Loss functions

Segmentation Losses

DiceLoss

class monai.losses.DiceLoss(include_background=True, to_onehot_y=False, sigmoid=False, softmax=False, other_act=None, squared_pred=False, jaccard=False, reduction=<LossReduction.MEAN: 'mean'>, smooth_nr=1e-05, smooth_dr=1e-05, batch=False)[source]

Compute average Dice loss between two tensors. It can support both multi-classes and multi-labels tasks. Input logits input (BNHW[D] where N is number of classes) is compared with ground truth target (BNHW[D]). Axis N of input is expected to have logit predictions for each class rather than being image channels, while the same axis of target can be 1 or N (one-hot format). The smooth_nr and smooth_dr parameters are values added to the intersection and union components of the inter-over-union calculation to smooth results respectively, these values should be small. The include_background class attribute can be set to False for an instance of DiceLoss to exclude the first category (channel index 0) which is by convention assumed to be background. If the non-background segmentations are small compared to the total image size they can get overwhelmed by the signal from the background so excluding it in such cases helps convergence.

Milletari, F. et. al. (2016) V-Net: Fully Convolutional Neural Networks forVolumetric Medical Image Segmentation, 3DV, 2016.

Parameters

  • include_background (bool) – if False channel index 0 (background category) is excluded from the calculation.

  • to_onehot_y (bool) – whether to convert y into the one-hot format. Defaults to False.

  • sigmoid (bool) – if True, apply a sigmoid function to the prediction.

  • softmax (bool) – if True, apply a softmax function to the prediction.

  • other_act (Optional[Callable]) – if don’t want to use sigmoid or softmax, use other callable function to execute other activation layers, Defaults to None. for example: other_act = torch.tanh.

  • squared_pred (bool) – use squared versions of targets and predictions in the denominator or not.

  • jaccard (bool) – compute Jaccard Index (soft IoU) instead of dice or not.

  • reduction (Union[LossReduction, str]) –

    {"none", "mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean".

    • "none": no reduction will be applied.

    • "mean": the sum of the output will be divided by the number of elements in the output.

    • "sum": the output will be summed.

  • smooth_nr (float) – a small constant added to the numerator to avoid zero.

  • smooth_dr (float) – a small constant added to the denominator to avoid nan.

  • batch (bool) – whether to sum the intersection and union areas over the batch dimension before the dividing. Defaults to False, a Dice loss value is computed independently from each item in the batch before any reduction.

Raises

  • TypeError – When other_act is not an Optional[Callable].

  • ValueError – When more than 1 of [sigmoid=True, softmax=True, other_act is not None]. Incompatible values.

forward(input, target)[source]
Parameters

  • input (Tensor) – the shape should be BNH[WD].

  • target (Tensor) – the shape should be BNH[WD].

Raises

ValueError – When self.reduction is not one of [“mean”, “sum”, “none”].

Return type

Tensor

monai.losses.Dice

alias of monai.losses.dice.DiceLoss

monai.losses.dice

alias of monai.losses.dice.DiceLoss

MaskedDiceLoss

class monai.losses.MaskedDiceLoss(include_background=True, to_onehot_y=False, sigmoid=False, softmax=False, other_act=None, squared_pred=False, jaccard=False, reduction=<LossReduction.MEAN: 'mean'>, smooth_nr=1e-05, smooth_dr=1e-05, batch=False)[source]

Add an additional masking process before DiceLoss, accept a binary mask ([0, 1]) indicating a region, input and target will be masked by the region: region with mask 1 will keep the original value, region with 0 mask will be converted to 0. Then feed input and target to normal DiceLoss computation. This has the effect of ensuring only the masked region contributes to the loss computation and hence gradient calculation.

Parameters

  • include_background (bool) – if False channel index 0 (background category) is excluded from the calculation.

  • to_onehot_y (bool) – whether to convert y into the one-hot format. Defaults to False.

  • sigmoid (bool) – if True, apply a sigmoid function to the prediction.

  • softmax (bool) – if True, apply a softmax function to the prediction.

  • other_act (Optional[Callable]) – if don’t want to use sigmoid or softmax, use other callable function to execute other activation layers, Defaults to None. for example: other_act = torch.tanh.

  • squared_pred (bool) – use squared versions of targets and predictions in the denominator or not.

  • jaccard (bool) – compute Jaccard Index (soft IoU) instead of dice or not.

  • reduction (Union[LossReduction, str]) –

    {"none", "mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean".

    • "none": no reduction will be applied.

