Iterative annotation to ease neural network training: Specialized machine learning in medical image analysis

Neural networks promise to bring robust, quantitative analysis to medical fields, but adoption is limited by the technicalities of training these networks. To address this translation gap between medical researchers and neural networks in the field of pathology, we have created an intuitive interface which utilizes the commonly used whole slide image (WSI) viewer, Aperio ImageScope (Leica Biosystems Imaging, Inc.), for the annotation and display of neural network predictions on WSIs. Leveraging this, we propose the use of a human-in-the-loop strategy to reduce the burden of WSI annotation. We track network performance improvements as a function of iteration and quantify the use of this pipeline for the segmentation of renal histologic findings on WSIs. More specifically, we present network performance when applied to segmentation of renal micro compartments, and demonstrate multi-class segmentation in human and mouse renal tissue slides. Finally, to show the adaptability of this technique to other medical imaging fields, we demonstrate its ability to iteratively segment human prostate glands from radiology imaging data.Comment: 15 pages, 7 figures, 2 supplemental figures (on the last page

Regularizing Deep Networks by Modeling and Predicting Label Structure

We construct custom regularization functions for use in supervised training of deep neural networks. Our technique is applicable when the ground-truth labels themselves exhibit internal structure; we derive a regularizer by learning an autoencoder over the set of annotations. Training thereby becomes a two-phase procedure. The first phase models labels with an autoencoder. The second phase trains the actual network of interest by attaching an auxiliary branch that must predict output via a hidden layer of the autoencoder. After training, we discard this auxiliary branch. We experiment in the context of semantic segmentation, demonstrating this regularization strategy leads to consistent accuracy boosts over baselines, both when training from scratch, or in combination with ImageNet pretraining. Gains are also consistent over different choices of convolutional network architecture. As our regularizer is discarded after training, our method has zero cost at test time; the performance improvements are essentially free. We are simply able to learn better network weights by building an abstract model of the label space, and then training the network to understand this abstraction alongside the original task.Comment: to appear at CVPR 201

Fine-graind Image Classification via Combining Vision and Language

Fine-grained image classification is a challenging task due to the large intra-class variance and small inter-class variance, aiming at recognizing hundreds of sub-categories belonging to the same basic-level category. Most existing fine-grained image classification methods generally learn part detection models to obtain the semantic parts for better classification accuracy. Despite achieving promising results, these methods mainly have two limitations: (1) not all the parts which obtained through the part detection models are beneficial and indispensable for classification, and (2) fine-grained image classification requires more detailed visual descriptions which could not be provided by the part locations or attribute annotations. For addressing the above two limitations, this paper proposes the two-stream model combining vision and language (CVL) for learning latent semantic representations. The vision stream learns deep representations from the original visual information via deep convolutional neural network. The language stream utilizes the natural language descriptions which could point out the discriminative parts or characteristics for each image, and provides a flexible and compact way of encoding the salient visual aspects for distinguishing sub-categories. Since the two streams are complementary, combining the two streams can further achieves better classification accuracy. Comparing with 12 state-of-the-art methods on the widely used CUB-200-2011 dataset for fine-grained image classification, the experimental results demonstrate our CVL approach achieves the best performance.Comment: 9 pages, to appear in CVPR 201