Breast cancer is one of the main causes of death worldwide. Histopathological cellularity assessment of residual tumors in post-surgical tissues is used to analyze a tumor's response to a therapy. Correct cellularity assessment increases the chances of getting an appropriate treatment and facilitates the patient's survival. In current clinical practice, tumor cellularity is manually estimated by pathologists; this process is tedious and prone to errors or low agreement rates between assessors. In this work, we evaluated three strong novel Deep Learning-based approaches for automatic assessment of tumor cellularity from post-treated breast surgical specimens stained with hematoxylin and eosin. We validated the proposed methods on the BreastPathQ SPIE challenge dataset that consisted of 2395 image patches selected from whole slide images acquired from 64 patients. Compared to expert pathologist scoring, our best performing method yielded the Cohen's kappa coefficient of 0.70 (vs. 0.42 previously known in literature) and the intra-class correlation coefficient of 0.89 (vs. 0.83). Our results suggest that Deep Learning-based methods have a significant potential to alleviate the burden on pathologists, enhance the diagnostic workflow, and, thereby, facilitate better clinical outcomes in breast cancer treatment.
Recent works by Akbar @cite_39 @cite_34 have compared the conventional approach based on segmentation and feature extraction and direct applications of deep CNNs to image patches in both regression and classification settings. Overall, they showed that the DL-based approach outperformed hand-crafted features in both accuracy and intra-class correlation (ICC) with expert pathologist annotations. Specifically, their best result was achieved by using a pre-trained Inception @cite_25 model that reached ICC of @math and @math with two expert pathologists. In this study we evaluate even wider range of DL-based approaches, including segmentation-based and segmentation-free, in both regression and classification settings. We provide appropriate performance comparisons with previously reported results. All the methods developed in this study are fully automatic and do not require any involvement of the human annotators at the test time.
@cite_34 @cite_25 @cite_39
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Our objective is to evaluate the efficacy of methods that use deep learning (DL) for the automatic fine-grained segmentation of optical coherence tomography (OCT) images of the retina. OCT images from 10 patients with mild non-proliferative diabetic retinopathy were used from a public (U. of Miami) dataset. For each patient, five images were available: one image of the fovea center, two images of the perifovea, and two images of the parafovea. For each image, two expert graders each manually annotated five retinal surfaces (i.e. boundaries between pairs of retinal layers). The first grader's annotations were used as ground truth and the second grader's annotations to compute inter-operator agreement. The proposed automated approach segments images using fully convolutional networks (FCNs) together with Gaussian process (GP)-based regression as a post-processing step to improve the quality of the estimates. Using 10-fold cross validation, the performance of the algorithms is determined by computing the per-pixel unsigned error (distance) between the automated estimates and the ground truth annotations generated by the first manual grader. We compare the proposed method against five state of the art automatic segmentation techniques. The results show that the proposed methods compare favorably with state of the art techniques, resulting in the smallest mean unsigned error values and associated standard deviations, and performance is comparable with human annotation of retinal layers from OCT when there is only mild retinopathy. The results suggest that semantic segmentation using FCNs, coupled with regression-based post-processing, can effectively solve the OCT segmentation problem on par with human capabilities with mild retinopathy. In this paper, we focus on improving the proposal classification stage in the object detection task and present implicit negative sub-categorization and sink diversion to lift the performance by strengthening loss function in this stage. First, based on the observation that the “background” class is generally very diverse and thus challenging to be handled as a single indiscriminative class in existing state-of-the-art methods, we propose to divide the background category into multiple implicit sub-categories to explicitly differentiate diverse patterns within it. Second, since the ground truth class inevitably has low-value probability scores for certain images, we propose to add a “sink” class and divert the probabilities of wrong classes to this class when necessary, such that the ground truth label will still have a higher probability than other wrong classes even though it has low probability output. Additionally, we propose to use dilated convolution, which is widely used in the semantic segmentation task, for efficient and valuable context information extraction. Extensive experiments on PASCAL VOC 2007 and 2012 data sets show that our proposed methods based on faster R-CNN implementation can achieve state-of-the-art mAPs, i.e., 84.1 , 82.6 , respectively, and obtain 2.5 improvement on ILSVRC DET compared with that of ResNet. We consider the task of learning a classifier for semantic segmentation using weak supervision in the form of image labels which specify the object classes present in the image. Our method uses deep convolutional neural networks (CNNs) and adopts an Expectation-Maximization (EM) based approach. We focus on the following three aspects of EM: (i) initialization; (ii) latent posterior estimation (E-step) and (iii) the parameter update (M-step). We show that saliency and attention maps, our bottom-up and top-down cues respectively, of simple images provide very good cues to learn an initialization for the EM-based algorithm. Intuitively, we show that before trying to learn to segment complex images, it is much easier and highly effective to first learn to segment a set of simple images and then move towards the complex ones. Next, in order to update the parameters, we propose minimizing the combination of the standard softmax loss and the KL divergence between the true latent posterior and the likelihood given by the CNN. We argue that this combination is more robust to wrong predictions made by the expectation step of the EM method. We support this argument with empirical and visual results. Extensive experiments and discussions show that: (i) our method is very simple and intuitive; (ii) requires only image-level labels; and (iii) consistently outperforms other weakly-supervised state-of-the-art methods with a very high margin on the PASCAL VOC 2012 dataset. Training deep fully convolutional neural networks (F-CNNs) for semantic image segmentation requires access to abundant labeled data. While large datasets of unlabeled image data are available in medical applications, access to manually labeled data is very limited. We propose to automatically create auxiliary labels on initially unlabeled data with existing tools and to use them for pre-training. For the subsequent fine-tuning of the network with manually labeled data, we introduce error corrective boosting (ECB), which emphasizes parameter updates on classes with lower accuracy. Furthermore, we introduce SkipDeconv-Net (SD-Net), a new F-CNN architecture for brain segmentation that combines skip connections with the unpooling strategy for upsampling. The SD-Net addresses challenges of severe class imbalance and errors along boundaries. With application to whole-brain MRI T1 scan segmentation, we generate auxiliary labels on a large dataset with FreeSurfer and fine-tune on two datasets with manual annotations. Our results show that the inclusion of auxiliary labels and ECB yields significant improvements. SD-Net segments a 3D scan in 7 secs in comparison to 30 hours for the closest multi-atlas segmentation method, while reaching similar performance. It also outperforms the latest state-of-the-art F-CNN models.