Suggestive Annotation: A Deep Active Learning Framework for Biomedical Image Segmentation

Image segmentation is a fundamental problem in biomedical image analysis. Recent advances in deep learning have achieved promising results on many biomedical image segmentation benchmarks. However, due to large variations in biomedical images (different modalities, image settings, objects, noise, etc), to utilize deep learning on a new application, it usually needs a new set of training data. This can incur a great deal of annotation effort and cost, because only biomedical experts can annotate effectively, and often there are too many instances in images (e.g., cells) to annotate. In this paper, we aim to address the following question: With limited effort (e.g., time) for annotation, what instances should be annotated in order to attain the best performance? We present a deep active learning framework that combines fully convolutional network (FCN) and active learning to significantly reduce annotation effort by making judicious suggestions on the most effective annotation areas. We utilize uncertainty and similarity information provided by FCN and formulate a generalized version of the maximum set cover problem to determine the most representative and uncertain areas for annotation. Extensive experiments using the 2015 MICCAI Gland Challenge dataset and a lymph node ultrasound image segmentation dataset show that, using annotation suggestions by our method, state-of-the-art segmentation performance can be achieved by using only 50% of training data.Comment: Accepted at MICCAI 201

Image Restoration Using Very Deep Convolutional Encoder-Decoder Networks with Symmetric Skip Connections

In this paper, we propose a very deep fully convolutional encoding-decoding framework for image restoration such as denoising and super-resolution. The network is composed of multiple layers of convolution and de-convolution operators, learning end-to-end mappings from corrupted images to the original ones. The convolutional layers act as the feature extractor, which capture the abstraction of image contents while eliminating noises/corruptions. De-convolutional layers are then used to recover the image details. We propose to symmetrically link convolutional and de-convolutional layers with skip-layer connections, with which the training converges much faster and attains a higher-quality local optimum. First, The skip connections allow the signal to be back-propagated to bottom layers directly, and thus tackles the problem of gradient vanishing, making training deep networks easier and achieving restoration performance gains consequently. Second, these skip connections pass image details from convolutional layers to de-convolutional layers, which is beneficial in recovering the original image. Significantly, with the large capacity, we can handle different levels of noises using a single model. Experimental results show that our network achieves better performance than all previously reported state-of-the-art methods.Comment: Accepted to Proc. Advances in Neural Information Processing Systems (NIPS'16). Content of the final version may be slightly different. Extended version is available at http://arxiv.org/abs/1606.0892

Automatic Labeled LiDAR Data Generation based on Precise Human Model

Following improvements in deep neural networks, state-of-the-art networks have been proposed for human recognition using point clouds captured by LiDAR. However, the performance of these networks strongly depends on the training data. An issue with collecting training data is labeling. Labeling by humans is necessary to obtain the ground truth label; however, labeling requires huge costs. Therefore, we propose an automatic labeled data generation pipeline, for which we can change any parameters or data generation environments. Our approach uses a human model named Dhaiba and a background of Miraikan and consequently generated realistic artificial data. We present 500k+ data generated by the proposed pipeline. This paper also describes the specification of the pipeline and data details with evaluations of various approaches.Comment: Accepted at ICRA201