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: 20,116 Bytes
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import numpy as np
import torch
import torch.distributed as dist
import torch.nn as nn
import torch.nn.functional as F
from entmax import entmax_bisect
from .dfr import DFRLoss # noqa: F401
logger = logging.getLogger("glint")
def pad_and_gather(tensor):
local_size = torch.tensor(tensor.size(), device=tensor.device)
all_sizes = [torch.zeros_like(local_size) for _ in range(dist.get_world_size())]
dist.all_gather(all_sizes, local_size)
max_size = torch.stack(all_sizes).max(dim=0)[0]
padded_tensor = torch.zeros(max_size.tolist(), device=tensor.device)
padded_tensor[: local_size[0]] = tensor
gathered_tensors = dist.nn.all_gather(padded_tensor)
gathered_tensors = [g[: s[0]] for g, s in zip(gathered_tensors, all_sizes)]
gathered_tensors = torch.cat(gathered_tensors, dim=0)
return gathered_tensors
def pad_and_gather_2nd_dim(tensor, mask):
local_size = torch.tensor(tensor.size(), device=tensor.device)
if local_size[1] == 0:
local_size = torch.tensor([local_size[0], 1, local_size[2]], device=tensor.device)
tensor = torch.zeros(
(local_size[0], 1, local_size[2]),
device=tensor.device,
requires_grad=True,
)
mask = torch.zeros((local_size[0], 1), device=mask.device, dtype=torch.bool)
all_sizes = [torch.zeros_like(local_size) for _ in range(dist.get_world_size())]
dist.all_gather(all_sizes, local_size)
max_len = max([i[1].item() for i in all_sizes])
padded_tensor = torch.zeros((local_size[0], max_len, local_size[2]), device=tensor.device)
padded_tensor[:, : local_size[1]] = tensor
padded_mask = torch.zeros((local_size[0], max_len), device=mask.device)
padded_mask[:, : local_size[1]] = mask
gathered_tensors = dist.nn.all_gather(padded_tensor)
gathered_masks = dist.nn.all_gather(padded_mask)
gathered_tensors = torch.cat(gathered_tensors, dim=0)
gathered_masks = torch.cat(gathered_masks, dim=0)
return gathered_tensors, gathered_masks
def _build_projection(embed_dim, hidden_dim, mode="mlp"):
if mode == "identity":
return nn.Identity()
if mode == "linear":
return nn.Linear(embed_dim, hidden_dim)
if mode == "mlp":
return nn.Sequential(
nn.Linear(embed_dim, hidden_dim),
nn.GELU(),
nn.Linear(hidden_dim, embed_dim),
)
raise ValueError(f"Unknown projection mode: {mode}")
class GatedConfidenceShift(nn.Module):
def __init__(
self,
embed_dim=768,
gate_hidden_dim=768,
sem_hidden_dim=768,
gate_proj_mode="mlp",
sem_proj_mode="identity",
gate_log_temperature=2.302585,
shift_w_init=0.0,
shift_w_no_weight_decay=True,
):
super().__init__()
self.text_gate_proj = _build_projection(embed_dim, gate_hidden_dim, gate_proj_mode)
self.vision_gate_proj = _build_projection(embed_dim, gate_hidden_dim, gate_proj_mode)
self.gate_log_temperature = nn.Parameter(torch.FloatTensor([gate_log_temperature]))
self.text_sem_proj = _build_projection(embed_dim, sem_hidden_dim, sem_proj_mode)
self.vision_sem_proj = _build_projection(embed_dim, sem_hidden_dim, sem_proj_mode)
self.shift_w = nn.Parameter(torch.tensor(float(shift_w_init)))
if shift_w_no_weight_decay:
self.shift_w._no_weight_decay = True
def _compute_gate_evidence(self, gate):
w = entmax_bisect(gate, alpha=2.0, n_iter=50, dim=-1)
return (w * gate).sum(dim=-1)
def forward(self, text_features, vision_tokens, need_attn_weights=False, repeat=True, **kwargs):
if repeat:
query = text_features.unsqueeze(0).expand(vision_tokens.shape[0], text_features.shape[0], -1)
else:
assert text_features.dim() == 3
query = text_features
text_gate = F.normalize(self.text_gate_proj(query), p=2, dim=-1)
vision_gate = F.normalize(self.vision_gate_proj(vision_tokens), p=2, dim=-1)
gate_scores = torch.bmm(text_gate, vision_gate.permute(0, 2, 1))
gate = torch.sigmoid(gate_scores * self.gate_log_temperature.exp())
weight = gate
gate_evidence = self._compute_gate_evidence(gate)
