Deep learning based digital cell profiles for risk stratification of urine cytology images.

Urine cytology is a test for the detection of high-grade bladder cancer. In clinical practice, the pathologist would manually scan the sample under the microscope to locate atypical and malignant cells. They would assess the morphology of these cells to make a diagnosis. Accurate identification of atypical and malignant cells in urine cytology is a challenging task and is an essential part of identifying different diagnosis with low-risk and high-risk malignancy. Computer-assisted identification of malignancy in urine cytology can be complementary to the clinicians for treatment management and in providing advice for carrying out further tests. In this study, we presented a method for identifying atypical and malignant cells followed by their profiling to predict the risk of diagnosis automatically. For cell detection and classification, we employed two different deep learning-based approaches. Based on the best performing network predictions at the cell level, we identified low-risk and high-risk cases using the count of atypical cells and the total count of atypical and malignant cells. The area under the receiver operating characteristic (ROC) curve shows that a total count of atypical and malignant cells is comparably better at diagnosis as compared to the count of malignant cells only. We obtained area under the ROC curve with the count of malignant cells and the total count of atypical and malignant cells as 0.81 and 0.83, respectively. Our experiments also demonstrate that the digital risk could be a better predictor of the final histopathology-based diagnosis. We also analyzed the variability in annotations at both cell and whole slide image level and also explored the possible inherent rationales behind this variability.

Fine-Grained Forecasting of COVID-19 Trends at the County Level in the United States.

The novel coronavirus (COVID-19) pandemic, first identified in Wuhan China in December 2019, has profoundly impacted various aspects of daily life, society, healthcare systems, and global health policies. There have been more than half a billion human infections and more than 6 million deaths globally attributable to COVID-19. Although treatments and vaccines to protect against COVID-19 are now available, people continue being hospitalized and dying due to COVID-19 infections. Real-time surveillance of population-level infections, hospitalizations, and deaths has helped public health officials better allocate healthcare resources and deploy mitigation strategies. However, producing reliable, real-time, short-term disease activity forecasts (one or two weeks into the future) remains a practical challenge. The recent emergence of robust time-series forecasting methodologies based on deep learning approaches has led to clear improvements in multiple research fields. We propose a recurrent neural network model named Fine-Grained Infection Forecast Network (FIGI-Net), which utilizes a stacked bidirectional LSTM structure designed to leverage fine-grained county-level data, to produce daily forecasts of COVID-19 infection trends up to two weeks in advance. We show that FIGI-Net improves existing COVID-19 forecasting approaches and delivers accurate county-level COVID-19 disease estimates. Specifically, FIGI-Net is capable of anticipating upcoming sudden changes in disease trends such as the onset of a new outbreak or the peak of an ongoing outbreak, a skill that multiple existing state-of-the-art models fail to achieve. This improved performance is observed across locations and periods. Our enhanced forecasting methodologies may help protect human populations against future disease outbreaks.

Human papilloma virus detection in oropharyngeal carcinomas with in situ hybridisation using hand crafted morphological features and deep central attention residual networks.

Human Papilloma Virus (HPV) is a major risk factor for the development of oropharyngeal cancer. Automatic detection of HPV in digitized pathology tissues using in situ hybridisation (ISH) is a difficult task due to the variability and complexity of staining patterns as well as the presence of imaging and staining artefacts. This paper proposes an intelligent image analysis framework to determine HPV status in digitized samples of oropharyngeal cancer tissue micro-arrays (TMA). The proposed pipeline mixes handcrafted feature extraction with a deep learning for epithelial region segmentation as a preliminary step. We apply a deep central attention learning technique to segment epithelial regions and within those assess the presence of regions representing ISH products. We then extract relevant morphological measurements from those regions which are then input into a supervised learning model for the identification of HPV status. The performance of the proposed method has been evaluated on 2009 TMA images of oropharyngeal carcinoma tissues captured with a ×20 objective. The experimental results show that our technique provides around 91% classification accuracy in detecting HPV status when compared with the histopatholgist gold standard. We also tested the performance of end-to-end deep learning classification methods to assess HPV status by learning directly from the original ISH processed images, rather than from the handcrafted features extracted from the segmented images. We examined the performance of sequential convolutional neural networks (CNN) architectures including three popular image recognition networks (VGG-16, ResNet and Inception V3) in their pre-trained and trained from scratch versions, however their highest classification accuracy was inferior (78%) to the hybrid pipeline presented here.

Simultaneous Cell Detection and Classification in Bone Marrow Histology Images.

Recently, deep learning frameworks have been shown to be successful and efficient in processing digital histology images for various detection and classification tasks. Among these tasks, cell detection and classification are key steps in many computer-assisted diagnosis systems. Traditionally, cell detection and classification is performed as a sequence of two consecutive steps by using two separate deep learning networks: one for detection and the other for classification. This strategy inevitably increases the computational complexity of the training stage. In this paper, we propose a synchronized deep autoencoder network for simultaneous detection and classification of cells in bone marrow histology images. The proposed network uses a single architecture to detect the positions of cells and classify the detected cells, in parallel. It uses a curve-support Gaussian model to compute probability maps that allow detecting irregularly shape cells precisely. Moreover, the network includes a novel neighborhood selection mechanism to boost the classification accuracy. We show that the performance of the proposed network is superior than traditional deep learning detection methods and very competitive compared to traditional deep learning classification networks. Runtime comparison also shows that our network requires less time to be trained.

Dual-Channel Active Contour Model for Megakaryocytic Cell Segmentation in Bone Marrow Trephine Histology Images.

Assessment of morphological features of megakaryocytes (MKs) (special kind of cells) in bone marrow trephine biopsies play an important role in the classification of different subtypes of Philadelphia-chromosome-negative myeloproliferative neoplasms (Ph-negative MPNs). In order to aid hematopathologists in the study of MKs, we propose a novel framework that can efficiently delineate the nuclei and cytoplasm of these cells in digitized images of bone marrow trephine biopsies. The framework first employs a supervised machine learning approach that utilizes color and texture features to delineate megakaryocytic nuclei. It then employs a novel dual-channel active contour model to delineate the boundary of megakaryocytic cytoplasm by using different deconvolved stain channels. Compared to other recent models, the proposed framework achieves accurate results for both megakaryocytic nuclear and cytoplasmic delineation.