A Probabilistic U-Net for segmentation of ambiguous images implemented in PyTorch
A Probabilistic U-Net for segmentation of ambiguous images implemented in PyTorch. This is a pytorch implementation of this paper https://arxiv.org/abs/1806.05034, for which the code can be found here: https://github.com/SimonKohl/probabilistic_unet.
In order to implement an Gaussian distribution with an axis aligned covariance matrix in PyTorch, I needed to wrap a Normal distribution in a Independent distribution. Therefore you need the add the following to the PyTorch source code at torch/distributions/kl.py (source: https://github.com/pytorch/pytorch/issues/13545).
def _kl_independent_independent(p, q): if p.reinterpreted_batch_ndims != q.reinterpreted_batch_ndims: raise NotImplementedError result = kl_divergence(p.base_dist, q.base_dist) return _sum_rightmost(result, p.reinterpreted_batch_ndims)
In order to train your own Probabilistic UNet in PyTorch, you should first write your own data loader. Then you can use the following code snippet to train the network
train_loader = define this yourself net = ProbabilisticUnet(no_channels,no_classes,filter_list,latent_dim,no_fcomb_convs,beta) net.to(device) optimizer = torch.optim.Adam(net.parameters(), lr=1e-4, weight_decay=0) for epoch in range(epochs): for step, (patch, mask) in enumerate(train_loader): patch = patch.to(device) mask = mask.to(device) mask = torch.unsqueeze(mask,1) net.forward(patch, mask, training=True) elbo = net.elbo(mask) reg_loss = l2_regularisation(net.posterior) + l2_regularisation(net.prior) + l2_regularisation(net.fcomb.layers) loss = -elbo + 1e-5 * reg_loss optimizer.zero_grad() loss.backward() optimizer.step()
One of the datasets used in the original paper is the LIDC dataset. I've preprocessed this data and stored them in a pickle file, which you can download here. After downloading the files you should place them in a folder called 'data'. After that, you can train your own Probabilistic UNet on the LIDC dataset using the simple train script provided in train_model.py.