Most of the current state-of-the-art methods for tumor segmentation are based on machine learning models trained on manually segmented images. This type of training data is particularly costly, as manual delineation of tumors is not only time-consuming but also requires medical expertise. On the other hand, images with a provided global label (indicating presence or absence of a tumor) are less informative but can be obtained at a substantially lower cost. In this paper, we propose to use both types of training data (fully-annotated and weakly-annotated) to train a deep learning model for segmentation. The idea of our approach is to extend segmentation networks with an additional branch performing image-level classification. The model is jointly trained for segmentation and classification tasks in order to exploit information contained in weakly-annotated images while preventing the network to learn features which are irrelevant for the segmentation task. We evaluate our method on the challenging task of brain tumor segmentation in Magnetic Resonance images from BRATS 2018 challenge. We show that the proposed approach provides a significant improvement of segmentation performance compared to the standard supervised learning. The observed improvement is proportional to the ratio between weakly-annotated and fully-annotated images available for training.
In standard semi-supervised learning @cite_3 for classification, the training data is composed both of labelled samples and unlabelled samples. Unlabelled samples can be used to encourage the model to satisfy some properties on relations between labels and the feature space. Common properties include smoothness (points close in the feature space should be close in the target space), clustering (labels form clusters in the feature space) and low density separation (decision boundaries should be in low density regions of the feature space). Semi-supervised learning based on these properties can be performed by graph-based methods such as the recent work of @cite_21 . The main idea of such methods is to propagate labels in a fully-connected graph whose nodes are samples (labelled and unlabelled) and whose edges are weighted by similarities between samples. The use of graph-based semi-supervised methods is difficult for segmentation, in particular because it implies computation of similarity metrics between samples, whereas each single image is generally composed of millions of samples (pixels or voxels).
@cite_21 @cite_3
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We present a novel cost function for semi-supervised learning of neural networks that encourages compact clustering of the latent space to facilitate separation. The key idea is to dynamically create a graph over embeddings of labeled and unlabeled samples of a training batch to capture underlying structure in feature space, and use label propagation to estimate its high and low density regions. We then devise a cost function based on Markov chains on the graph that regularizes the latent space to form a single compact cluster per class, while avoiding to disturb existing clusters during optimization. We evaluate our approach on three benchmarks and compare to state-of-the art with promising results. Our approach combines the benefits of graph-based regularization with efficient, inductive inference, does not require modifications to a network architecture, and can thus be easily applied to existing networks to enable an effective use of unlabeled data. Abstract Machine learning (ML) algorithms have made a tremendous impact in the field of medical imaging. While medical imaging datasets have been growing in size, a challenge for supervised ML algorithms that is frequently mentioned is the lack of annotated data. As a result, various methods that can learn with less other types of supervision, have been proposed. We give an overview of semi-supervised, multiple instance, and transfer learning in medical imaging, both in diagnosis or segmentation tasks. We also discuss connections between these learning scenarios, and opportunities for future research. A dataset with the details of the surveyed papers is available via https: figshare.com articles Database_of_surveyed_literature_in_Not-so-supervised_a_survey_of_semi-supervised_multi-instance_and_transfer_learning_in_medical_image_analysis_ 7479416 .