return_docstrings,
+)
+from transformers.models.clip.configuration_clip import CLIPConfig, CLIPTextConfig, CLIPVisionConfig
+from transformers.models.clip.modeling_clip import *
+
+from .configuration_biomed_clip import BiomedCLIPTextProjectionConfig, BiomedCLIPConfig
+
+
+logger = logging.get_logger(__name__)
+
+
+
+# contrastive loss function, adapted from
+# https://sachinruk.github.io/blog/2021-03-07-clip.html
+def contrastive_loss(logits: torch.Tensor) -> torch.Tensor:
+    return nn.functional.cross_entropy(logits, torch.arange(len(logits), device=logits.device))
+
+
+def clip_loss(similarity: torch.Tensor) -> torch.Tensor:
+    caption_loss = contrastive_loss(similarity)
+    image_loss = contrastive_loss(similarity.t())
+    return (caption_loss + image_loss) / 2.0
+
+
+class BiomedCLIPVisionEmbeddings(CLIPVisionEmbeddings):
+    def __init__(self, config: CLIPVisionConfig):
+        super().__init__(config)
+
+        self.patch_embedding = nn.Conv2d(
+            in_channels=config.num_channels,
+            out_channels=self.embed_dim,
+            kernel_size=self.patch_size,
+            stride=self.patch_size,
+            # True in open_clip
+            bias=True,
+        )
+
+# TODO
+class BiomedCLIPTextEmbeddings(nn.Module):
+    def __init__(self, config: CLIPTextConfig):
+        super().__init__()
+        embed_dim = config.hidden_size
+
+        self.token_embedding = nn.Embedding(config.vocab_size, embed_dim)
+        self.position_embedding = nn.Embedding(config.max_position_embeddings, embed_dim)
+        self.token_type_embedding = nn.Embedding(config.type_vocab_size, embed_dim)
+
+        self.layer_norm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        # position_ids (1, len position emb) is contiguous in memory and exported when serialized
+        self.position_embedding_type = getattr(config, "position_embedding_type", "absolute")
+
+        # position_ids (1, len position emb) is contiguous in memory and exported when serialized
+        self.register_buffer(
+            "position_ids", torch.arange(config.max_position_embeddings).expand((1, -1)), persistent=False
+        )
+        self.register_buffer(
+            "token_type_ids", torch.zeros(self.position_ids.size(), dtype=torch.long), persistent=False
+        )
+
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        token_type_ids: Optional[torch.LongTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        past_key_values_length: int = 0,
+    ) -> torch.Tensor:
+        
+        if input_ids is not None:
+            input_shape = input_ids.size()
+        else:
+            input_shape = inputs_embeds.size()[:-1]
+
+        seq_length = input_shape[1]
+
+        if position_ids is None:
+            position_ids = self.position_ids[:, past_key_values_length : seq_length + past_key_values_length]
+
+        # Setting the token_type_ids to the registered buffer in constructor where it is all zeros, which usually occurs
+        # when its auto-generated, registered buffer helps users when tracing the model without passing token_type_ids, solves
+        # issue #5664
+        if token_type_ids is None:
+            if hasattr(self, "token_type_ids"):
+                buffered_token_type_ids = self.token_type_ids[:, :seq_length]
+                buffered_token_type_ids_expanded = buffered_token_type_ids.expand(input_shape[0], seq_length)
+                token_type_ids = buffered_token_type_ids_expanded
+            else:
+                token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=self.position_ids.device)
+
+        if inputs_embeds is None:
+            inputs_embeds = self.token_embedding(input_ids)
+        token_type_embeddings = self.token_type_embedding(token_type_ids)
+
+        embeddings = inputs_embeds + token_type_embeddings
+        if self.position_embedding_type == "absolute":
+            position_embeddings = self.position_embedding(position_ids)
+            embeddings += position_embeddings
+            
+        embeddings = self.layer_norm(embeddings)
+        embeddings = self.dropout(embeddings)
+        return embeddings
+
+
+class BiomedCLIPAttention(nn.Module):
+    def __init__(self, config, position_embedding_type=None):
+        super().__init__()
+        super().__init__()
+        self.config = config
+        self.embed_dim = config.hidden_size
+        self.num_heads = config.num_attention_heads
+        self.head_dim = self.embed_dim // self.num_heads
+        if self.head_dim * self.num_heads != self.embed_dim:
+            raise ValueError(
+                f"embed_dim must be divisible by num_heads (got `embed_dim`: {self.embed_dim} and `num_heads`:"
+                f" {self.num_heads})."