    • "mean": the sum of the output will be divided by the number of elements in the output.

    • "sum": the output will be summed.

  • smooth_nr (float) – a small constant added to the numerator to avoid zero.

  • smooth_dr (float) – a small constant added to the denominator to avoid nan.

  • batch (bool) – whether to sum the intersection and union areas over the batch dimension before the dividing. Defaults to False, a Dice loss value is computed independently from each item in the batch before any reduction.

Raises

  • TypeError – When other_act is not an Optional[Callable].

  • ValueError – When more than 1 of [sigmoid=True, softmax=True, other_act is not None]. Incompatible values.

forward(input, target, mask=None)[source]
Parameters

  • input (Tensor) – the shape should be BNH[WD].

  • target (Tensor) – the shape should be BNH[WD].

  • mask (Optional[Tensor]) – the shape should B1H[WD] or 11H[WD].

Return type

Tensor

GeneralizedDiceLoss

class monai.losses.GeneralizedDiceLoss(include_background=True, to_onehot_y=False, sigmoid=False, softmax=False, other_act=None, w_type=<Weight.SQUARE: 'square'>, reduction=<LossReduction.MEAN: 'mean'>, smooth_nr=1e-05, smooth_dr=1e-05, batch=False)[source]

Compute the generalised Dice loss defined in:

Sudre, C. et. al. (2017) Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations. DLMIA 2017.

Adapted from:

https://github.com/NifTK/NiftyNet/blob/v0.6.0/niftynet/layer/loss_segmentation.py#L279

Parameters

  • include_background (bool) – If False channel index 0 (background category) is excluded from the calculation.

  • to_onehot_y (bool) – whether to convert y into the one-hot format. Defaults to False.

  • sigmoid (bool) – If True, apply a sigmoid function to the prediction.

  • softmax (bool) – If True, apply a softmax function to the prediction.

  • other_act (Optional[Callable]) – if don’t want to use sigmoid or softmax, use other callable function to execute other activation layers, Defaults to None. for example: other_act = torch.tanh.

  • squared_pred – use squared versions of targets and predictions in the denominator or not.

  • w_type (Union[Weight, str]) – {"square", "simple", "uniform"} Type of function to transform ground truth volume to a weight factor. Defaults to "square".

  • reduction (Union[LossReduction, str]) –

    {"none", "mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean".

    • "none": no reduction will be applied.

    • "mean": the sum of the output will be divided by the number of elements in the output.

    • "sum": the output will be summed.

  • smooth_nr (float) – a small constant added to the numerator to avoid zero.

  • smooth_dr (float) – a small constant added to the denominator to avoid nan.

  • batch (bool) – whether to sum the intersection and union areas over the batch dimension before the dividing. Defaults to False, intersection over union is computed from each item in the batch.

Raises

  • TypeError – When other_act is not an Optional[Callable].

  • ValueError – When more than 1 of [sigmoid=True, softmax=True, other_act is not None]. Incompatible values.

forward(input, target)[source]
Parameters

  • input (Tensor) – the shape should be BNH[WD].

  • target (Tensor) – the shape should be BNH[WD].

Raises

ValueError – When self.reduction is not one of [“mean”, “sum”, “none”].

Return type

Tensor

monai.losses.generalized_dice

alias of monai.losses.dice.GeneralizedDiceLoss

GeneralizedWassersteinDiceLoss

class monai.losses.GeneralizedWassersteinDiceLoss(dist_matrix, weighting_mode='default', reduction=<LossReduction.MEAN: 'mean'>, smooth_nr=1e-05, smooth_dr=1e-05)[source]

Compute the generalized Wasserstein Dice Loss defined in:

Fidon L. et al. (2017) Generalised Wasserstein Dice Score for Imbalanced Multi-class Segmentation using Holistic Convolutional Networks. BrainLes 2017.

Or its variant (use the option weighting_mode=”GDL”) defined in the Appendix of:

Tilborghs, S. et al. (2020) Comparative study of deep learning methods for the automatic segmentation of lung, lesion and lesion type in CT scans of COVID-19 patients. arXiv preprint arXiv:2007.15546

Adapted from:

https://github.com/LucasFidon/GeneralizedWassersteinDiceLoss

Parameters

  • dist_matrix (Union[ndarray, Tensor]) – 2d tensor or 2d numpy array; matrix of distances between the classes.

  • must have dimension C x C where C is the number of classes. (It) –

  • weighting_mode (str) –

    {"default", "GDL"} Specifies how to weight the class-specific sum of errors. Default to "default".

