arXiv subjects

Konstantinos Kamnitsas

Publications and source records attributed to Konstantinos Kamnitsas.

At least 55 records · Page 3Linked to original sources

arXiv2020

Stochastic Segmentation Networks: Modelling Spatially Correlated Aleatoric Uncertainty

In image segmentation, there is often more than one plausible solution for a given input. In medical imaging, for example, experts will often disagree about the exact location of object boundaries. Estimating this inherent uncertainty and predicting multiple plausible hypotheses is of great interest in many applications, yet this ability is lacking in most current deep learning methods. In this paper, we introduce stochastic segmentation networks (SSNs), an efficient probabilistic method for modelling aleatoric uncertainty with any image segmentation network architecture. In contrast to approaches that produce pixel-wise estimates, SSNs model joint distributions over entire label maps and thus can generate multiple spatially coherent hypotheses for a single image. By using a low-rank multivariate normal distribution over the logit space to model the probability of the label map given the image, we obtain a spatially consistent probability distribution that can be efficiently computed by a neural network without any changes to the underlying architecture. We tested our method on the segmentation of real-world medical data, including lung nodules in 2D CT and brain tumours in 3D multimodal MRI scans. SSNs outperform state-of-the-art for modelling correlated uncertainty in ambiguous images while being much simpler, more flexible, and more efficient.

cs.CV↗

arXiv2020

Explainable Anatomical Shape Analysis through Deep Hierarchical Generative Models

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer's disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating high-throughput analysis of normal anatomy and pathology in large-scale studies of volumetric imaging.

eess.IV↗

arXiv2019

Domain Generalization via Model-Agnostic Learning of Semantic Features

Generalization capability to unseen domains is crucial for machine learning models when deploying to real-world conditions. We investigate the challenging problem of domain generalization, i.e., training a model on multi-domain source data such that it can directly generalize to target domains with unknown statistics. We adopt a model-agnostic learning paradigm with gradient-based meta-train and meta-test procedures to expose the optimization to domain shift. Further, we introduce two complementary losses which explicitly regularize the semantic structure of the feature space. Globally, we align a derived soft confusion matrix to preserve general knowledge about inter-class relationships. Locally, we promote domain-independent class-specific cohesion and separation of sample features with a metric-learning component. The effectiveness of our method is demonstrated with new state-of-the-art results on two common object recognition benchmarks. Our method also shows consistent improvement on a medical image segmentation task.

cs.CV↗

arXiv2019

Overfitting of neural nets under class imbalance: Analysis and improvements for segmentation

Overfitting in deep learning has been the focus of a number of recent works, yet its exact impact on the behavior of neural networks is not well understood. This study analyzes overfitting by examining how the distribution of logits alters in relation to how much the model overfits. Specifically, we find that when training with few data samples, the distribution of logit activations when processing unseen test samples of an under-represented class tends to shift towards and even across the decision boundary, while the over-represented class seems unaffected. In image segmentation, foreground samples are often heavily under-represented. We observe that sensitivity of the model drops as a result of overfitting, while precision remains mostly stable. Based on our analysis, we derive asymmetric modifications of existing loss functions and regularizers including a large margin loss, focal loss, adversarial training and mixup, which specifically aim at reducing the shift observed when embedding unseen samples of the under-represented class. We study the case of binary segmentation of brain tumor core and show that our proposed simple modifications lead to significantly improved segmentation performance over the symmetric variants.

cs.LG↗

arXiv2019

Data Efficient Unsupervised Domain Adaptation for Cross-Modality Image Segmentation

Deep learning models trained on medical images from a source domain (e.g. imaging modality) often fail when deployed on images from a different target domain, despite imaging common anatomical structures. Deep unsupervised domain adaptation (UDA) aims to improve the performance of a deep neural network model on a target domain, using solely unlabelled target domain data and labelled source domain data. However, current state-of-the-art methods exhibit reduced performance when target data is scarce. In this work, we introduce a new data efficient UDA method for multi-domain medical image segmentation. The proposed method combines a novel VAE-based feature prior matching, which is data-efficient, and domain adversarial training to learn a shared domain-invariant latent space which is exploited during segmentation. Our method is evaluated on a public multi-modality cardiac image segmentation dataset by adapting from the labelled source domain (3D MRI) to the unlabelled target domain (3D CT). We show that by using only one single unlabelled 3D CT scan, the proposed architecture outperforms the state-of-the-art in the same setting. Finally, we perform ablation studies on prior matching and domain adversarial training to shed light on the theoretical grounding of the proposed method.

