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Register a new userLabelling Vertebrae with 2D Reformations of Multidetector CT Images: An Adversarial Approach for Incorporating Prior Knowledge of Spine Anatomy
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Anjany Kumar Sekuboyina
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Purpose: To use and test a labelling algorithm that operates on two-dimensional (2D) reformations, rather than three-dimensional (3D) data to locate and identify vertebrae. Methods: We improved the Btrfly Net (described by Sekuboyina et al) that works on sagittal and coronal maximum intensity projections (MIP) and augmented it with two additional components: spine-localization and adversarial a priori-learning. Furthermore, we explored two variants of adversarial training schemes that incorporated the anatomical a priori knowledge into the Btrfly Net. We investigated the superiority of the proposed approach for labelling vertebrae on three datasets: a public benchmarking dataset of 302 CT scans and two in-house datasets with a total of 238 CT scans. We employed Wilcoxon signed-rank test to compute the statistical significance of the improvement in performance observed due to various architectural components in our approach. Results: On the public dataset, our approach using the described Btrfly(pe-eb) network performed on par with current state-of-the-art methods achieving a statistically significant (p < .001) vertebrae identification rate of 88.5+/-0.2 % and localization distances of less than 7-mm. On the in-house datasets that had a higher inter-scan data variability, we obtained an identification rate of 85.1+/-1.2%. Conclusion: An identification performance comparable to existing 3D approaches was achieved when labelling vertebrae on 2D MIPs. The performance was further improved using the proposed adversarial training regime that effectively enforced local spine a priori knowledge during training. Lastly, spine-localization increased the generalizability of our approach by homogenizing the content in the MIPs.
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Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse.
Recent studies have highlighted the high correlation between cardiovascular diseases (CVD) and lung cancer, and both are associated with significant morbidity and mortality. Low-Dose CT (LCDT) scans have led to significant improvements in the accuracy of lung cancer diagnosis and thus the reduction of cancer deaths. However, the high correlation between lung cancer and CVD has not been well explored for mortality prediction. This paper introduces a knowledge-based analytical method using deep convolutional neural network (CNN) for all-cause mortality prediction. The underlying approach combines structural image features extracted from CNNs, based on LDCT volume in different scale, and clinical knowledge obtained from quantitative measurements, to comprehensively predict the mortality risk of lung cancer screening subjects. The introduced method is referred to here as the Knowledge-based Analysis of Mortality Prediction Network, or KAMP-Net. It constitutes a collaborative framework that utilizes both imaging features and anatomical information, instead of completely relying on automatic feature extraction. Our work demonstrates the feasibility of incorporating quantitative clinical measurements to assist CNNs in all-cause mortality prediction from chest LDCT images. The results of this study confirm that radiologist defined features are an important complement to CNNs to achieve a more comprehensive feature extraction. Thus, the proposed KAMP-Net has shown to achieve a superior performance when compared to other methods. Our code is available at https://github.com/DIAL-RPI/KAMP-Net.
The task of morphological classification is complex for simple parameterization, but important for research in the galaxy evolution field. Future galaxy surveys (e.g. EUCLID) will collect data about more than a $10^9$ galaxies. To obtain morphological information one needs to involve people to mark up galaxy images, which requires either a considerable amount of money or a huge number of volunteers. We propose an effective semi-supervised approach for galaxy morphology classification task, based on active learning of adversarial autoencoder (AAE) model. For a binary classification problem (top level question of Galaxy Zoo 2 decision tree) we achieved accuracy 93.1% on the test part with only 0.86 millions markup actions, this model can easily scale up on any number of images. Our best model with additional markup achieves accuracy of 95.5%. To the best of our knowledge it is a first time AAE semi-supervised learning model used in astronomy.
Though large-scale datasets are essential for training deep learning systems, it is expensive to scale up the collection of medical imaging datasets. Synthesizing the objects of interests, such as lung nodules, in medical images based on the distribu
tion of annotated datasets can be helpful for improving the supervised learning tasks, especially when the datasets are limited by size and class balance. In this paper, we propose the class-aware adversarial synthesis framework to synthesize lung nodules in CT images. The framework is built with a coarse-to-fine patch in-painter (generator) and two class-aware discriminators. By conditioning on the random latent variables and the target nodule labels, the trained networks are able to generate diverse nodules given the same context. By evaluating on the public LIDC-IDRI dataset, we demonstrate an example application of the proposed framework for improving the accuracy of the lung nodule malignancy estimation as a binary classification problem, which is important in the lung screening scenario. We show that combining the real image patches and the synthetic lung nodules in the training set can improve the mean AUC classification score across different network architectures by 2%.
Despite the recent works on knowledge distillation (KD) have achieved a further improvement through elaborately modeling the decision boundary as the posterior knowledge, their performance is still dependent on the hypothesis that the target network has a powerful capacity (representation ability). In this paper, we propose a knowledge representing (KR) framework mainly focusing on modeling the parameters distribution as prior knowledge. Firstly, we suggest a knowledge aggregation scheme in order to answer how to represent the prior knowledge from teacher network. Through aggregating the parameters distribution from teacher network into more abstract level, the scheme is able to alleviate the phenomenon of residual accumulation in the deeper layers. Secondly, as the critical issue of what the most important prior knowledge is for better distilling, we design a sparse recoding penalty for constraining the student network to learn with the penalized gradients. With the proposed penalty, the student network can effectively avoid the over-regularization during knowledge distilling and converge faster. The quantitative experiments exhibit that the proposed framework achieves the state-ofthe-arts performance, even though the target network does not have the expected capacity. Moreover, the framework is flexible enough for combining with other KD methods based on the posterior knowledge.
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