InfiNet: Fully Convolutional Networks for Infant Brain MRI Segmentation

We present a novel, parameter-efficient and practical fully convolutional neural network architecture, termed InfiNet, aimed at voxel-wise semantic segmentation of infant brain MRI images at iso-intense stage, which can be easily extended for other segmentation tasks involving multi-modalities. InfiNet consists of double encoder arms for T1 and T2 input scans that feed into a joint-decoder arm that terminates in the classification layer. The novelty of InfiNet lies in the manner in which the decoder upsamples lower resolution input feature map(s) from multiple encoder arms. Specifically, the pooled indices computed in the max-pooling layers of each of the encoder blocks are related to the corresponding decoder block to perform non-linear learning-free upsampling. The sparse maps are concatenated with intermediate encoder representations (skip connections) and convolved with trainable filters to produce dense feature maps. InfiNet is trained end-to-end to optimize for the Generalized Dice Loss, which is well-suited for high class imbalance. InfiNet achieves the whole-volume segmentation in under 50 seconds and we demonstrate competitive performance against multiple state-of-the art deep architectures and their multi-modal variants.Comment: 4 pages, 3 figures, conference, IEEE ISBI, 201

Webly Supervised Learning for Skin Lesion Classification

Within medical imaging, manual curation of sufficient well-labeled samples is cost, time and scale-prohibitive. To improve the representativeness of the training dataset, for the first time, we present an approach to utilize large amounts of freely available web data through web-crawling. To handle noise and weak nature of web annotations, we propose a two-step transfer learning based training process with a robust loss function, termed as Webly Supervised Learning (WSL) to train deep models for the task. We also leverage search by image to improve the search specificity of our web-crawling and reduce cross-domain noise. Within WSL, we explicitly model the noise structure between classes and incorporate it to selectively distill knowledge from the web data during model training. To demonstrate improved performance due to WSL, we benchmarked on a publicly available 10-class fine-grained skin lesion classification dataset and report a significant improvement of top-1 classification accuracy from 71.25 % to 80.53 % due to the incorporation of web-supervision.Comment: Accepted to International Conference on Medical Image Computing and Computer-Assisted Intervention 2018 Added Acknowledgements section, rest is unchanged. In MICCAI 2018. Springer, Cha

Competition vs. Concatenation in Skip Connections of Fully Convolutional Networks

Increased information sharing through short and long-range skip connections between layers in fully convolutional networks have demonstrated significant improvement in performance for semantic segmentation. In this paper, we propose Competitive Dense Fully Convolutional Networks (CDFNet) by introducing competitive maxout activations in place of naive feature concatenation for inducing competition amongst layers. Within CDFNet, we propose two architectural contributions, namely competitive dense block (CDB) and competitive unpooling block (CUB) to induce competition at local and global scales for short and long-range skip connections respectively. This extension is demonstrated to boost learning of specialized sub-networks targeted at segmenting specific anatomies, which in turn eases the training of complex tasks. We present the proof-of-concept on the challenging task of whole body segmentation in the publicly available VISCERAL benchmark and demonstrate improved performance over multiple learning and registration based state-of-the-art methods.Comment: Paper accepted on MICCAI-MLMI 2018 worksho