eess.IV↗

arXiv2019

Multiple Landmark Detection using Multi-Agent Reinforcement Learning

The detection of anatomical landmarks is a vital step for medical image analysis and applications for diagnosis, interpretation and guidance. Manual annotation of landmarks is a tedious process that requires domain-specific expertise and introduces inter-observer variability. This paper proposes a new detection approach for multiple landmarks based on multi-agent reinforcement learning. Our hypothesis is that the position of all anatomical landmarks is interdependent and non-random within the human anatomy, thus finding one landmark can help to deduce the location of others. Using a Deep Q-Network (DQN) architecture we construct an environment and agent with implicit inter-communication such that we can accommodate K agents acting and learning simultaneously, while they attempt to detect K different landmarks. During training the agents collaborate by sharing their accumulated knowledge for a collective gain. We compare our approach with state-of-the-art architectures and achieve significantly better accuracy by reducing the detection error by 50%, while requiring fewer computational resources and time to train compared to the naive approach of training K agents separately.

cs.CV↗

arXiv2019

Controlling Meshes via Curvature: Spin Transformations for Pose-Invariant Shape Processing

We investigate discrete spin transformations, a geometric framework to manipulate surface meshes by controlling mean curvature. Applications include surface fairing -- flowing a mesh onto say, a reference sphere -- and mesh extrusion -- e.g., rebuilding a complex shape from a reference sphere and curvature specification. Because they operate in curvature space, these operations can be conducted very stably across large deformations with no need for remeshing. Spin transformations add to the algorithmic toolbox for pose-invariant shape analysis. Mathematically speaking, mean curvature is a shape invariant and in general fully characterizes closed shapes (together with the metric). Computationally speaking, spin transformations make that relationship explicit. Our work expands on a discrete formulation of spin transformations. Like their smooth counterpart, discrete spin transformations are naturally close to conformal (angle-preserving). This quasi-conformality can nevertheless be relaxed to satisfy the desired trade-off between area distortion and angle preservation. We derive such constraints and propose a formulation in which they can be efficiently incorporated. The approach is showcased on subcortical structures.

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arXiv2018

Towards continual learning in medical imaging

This work investigates continual learning of two segmentation tasks in brain MRI with neural networks. To explore in this context the capabilities of current methods for countering catastrophic forgetting of the first task when a new one is learned, we investigate elastic weight consolidation, a recently proposed method based on Fisher information, originally evaluated on reinforcement learning of Atari games. We use it to sequentially learn segmentation of normal brain structures and then segmentation of white matter lesions. Our findings show this recent method reduces catastrophic forgetting, while large room for improvement exists in these challenging settings for continual learning.

cs.CV↗

arXiv2018

Generative adversarial networks and adversarial methods in biomedical image analysis

Generative adversarial networks (GANs) and other adversarial methods are based on a game-theoretical perspective on joint optimization of two neural networks as players in a game. Adversarial techniques have been extensively used to synthesize and analyze biomedical images. We provide an introduction to GANs and adversarial methods, with an overview of biomedical image analysis tasks that have benefited from such methods. We conclude with a discussion of strengths and limitations of adversarial methods in biomedical image analysis, and propose potential future research directions.

cs.CV↗

arXiv2018

Semi-Supervised Learning via Compact Latent Space Clustering

We present a novel cost function for semi-supervised learning of neural networks that encourages compact clustering of the latent space to facilitate separation. The key idea is to dynamically create a graph over embeddings of labeled and unlabeled samples of a training batch to capture underlying structure in feature space, and use label propagation to estimate its high and low density regions. We then devise a cost function based on Markov chains on the graph that regularizes the latent space to form a single compact cluster per class, while avoiding to disturb existing clusters during optimization. We evaluate our approach on three benchmarks and compare to state-of-the art with promising results. Our approach combines the benefits of graph-based regularization with efficient, inductive inference, does not require modifications to a network architecture, and can thus be easily applied to existing networks to enable an effective use of unlabeled data.

