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Ultra-high resolution image segmentation has raised increasing interests in recent years due to its realistic applications. In this paper, we innovate the widely used high-resolution image segmentation pipeline, in which an ultra-high resolution image is partitioned into regular patches for local segmentation and then the local results are merged into a high-resolution semantic mask. In particular, we introduce a novel locality-aware context fusion based segmentation model to process local patches, where the relevance between local patch and its various contexts are jointly and complementarily utilized to handle the semantic regions with large variations. Additionally, we present the alternating local enhancement module that restricts the negative impact of redundant information introduced from the contexts, and thus is endowed with the ability of fixing the locality-aware features to produce refined results. Furthermore, in comprehensive experiments, we demonstrate that our model outperforms other state-of-the-art methods in public benchmarks. Our released codes are available at: //github.com/liqiokkk/FCtL.

Generalization is an important attribute of machine learning models, particularly for those that are to be deployed in a medical context, where unreliable predictions can have real world consequences. While the failure of models to generalize across datasets is typically attributed to a mismatch in the data distributions, performance gaps are often a consequence of biases in the 'ground-truth' label annotations. This is particularly important in the context of medical image segmentation of pathological structures (e.g. lesions), where the annotation process is much more subjective, and affected by a number underlying factors, including the annotation protocol, rater education/experience, and clinical aims, among others. In this paper, we show that modeling annotation biases, rather than ignoring them, poses a promising way of accounting for differences in annotation style across datasets. To this end, we propose a generalized conditioning framework to (1) learn and account for different annotation styles across multiple datasets using a single model, (2) identify similar annotation styles across different datasets in order to permit their effective aggregation, and (3) fine-tune a fully trained model to a new annotation style with just a few samples. Next, we present an image-conditioning approach to model annotation styles that correlate with specific image features, potentially enabling detection biases to be more easily identified.

Knowledge graphs represent factual knowledge about the world as relationships between concepts and are critical for intelligent decision making in enterprise applications. New knowledge is inferred from the existing facts in the knowledge graphs by encoding the concepts and relations into low-dimensional feature vector representations. The most effective representations for this task, called Knowledge Graph Embeddings (KGE), are learned through neural network architectures. Due to their impressive predictive performance, they are increasingly used in high-impact domains like healthcare, finance and education. However, are the black-box KGE models adversarially robust for use in domains with high stakes? This thesis argues that state-of-the-art KGE models are vulnerable to data poisoning attacks, that is, their predictive performance can be degraded by systematically crafted perturbations to the training knowledge graph. To support this argument, two novel data poisoning attacks are proposed that craft input deletions or additions at training time to subvert the learned model's performance at inference time. These adversarial attacks target the task of predicting the missing facts in knowledge graphs using KGE models, and the evaluation shows that the simpler attacks are competitive with or outperform the computationally expensive ones. The thesis contributions not only highlight and provide an opportunity to fix the security vulnerabilities of KGE models, but also help to understand the black-box predictive behaviour of KGE models.

Since hardware resources are limited, the objective of training deep learning models is typically to maximize accuracy subject to the time and memory constraints of training and inference. We study the impact of model size in this setting, focusing on Transformer models for NLP tasks that are limited by compute: self-supervised pretraining and high-resource machine translation. We first show that even though smaller Transformer models execute faster per iteration, wider and deeper models converge in significantly fewer steps. Moreover, this acceleration in convergence typically outpaces the additional computational overhead of using larger models. Therefore, the most compute-efficient training strategy is to counterintuitively train extremely large models but stop after a small number of iterations. This leads to an apparent trade-off between the training efficiency of large Transformer models and the inference efficiency of small Transformer models. However, we show that large models are more robust to compression techniques such as quantization and pruning than small models. Consequently, one can get the best of both worlds: heavily compressed, large models achieve higher accuracy than lightly compressed, small models.

The U-Net was presented in 2015. With its straight-forward and successful architecture it quickly evolved to a commonly used benchmark in medical image segmentation. The adaptation of the U-Net to novel problems, however, comprises several degrees of freedom regarding the exact architecture, preprocessing, training and inference. These choices are not independent of each other and substantially impact the overall performance. The present paper introduces the nnU-Net ('no-new-Net'), which refers to a robust and self-adapting framework on the basis of 2D and 3D vanilla U-Nets. We argue the strong case for taking away superfluous bells and whistles of many proposed network designs and instead focus on the remaining aspects that make out the performance and generalizability of a method. We evaluate the nnU-Net in the context of the Medical Segmentation Decathlon challenge, which measures segmentation performance in ten disciplines comprising distinct entities, image modalities, image geometries and dataset sizes, with no manual adjustments between datasets allowed. At the time of manuscript submission, nnU-Net achieves the highest mean dice scores across all classes and seven phase 1 tasks (except class 1 in BrainTumour) in the online leaderboard of the challenge.

Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.

Medical image segmentation requires consensus ground truth segmentations to be derived from multiple expert annotations. A novel approach is proposed that obtains consensus segmentations from experts using graph cuts (GC) and semi supervised learning (SSL). Popular approaches use iterative Expectation Maximization (EM) to estimate the final annotation and quantify annotator's performance. Such techniques pose the risk of getting trapped in local minima. We propose a self consistency (SC) score to quantify annotator consistency using low level image features. SSL is used to predict missing annotations by considering global features and local image consistency. The SC score also serves as the penalty cost in a second order Markov random field (MRF) cost function optimized using graph cuts to derive the final consensus label. Graph cut obtains a global maximum without an iterative procedure. Experimental results on synthetic images, real data of Crohn's disease patients and retinal images show our final segmentation to be accurate and more consistent than competing methods.

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.

Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.