+            )
+        self.scale = self.head_dim**-0.5
+        self.dropout = nn.Dropout(config.attention_dropout)
+
+        self.k_proj = nn.Linear(self.embed_dim, self.embed_dim)
+        self.v_proj = nn.Linear(self.embed_dim, self.embed_dim)
+        self.q_proj = nn.Linear(self.embed_dim, self.embed_dim)
+        self.out_proj = nn.Linear(self.embed_dim, self.embed_dim)
+
+    def transpose_for_scores(self, x: torch.Tensor) -> torch.Tensor:
+        new_x_shape = x.size()[:-1] + (self.num_heads, self.head_dim)
+        x = x.view(new_x_shape)
+        return x.permute(0, 2, 1, 3)
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.FloatTensor] = None,
+        past_key_value: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
+        output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.Tensor]:
+        
+        mixed_query_layer = self.q_proj(hidden_states)
+
+        # If this is instantiated as a cross-attention module, the keys
+        # and values come from an encoder; the attention mask needs to be
+        # such that the encoder's padding tokens are not attended to.
+        is_cross_attention = encoder_hidden_states is not None
+
+        key_layer = self.transpose_for_scores(self.k_proj(hidden_states))
+        value_layer = self.transpose_for_scores(self.v_proj(hidden_states))
+
+        query_layer = self.transpose_for_scores(mixed_query_layer)
+
+
+        # Take the dot product between "query" and "key" to get the raw attention scores.
+        attention_scores = torch.matmul(query_layer, key_layer.transpose(-1, -2))
+
+
+        attention_scores = attention_scores / math.sqrt(self.head_dim)
+        if attention_mask is not None:
+            # Apply the attention mask is (precomputed for all layers in BertModel forward() function)
+            attention_scores = attention_scores + attention_mask
+
+        # Normalize the attention scores to probabilities.
+        attention_probs = nn.functional.softmax(attention_scores, dim=-1)
+
+        # This is actually dropping out entire tokens to attend to, which might
+        # seem a bit unusual, but is taken from the original Transformer paper.
+        attention_probs = self.dropout(attention_probs)
+
+
+        context_layer = torch.matmul(attention_probs, value_layer)
+
+        context_layer = context_layer.permute(0, 2, 1, 3).contiguous()
+        new_context_layer_shape = context_layer.size()[:-2] + (self.embed_dim,)
+        context_layer = context_layer.view(new_context_layer_shape).contiguous()
+
+        outputs = self.out_proj(context_layer)
+        return outputs, attention_probs
+
+        
+
+
+class BiomedCLIPEncoderLayer(nn.Module):
+    def __init__(self, config: BiomedCLIPConfig, norm='pre'):
+        super().__init__()
+        self.embed_dim = config.hidden_size
+        # pre-norm
+        self.layer_norm1 = nn.LayerNorm(self.embed_dim, eps=config.layer_norm_eps)
+        self.self_attn = BiomedCLIPAttention(config)
+        self.layer_norm2 = nn.LayerNorm(self.embed_dim, eps=config.layer_norm_eps)
+        self.mlp = CLIPMLP(config)
+        self.norm = norm
+
+        if self.norm == 'pre':
+            self.forward = self.pre_norm_forward
+        elif self.norm == 'post':
+            self.forward = self.post_norm_forward
+        
+
+    def pre_norm_forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: torch.Tensor,
+        output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.FloatTensor]:
+        """
+        Args:
+            hidden_states (`torch.FloatTensor`): input to the layer of shape `(batch, seq_len, embed_dim)`
+            attention_mask (`torch.FloatTensor`): attention mask of size
+                `(batch, 1, tgt_len, src_len)` where padding elements are indicated by very large negative values.
+                `(config.encoder_attention_heads,)`.
+            output_attentions (`bool`, *optional*):
+                Whether or not to return the attentions tensors of all attention layers. See `attentions` under
+                returned tensors for more detail.
+        """
+        residual = hidden_states
+
+        hidden_states = self.layer_norm1(hidden_states)
+        hidden_states, attn_weights = self.self_attn(
+            hidden_states=hidden_states,
+            attention_mask=attention_mask,
+            output_attentions=output_attentions,
+        )
+        hidden_states = residual + hidden_states
+
+        residual = hidden_states
+        hidden_states = self.layer_norm2(hidden_states)
+        hidden_states = self.mlp(hidden_states)
+        hidden_states = residual + hidden_states
+
+        outputs = (hidden_states,)
+
+        if output_attentions:
+            outputs += (attn_weights,)
+
+        return outputs
+    
+    def post_norm_forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: torch.Tensor,
+        output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.FloatTensor]:
+        """
+        Args:
+            hidden_states (`torch.FloatTensor`): input to the layer of shape `(batch, seq_len, embed_dim)`
+            attention_mask (`torch.FloatTensor`): attention mask of size
+                `(batch, 1, tgt_len, src_len)` where padding elements are indicated by very large negative values.