cs.LG↗

arXiv2018

Autofocus Layer for Semantic Segmentation

We propose the autofocus convolutional layer for semantic segmentation with the objective of enhancing the capabilities of neural networks for multi-scale processing. Autofocus layers adaptively change the size of the effective receptive field based on the processed context to generate more powerful features. This is achieved by parallelising multiple convolutional layers with different dilation rates, combined by an attention mechanism that learns to focus on the optimal scales driven by context. By sharing the weights of the parallel convolutions we make the network scale-invariant, with only a modest increase in the number of parameters. The proposed autofocus layer can be easily integrated into existing networks to improve a model's representational power. We evaluate our models on the challenging tasks of multi-organ segmentation in pelvic CT and brain tumor segmentation in MRI and achieve very promising performance.

cs.CV↗

arXiv2018

Automatic View Planning with Multi-scale Deep Reinforcement Learning Agents

We propose a fully automatic method to find standardized view planes in 3D image acquisitions. Standard view images are important in clinical practice as they provide a means to perform biometric measurements from similar anatomical regions. These views are often constrained to the native orientation of a 3D image acquisition. Navigating through target anatomy to find the required view plane is tedious and operator-dependent. For this task, we employ a multi-scale reinforcement learning (RL) agent framework and extensively evaluate several Deep Q-Network (DQN) based strategies. RL enables a natural learning paradigm by interaction with the environment, which can be used to mimic experienced operators. We evaluate our results using the distance between the anatomical landmarks and detected planes, and the angles between their normal vector and target. The proposed algorithm is assessed on the mid-sagittal and anterior-posterior commissure planes of brain MRI, and the 4-chamber long-axis plane commonly used in cardiac MRI, achieving accuracy of 1.53mm, 1.98mm and 4.84mm, respectively.

cs.CV↗

arXiv2018

Domain Adaptation for MRI Organ Segmentation using Reverse Classification Accuracy

The variations in multi-center data in medical imaging studies have brought the necessity of domain adaptation. Despite the advancement of machine learning in automatic segmentation, performance often degrades when algorithms are applied on new data acquired from different scanners or sequences than the training data. Manual annotation is costly and time consuming if it has to be carried out for every new target domain. In this work, we investigate automatic selection of suitable subjects to be annotated for supervised domain adaptation using the concept of reverse classification accuracy (RCA). RCA predicts the performance of a trained model on data from the new domain and different strategies of selecting subjects to be included in the adaptation via transfer learning are evaluated. We perform experiments on a two-center MR database for the task of organ segmentation. We show that subject selection via RCA can reduce the burden of annotation of new data for the target domain.

cs.CV↗

arXiv2017

Anatomically Constrained Neural Networks (ACNN): Application to Cardiac Image Enhancement and Segmentation

Incorporation of prior knowledge about organ shape and location is key to improve performance of image analysis approaches. In particular, priors can be useful in cases where images are corrupted and contain artefacts due to limitations in image acquisition. The highly constrained nature of anatomical objects can be well captured with learning based techniques. However, in most recent and promising techniques such as CNN based segmentation it is not obvious how to incorporate such prior knowledge. State-of-the-art methods operate as pixel-wise classifiers where the training objectives do not incorporate the structure and inter-dependencies of the output. To overcome this limitation, we propose a generic training strategy that incorporates anatomical prior knowledge into CNNs through a new regularisation model, which is trained end-to-end. The new framework encourages models to follow the global anatomical properties of the underlying anatomy (e.g. shape, label structure) via learned non-linear representations of the shape. We show that the proposed approach can be easily adapted to different analysis tasks (e.g. image enhancement, segmentation) and improve the prediction accuracy of the state-of-the-art models. The applicability of our approach is shown on multi-modal cardiac datasets and public benchmarks. Additionally, we demonstrate how the learned deep models of 3D shapes can be interpreted and used as biomarkers for classification of cardiac pathologies.

cs.CV↗

arXiv2017

Ensembles of Multiple Models and Architectures for Robust Brain Tumour Segmentation

