We present a novel approach to train pixel resolution segmentation models on whole slide images in a weakly supervised setup. The model is trained to classify patches extracted from slides. This leads the training to be made under noisy labeled data. We solve the problem with two complementary strategies. First, the patches are sampled online using the model's knowledge by focusing on regions where the model's confidence is higher. Second, we propose an extension of the KL divergence that is robust to noisy labels. Our preliminary experiment on CAMELYON 16 data set show promising results. The model can successfully segment tumor areas with strong morphological consistency.
Image segmentation at pixel-level under weak supervision has been studied in @cite_0 @cite_14 @cite_5 . These approaches propose to work under the Multiple Instance Learning framework (MIL). The images are seen as bag of pixels or patches. The elements of the bags have an underlying label that is not available. However a label at the bag level is available and relate to the label of its elements. A negative (i.e. @math ) bag contains only negative elements, while a positive (i.e. @math ) bag contains at least one positive element. A convolutional neural network (CNN) is used to produce pixel (patch) level features that are aggregated through a pooling function to form the bag level class prediction. However these approaches need the image to fit into memory and do not scale on WSIs that contain giga pixels.
@cite_0 @cite_5 @cite_14
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Convolutional Neural Networks (CNN) are state-of-the-art models for many image classification tasks. However, to recognize cancer subtypes automatically, training a CNN on gigapixel resolution Whole Slide Tissue Images (WSI) is currently computationally impossible. The differentiation of cancer subtypes is based on cellular-level visual features observed on image patch scale. Therefore, we argue that in this situation, training a patch-level classifier on image patches will perform better than or similar to an image-level classifier. The challenge becomes how to intelligently combine patch-level classification results and model the fact that not all patches will be discriminative. We propose to train a decision fusion model to aggregate patch-level predictions given by patch-level CNNs, which to the best of our knowledge has not been shown before. Furthermore, we formulate a novel Expectation-Maximization (EM) based method that automatically locates discriminative patches robustly by utilizing the spatial relationships of patches. We apply our method to the classification of glioma and non-small-cell lung carcinoma cases into subtypes. The classification accuracy of our method is similar to the inter-observer agreement between pathologists. Although it is impossible to train CNNs on WSIs, we experimentally demonstrate using a comparable non-cancer dataset of smaller images that a patch-based CNN can outperform an image-based CNN. This paper addresses the problem of weakly supervised semantic image segmentation. Our goal is to label every pixel in a new image, given only image-level object labels associated with training images. Our problem statement differs from common semantic segmentation, where pixel-wise annotations are typically assumed available in training. We specify a novel deep architecture which fuses three distinct computation processes toward semantic segmentation &#x2013; namely, (i) the bottom-up computation of neural activations in a CNN for the image-level prediction of object classes, (ii) the top-down estimation of conditional likelihoods of the CNNs activations given the predicted objects, resulting in probabilistic attention maps per object class, and (iii) the lateral attention-message passing from neighboring neurons at the same CNN layer. The fusion of (i)-(iii) is realized via a conditional random field as recurrent network aimed at generating a smooth and boundary-preserving segmentation. Unlike existing work, we formulate a unified end-to-end learning of all components of our deep architecture. Evaluation on the benchmark PASCAL VOC 2012 dataset demonstrates that we outperform reasonable weakly supervised baselines and state-of-the-art approaches. Convolutional neural networks (CNNs) have shown great performance as general feature representations for object recognition applications. However, for multi-label images that contain multiple objects from different categories, scales and locations, global CNN features are not optimal. In this paper, we incorporate local information to enhance the feature discriminative power. In particular, we first extract object proposals from each image. With each image treated as a bag and object proposals extracted from it treated as instances, we transform the multi-label recognition problem into a multi-class multi-instance learning problem. Then, in addition to extracting the typical CNN feature representation from each proposal, we propose to make use of ground-truth bounding box annotations (strong labels) to add another level of local information by using nearest-neighbor relationships of local regions to form a multi-view pipeline. The proposed multi-view multiinstance framework utilizes both weak and strong labels effectively, and more importantly it has the generalization ability to even boost the performance of unseen categories by partial strong labels from other categories. Our framework is extensively compared with state-of-the-art handcrafted feature based methods and CNN based methods on two multi-label benchmark datasets. The experimental results validate the discriminative power and the generalization ability of the proposed framework. With strong labels, our framework is able to achieve state-of-the-art results in both datasets. Convolutional neural networks (CNN) have been widely used for visual recognition tasks including semantic segmentation of images. While the existing methods consider uniformly sampled single-or multi-scale patches from the neighborhood of each voxel, this approach might be sub-optimal as it captures and processes unnecessary details far away from the center of the patch. We instead propose to train CNNs with non-uniformly sampled patches that allow a wider extent for the sampled patches. This results in more captured contextual information, which is in particular of interest for biomedical image analysis, where the anatomical location of imaging features are often crucial. We evaluate and compare this strategy for white matter hyperintensity segmentation on a test set of 46 MRI scans. We show that the proposed method not only outperforms identical CNNs with uniform patches of the same size (0.780 Dice coefficient compared to 0.736), but also gets very close to the performance of an independent human expert (0.796 Dice coefficient).