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Register a new userDeep learning cardiac motion analysis for human survival prediction
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Added by
Declan O'Regan
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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Motion analysis is used in computer vision to understand the behaviour of moving objects in sequences of images. Optimising the interpretation of dynamic biological systems requires accurate and precise motion tracking as well as efficient representations of high-dimensional motion trajectories so that these can be used for prediction tasks. Here we use image sequences of the heart, acquired using cardiac magnetic resonance imaging, to create time-resolved three-dimensional segmentations using a fully convolutional network trained on anatomical shape priors. This dense motion model formed the input to a supervised denoising autoencoder (4Dsurvival), which is a hybrid network consisting of an autoencoder that learns a task-specific latent code representation trained on observed outcome data, yielding a latent representation optimised for survival prediction. To handle right-censored survival outcomes, our network used a Cox partial likelihood loss function. In a study of 302 patients the predictive accuracy (quantified by Harrells C-index) was significantly higher (p < .0001) for our model C=0.73 (95$%$ CI: 0.68 - 0.78) than the human benchmark of C=0.59 (95$%$ CI: 0.53 - 0.65). This work demonstrates how a complex computer vision task using high-dimensional medical image data can efficiently predict human survival.
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Deriving interpretable prognostic features from deep-learning-based prognostic histopathology models remains a challenge. In this study, we developed a deep learning system (DLS) for predicting disease specific survival for stage II and III colorectal cancer using 3,652 cases (27,300 slides). When evaluated on two validation datasets containing 1,239 cases (9,340 slides) and 738 cases (7,140 slides) respectively, the DLS achieved a 5-year disease-specific survival AUC of 0.70 (95%CI 0.66-0.73) and 0.69 (95%CI 0.64-0.72), and added significant predictive value to a set of 9 clinicopathologic features. To interpret the DLS, we explored the ability of different human-interpretable features to explain the variance in DLS scores. We observed that clinicopathologic features such as T-category, N-category, and grade explained a small fraction of the variance in DLS scores (R2=18% in both validation sets). Next, we generated human-interpretable histologic features by clustering embeddings from a deep-learning based image-similarity model and showed that they explain the majority of the variance (R2 of 73% to 80%). Furthermore, the clustering-derived feature most strongly associated with high DLS scores was also highly prognostic in isolation. With a distinct visual appearance (poorly differentiated tumor cell clusters adjacent to adipose tissue), this feature was identified by annotators with 87.0-95.5% accuracy. Our approach can be used to explain predictions from a prognostic deep learning model and uncover potentially-novel prognostic features that can be reliably identified by people for future validation studies.
Learning curves model a classifiers test error as a function of the number of training samples. Prior works show that learning curves can be used to select model parameters and extrapolate performance. We investigate how to use learning curves to evaluate design choices, such as pretraining, architecture, and data augmentation. We propose a method to robustly estimate learning curves, abstract their parameters into error and data-reliance, and evaluate the effectiveness of different parameterizations. Our experiments exemplify use of learning curves for analysis and yield several interesting observations.
Effectively measuring the similarity between two human motions is necessary for several computer vision tasks such as gait analysis, person identi- fication and action retrieval. Nevertheless, we believe that traditional approaches such as L2 distance or Dynamic Time Warping based on hand-crafted local pose metrics fail to appropriately capture the semantic relationship across motions and, as such, are not suitable for being employed as metrics within these tasks. This work addresses this limitation by means of a triplet-based deep metric learning specifically tailored to deal with human motion data, in particular with the prob- lem of varying input size and computationally expensive hard negative mining due to motion pair alignment. Specifically, we propose (1) a novel metric learn- ing objective based on a triplet architecture and Maximum Mean Discrepancy; as well as, (2) a novel deep architecture based on attentive recurrent neural networks. One benefit of our objective function is that it enforces a better separation within the learned embedding space of the different motion categories by means of the associated distribution moments. At the same time, our attentive recurrent neural network allows processing varying input sizes to a fixed size of embedding while learning to focus on those motion parts that are semantically distinctive. Our ex- periments on two different datasets demonstrate significant improvements over conventional human motion metrics.
Advances in deep learning (DL) have resulted in impressive accuracy in some medical image classification tasks, but often deep models lack interpretability. The ability of these models to explain their decisions is important for fostering clinical trust and facilitating clinical translation. Furthermore, for many problems in medicine there is a wealth of existing clinical knowledge to draw upon, which may be useful in generating explanations, but it is not obvious how this knowledge can be encoded into DL models - most models are learnt either from scratch or using transfer learning from a different domain. In this paper we address both of these issues. We propose a novel DL framework for image-based classification based on a variational autoencoder (VAE). The framework allows prediction of the output of interest from the latent space of the autoencoder, as well as visualisation (in the image domain) of the effects of crossing the decision boundary, thus enhancing the interpretability of the classifier. Our key contribution is that the VAE disentangles the latent space based on `explanations drawn from existing clinical knowledge. The framework can predict outputs as well as explanations for these outputs, and also raises the possibility of discovering new biomarkers that are separate (or disentangled) from the existing knowledge. We demonstrate our framework on the problem of predicting response of patients with cardiomyopathy to cardiac resynchronization therapy (CRT) from cine cardiac magnetic resonance images. The sensitivity and specificity of the proposed model on the task of CRT response prediction are 88.43% and 84.39% respectively, and we showcase the potential of our model in enhancing understanding of the factors contributing to CRT response.
Constraint-based learning reduces the burden of collecting labels by having users specify general properties of structured outputs, such as constraints imposed by physical laws. We propose a novel framework for simultaneously learning these constraints and using them for supervision, bypassing the difficulty of using domain expertise to manually specify constraints. Learning requires a black-box simulator of structured outputs, which generates valid labels, but need not model their corresponding inputs or the input-label relationship. At training time, we constrain the model to produce outputs that cannot be distinguished from simulated labels by adversarial training. Providing our framework with a small number of labeled inputs gives rise to a new semi-supervised structured prediction model; we evaluate this model on multiple tasks --- tracking, pose estimation and time series prediction --- and find that it achieves high accuracy with only a small number of labeled inputs. In some cases, no labels are required at all.
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