    • "default": (recommended) use the original weighting method as in:

      Fidon L. et al. (2017) Generalised Wasserstein Dice Score for Imbalanced Multi-class Segmentation using Holistic Convolutional Networks. BrainLes 2017.

    • "GDL": use a GDL-like weighting method as in the Appendix of:

      Tilborghs, S. et al. (2020) Comparative study of deep learning methods for the automatic segmentation of lung, lesion and lesion type in CT scans of COVID-19 patients. arXiv preprint arXiv:2007.15546

  • reduction (Union[LossReduction, str]) –

    {"none", "mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean".

    • "none": no reduction will be applied.

    • "mean": the sum of the output will be divided by the number of elements in the output.

    • "sum": the output will be summed.

  • smooth_nr (float) – a small constant added to the numerator to avoid zero.

  • smooth_dr (float) – a small constant added to the denominator to avoid nan.

Raises

ValueError – When dist_matrix is not a square matrix.

Example

import torch
import numpy as np
from monai.losses import GeneralizedWassersteinDiceLoss

# Example with 3 classes (including the background: label 0).
# The distance between the background class (label 0) and the other classes is the maximum, equal to 1.
# The distance between class 1 and class 2 is 0.5.
dist_mat = np.array([[0.0, 1.0, 1.0], [1.0, 0.0, 0.5], [1.0, 0.5, 0.0]], dtype=np.float32)
wass_loss = GeneralizedWassersteinDiceLoss(dist_matrix=dist_mat)

pred_score = torch.tensor([[1000, 0, 0], [0, 1000, 0], [0, 0, 1000]], dtype=torch.float32)
grnd = torch.tensor([0, 1, 2], dtype=torch.int64)
wass_loss(pred_score, grnd)  # 0
forward(input, target)[source]
Parameters

  • input (Tensor) – the shape should be BNH[WD].

  • target (Tensor) – the shape should be BNH[WD].

Return type

Tensor

wasserstein_distance_map(flat_proba, flat_target)[source]

Compute the voxel-wise Wasserstein distance between the flattened prediction and the flattened labels (ground_truth) with respect to the distance matrix on the label space M. This corresponds to eq. 6 in:

Fidon L. et al. (2017) Generalised Wasserstein Dice Score for Imbalanced Multi-class Segmentation using Holistic Convolutional Networks. BrainLes 2017.

Parameters

  • flat_proba (Tensor) – the probabilities of input(predicted) tensor.

  • flat_target (Tensor) – the target tensor.

Return type

Tensor

monai.losses.generalized_wasserstein_dice

alias of monai.losses.dice.GeneralizedWassersteinDiceLoss

DiceCELoss

class monai.losses.DiceCELoss(include_background=True, to_onehot_y=False, sigmoid=False, softmax=False, other_act=None, squared_pred=False, jaccard=False, reduction='mean', smooth_nr=1e-05, smooth_dr=1e-05, batch=False, ce_weight=None)[source]

Compute both Dice loss and Cross Entropy Loss, and return the sum of these two losses. Input logits input (BNHW[D] where N is number of classes) is compared with ground truth target (BNHW[D]). Axis N of input is expected to have logit predictions for each class rather than being image channels, while the same axis of target can be 1 or N (one-hot format). The smooth_nr and smooth_dr parameters are values added for dice loss part to the intersection and union components of the inter-over-union calculation to smooth results respectively, these values should be small. The include_background class attribute can be set to False for an instance of the loss to exclude the first category (channel index 0) which is by convention assumed to be background. If the non-background segmentations are small compared to the total image size they can get overwhelmed by the signal from the background so excluding it in such cases helps convergence.

Parameters

  • is only used for cross entropy loss (ce_weight) –

  • is used for both losses and other (reduction) –

  • are only used for dice loss. (parameters) –

  • include_background (bool) – if False channel index 0 (background category) is excluded from the calculation.

  • to_onehot_y (bool) – whether to convert y into the one-hot format. Defaults to False.

  • sigmoid (bool) – if True, apply a sigmoid function to the prediction.

  • softmax (bool) – if True, apply a softmax function to the prediction.

  • other_act (Optional[Callable]) – if don’t want to use sigmoid or softmax, use other callable function to execute other activation layers, Defaults to None. for example: other_act = torch.tanh.

  • squared_pred (bool) – use squared versions of targets and predictions in the denominator or not.

  • jaccard (bool) – compute Jaccard Index (soft IoU) instead of dice or not.

