Feature Extraction
Transformers
Safetensors
medical
radiology
vision-language
chest-ct
3d-medical-imaging
glint
custom_code
Instructions to use Deepnoid/GLINT-CT with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use Deepnoid/GLINT-CT with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("feature-extraction", model="Deepnoid/GLINT-CT", trust_remote_code=True)# pip install -U transformers accelerate # Load model directly from transformers import AutoModel model = AutoModel.from_pretrained("Deepnoid/GLINT-CT", trust_remote_code=True, device_map="auto") - Notebooks
- Google Colab
- Kaggle
File size: 13,719 Bytes
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import torch
import torch.nn as nn
import torch.nn.functional as F
from .align_layers import build_align_layer
from .common_layers import BasePreTrainedModel
from .configuration_glint import GLINTConfig
from .losses import LossFunctions
from .text_encoders import build_text_encoder
from .vision_encoders import build_vision_encoder
logger = logging.getLogger("glint")
class GLINTModel(BasePreTrainedModel):
config_class = GLINTConfig
# only relevant when vision_only=True drops these submodules; in VLM mode every key loads
_keys_to_ignore_on_load_unexpected = [
r"^text_model\.",
r"^align_layer\.",
r"^loss_fns\.",
r"^dfr_module\.",
r"^vision_layer_norm\.",
r"^text_layer_norm\.",
]
def build_vision_model(self, config):
vision_config = config.vision_config
vision_model = build_vision_encoder(vision_config)
return vision_model
def build_text_model(self, config):
text_config = config.text_config
text_model = build_text_encoder(text_config)
return text_model
def build_align_layer_model(self, config):
align_layer_config = config.align_layer_config
align_layer = build_align_layer(align_layer_config)
return align_layer
def build_dfr_module(self, config):
from .dfr import DFRModule
dfr_module = DFRModule(config.dfr_config)
return dfr_module
def __init__(self, config: GLINTConfig):
super().__init__(config)
logger.info("Build vision model ...")
self.vision_model = self.build_vision_model(config)
if getattr(config, "vision_only", False):
logger.info("vision_only=True: skipping text model, align layer, losses and DFR module.")
return
logger.info("Build text model ...")
self.text_model = self.build_text_model(config)
logger.info("Build align layer model ...")
self.align_layer = self.build_align_layer_model(config)
logger.info("Build loss functions ...")
loss_cfg = config.kwargs["loss"]
self.loss_fns = LossFunctions(loss_cfg)
if hasattr(config, "dfr_config") and config.dfr_config is not None:
logger.info("Build dfr module ...")
self.dfr_module = self.build_dfr_module(config)
self.vision_layer_norm = (
nn.LayerNorm(config.align_layer_config.hidden_size) if config.use_vision_layer_norm else None
)
self.text_layer_norm = nn.LayerNorm(config.text_config.hidden_size) if config.use_text_layer_norm else None
self.compute_logits_type = config.kwargs.get("compute_logits_type")
self.module_to_update = config.kwargs.get("module_to_update")
def forward_vision_model(self, pixel_values, output_hidden_states=False):
vision_model_type = self.config.vision_config.model_type
vision_hidden_states = None
use_cls_token = getattr(self.config.vision_config, "use_cls_token", False)
if vision_model_type == "dinov2":
vision_outputs = self.vision_model(pixel_values, output_hidden_states=output_hidden_states)
vision_tokens = vision_outputs["last_hidden_state"]
if not use_cls_token:
vision_tokens = vision_tokens[:, 1:, :]
vision_hidden_states = vision_outputs.get("hidden_states", None)
elif vision_model_type == "dinov3_vit":
vision_outputs = self.vision_model(pixel_values, output_hidden_states=output_hidden_states)
