This work tackles the automatic fine-grained slide quality assessment problem for digitized direct smears test using the Gram staining protocol. Automatic quality assessment can provide useful information for the pathologists and the whole digital pathology workflow. For instance, if the system found a slide to have a low staining quality, it could send a request to the automatic slide preparation system to remake the slide. If the system detects severe damage in the slides, it could notify the experts that manual microscope reading may be required. In order to address the quality assessment problem, we propose a deep neural network based framework to automatically assess the slide quality in a semantic way. Specifically, the first step of our framework is to perform dense fine-grained region classification on the whole slide and calculate the region histogram of the label distributions. Next, our framework will generate assessments of the slide quality from various perspectives: staining quality, information density, damage level and which regions are more valuable for subsequent high-magnification analysis. To make the information more accessible, we present our results in the form of a heat map and text summaries. Additionally, in order to stimulate research in this direction, we propose a novel dataset for slide quality assessment. Experiments show that the proposed framework outperforms recent related works.
More recently, deep learning methods are also being investigated in several microscopic medical applications @cite_12 @cite_27 . However, these works address different problems thus their frameworks are not suitable for our proposed tasks. Perhaps the most similar work to us is @cite_22 where the authors use SVM to select the regions of interest in a coarse-grain style using hand-crafted feature descriptors. In contrast, we differ significantly: 1. We propose a novel fine-grained slide quality assessment problem with a new larger, improved, and more difficult dataset. 2. We propose a novel DNN based framework that is 20x faster in training, 4x faster in testing and more accurate compared to @cite_22 in the region classification task.
@cite_27 @cite_22 @cite_12
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In this paper, we study the problem of learning from weakly labeled data, where labels of the training examples are incomplete. This includes, for example, (i) semi-supervised learning where labels are partially known; (ii) multi-instance learning where labels are implicitly known; and (iii) clustering where labels are completely unknown. Unlike supervised learning, learning with weak labels involves a difficult Mixed-Integer Programming (MIP) problem. Therefore, it can suffer from poor scalability and may also get stuck in local minimum. In this paper, we focus on SVMs and propose the WELLSVM via a novel label generation strategy. This leads to a convex relaxation of the original MIP, which is at least as tight as existing convex Semi-Definite Programming (SDP) relaxations. Moreover, the WELLSVM can be solved via a sequence of SVM subproblems that are much more scalable than previous convex SDP relaxations. Experiments on three weakly labeled learning tasks, namely, (i) semi-supervised learning; (ii) multi-instance learning for locating regions of interest in content-based information retrieval; and (iii) clustering, clearly demonstrate improved performance, and WELLSVM is also readily applicable on large data sets. We consider the semi-supervised multi-class classification problem of learning from sparse labelled and abundant unlabelled training data. To address this problem, existing semi-supervised deep learning methods often rely on the up-to-date “network-in-training” to formulate the semi-supervised learning objective. This ignores both the discriminative feature representation and the model inference uncertainty revealed by the network in the preceding learning iterations, referred to as the memory of model learning. In this work, we propose a novel Memory-Assisted Deep Neural Network (MA-DNN) capable of exploiting the memory of model learning to enable semi-supervised learning. Specifically, we introduce a memory mechanism into the network training process as an assimilation-accommodation interaction between the network and an external memory module. Experiments demonstrate the advantages of the proposed MA-DNN model over the state-of-the-art semi-supervised deep learning methods on three image classification benchmark datasets: SVHN, CIFAR10, and CIFAR100. This paper studies the effectiveness of accomplishing high-level tasks with a minimum of manual annotation and good feature representations for medical images. In medical image analysis, objects like cells are characterized by significant clinical features. Previously developed features like SIFT and HARR are unable to comprehensively represent such objects. Therefore, feature representation is especially important. In this paper, we study automatic extraction of feature representation through deep learning (DNN). Furthermore, detailed annotation of objects is often an ambiguous and challenging task. We use multiple instance learning (MIL) framework in classification training with deep learning features. Several interesting conclusions can be drawn from our work: (1) automatic feature learning outperforms manual feature; (2) the unsupervised approach can achieve performance that's close to fully supervised approach (93.56 ) vs. (94.52 ); and (3) the MIL performance of coarse label (96.30 ) outweighs the supervised performance of fine label (95.40 ) in supervised deep learning features. We study the problem of selecting a subset of big data to train a classifier while incurring minimal performance loss. We show the connection of submodularity to the data likelihood functions for Naive Bayes (NB) and Nearest Neighbor (NN) classifiers, and formulate the data subset selection problems for these classifiers as constrained submodular maximization. Furthermore, we apply this framework to active learning and propose a novel scheme called filtered active submodular selection (FASS), where we combine the uncertainty sampling method with a submodular data subset selection framework. We extensively evaluate the proposed framework on text categorization and handwritten digit recognition tasks with four different classifiers, including deep neural network (DNN) based classifiers. Empirical results indicate that the proposed framework yields significant improvement over the state-of-the-art algorithms on all classifiers.