+                `(config.encoder_attention_heads,)`.
+            output_attentions (`bool`, *optional*):
+                Whether or not to return the attentions tensors of all attention layers. See `attentions` under
+                returned tensors for more detail.
+        """
+        residual = hidden_states
+
+        hidden_states, attn_weights = self.self_attn(
+            hidden_states=hidden_states,
+            attention_mask=attention_mask,
+            output_attentions=output_attentions,
+        )
+        hidden_states = residual + hidden_states
+        
+        hidden_states = self.layer_norm1(hidden_states)
+        
+        residual = hidden_states
+        hidden_states = self.mlp(hidden_states)
+        hidden_states = residual + hidden_states
+        hidden_states = self.layer_norm2(hidden_states)
+        outputs = (hidden_states,)
+
+        if output_attentions:
+            outputs += (attn_weights,)
+
+        return outputs
+
+
+class BiomedCLIPTextProjection(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+        self.fc1 = nn.Linear(config.hidden_size, config.intermediate_size, bias=False)
+        self.activation_fn = ACT2FN[config.hidden_act]
+        self.fc2 = nn.Linear(config.intermediate_size, config.projection_dim, bias=False)
+
+    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.fc1(hidden_states)
+        hidden_states = self.activation_fn(hidden_states)
+        hidden_states = self.fc2(hidden_states)
+        return hidden_states
+
+
+class BiomedCLIPEncoder(nn.Module):
+    """
+    Transformer encoder consisting of `config.num_hidden_layers` self attention layers. Each layer is a
+    [`BiomedCLIPEncoderLayer`].
+    Args:
+        config: BiomedCLIPConfig
+    """
+    def __init__(self, config, norm='pre'):
+        super().__init__()
+        self.config = config
+        self.norm = norm
+        self.layers = nn.ModuleList([BiomedCLIPEncoderLayer(config, norm) for _ in range(config.num_hidden_layers)])
+        self.gradient_checkpointing = False
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.FloatTensor] = None,
+        past_key_values: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = False,
+        output_hidden_states: Optional[bool] = False,
+        return_dict: Optional[bool] = True,
+    ) :
+        all_hidden_states = () if output_hidden_states else None
+        all_self_attentions = () if output_attentions else None
+        all_cross_attentions = () if output_attentions and self.config.add_cross_attention else None
+
+        if self.gradient_checkpointing and self.training:
+            if use_cache:
+                logger.warning_once(
+                    "`use_cache=True` is incompatible with gradient checkpointing. Setting `use_cache=False`..."
+                )
+                use_cache = False
+
+        next_decoder_cache = () if use_cache else None
+        for i, layer_module in enumerate(self.layers):
+            if output_hidden_states:
+                all_hidden_states = all_hidden_states + (hidden_states,)
+
+            layer_head_mask = head_mask[i] if head_mask is not None else None
+            past_key_value = past_key_values[i] if past_key_values is not None else None
+
+            if self.gradient_checkpointing and self.training:
+                layer_outputs = self._gradient_checkpointing_func(
+                    layer_module.__call__,
+                    hidden_states,
+                    attention_mask,
+                    output_attentions,
+                )
+            else:
+                layer_outputs = layer_module(
+                    hidden_states,
+                    attention_mask,
+                    output_attentions,
+                )
+
+            hidden_states = layer_outputs[0]
+            if use_cache:
+                next_decoder_cache += (layer_outputs[-1],)
+            if output_attentions:
+                all_self_attentions = all_self_attentions + (layer_outputs[1],)
+                if self.config.add_cross_attention:
+                    all_cross_attentions = all_cross_attentions + (layer_outputs[2],)
+
+        if output_hidden_states:
+            all_hidden_states = all_hidden_states + (hidden_states,)
+
+        if not return_dict:
+            return tuple(
+                v
+                for v in [
+                    hidden_states,
+                    next_decoder_cache,
+                    all_hidden_states,
+                    all_self_attentions,
+                    all_cross_attentions,
+                ]
+                if v is not None
+            )
+        return BaseModelOutputWithPastAndCrossAttentions(
+            last_hidden_state=hidden_states,
+            past_key_values=next_decoder_cache,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attentions,
+            cross_attentions=all_cross_attentions,
+        )
+
+
+
+class BiomedCLIPTextTransformer(CLIPPreTrainedModel):
+    def __init__(self, config: CLIPTextConfig):
+        super().__init__(config)
+        self.config = config
+        embed_dim = config.hidden_size
+        self.embeddings = BiomedCLIPTextEmbeddings(config)
+        self.encoder = BiomedCLIPEncoder(config, norm='post')
+        # no final_ln
+        # self.final_layer_norm = nn.LayerNorm(embed_dim, eps=config.layer_norm_eps)
+
+        # For `pooled_output` computation
+
+    def forward(
+        self,
+        input_ids: Optional[torch.Tensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        token_type_ids: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        encoder_hidden_states: Optional[torch.Tensor] = None,
+        encoder_attention_mask: Optional[torch.Tensor] = None,
+        past_key_values: Optional[List[torch.FloatTensor]] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple[torch.Tensor], BaseModelOutputWithPoolingAndCrossAttentions]:
+        r"""
+        encoder_hidden_states  (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+            Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
+            the model is configured as a decoder.