original_output = vision_outputs["last_hidden_state"]
patch_tokens = original_output[:, 1 + self.config.vision_config.num_register_tokens :, :]
if use_cls_token:
cls_token = original_output[:, :1, :]
vision_tokens = torch.cat([cls_token, patch_tokens], dim=1)
else:
vision_tokens = patch_tokens
vision_hidden_states = vision_outputs.get("hidden_states", None)
elif vision_model_type == "vjepa2":
vision_outputs = self.vision_model(
pixel_values, skip_predictor=True, output_hidden_states=output_hidden_states
)
vision_tokens = vision_outputs["last_hidden_state"]
vision_hidden_states = vision_outputs.get("hidden_states", None)
elif vision_model_type == "vjepa2.1":
vision_outputs = self.vision_model(pixel_values, output_hidden_states=output_hidden_states)
vision_tokens = vision_outputs["last_hidden_state"]
vision_hidden_states = vision_outputs.get("hidden_states", None)
else:
raise NotImplementedError
outputs = {}
vision_tokens = self.align_layer(vision_tokens)
if self.vision_layer_norm is not None:
vision_tokens = self.vision_layer_norm(vision_tokens)
outputs["vision_tokens"] = vision_tokens
outputs["vision_hidden_states"] = vision_hidden_states
return outputs
def forward_text_model(self, encoded_input):
text_outputs = {}
text_model_type = self.config.text_config.model_type
if text_model_type == "mpnet":
model_output = self.text_model(encoded_input["input_ids"], attention_mask=encoded_input["attention_mask"])
token_embeddings = model_output[0]
else:
raise NotImplementedError
if self.config.text_config.use_cls_token:
text_features = token_embeddings[:, 0, :]
else:
input_mask_expanded = (
encoded_input["attention_mask"].unsqueeze(-1).expand(token_embeddings.size()).to(token_embeddings.dtype)
)
text_features = torch.sum(token_embeddings * input_mask_expanded, 1) / torch.clamp(
input_mask_expanded.sum(1), min=1e-9
)
if self.text_layer_norm is not None:
text_features = self.text_layer_norm(text_features)
text_outputs["text_features"] = text_features
text_outputs["text_features_norm"] = F.normalize(text_features, p=2, dim=1)
return text_outputs
def forward(
self,
pixel_values=None,
enc_sents=None,
neg_enc_sents=None,
return_loss=True,
forward_accum_outputs=False,
forward_accum_loss=False,
**kwargs,
):
if forward_accum_outputs:
return self.forward_accum_outputs(
pixel_values=pixel_values,
enc_sents=enc_sents,
neg_enc_sents=neg_enc_sents,
**kwargs,
)
if forward_accum_loss:
return self.forward_accum_loss(**kwargs)
if getattr(self.config, "vision_only", False):
return self.vision_model(pixel_values)
outputs = {}
use_dfr_module = hasattr(self, "dfr_module") and self.dfr_module is not None
vision_outputs = self.forward_vision_model(pixel_values, output_hidden_states=use_dfr_module)
if use_dfr_module:
dfr_outputs = self.dfr_module(
pixel_values=pixel_values,
student_hidden_states=vision_outputs["vision_hidden_states"],
cached_teacher_features=kwargs.get("cached_teacher_features"),
)
outputs.update(dfr_outputs)
outputs.update(vision_outputs)
if return_loss:
loss = 0
losses = {}
for loss_type, loss_fn in self.loss_fns.loss_dict.items():
loss_ratio = self.loss_fns.loss_ratio[loss_type]
if loss_fn.__class__.__name__ == "AlignmentLoss":
loss_outputs = loss_fn(
enc_sents=enc_sents,
neg_enc_sents=neg_enc_sents,
vision_tokens=outputs["vision_tokens"],
forward_text_model=self.forward_text_model,
)
_losses = loss_outputs["losses"]
loop_loss = _losses.pop("loss")
losses.update(_losses)
elif loss_fn.__class__.__name__ == "DFRLoss":
loss_outputs = loss_fn(
proj_student_features=outputs["proj_student_features"],
teacher_features=outputs["teacher_features"],
)
_losses = loss_outputs["losses"]
loop_loss = _losses.pop("loss")
