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label-set-loss-functions

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Label-set loss functions for partial supervision in image segmentation

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# Label-set Loss Functions for Partial Supervision
Label-set loss functions are loss functions 
that can handle partially segmented images,
i.e. images for which some, but not all, regions of interest
are segmented.

## Installation
```bash
pip install git+https://github.com/LucasFidon/label-set-loss-functions.git
```

## Example
```python
import torch
from label_set_loss_functions.loss import LeafDiceLoss, MarginalizedDiceLoss

# Example with 4 classes (labels 0 to 3) and one super class (label 4) that contains the labels 2 and 3
labels_superset_map = {4: [2, 3]}

# partial segmentation in 1D with 3 voxels (ground truth).
# Dimensions: num batch x num leaf labels x num voxels = 1 x 3
partial_seg = torch.tensor([[0, 1, 4]], dtype=torch.int64).cuda()

# We define two predicted score maps that are equivalent wrt the partial annotation
# Dimensions: num batch x num leaf labels x num voxels = 1 x 4 x 3
score_pred1 = torch.tensor([[[100, 0, 0], [0, 100, 0], [0, 0, 100], [0, 0, 0]]], dtype=torch.float32).cuda()
score_pred2 = torch.tensor([[[100, 0, 0], [0, 100, 0], [0, 0, 0], [0, 0, 100]]], dtype=torch.float32).cuda()

# Marginalized Dice loss
marg_dice = MarginalizedDiceLoss(labels_superset_map)
marg_dice(score_pred1, partial_seg)  # approximately 0
marg_dice(score_pred2, partial_seg)  # approximately 0

# Leaf-Dice loss
leaf_dice = LeafDiceLoss(labels_superset_map)
leaf_dice(score_pred1, partial_seg)  # 0.5
leaf_dice(score_pred2, partial_seg)  # 0.5
```

## List of label-set loss functions implemented
```python
# Leaf-Dice loss
from label_set_loss_functions.loss import LeafDiceLoss

# Marginalized Dice loss 
from label_set_loss_functions.loss import MarginalizedDiceLoss

# Marginalized Cross Entropy loss
from label_set_loss_functions.loss import MarginalizedCrossEntropyLoss

# Marginalized Focal loss
from label_set_loss_functions.loss import MarginalizedFocalLoss

# Marginalized Dice loss + marginalized Cross Entropy loss
from label_set_loss_functions.loss import MarginalizedDiceCE

# Marginalized Dice loss + marginalized Focal loss
from label_set_loss_functions.loss import MarginalizedDiceFocalLoss

# Leaf-Dice loss + marginalized Focal loss
from label_set_loss_functions.loss import LeafDiceFocalLoss

# Leaf-Dice loss + marginalized Cross Entropy loss
from label_set_loss_functions.loss import LeafDiceCE
```

## How to cite
If you use the label-set loss functions in you work, please cite

L. Fidon, M. Aertsen, D. Emam, N. Mufti, F. Guffens, T. Deprest, P. Demaerel, A. L. David, A. Melbourne, S. Ourselin, J. Deprest, T. Vercauteren.
[Label-set Loss Functions for Partial Supervision: Application to Fetal Brain 3D MRI Parcellation][arxiv]
International Conference on Medical Image Computing and Computer-Assisted Intervention. Springer, Cham, 2021.

Bibtex:
```
@inproceedings{fidon2021partial,
  title={Label-set Loss Functions for Partial Supervision: Application to Fetal Brain {3D MRI} Parcellation},
  author={Fidon, Lucas and Aertsen, Michael and Emam, Doaa and Mufti, Nada and Guffens, Fr{\'e}d{\'e}ric and Deprest, Thomas and Demaerel, Philippe and L. David, Anna and Melbourne, Andrew and Ourselin, S{\'e}bastien and Deprest, Jan and Vercauteren, Tom},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  year={2021},
  organization={Springer}
}
```
[arxiv]: https://arxiv.org/abs/2107.03846

label-set-loss-functions

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