shift = self.shift_w * gate_evidence
sem_text_norm = F.normalize(self.text_sem_proj(query), p=2, dim=-1)
sem_patches_norm = F.normalize(self.vision_sem_proj(vision_tokens), p=2, dim=-1)
aggregated = torch.bmm(weight, sem_patches_norm)
aggregated_norm = F.normalize(aggregated, p=2, dim=-1)
cos_sim = (sem_text_norm * aggregated_norm).sum(dim=-1)
logits = (cos_sim + shift).T
if need_attn_weights:
sem_scores = torch.bmm(sem_text_norm, sem_patches_norm.permute(0, 2, 1))
if "loss_temperature" in kwargs:
scaled_sem = (sem_scores / kwargs["loss_temperature"]).sigmoid()
elif "logit_scale" in kwargs:
scaled_sem = (sem_scores * kwargs["logit_scale"] + kwargs.get("logit_bias", 0.0)).sigmoid()
else:
scaled_sem = sem_scores.sigmoid()
similarity_scores = [scaled_sem * weight]
_comp = {"gate": gate, "semantic": scaled_sem, "weight": weight}
else:
similarity_scores = None
_comp = None
return logits, similarity_scores, _comp
def multi_positive_nce_loss(
logits,
group_map,
temperature,
additional_neg_mask=None,
):
scaled_logits = torch.exp(logits / temperature)
np_total = group_map.size(0)
pos_logits = scaled_logits[torch.arange(np_total), group_map]
row_loss = get_row_loss(
scaled_logits[:np_total],
pos_logits,
)
neg_mask = torch.ones_like(scaled_logits)
if additional_neg_mask is not None:
neg_mask[-len(additional_neg_mask) :, :] = additional_neg_mask
neg_mask[torch.arange(np_total), group_map] = 0
column_loss = get_col_loss(
scaled_logits,
pos_logits,
neg_mask,
group_map,
)
losses = {}
losses["per_text_loss"] = row_loss.mean()
losses["per_image_loss"] = column_loss.mean()
losses["mpnce_loss"] = (losses["per_text_loss"] + losses["per_image_loss"]) / 2
losses["loss"] = losses["mpnce_loss"]
return losses
def multi_positive_nce_local_loss(
logits_per_text,
logits_per_image,
group_map,
local_group_map,
local_group_map_per_image,
temperature,
local_rank,
B_local,
additional_neg_mask=None,
):
logits_per_text = torch.exp(logits_per_text / temperature)
pos_logits_per_text = logits_per_text[torch.arange(logits_per_text.size(0)), local_group_map]
row_loss = get_row_loss(
logits_per_text,
pos_logits_per_text,
)
logits_per_image = torch.exp(logits_per_image / temperature)
local_start_idx = torch.where(group_map == local_rank * B_local)[0][0]
local_end_idx = local_start_idx + len(local_group_map_per_image)
pos_text_indices = torch.LongTensor(range(local_start_idx, local_end_idx))
pos_logits_per_image = logits_per_image[pos_text_indices, local_group_map_per_image]
neg_mask = torch.ones_like(logits_per_image)
if additional_neg_mask is not None:
neg_mask[-len(additional_neg_mask) :, :] = additional_neg_mask
neg_mask[pos_text_indices, local_group_map_per_image] = 0
column_loss = get_col_loss(
logits_per_image,
pos_logits_per_image,
neg_mask,
local_group_map_per_image,
)
losses = {}
losses["per_text_loss"] = row_loss.mean()
losses["per_image_loss"] = column_loss.mean()
losses["mpnce_loss"] = (losses["per_text_loss"] + losses["per_image_loss"]) / 2
losses["loss"] = losses["mpnce_loss"]
return losses
def get_row_loss(
logits: torch.Tensor,
pos_logits: torch.Tensor,
eps: float = 1e-8,
):
row_sum_logits = logits.sum(dim=1)
p_row = pos_logits / (row_sum_logits + eps)
return -torch.log(p_row + eps)
def get_col_loss(
logits: torch.Tensor,
pos_logits: torch.Tensor,
neg_mask: torch.Tensor,
group_map: torch.Tensor,
eps: float = 1e-8,
):
neg_logits = logits * neg_mask
sum_neg_logits = neg_logits.sum(dim=0)
sum_neg_logits = sum_neg_logits[group_map]
p_column = pos_logits / (pos_logits + sum_neg_logits + eps)
return -torch.log(p_column + eps)
class LossFunctions(nn.Module):
def __init__(self, loss_cfg, **kwargs):
super().__init__()
self.loss_ratio = dict()
self.loss_dict = nn.ModuleDict()
for loss_type, ratio in zip(loss_cfg["apply"], loss_cfg["ratio"]):
logger.info(f"Build {loss_type} loss function ...")
