I\'m interested in taking advantage of some partially labeled data that I have in a deep learning task. I\'m using a fully convolutional approach, not sampling patches from
You could treat this as a semi-supervised problem. Use the full dataset without labels to train a bottleneck autoencoder structure (or a GAN approach). This pretrained model can then be adjusted (e.g. removing the last layers, adding a better layer structure at the end on top of the bottleneck features) and finetuned on the labeled data.