SNER: Semi-supervised Named Entity Recognition for Large Volume of Diabetes Data.

The medical literature and records on diabetes provide crucial resources for diabetes prevention and treatment. However, extracting entities from these textual diabetes data is crucial but challenging. Named entity recognition (NER) - an important corner-stone technology of natural language processing - has been studied well in the general medical field. However, there is still a lack of effective NER methods to handle diabetes data. Briefly, there are three challenges in the real world, including 1) the large volume of diabetes-related data to be processed, 2) the lack of labeled data, and 3) the high costs of manual labeling. To mitigate those challenges, this paper proposes a novel NER method based on semi-supervised learning, namely SNER, for diabetes data processing. It utilizes large amounts of unlabeled data to solve the problem of lack of labeled data. Specifically, it filters the predicted labels based on their confidence and uncertainty scores to reduce the noise entering the model and divide them into positive pseudo-labels and negative pseudo-labels. Also, it utilizes negative pseudo-labels reasonably to improve the training effect of pseudo-labels. Experiments on two public diabetes datasets show that SNER achieves the best performance compared with existing state-of-the-art models.

Label-Free Virtual HER2 Immunohistochemical Staining of Breast Tissue using Deep Learning.

The immunohistochemical (IHC) staining of the human epidermal growth factor receptor 2 (HER2) biomarker is widely practiced in breast tissue analysis, preclinical studies, and diagnostic decisions, guiding cancer treatment and investigation of pathogenesis. HER2 staining demands laborious tissue treatment and chemical processing performed by a histotechnologist, which typically takes one day to prepare in a laboratory, increasing analysis time and associated costs. Here, we describe a deep learning-based virtual HER2 IHC staining method using a conditional generative adversarial network that is trained to rapidly transform autofluorescence microscopic images of unlabeled/label-free breast tissue sections into bright-field equivalent microscopic images, matching the standard HER2 IHC staining that is chemically performed on the same tissue sections. The efficacy of this virtual HER2 staining framework was demonstrated by quantitative analysis, in which three board-certified breast pathologists blindly graded the HER2 scores of virtually stained and immunohistochemically stained HER2 whole slide images (WSIs) to reveal that the HER2 scores determined by inspecting virtual IHC images are as accurate as their immunohistochemically stained counterparts. A second quantitative blinded study performed by the same diagnosticians further revealed that the virtually stained HER2 images exhibit a comparable staining quality in the level of nuclear detail, membrane clearness, and absence of staining artifacts with respect to their immunohistochemically stained counterparts. This virtual HER2 staining framework bypasses the costly, laborious, and time-consuming IHC staining procedures in laboratory and can be extended to other types of biomarkers to accelerate the IHC tissue staining used in life sciences and biomedical workflow.