  • reduction (str) –

    {"mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean". The dice loss should as least reduce the spatial dimensions, which is different from cross entropy loss, thus here the none option cannot be used.

    • "mean": the sum of the output will be divided by the number of elements in the output.

    • "sum": the output will be summed.

  • smooth_nr (float) – a small constant added to the numerator to avoid zero.

  • smooth_dr (float) – a small constant added to the denominator to avoid nan.

  • batch (bool) – whether to sum the intersection and union areas over the batch dimension before the dividing. Defaults to False, a Dice loss value is computed independently from each item in the batch before any reduction.

  • ce_weight (Optional[Tensor]) – a rescaling weight given to each class for cross entropy loss. See torch.nn.CrossEntropyLoss() for more information.

forward(input, target)[source]
Parameters

  • input (Tensor) – the shape should be BNH[WD].

  • target (Tensor) – the shape should be BNH[WD] or B1H[WD].

Raises

  • ValueError – When number of dimensions for input and target are different.

  • ValueError – When number of channels for target is nither 1 or the same as input.

Return type

Tensor

FocalLoss

class monai.losses.FocalLoss(gamma=2.0, weight=None, reduction=<LossReduction.MEAN: 'mean'>)[source]

Reimplementation of the Focal Loss described in:

  • “Focal Loss for Dense Object Detection”, T. Lin et al., ICCV 2017

  • “AnatomyNet: Deep learning for fast and fully automated whole‐volume segmentation of head and neck anatomy”, Zhu et al., Medical Physics 2018

Parameters

  • gamma (float) – value of the exponent gamma in the definition of the Focal loss.

  • weight (Optional[Tensor]) – weights to apply to the voxels of each class. If None no weights are applied. This corresponds to the weights lpha in [1].

  • reduction (Union[LossReduction, str]) –

    {"none", "mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean".

    • "none": no reduction will be applied.

    • "mean": the sum of the output will be divided by the number of elements in the output.

    • "sum": the output will be summed.

Example

import torch
from monai.losses import FocalLoss

pred = torch.tensor([[1, 0], [0, 1], [1, 0]], dtype=torch.float32)
grnd = torch.tensor([[0], [1], [0]], dtype=torch.int64)
fl = FocalLoss()
fl(pred, grnd)
forward(logits, target)[source]
Parameters

  • logits (Tensor) – the shape should be BCH[WD]. where C (greater than 1) is the number of classes. Softmax over the logits is integrated in this module for improved numerical stability.

  • target (Tensor) – the shape should be B1H[WD] or BCH[WD]. If the target’s shape is B1H[WD], the target that this loss expects should be a class index in the range [0, C-1] where C is the number of classes.

Raises

  • ValueError – When target ndim differs from logits.

  • ValueError – When target channel is not 1 and target shape differs from logits.

  • ValueError – When self.reduction is not one of [“mean”, “sum”, “none”].

Return type

Tensor

TverskyLoss

class monai.losses.TverskyLoss(include_background=True, to_onehot_y=False, sigmoid=False, softmax=False, other_act=None, alpha=0.5, beta=0.5, reduction=<LossReduction.MEAN: 'mean'>, smooth_nr=1e-05, smooth_dr=1e-05, batch=False)[source]

Compute the Tversky loss defined in:

Sadegh et al. (2017) Tversky loss function for image segmentation using 3D fully convolutional deep networks. (https://arxiv.org/abs/1706.05721)

Adapted from:

https://github.com/NifTK/NiftyNet/blob/v0.6.0/niftynet/layer/loss_segmentation.py#L631

Parameters

  • include_background (bool) – If False channel index 0 (background category) is excluded from the calculation.

  • to_onehot_y (bool) – whether to convert y into the one-hot format. Defaults to False.

  • sigmoid (bool) – If True, apply a sigmoid function to the prediction.

  • softmax (bool) – If True, apply a softmax function to the prediction.

  • other_act (Optional[Callable]) – if don’t want to use sigmoid or softmax, use other callable function to execute other activation layers, Defaults to None. for example: other_act = torch.tanh.

  • alpha (float) – weight of false positives

  • beta (float) – weight of false negatives

  • reduction (Union[LossReduction, str]) –

    {"none", "mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean".

    • "none": no reduction will be applied.

    • "mean": the sum of the output will be divided by the number of elements in the output.

    • "sum": the output will be summed.

  • smooth_nr (float) – a small constant added to the numerator to avoid zero.

  • smooth_dr (float) – a small constant added to the denominator to avoid nan.