+        encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
+            the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+        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)`):
+            Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.
+            If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
+            don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
+            `decoder_input_ids` of shape `(batch_size, sequence_length)`.
+        use_cache (`bool`, *optional*):
+            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
+            `past_key_values`).
+        """
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        if self.config.is_decoder:
+            use_cache = use_cache if use_cache is not None else self.config.use_cache
+        else:
+            use_cache = False
+
+        if input_ids is not None and inputs_embeds is not None:
+            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
+        elif input_ids is not None:
+            input_shape = input_ids.size()
+        elif inputs_embeds is not None:
+            input_shape = inputs_embeds.size()[:-1]
+        else:
+            raise ValueError("You have to specify either input_ids or inputs_embeds")
+
+        batch_size, seq_length = input_shape
+        device = input_ids.device if input_ids is not None else inputs_embeds.device
+
+        # past_key_values_length
+        past_key_values_length = past_key_values[0][0].shape[2] if past_key_values is not None else 0
+
+        if token_type_ids is None:
+            if hasattr(self.embeddings, "token_type_ids"):
+                buffered_token_type_ids = self.embeddings.token_type_ids[:, :seq_length]
+                buffered_token_type_ids_expanded = buffered_token_type_ids.expand(batch_size, seq_length)
+                token_type_ids = buffered_token_type_ids_expanded
+            else:
+                token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=device)
+
+        embedding_output = self.embeddings(
+            input_ids=input_ids,
+            position_ids=position_ids,
+            token_type_ids=token_type_ids,
+            inputs_embeds=inputs_embeds,
+            past_key_values_length=past_key_values_length,
+        )
+
+        if attention_mask is None:
+            attention_mask = torch.ones((batch_size, seq_length + past_key_values_length), device=device)
+
+        # We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length]
+        # ourselves in which case we just need to make it broadcastable to all heads.
+        extended_attention_mask = self.get_extended_attention_mask(attention_mask, input_shape)
+
+        # If a 2D or 3D attention mask is provided for the cross-attention
+        # we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length]
+        if self.config.is_decoder and encoder_hidden_states is not None:
+            encoder_batch_size, encoder_sequence_length, _ = encoder_hidden_states.size()
+            encoder_hidden_shape = (encoder_batch_size, encoder_sequence_length)
+            if encoder_attention_mask is None:
+                encoder_attention_mask = torch.ones(encoder_hidden_shape, device=device)
+
+            if use_sdpa_attention_masks:
+                # Expand the attention mask for SDPA.
+                # [bsz, seq_len] -> [bsz, 1, seq_len, seq_len]
+                encoder_extended_attention_mask = _prepare_4d_attention_mask_for_sdpa(
+                    encoder_attention_mask, embedding_output.dtype, tgt_len=seq_length
+                )
+            else:
+                encoder_extended_attention_mask = self.invert_attention_mask(encoder_attention_mask)
+        else:
+            encoder_extended_attention_mask = None
+
+                
+        encoder_outputs = self.encoder(
+            embedding_output,
+            attention_mask=extended_attention_mask,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        sequence_output = encoder_outputs[0]
+
+        return (sequence_output, sequence_output[:, 0, :])
+        
+    
+
+class BiomedCLIPVisionTransformer(nn.Module):
+    def __init__(self, config: CLIPVisionConfig):
+        super().__init__()
+        self.config = config
+        embed_dim = config.hidden_size
+
+        self.embeddings = BiomedCLIPVisionEmbeddings(config)
+        # No pre_norm in open_clip Vision Tower
+        # self.pre_layrnorm = nn.LayerNorm(embed_dim, eps=config.layer_norm_eps)
+        self.encoder = BiomedCLIPEncoder(config)
+        self.post_layernorm = nn.LayerNorm(embed_dim, eps=config.layer_norm_eps)
+
+    def forward(
+        self,
+        pixel_values: Optional[torch.FloatTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, BaseModelOutputWithPooling]:
+        r"""
+        Returns:
+        """
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        if pixel_values is None:
+            raise ValueError("You have to specify pixel_values")
+
+        hidden_states = self.embeddings(pixel_values)
+        # hidden_states = self.pre_layrnorm(hidden_states)
+
+        encoder_outputs = self.encoder(
+            hidden_states=hidden_states,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        last_hidden_state = encoder_outputs[0]
+        pooled_output = last_hidden_state[:, 0, :]
+        pooled_output = self.post_layernorm(pooled_output)
+
+        if not return_dict:
+            return (last_hidden_state, pooled_output) + encoder_outputs[1:]
+
+        return BaseModelOutputWithPooling(
+            last_hidden_state=last_hidden_state,
+            pooler_output=pooled_output,
+            hidden_states=encoder_outputs.hidden_states,
+            attentions=encoder_outputs.attentions,
+        )
+
+
+class BiomedCLIPModel(CLIPPreTrainedModel):
+    config_class = BiomedCLIPConfig
+    _no_split_modules = ["BiomedCLIPTextEmbeddings", "BiomedCLIPEncoderLayer"]
+
+    def __init__(self, config: BiomedCLIPConfig):
+        super().__init__(config)
+
+        if not isinstance(config.text_config, CLIPTextConfig):
+            raise ValueError(
+                "config.text_config is expected to be of type CLIPTextConfig but is of type"
+                f" {type(config.text_config)}."