Deep learning approaches such as convolutional neural nets have consistently outperformed previous methods on challenging tasks such as dense, semantic segmentation. However, the various proposed networks perform differently, with behaviour largely influenced by architectural choices and training settings. This paper explores Ensembles of Multiple Models and Architectures (EMMA) for robust performance through aggregation of predictions from a wide range of methods. The approach reduces the influence of the meta-parameters of individual models and the risk of overfitting the configuration to a particular database. EMMA can be seen as an unbiased, generic deep learning model which is shown to yield excellent performance, winning the first position in the BRATS 2017 competition among 50+ participating teams.

cs.CV↗

arXiv2017

Context-Sensitive Super-Resolution for Fast Fetal Magnetic Resonance Imaging

3D Magnetic Resonance Imaging (MRI) is often a trade-off between fast but low-resolution image acquisition and highly detailed but slow image acquisition. Fast imaging is required for targets that move to avoid motion artefacts. This is in particular difficult for fetal MRI. Spatially independent upsampling techniques, which are the state-of-the-art to address this problem, are error prone and disregard contextual information. In this paper we propose a context-sensitive upsampling method based on a residual convolutional neural network model that learns organ specific appearance and adopts semantically to input data allowing for the generation of high resolution images with sharp edges and fine scale detail. By making contextual decisions about appearance and shape, present in different parts of an image, we gain a maximum of structural detail at a similar contrast as provided by high-resolution data. We experiment on $145$ fetal scans and show that our approach yields an increased PSNR of $1.25$ $dB$ when applied to under-sampled fetal data \emph{cf.} baseline upsampling. Furthermore, our method yields an increased PSNR of $1.73$ $dB$ when utilizing under-sampled fetal data to perform brain volume reconstruction on motion corrupted captured data.

cs.CV↗

arXiv2017

SonoNet: Real-Time Detection and Localisation of Fetal Standard Scan Planes in Freehand Ultrasound

Identifying and interpreting fetal standard scan planes during 2D ultrasound mid-pregnancy examinations are highly complex tasks which require years of training. Apart from guiding the probe to the correct location, it can be equally difficult for a non-expert to identify relevant structures within the image. Automatic image processing can provide tools to help experienced as well as inexperienced operators with these tasks. In this paper, we propose a novel method based on convolutional neural networks which can automatically detect 13 fetal standard views in freehand 2D ultrasound data as well as provide a localisation of the fetal structures via a bounding box. An important contribution is that the network learns to localise the target anatomy using weak supervision based on image-level labels only. The network architecture is designed to operate in real-time while providing optimal output for the localisation task. We present results for real-time annotation, retrospective frame retrieval from saved videos, and localisation on a very large and challenging dataset consisting of images and video recordings of full clinical anomaly screenings. We found that the proposed method achieved an average F1-score of 0.798 in a realistic classification experiment modelling real-time detection, and obtained a 90.09% accuracy for retrospective frame retrieval. Moreover, an accuracy of 77.8% was achieved on the localisation task.

cs.CV↗

arXiv2017

Reverse Classification Accuracy: Predicting Segmentation Performance in the Absence of Ground Truth

When integrating computational tools such as automatic segmentation into clinical practice, it is of utmost importance to be able to assess the level of accuracy on new data, and in particular, to detect when an automatic method fails. However, this is difficult to achieve due to absence of ground truth. Segmentation accuracy on clinical data might be different from what is found through cross-validation because validation data is often used during incremental method development, which can lead to overfitting and unrealistic performance expectations. Before deployment, performance is quantified using different metrics, for which the predicted segmentation is compared to a reference segmentation, often obtained manually by an expert. But little is known about the real performance after deployment when a reference is unavailable. In this paper, we introduce the concept of reverse classification accuracy (RCA) as a framework for predicting the performance of a segmentation method on new data. In RCA we take the predicted segmentation from a new image to train a reverse classifier which is evaluated on a set of reference images with available ground truth. The hypothesis is that if the predicted segmentation is of good quality, then the reverse classifier will perform well on at least some of the reference images. We validate our approach on multi-organ segmentation with different classifiers and segmentation methods. Our results indicate that it is indeed possible to predict the quality of individual segmentations, in the absence of ground truth. Thus, RCA is ideal for integration into automatic processing pipelines in clinical routine and as part of large-scale image analysis studies.

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