Capsules for biomedical image segmentation.

Our work expands the use of capsule networks to the task of object segmentation for the first time in the literature. This is made possible via the introduction of locally-constrained routing and transformation matrix sharing, which reduces the parameter/memory burden and allows for the segmentation of objects at large resolutions. To compensate for the loss of global information in constraining the routing, we propose the concept of "deconvolutional" capsules to create a deep encoder-decoder style network, called SegCaps. We extend the masked reconstruction regularization to the task of segmentation and perform thorough ablation experiments on each component of our method. The proposed convolutional-deconvolutional capsule network, SegCaps, shows state-of-the-art results while using a fraction of the parameters of popular segmentation networks. To validate our proposed method, we perform experiments segmenting pathological lungs from clinical and pre-clinical thoracic computed tomography (CT) scans and segmenting muscle and adipose (fat) tissue from magnetic resonance imaging (MRI) scans of human subjects' thighs. Notably, our experiments in lung segmentation represent the largest-scale study in pathological lung segmentation in the literature, where we conduct experiments across five extremely challenging datasets, containing both clinical and pre-clinical subjects, and nearly 2000 computed-tomography scans. Our newly developed segmentation platform outperforms other methods across all datasets while utilizing less than 5% of the parameters in the popular U-Net for biomedical image segmentation. Further, we demonstrate capsules' ability to generalize to unseen handling of rotations/reflections on natural images.

INN: Inflated Neural Networks for IPMN Diagnosis.

Intraductal papillary mucinous neoplasm (IPMN) is a precursor to pancreatic ductal adenocarcinoma. While over half of patients are diagnosed with pancreatic cancer at a distant stage, patients who are diagnosed early enjoy a much higher 5-year survival rate of 34% compared to 3% in the former; hence, early diagnosis is key. Unique challenges in the medical imaging domain such as extremely limited annotated data sets and typically large 3D volumetric data have made it difficult for deep learning to secure a strong foothold. In this work, we construct two novel "inflated" deep network architectures, InceptINN and DenseINN, for the task of diagnosing IPMN from multisequence (T1 and T2) MRI. These networks inflate their 2D layers to 3D and bootstrap weights from their 2D counterparts (Inceptionv3 and DenseNet121 respectively) trained on ImageNet to the new 3D kernels. We also extend the inflation process by further expanding the pre-trained kernels to handle any number of input modalities and different fusion strategies. This is one of the first studies to train an end-to-end deep network on multisequence MRI for IPMN diagnosis, and shows that our proposed novel inflated network architectures are able to handle the extremely limited training data (139 MRI scans), while providing an absolute improvement of 8.76% in accuracy for diagnosing IPMN over the current state-of-the-art. Code is publicly available at https://github.com/lalonderodney/INN-Inflated-Neural-Nets.