+            )
+
+        if not isinstance(config.vision_config, CLIPVisionConfig):
+            raise ValueError(
+                "config.vision_config is expected to be of type CLIPVisionConfig but is of type"
+                f" {type(config.vision_config)}."
+            )
+
+        text_config = config.text_config
+        text_projection_config = config.text_projection_config
+        vision_config = config.vision_config
+        
+
+        self.projection_dim = config.projection_dim
+        self.text_embed_dim = text_config.hidden_size
+        self.vision_embed_dim = vision_config.hidden_size
+
+        self.text_model = BiomedCLIPTextTransformer(text_config)
+        self.vision_model = BiomedCLIPVisionTransformer(vision_config)
+        
+        self.visual_projection = nn.Linear(self.vision_embed_dim, self.projection_dim, bias=False)
+        
+        self.text_projection = BiomedCLIPTextProjection(text_projection_config)
+        
+        self.logit_scale = nn.Parameter(torch.tensor(self.config.logit_scale_init_value))
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_text_features(
+        self,
+        input_ids: Optional[torch.Tensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        token_type_ids: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.Tensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> torch.FloatTensor:
+        r"""
+        Returns:
+            text_features (`torch.FloatTensor` of shape `(batch_size, output_dim`): The text embeddings obtained by
+            applying the projection layer to the pooled output of [`CLIPTextModel`].
+        Examples:
+        ```python
+        >>> from transformers import AutoTokenizer, CLIPModel
+        >>> model = CLIPModel.from_pretrained("openai/clip-vit-base-patch32")
+        >>> tokenizer = AutoTokenizer.from_pretrained("openai/clip-vit-base-patch32")
+        >>> inputs = tokenizer(["a photo of a cat", "a photo of a dog"], padding=True, return_tensors="pt")
+        >>> text_features = model.get_text_features(**inputs)
+        ```"""
+        # Use CLIP model's config for some fields (if specified) instead of those of vision & text components.
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        text_outputs = self.text_model(
+            input_ids=input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        pooled_output = text_outputs[1]
+        text_features = self.text_projection(pooled_output)
+
+        return text_features
+
+    def get_image_features(
+        self,
+        pixel_values: Optional[torch.FloatTensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> torch.FloatTensor:
+        r"""
+        Returns:
+            image_features (`torch.FloatTensor` of shape `(batch_size, output_dim`): The image embeddings obtained by
+            applying the projection layer to the pooled output of [`CLIPVisionModel`].
+        Examples:
+        ```python
+        >>> from PIL import Image
+        >>> import requests
+        >>> from transformers import AutoProcessor, CLIPModel
+        >>> model = CLIPModel.from_pretrained("openai/clip-vit-base-patch32")
+        >>> processor = AutoProcessor.from_pretrained("openai/clip-vit-base-patch32")
+        >>> url = "http://images.cocodataset.org/val2017/000000039769.jpg"
+        >>> image = Image.open(requests.get(url, stream=True).raw)
+        >>> inputs = processor(images=image, return_tensors="pt")
+        >>> image_features = model.get_image_features(**inputs)
+        ```"""
+        # Use CLIP model's config for some fields (if specified) instead of those of vision & text components.