if loss_cfg[loss_type] is None:
loss_cfg[loss_type] = dict()
if torch.distributed.is_available() and torch.distributed.is_initialized():
loss_cfg[loss_type]["rank"] = torch.distributed.get_rank()
loss_cfg[loss_type]["world_size"] = torch.distributed.get_world_size()
self.loss_dict[loss_type] = LOSS_REGISTRY[loss_type](**loss_cfg[loss_type])
self.loss_ratio[loss_type] = ratio
class AlignmentLoss(nn.Module):
def __init__(
self,
vl_logit_type="gate_confidence_shift",
vl_logit_kwargs={},
loss_type="mpnce",
loss_kwargs={},
local_loss=False,
**kwargs,
):
super().__init__()
self.vl_logit_type = vl_logit_type
self.init_vl_logit_kwargs(vl_logit_kwargs)
self.loss_type = loss_type
self.init_loss_kwargs(loss_kwargs)
self.local_loss = local_loss
def forward(
self,
enc_sents,
vision_tokens,
forward_text_model=None,
ddp_gather=True,
need_attn_weights=False,
compute_loss=True,
text_feats_list=None,
neg_enc_sents=None,
neg_text_feats_list=None,
**kwargs,
):
outputs = {}
B_local = len(vision_tokens)
local_rank = dist.get_rank() if (ddp_gather and dist.is_initialized()) else 0
text_features, group_map, local_text_features, local_group_map = self.get_text_features(
enc_sents, forward_text_model, ddp_gather, text_feats_list
)
local_vision_tokens = vision_tokens
if ddp_gather and dist.is_initialized():
vision_tokens = torch.cat(dist.nn.all_gather(vision_tokens), dim=0)
if not compute_loss:
logits_outputs = self.compute_logits(text_features, vision_tokens, need_attn_weights)
logits = logits_outputs["logits"]
if self.loss_type == "mpnce":
logits = logits / self.loss_temperature.exp()
logits_outputs["logits"] = logits
outputs.update(logits_outputs)
return outputs
if neg_enc_sents or neg_text_feats_list:
hidden_dim = vision_tokens.shape[-1]
(
neg_text_features,
neg_text_mask,
local_neg_text_features,
local_neg_text_mask,
) = self.get_neg_text_features(
neg_enc_sents,
forward_text_model,
hidden_dim,
ddp_gather,
neg_text_feats_list,
device=vision_tokens.device,
)
else:
(
neg_text_features,
neg_text_mask,
local_neg_text_features,
local_neg_text_mask,
) = (None, None, None, None)
if not (self.local_loss and self.training):
logits_outputs = self.compute_logits(text_features, vision_tokens, need_attn_weights)
logits = logits_outputs["logits"]
if neg_text_features is not None:
neg_logits_outputs = self.compute_logits(
neg_text_features, vision_tokens, need_attn_weights, repeat=False
)
logits = torch.cat([logits, neg_logits_outputs["logits"]], dim=0)
outputs["logits"] = logits
losses = self.compute_loss(
logits,
group_map,
additional_neg_mask=neg_text_mask,
text_features=text_features,
)
else:
logits_outputs_per_text = self.compute_logits(local_text_features, vision_tokens, need_attn_weights)
logits_per_text = logits_outputs_per_text["logits"]
outputs["logits_per_text"] = logits_per_text
logits_outputs_per_image = self.compute_logits(text_features, local_vision_tokens, need_attn_weights)
logits_per_image = logits_outputs_per_image["logits"]
if local_neg_text_features is not None:
neg_logits_outputs = self.compute_logits(
local_neg_text_features,
local_vision_tokens,
need_attn_weights,
repeat=False,
)
logits_per_image = torch.cat([logits_per_image, neg_logits_outputs["logits"]], dim=0)
outputs["logits_per_image"] = logits_per_image
local_group_map_per_image = local_group_map - local_rank * B_local
losses = self.compute_local_loss(
logits_per_text,
logits_per_image,
group_map,
local_group_map,
local_group_map_per_image,
local_rank,
B_local,
additional_neg_mask=local_neg_text_mask,
text_features=text_features,
)
outputs["losses"] = losses
return outputs
def get_feats_list(self, text_feats_list, ddp_gather=True):
text_features = list()
group_list = list()
B_local = sum([len(i) for i in text_feats_list])
local_rank = dist.get_rank() if (ddp_gather and dist.is_initialized()) else 0
local_index = 0
for i, features in enumerate(text_feats_list):
for j, feats in enumerate(features):
text_features.append(feats)
group_list.extend([local_index + local_rank * B_local] * feats.size(0))
local_index += 1
return text_features, group_list
def get_text_features(
self,
enc_sents,
forward_text_model,
ddp_gather=True,
text_feats_list=None,
):
if text_feats_list is not None:
text_features, group_list = self.get_feats_list(text_feats_list, ddp_gather)
else:
text_features = list()
group_list = list()
B_local = len(enc_sents)
local_rank = dist.get_rank() if (ddp_gather and dist.is_initialized()) else 0
for i, kp in enumerate(enc_sents):
feats = forward_text_model(kp)
feat = feats["text_features"]
text_features.append(feat)
global_index = i + local_rank * B_local
group_list.extend([global_index] * feat.size(0))
text_features = torch.cat(text_features, dim=0)
group_map = torch.tensor(group_list, device=text_features.device)
local_text_features = text_features
local_group_map = group_map
if ddp_gather and dist.is_initialized():
text_features = pad_and_gather(text_features)
group_map = pad_and_gather(group_map)
group_map = group_map.long()
return text_features, group_map, local_text_features, local_group_map
def get_neg_feats_list(self, neg_text_feats_list, hidden_dim=None, device=None):
text_features = list()
for i, features in enumerate(neg_text_feats_list):
for j, feats in enumerate(features):
text_features.append(feats)
return text_features
def get_neg_text_features(
self,
neg_enc_sents,
forward_text_model,
hidden_dim,
ddp_gather=True,
neg_text_feats_list=None,
device=None,
):
if neg_text_feats_list is not None:
neg_feats_list = self.get_neg_feats_list(neg_text_feats_list, hidden_dim, device)
else:
neg_feats_list = list()
for i, kp in enumerate(neg_enc_sents):
if isinstance(kp["input_ids"], torch.Tensor):
feats = forward_text_model(kp)
feat = feats["text_features"]
else:
feat = torch.zeros((0, hidden_dim)).to(device)
neg_feats_list.append(feat)
neg_text_features = torch.nn.utils.rnn.pad_sequence(neg_feats_list, batch_first=True, padding_value=0)
neg_text_mask = torch.zeros(
len(neg_feats_list),
neg_text_features.size(1),
dtype=torch.bool,
device=neg_text_features.device,
)
for i, feat in enumerate(neg_feats_list):
neg_text_mask[i, : feat.size(0)] = True
local_neg_text_features = neg_text_features
local_neg_text_mask = neg_text_mask
if ddp_gather and dist.is_initialized():
neg_text_features, neg_text_mask = pad_and_gather_2nd_dim(neg_text_features, neg_text_mask)
local_neg_text_mask = local_neg_text_mask.T
neg_text_mask = neg_text_mask.T
return (
neg_text_features,
neg_text_mask,
local_neg_text_features,
local_neg_text_mask,
)
def init_vl_logit_kwargs(self, vl_logit_kwargs):
self.vl_logit_kwargs = {}
if self.vl_logit_type != "gate_confidence_shift":
raise NotImplementedError(f"Unsupported vl_logit_type: {self.vl_logit_type}")
vl_logit_kwargs.pop("attn_temperature", None)
self.sga = GatedConfidenceShift(**vl_logit_kwargs)
def compute_logits(self, text_features, vision_tokens, need_attn_weights, repeat=True):
outputs = {}
sim_scale_kwargs = {}
if hasattr(self, "loss_temperature"):
sim_scale_kwargs["loss_temperature"] = self.loss_temperature.exp()
logits, attn_weights_list, sim_components = self.sga(
text_features,
vision_tokens,
need_attn_weights,
repeat=repeat,
**sim_scale_kwargs,
**self.vl_logit_kwargs,
)
outputs["logits"] = logits
outputs["attn_weights"] = attn_weights_list
if sim_components is not None:
outputs["sim_components"] = sim_components
return outputs
def init_loss_kwargs(self, loss_kwargs):
self.loss_kwargs = {}
if self.loss_type != "mpnce":
raise NotImplementedError(f"Unsupported loss_type: {self.loss_type}")
self.loss_temperature = nn.Parameter(torch.FloatTensor([np.log(loss_kwargs["temperature"])]))
def compute_loss(self, logits, group_map, additional_neg_mask=None, **kwargs):
return multi_positive_nce_loss(
logits,
group_map,
additional_neg_mask=additional_neg_mask,
temperature=self.loss_temperature.exp(),
**self.loss_kwargs,
)
def compute_local_loss(
self,
logits_per_text,
logits_per_image,
group_map,
local_group_map,
local_group_map_per_image,
local_rank,
B_local,
additional_neg_mask=None,
**kwargs,
):
return multi_positive_nce_local_loss(
logits_per_text,
logits_per_image,
group_map,
local_group_map,
local_group_map_per_image,
temperature=self.loss_temperature.exp(),
local_rank=local_rank,
B_local=B_local,
additional_neg_mask=additional_neg_mask,
**self.loss_kwargs,
)
LOSS_REGISTRY = {"AlignmentLoss": AlignmentLoss, "DFRLoss": DFRLoss}
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