MNT: Update `hi-ml-multimodal` (#928)

Users (including ourselves) keep having issues installing
`hi-ml-multimodal`. I've unpinned the requirements so it's easy to
install and use. I've had to update some bits that were using ancient
versions of e.g. TorchVision. I've checked the notebook and it's working
fine.

Related issues:
- https://github.com/microsoft/hi-ml/issues/927
- https://github.com/microsoft/hi-ml/issues/916
- https://github.com/microsoft/hi-ml/issues/850

Fixes #850.
Fixes #916.
Fixes #927.

hi-ml-multimodal/requirements_run.txt

@@ -1,9 +1,10 @@
-huggingface-hub==0.6.0
+huggingface-hub
-pillow==10.0.1
+matplotlib
-pydicom==2.2.2
+Pillow
-scikit-image==0.18.1
+pydicom
-SimpleITK==2.1.1
+scikit-image
-timm==0.6.5
+SimpleITK
-torch==1.9.0
+timm
-torchvision>0.9,<=0.10.0
+torch
-transformers==4.17.0
+torchvision
+transformers

hi-ml-multimodal/src/health_multimodal/image/model/pretrained.py

@@ -10,7 +10,7 @@ from pathlib import Path
 
 from torch.hub import load_state_dict_from_url
 from torchvision.datasets.utils import download_url
-from torchvision.models.resnet import model_urls
+from torchvision.models.resnet import ResNet50_Weights
 
 from .model import ImageModel
 from .types import ImageEncoderType, ImageEncoderWeightTypes
@@ -75,7 +75,7 @@ def get_biovil_image_encoder(pretrained: bool = True) -> ImageModel:
     return image_model
 
 
-def get_biovil_t_image_encoder() -> ImageModel:
+def get_biovil_t_image_encoder(**kwargs) -> ImageModel:
     """Download weights from Hugging Face and instantiate the image model."""
 
     biovilt_checkpoint_path = _download_biovil_t_image_model_weights()
@@ -84,14 +84,15 @@ def get_biovil_t_image_encoder() -> ImageModel:
         img_encoder_type=model_type,
         joint_feature_size=JOINT_FEATURE_SIZE,
         pretrained_model_path=biovilt_checkpoint_path,
+        **kwargs,
     )
     return image_model
 
 
 def get_imagenet_init_encoder() -> ImageModel:
     """Download ImageNet pre-trained weights and instantiate the image model."""
-
+    url = ResNet50_Weights.IMAGENET1K_V1.url
-    state_dict = load_state_dict_from_url(model_urls[ImageEncoderType.RESNET50])
+    state_dict = load_state_dict_from_url(url)
     image_model = ImageModel(
         img_encoder_type=ImageEncoderType.RESNET50,
         joint_feature_size=JOINT_FEATURE_SIZE,

hi-ml-multimodal/src/health_multimodal/image/model/resnet.py

@@ -7,7 +7,9 @@ from typing import Any, List, Tuple, Type, Union
 
 import torch
 from torch.hub import load_state_dict_from_url
-from torchvision.models.resnet import model_urls, ResNet, BasicBlock, Bottleneck
+from torchvision.models.resnet import ResNet, BasicBlock, Bottleneck
+from torchvision.models.resnet import ResNet18_Weights
+from torchvision.models.resnet import ResNet50_Weights
 
 TypeSkipConnections = Tuple[torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor]
 
@@ -49,7 +51,7 @@ class ResNetHIML(ResNet):
 
 
 def _resnet(
-    arch: str,
+    url: str,
     block: Type[Union[BasicBlock, Bottleneck]],
     layers: List[int],
     pretrained: bool,
@@ -62,7 +64,7 @@ def _resnet(
     """
     model = ResNetHIML(block=block, layers=layers, **kwargs)
     if pretrained:
-        state_dict = load_state_dict_from_url(model_urls[arch], progress=progress)
+        state_dict = load_state_dict_from_url(url, progress=progress)
         model.load_state_dict(state_dict)
     return model
 
@@ -74,7 +76,8 @@ def resnet18(pretrained: bool = False, progress: bool = True, **kwargs: Any) ->
     :param pretrained: If ``True``, returns a model pre-trained on ImageNet.
     :param progress: If ``True``, displays a progress bar of the download to ``stderr``.
     """
-    return _resnet('resnet18', BasicBlock, [2, 2, 2, 2], pretrained, progress, **kwargs)
+    url = ResNet18_Weights.IMAGENET1K_V1.url
+    return _resnet(url, BasicBlock, [2, 2, 2, 2], pretrained, progress, **kwargs)
 
 
 def resnet50(pretrained: bool = False, progress: bool = True, **kwargs: Any) -> ResNetHIML:
@@ -84,4 +87,5 @@ def resnet50(pretrained: bool = False, progress: bool = True, **kwargs: Any) ->
     :param pretrained: If ``True``, returns a model pre-trained on ImageNet
     :param progress: If ``True``, displays a progress bar of the download to ``stderr``.
     """
-    return _resnet('resnet50', Bottleneck, [3, 4, 6, 3], pretrained, progress, **kwargs)
+    url = ResNet50_Weights.IMAGENET1K_V1.url
+    return _resnet(url, Bottleneck, [3, 4, 6, 3], pretrained, progress, **kwargs)

hi-ml-multimodal/src/health_multimodal/image/model/transformer.py

@@ -11,7 +11,6 @@ from typing import Any, Callable, Optional, Set, Tuple
 import torch
 import torch.nn as nn
 from timm.models.layers import DropPath, Mlp, trunc_normal_
-from transformers.pytorch_utils import torch_int_div
 
 
 @dataclass
@@ -265,7 +264,7 @@ class SinePositionEmbedding:
             x_embed = x_embed / (x_embed[:, :, -1:] + 1e-6) * self.scale
 
         dim_t = torch.arange(self.embedding_dim, dtype=torch.float32)
-        dim_t = self.temperature ** (2 * torch_int_div(dim_t, 2) / self.embedding_dim)
+        dim_t = self.temperature ** (2 * torch.div(dim_t, 2, rounding_mode="floor") / self.embedding_dim)
 
         pos_x = x_embed[:, :, :, None] / dim_t
         pos_y = y_embed[:, :, :, None] / dim_t

hi-ml-multimodal/src/health_multimodal/text/model/modelling_cxrbert.py

@@ -3,6 +3,7 @@
 #  Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
 #  ------------------------------------------------------------------------------------------
 
+from dataclasses import dataclass
 from typing import Any, Optional, Tuple, Union
 
 import torch
@@ -17,9 +18,10 @@ from health_multimodal.text.model.configuration_cxrbert import CXRBertConfig
 BERTTupleOutput = Tuple[T, T, T, T, T]
 
 
+@dataclass
 class CXRBertOutput(ModelOutput):
     last_hidden_state: torch.FloatTensor
-    logits: torch.FloatTensor
+    logits: Optional[torch.FloatTensor] = None
     cls_projected_embedding: Optional[torch.FloatTensor] = None
     hidden_states: Optional[Tuple[torch.FloatTensor]] = None
     attentions: Optional[Tuple[torch.FloatTensor]] = None