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        vision_outputs = self.vision_model(
+            pixel_values=pixel_values,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        pooled_output = vision_outputs[1]  # pooled_output
+        image_features = self.visual_projection(pooled_output)
+
+        return image_features
+
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        pixel_values: Optional[torch.FloatTensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        token_type_ids: Optional[torch.LongTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        return_loss: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, CLIPOutput]:
+        r"""
+        Returns:
+        Examples:
+        ```python
+        >>> from PIL import Image
+        >>> import requests
+        >>> from transformers import AutoProcessor, CLIPModel
+        >>> model = CLIPModel.from_pretrained("openai/clip-vit-base-patch32")
+        >>> processor = AutoProcessor.from_pretrained("openai/clip-vit-base-patch32")
+        >>> url = "http://images.cocodataset.org/val2017/000000039769.jpg"
+        >>> image = Image.open(requests.get(url, stream=True).raw)
+        >>> inputs = processor(
+        ...     text=["a photo of a cat", "a photo of a dog"], images=image, return_tensors="pt", padding=True
+        ... )
+        >>> outputs = model(**inputs)
+        >>> logits_per_image = outputs.logits_per_image  # this is the image-text similarity score
+        >>> probs = logits_per_image.softmax(dim=1)  # we can take the softmax to get the label probabilities
+        ```"""
+        # Use CLIP model's config for some fields (if specified) instead of those of vision & text components.
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        vision_outputs = self.vision_model(
+            pixel_values=pixel_values,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        text_outputs = self.text_model(
+            input_ids=input_ids,
+            token_type_ids=token_type_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        image_embeds = vision_outputs[1]
+        image_embeds = self.visual_projection(image_embeds)
+
+        text_embeds = text_outputs[1]
+        text_embeds = self.text_projection(text_embeds)
+
+        # normalized features
+        image_embeds = image_embeds / image_embeds.norm(p=2, dim=-1, keepdim=True)
+        text_embeds = text_embeds / text_embeds.norm(p=2, dim=-1, keepdim=True)
+
+        # cosine similarity as logits
+        logit_scale = self.logit_scale.exp()
+        logits_per_text = torch.matmul(text_embeds, image_embeds.t()) * logit_scale
+        logits_per_image = logits_per_text.t()
+
+        loss = None
+        if return_loss:
+            loss = clip_loss(logits_per_text)
+
+        if not return_dict:
+            output = (logits_per_image, logits_per_text, text_embeds, image_embeds, text_outputs, vision_outputs)
+            return ((loss,) + output) if loss is not None else output
+
+        return CLIPOutput(
+            loss=loss,
+            logits_per_image=logits_per_image,
+            logits_per_text=logits_per_text,
+            text_embeds=text_embeds,
+            image_embeds=image_embeds,
+            text_model_output=text_outputs,
+            vision_model_output=vision_outputs,
+        )
+
+
+class BiomedCLIPForImageClassification(CLIPPreTrainedModel):
+    main_input_name = "pixel_values"
+
+    def __init__(self, config: BiomedCLIPConfig) -> None:
+        super().__init__(config)
+
+        self.num_labels = config.num_labels
+        self.vision_model = BiomedCLIPVisionTransformer(config.vision_config)
+
+        # Classifier head
+        self.classifier = (
+            nn.Linear(config.vision_config.hidden_size, config.num_labels) if config.num_labels > 0 else nn.Identity()
+        )
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def forward(
+        self,
+        pixel_values: Optional[torch.Tensor] = None,
+        labels: Optional[torch.Tensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[tuple, ImageClassifierOutput]:
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the image classification/regression loss. Indices should be in `[0, ...,
+            config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
+            `config.num_labels > 1` a classification loss is computed (Cross-Entropy).
+        """
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.vision_model(
+            pixel_values,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output = outputs[0]
+
+        # average pool the patch tokens
+        sequence_output = torch.mean(sequence_output[:, 1:, :], dim=1)
+        # apply classifier
+        logits = self.classifier(sequence_output)
+
+        loss = None
+        if labels is not None:
+            # move labels to correct device to enable model parallelism
+            labels = labels.to(logits.device)
+            if self.config.problem_type is None:
+                if self.num_labels == 1:
+                    self.config.problem_type = "regression"
+                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
+                    self.config.problem_type = "single_label_classification"
+                else:
+                    self.config.problem_type = "multi_label_classification"
+
+            if self.config.problem_type == "regression":
+                loss_fct = MSELoss()
+                if self.num_labels == 1:
+                    loss = loss_fct(logits.squeeze(), labels.squeeze())
+                else:
+                    loss = loss_fct(logits, labels)
+            elif self.config.problem_type == "single_label_classification":
+                loss_fct = CrossEntropyLoss()
+                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
+            elif self.config.problem_type == "multi_label_classification":
+                loss_fct = BCEWithLogitsLoss()
+                loss = loss_fct(logits, labels)
+
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return ImageClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )

text_encoder_BiomedCLIP/preprocessor_config.json

@@ -0,0 +1,20 @@
+{
+  "crop_size": 224,
+  "do_center_crop": true,
+  "do_normalize": true,
+  "do_resize": true,
+  "image_processor_type": "CLIPImageProcessor",
+  "tokenizer_type": "BertTokenizer",
+  "image_mean": [
+    0.48145466,
+    0.4578275,
+    0.40821073
+  ],
+  "image_std": [
+    0.26862954,
+    0.26130258,
+    0.27577711
+  ],
+  "resample": 3,
+  "size": 224
+}

text_encoder_BiomedCLIP/processing_biomed_clip.py

@@ -0,0 +1,146 @@
+# coding=utf-8
+# Copyright 2021 The HuggingFace Inc. team.