losses.update(_losses)
else:
raise NotImplementedError
loss += loop_loss * loss_ratio
losses["loss"] = loss
outputs["loss"] = loss
outputs["losses"] = losses
return outputs
def compute_logits(
self,
pixel_values,
enc_sents,
**kwargs,
):
vision_outputs = self.forward_vision_model(pixel_values)
outputs = {}
if self.compute_logits_type == "vl_alignment":
loss_fn = self.loss_fns.loss_dict["AlignmentLoss"]
splited_sentences = [
{
"input_ids": enc_sents[0]["input_ids"][i : i + 1],
"attention_mask": enc_sents[0]["attention_mask"][i : i + 1],
}
for i in range(enc_sents[0]["input_ids"].size(0))
]
loss_outputs = loss_fn(
splited_sentences,
vision_outputs["vision_tokens"],
self.forward_text_model,
ddp_gather=False,
need_attn_weights=True,
compute_loss=False,
)
outputs.update(loss_outputs)
similarity_scores = loss_outputs["attn_weights"][0]
if getattr(self.config.vision_config, "use_cls_token", False):
similarity_scores = similarity_scores[:, :, 1:]
outputs["similarity_scores"] = similarity_scores
if "sim_components" in loss_outputs:
comp = loss_outputs["sim_components"]
if getattr(self.config.vision_config, "use_cls_token", False):
comp = {k: v[:, :, 1:] for k, v in comp.items()}
outputs["sim_components"] = comp
logits = loss_outputs["logits"]
logits = logits.T
else:
raise NotImplementedError
outputs["logits"] = logits
return outputs
def forward_accum_outputs(
self,
pixel_values,
enc_sents=None,
neg_enc_sents=None,
**kwargs,
):
use_dfr_module = hasattr(self, "dfr_module") and self.dfr_module is not None
outputs = {}
vision_outputs = self.forward_vision_model(pixel_values, output_hidden_states=use_dfr_module)
outputs.update(vision_outputs)
if use_dfr_module:
dfr_outputs = self.dfr_module(
pixel_values=pixel_values,
student_hidden_states=vision_outputs["vision_hidden_states"],
cached_teacher_features=kwargs.get("cached_teacher_features"),
)
outputs.update(dfr_outputs)
text_outputs = []
for kp in enc_sents:
text_outputs.append(self.forward_text_model(kp)["text_features"])
text_outputs = {"text_features": text_outputs}
outputs.update(text_outputs)
if neg_enc_sents is not None:
negative_text_outputs = []
for kp in neg_enc_sents:
if isinstance(kp["input_ids"], torch.Tensor):
negative_text_outputs.append(self.forward_text_model(kp)["text_features"])
else:
negative_text_outputs.append(
torch.zeros((0, self.config.text_config.hidden_size)).to(pixel_values.device)
)
negative_text_outputs = {"negative_text_features": negative_text_outputs}
outputs.update(negative_text_outputs)
if "ids_mask" in kwargs:
outputs["ids_mask"] = kwargs["ids_mask"]
outputs["mask"] = kwargs["mask"]
return outputs
def forward_accum_loss(
self,
vision_tokens,
text_features,
negative_text_features=None,
**kwargs,
):
outputs = {}
losses = {}
loss = 0
for loss_type, loss_fn in self.loss_fns.loss_dict.items():
loss_ratio = self.loss_fns.loss_ratio[loss_type]
if loss_fn.__class__.__name__ == "AlignmentLoss":
loss_outputs = loss_fn(
enc_sents=None,
neg_enc_sents=None,
vision_tokens=vision_tokens,
forward_text_model=None,
text_feats_list=text_features,
neg_text_feats_list=negative_text_features,
)
_losses = loss_outputs["losses"]
loop_loss = _losses.pop("loss")
losses.update(_losses)
elif loss_fn.__class__.__name__ == "DFRLoss":
loss_outputs = loss_fn(
proj_student_features=kwargs.get("proj_student_features"),
teacher_features=kwargs.get("teacher_features"),
)
_losses = loss_outputs["losses"]
loop_loss = _losses.pop("loss")
losses.update(_losses)
else:
raise NotImplementedError
loss += loop_loss * loss_ratio
losses["loss"] = loss
outputs["loss"] = loss
outputs["losses"] = losses
return outputs
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