From Fully-Supervised Single-Task to Semi-Supervised Multi-Task Deep Learning Architectures for Segmentation in Medical Imaging Applications

Medical imaging is routinely performed in clinics worldwide for the diagnosis and treatment of numerous medical conditions in children and adults. With the advent of these medical imaging modalities, radiologists can visualize both the structure of the body as well as the tissues within the body. However, analyzing these high-dimensional (2D/3D/4D) images demands a significant amount of time and effort from radiologists. Hence, there is an ever-growing need for medical image computing tools to extract relevant information from the image data to help radiologists perform efficiently. Image analysis based on machine learning has pivotal potential to improve the entire medical imaging pipeline, providing support for clinical decision-making and computer-aided diagnosis. To be effective in addressing challenging image analysis tasks such as classification, detection, registration, and segmentation, specifically for medical imaging applications, deep learning approaches have shown significant improvement in performance. While deep learning has shown its potential in a variety of medical image analysis problems including segmentation, motion estimation, etc., generalizability is still an unsolved problem and many of these successes are achieved at the cost of a large pool of datasets. For most practical applications, getting access to a copious dataset can be very difficult, often impossible. Annotation is tedious and time-consuming. This cost is further amplified when annotation must be done by a clinical expert in medical imaging applications. Additionally, the applications of deep learning in the real-world clinical setting are still limited due to the lack of reliability caused by the limited prediction capabilities of some deep learning models. Moreover, while using a CNN in an automated image analysis pipeline, it’s critical to understand which segmentation results are problematic and require further manual examination. To this extent, the estimation of uncertainty calibration in a semi-supervised setting for medical image segmentation is still rarely reported. This thesis focuses on developing and evaluating optimized machine learning models for a variety of medical imaging applications, ranging from fully-supervised, single-task learning to semi-supervised, multi-task learning that makes efficient use of annotated training data. The contributions of this dissertation are as follows: (1) developing a fully-supervised, single-task transfer learning for the surgical instrument segmentation from laparoscopic images; and (2) utilizing supervised, single-task, transfer learning for segmenting and digitally removing the surgical instruments from endoscopic/laparoscopic videos to allow the visualization of the anatomy being obscured by the tool. The tool removal algorithms use a tool segmentation mask and either instrument-free reference frames or previous instrument-containing frames to fill in (inpaint) the instrument segmentation mask; (3) developing fully-supervised, single-task learning via efficient weight pruning and learned group convolution for accurate left ventricle (LV), right ventricle (RV) blood pool and myocardium localization and segmentation from 4D cine cardiac MR images; (4) demonstrating the use of our fully-supervised memory-efficient model to generate dynamic patient-specific right ventricle (RV) models from cine cardiac MRI dataset via an unsupervised learning-based deformable registration field; and (5) integrating a Monte Carlo dropout into our fully-supervised memory-efficient model with inherent uncertainty estimation, with the overall goal to estimate the uncertainty associated with the obtained segmentation and error, as a means to flag regions that feature less than optimal segmentation results; (6) developing semi-supervised, single-task learning via self-training (through meta pseudo-labeling) in concert with a Teacher network that instructs the Student network by generating pseudo-labels given unlabeled input data; (7) proposing largely-unsupervised, multi-task learning to demonstrate the power of a simple combination of a disentanglement block, variational autoencoder (VAE), generative adversarial network (GAN), and a conditioning layer-based reconstructor for performing two of the foremost critical tasks in medical imaging — segmentation of cardiac structures and reconstruction of the cine cardiac MR images; (8) demonstrating the use of 3D semi-supervised, multi-task learning for jointly learning multiple tasks in a single backbone module – uncertainty estimation, geometric shape generation, and cardiac anatomical structure segmentation of the left atrial cavity from 3D Gadolinium-enhanced magnetic resonance (GE-MR) images. This dissertation summarizes the impact of the contributions of our work in terms of demonstrating the adaptation and use of deep learning architectures featuring different levels of supervision to build a variety of image segmentation tools and techniques that can be used across a wide spectrum of medical image computing applications centered on facilitating and promoting the wide-spread computer-integrated diagnosis and therapy data science

Budget-aware Semi-Supervised Semantic and Instance Segmentation

Methods that move towards less supervised scenarios are key for image segmentation, as dense labels demand significant human intervention. Generally, the annotation burden is mitigated by labeling datasets with weaker forms of supervision, e.g. image-level labels or bounding boxes. Another option are semi-supervised settings, that commonly leverage a few strong annotations and a huge number of unlabeled/weakly-labeled data. In this paper, we revisit semi-supervised segmentation schemes and narrow down significantly the annotation budget (in terms of total labeling time of the training set) compared to previous approaches. With a very simple pipeline, we demonstrate that at low annotation budgets, semi-supervised methods outperform by a wide margin weakly-supervised ones for both semantic and instance segmentation. Our approach also outperforms previous semi-supervised works at a much reduced labeling cost. We present results for the Pascal VOC benchmark and unify weakly and semi-supervised approaches by considering the total annotation budget, thus allowing a fairer comparison between methods.Comment: To appear in CVPR-W 2019 (DeepVision workshop

Coarse-to-Fine Annotation Enrichment for Semantic Segmentation Learning

Rich high-quality annotated data is critical for semantic segmentation learning, yet acquiring dense and pixel-wise ground-truth is both labor- and time-consuming. Coarse annotations (e.g., scribbles, coarse polygons) offer an economical alternative, with which training phase could hardly generate satisfactory performance unfortunately. In order to generate high-quality annotated data with a low time cost for accurate segmentation, in this paper, we propose a novel annotation enrichment strategy, which expands existing coarse annotations of training data to a finer scale. Extensive experiments on the Cityscapes and PASCAL VOC 2012 benchmarks have shown that the neural networks trained with the enriched annotations from our framework yield a significant improvement over that trained with the original coarse labels. It is highly competitive to the performance obtained by using human annotated dense annotations. The proposed method also outperforms among other state-of-the-art weakly-supervised segmentation methods.Comment: CIKM 2018 International Conference on Information and Knowledge Managemen