+#
+# 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.
+"""
+Image/Text processor class for CLIP
+"""
+
+import warnings
+
+from transformers.processing_utils import ProcessorMixin
+from transformers.tokenization_utils_base import BatchEncoding
+
+
+class BiomedCLIPProcessor(ProcessorMixin):
+    r"""
+    Constructs a CLIP processor which wraps a CLIP image processor and a CLIP tokenizer into a single processor.
+    [`CLIPProcessor`] offers all the functionalities of [`CLIPImageProcessor`] and [`CLIPTokenizerFast`]. See the
+    [`~CLIPProcessor.__call__`] and [`~CLIPProcessor.decode`] for more information.
+    Args:
+        image_processor ([`CLIPImageProcessor`], *optional*):
+            The image processor is a required input.
+        tokenizer ([`CLIPTokenizerFast`], *optional*):
+            The tokenizer is a required input.
+    """
+
+    attributes = ["image_processor", "tokenizer"]
+    image_processor_class = "CLIPImageProcessor"
+    tokenizer_class = ("BertTokenizer", "BertTokenizerFast")
+
+    def __init__(self, image_processor=None, tokenizer=None, **kwargs):
+        feature_extractor = None
+        if "feature_extractor" in kwargs:
+            warnings.warn(
+                "The `feature_extractor` argument is deprecated and will be removed in v5, use `image_processor`"
+                " instead.",
+                FutureWarning,
+            )
+            feature_extractor = kwargs.pop("feature_extractor")
+
+        image_processor = image_processor if image_processor is not None else feature_extractor
+        if image_processor is None:
+            raise ValueError("You need to specify an `image_processor`.")
+        if tokenizer is None:
+            raise ValueError("You need to specify a `tokenizer`.")
+
+        super().__init__(image_processor, tokenizer)
+
+    def __call__(self, text=None, images=None, return_tensors=None, **kwargs):
+        """
+        Main method to prepare for the model one or several sequences(s) and image(s). This method forwards the `text`
+        and `kwargs` arguments to CLIPTokenizerFast's [`~CLIPTokenizerFast.__call__`] if `text` is not `None` to encode
+        the text. To prepare the image(s), this method forwards the `images` and `kwrags` arguments to
+        CLIPImageProcessor's [`~CLIPImageProcessor.__call__`] if `images` is not `None`. Please refer to the doctsring
+        of the above two methods for more information.
+        Args:
+            text (`str`, `List[str]`, `List[List[str]]`):
+                The sequence or batch of sequences to be encoded. Each sequence can be a string or a list of strings
+                (pretokenized string). If the sequences are provided as list of strings (pretokenized), you must set
+                `is_split_into_words=True` (to lift the ambiguity with a batch of sequences).
+            images (`PIL.Image.Image`, `np.ndarray`, `torch.Tensor`, `List[PIL.Image.Image]`, `List[np.ndarray]`, `List[torch.Tensor]`):
+                The image or batch of images to be prepared. Each image can be a PIL image, NumPy array or PyTorch
+                tensor. Both channels-first and channels-last formats are supported.
+            return_tensors (`str` or [`~utils.TensorType`], *optional*):
+                If set, will return tensors of a particular framework. Acceptable values are:
+                - `'tf'`: Return TensorFlow `tf.constant` objects.
+                - `'pt'`: Return PyTorch `torch.Tensor` objects.
+                - `'np'`: Return NumPy `np.ndarray` objects.
+                - `'jax'`: Return JAX `jnp.ndarray` objects.
+        Returns:
+            [`BatchEncoding`]: A [`BatchEncoding`] with the following fields:
+            - **input_ids** -- List of token ids to be fed to a model. Returned when `text` is not `None`.
+            - **attention_mask** -- List of indices specifying which tokens should be attended to by the model (when
+              `return_attention_mask=True` or if *"attention_mask"* is in `self.model_input_names` and if `text` is not
+              `None`).
+            - **pixel_values** -- Pixel values to be fed to a model. Returned when `images` is not `None`.