  • batch (bool) – whether to sum the intersection and union areas over the batch dimension before the dividing. Defaults to False, a Dice loss value is computed independently from each item in the batch before any reduction.

Raises

  • TypeError – When other_act is not an Optional[Callable].

  • ValueError – When more than 1 of [sigmoid=True, softmax=True, other_act is not None]. Incompatible values.

forward(input, target)[source]
Parameters

  • input (Tensor) – the shape should be BNH[WD].

  • target (Tensor) – the shape should be BNH[WD].

Raises

ValueError – When self.reduction is not one of [“mean”, “sum”, “none”].

Return type

Tensor

Registration Losses

BendingEnergyLoss

class monai.losses.BendingEnergyLoss(reduction=<LossReduction.MEAN: 'mean'>)[source]

Calculate the bending energy based on second-order differentiation of pred using central finite difference.

Adapted from:

DeepReg (https://github.com/DeepRegNet/DeepReg)

Parameters

reduction (Union[LossReduction, str]) –

{"none", "mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean".

  • "none": no reduction will be applied.

  • "mean": the sum of the output will be divided by the number of elements in the output.

  • "sum": the output will be summed.

forward(pred)[source]
Parameters

pred (Tensor) – the shape should be BCH(WD)

Raises

ValueError – When self.reduction is not one of [“mean”, “sum”, “none”].

Return type

Tensor

LocalNormalizedCrossCorrelationLoss

class monai.losses.LocalNormalizedCrossCorrelationLoss(in_channels, ndim=3, kernel_size=3, kernel_type='rectangular', reduction=<LossReduction.MEAN: 'mean'>, smooth_nr=1e-07, smooth_dr=1e-07)[source]

Local squared zero-normalized cross-correlation. The loss is based on a moving kernel/window over the y_true/y_pred, within the window the square of zncc is calculated. The kernel can be a rectangular / triangular / gaussian window. The final loss is the averaged loss over all windows.

Adapted from:

https://github.com/voxelmorph/voxelmorph/blob/legacy/src/losses.py DeepReg (https://github.com/DeepRegNet/DeepReg)

Parameters

  • in_channels (int) – number of input channels

  • ndim (int) – number of spatial ndimensions, {1, 2, 3}. Defaults to 3.

  • kernel_size (int) – kernel spatial size, must be odd.

  • kernel_type (str) – {"rectangular", "triangular", "gaussian"}. Defaults to "rectangular".

  • reduction (Union[LossReduction, str]) –

    {"none", "mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean".

    • "none": no reduction will be applied.

    • "mean": the sum of the output will be divided by the number of elements in the output.

    • "sum": the output will be summed.

  • smooth_nr (float) – a small constant added to the numerator to avoid nan.

  • smooth_dr (float) – a small constant added to the denominator to avoid nan.

forward(pred, target)[source]
Parameters

  • pred (Tensor) – the shape should be BNH[WD].

  • target (Tensor) – the shape should be BNH[WD].

Raises

ValueError – When self.reduction is not one of [“mean”, “sum”, “none”].

Return type

Tensor

GlobalMutualInformationLoss

class monai.losses.GlobalMutualInformationLoss(num_bins=23, sigma_ratio=0.5, reduction=<LossReduction.MEAN: 'mean'>, smooth_nr=1e-07, smooth_dr=1e-07)[source]

Differentiable global mutual information loss via Parzen windowing method.

Reference:

https://dspace.mit.edu/handle/1721.1/123142, Section 3.1, equation 3.1-3.5, Algorithm 1

Parameters

  • num_bins (int) – number of bins for intensity

  • sigma_ratio (float) – a hyper param for gaussian function

  • reduction (Union[LossReduction, str]) –

    {"none", "mean", "sum"} Specifies the reduction to apply to the output. Defaults to "mean".

    • "none": no reduction will be applied.

    • "mean": the sum of the output will be divided by the number of elements in the output.

    • "sum": the output will be summed.

  • smooth_nr (float) – a small constant added to the numerator to avoid nan.

  • smooth_dr (float) – a small constant added to the denominator to avoid nan.

forward(pred, target)[source]
Parameters

  • pred (Tensor) – the shape should be B[NDHW].

  • target (Tensor) – the shape should be same as the pred shape.

Raises

ValueError – When self.reduction is not one of [“mean”, “sum”, “none”].

Return type

Tensor

parzen_windowing(pred)[source]
Parameters

pred (Tensor) – the shape should be B[NDHW].

Return type

Tuple[Tensor, Tensor]