+        """
+        tokenizer_kwargs, image_processor_kwargs = {}, {}
+        if kwargs:
+            tokenizer_kwargs = {k: v for k, v in kwargs.items() if k not in self.image_processor._valid_processor_keys}
+            image_processor_kwargs = {
+                k: v for k, v in kwargs.items() if k in self.image_processor._valid_processor_keys
+            }
+
+        if text is None and images is None:
+            raise ValueError("You have to specify either text or images. Both cannot be none.")
+
+        if text is not None:
+            encoding = self.tokenizer(text, return_tensors=return_tensors, **tokenizer_kwargs)
+
+        if images is not None:
+            image_features = self.image_processor(images, return_tensors=return_tensors, **image_processor_kwargs)
+
+        if text is not None and images is not None:
+            encoding["pixel_values"] = image_features.pixel_values
+            return encoding
+        elif text is not None:
+            return encoding
+        else:
+            return BatchEncoding(data=dict(**image_features), tensor_type=return_tensors)
+
+    def batch_decode(self, *args, **kwargs):
+        """
+        This method forwards all its arguments to CLIPTokenizerFast's [`~PreTrainedTokenizer.batch_decode`]. Please
+        refer to the docstring of this method for more information.
+        """
+        return self.tokenizer.batch_decode(*args, **kwargs)
+
+    def decode(self, *args, **kwargs):
+        """
+        This method forwards all its arguments to CLIPTokenizerFast's [`~PreTrainedTokenizer.decode`]. Please refer to
+        the docstring of this method for more information.
+        """
+        return self.tokenizer.decode(*args, **kwargs)
+
+    @property
+    def model_input_names(self):
+        tokenizer_input_names = self.tokenizer.model_input_names
+        image_processor_input_names = self.image_processor.model_input_names
+        return list(dict.fromkeys(tokenizer_input_names + image_processor_input_names))
+
+    @property
+    def feature_extractor_class(self):
+        warnings.warn(
+            "`feature_extractor_class` is deprecated and will be removed in v5. Use `image_processor_class` instead.",
+            FutureWarning,
+        )
+        return self.image_processor_class
+
+    @property
+    def feature_extractor(self):
+        warnings.warn(
+            "`feature_extractor` is deprecated and will be removed in v5. Use `image_processor` instead.",
+            FutureWarning,
+        )
+        return self.image_processor

text_encoder_BiomedCLIP/pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5bdc400de59a85620ddc7584d06913dc901c47f22647899c6addec71b9a5c9a2
+size 783733062

tokenizer_BiomedCLIP/special_tokens_map.json

@@ -0,0 +1,7 @@
+{
+  "cls_token": "[CLS]",
+  "mask_token": "[MASK]",
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "unk_token": "[UNK]"
+}

tokenizer_BiomedCLIP/tokenizer_config.json

@@ -0,0 +1,15 @@
+{
+  "clean_up_tokenization_spaces": true,
+  "cls_token": "[CLS]",
+  "do_basic_tokenize": true,
+  "do_lower_case": true,
+  "mask_token": "[MASK]",
+  "model_max_length": 1000000000000000019884624838656,
+  "never_split": null,
+  "pad_token": "[PAD]",
+  "sep_token": "[SEP]",
+  "strip_accents": null,
+  "tokenize_chinese_chars": true,
+  "tokenizer_class": "BertTokenizer",
+  "unk_token": "[UNK]"
+}

vae/config.json

@@ -0,0 +1,31 @@
+{
+  "_class_name": "AutoencoderKL",
+  "_diffusers_version": "0.29.2",
+  "_name_or_path": "/mnt/petrelfs/wuhaoning/MedicalGen/MRI_diffusion/train_vae/MedGen_MRI_CT_240930-000404/checkpoint_lastest/",
+  "act_fn": "silu",
+  "block_out_channels": [
+    128,
+    256,
+    512,
+    512
+  ],
+  "down_block_types": [
+    "DownEncoderBlock2D",
+    "DownEncoderBlock2D",
+    "DownEncoderBlock2D",
+    "DownEncoderBlock2D"
+  ],
+  "in_channels": 1,
+  "latent_channels": 16,
+  "layers_per_block": 2,
+  "norm_num_groups": 32,
+  "out_channels": 1,
+  "sample_size": 512,
+  "scaling_factor": 1.003,
+  "up_block_types": [
+    "UpDecoderBlock2D",
+    "UpDecoderBlock2D",
+    "UpDecoderBlock2D",
+    "UpDecoderBlock2D"
+  ]
+}

vae/diffusion_pytorch_model.safetensors

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+version https://git-lfs.github.com/spec/v1
+oid sha256:9eb7d0e0e2f647d82f02eb285d8fb885b1247d1ec9342c5770855a27809ec6f8
+size 335293452