Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of clinical notes can use observed frequencies of clinical terms as predictive features for downstream applications such as clinical decision making and patient trajectory prediction. However, due to the vast number of highly similar and related clinical concepts, a more effective modeling strategy is to represent clinical terms as semantic embeddings via representation learning and use the low dimensional embeddings as feature vectors for predictive modeling. To achieve efficient representation, fine-tuning pretrained language models with biomedical knowledge graphs may generate better embeddings for biomedical terms than those from standard language models alone. These embeddings can effectively discriminate synonymous pairs of from those that are unrelated. However, they often fail to capture different degrees of similarity or relatedness for concepts that are hierarchical in nature. To overcome this limitation, we propose HiPrBERT, a novel biomedical term representation model trained on additionally complied data that contains hierarchical structures for various biomedical terms. We modify an existing contrastive loss function to extract information from these hierarchies. Our numerical experiments demonstrate that HiPrBERT effectively learns the pair-wise distance from hierarchical information, resulting in a substantially more informative embeddings for further biomedical applications

Recently, knowledge-enhanced methods leveraging auxiliary knowledge graphs have emerged in relation extraction, surpassing traditional text-based approaches. However, to our best knowledge, there is currently no public dataset available that encompasses both evidence sentences and knowledge graphs for knowledge-enhanced relation extraction. To address this gap, we introduce the Knowledge-Enhanced Relation Extraction Dataset (KERED). KERED annotates each sentence with a relational fact, and it provides knowledge context for entities through entity linking. Using our curated dataset, We compared contemporary relation extraction methods under two prevalent task settings: sentence-level and bag-level. The experimental result shows the knowledge graphs provided by KERED can support knowledge-enhanced relation extraction methods. We believe that KERED offers high-quality relation extraction datasets with corresponding knowledge graphs for evaluating the performance of knowledge-enhanced relation extraction methods. Our dataset is available at: \url{https://figshare.com/projects/KERED/134459}

Fully automatic segmentation methods, such as liver and liver tumor segmentation, brain and brain tumor segmentation, optic disc segmentation, cell segmentation, lung segmentation, pulmonary nodule segmentation, and cardiac image segmentation [2], are essential for the diagnosis of serious diseases [3]. Therefore, it is important to improve the efficiency and accuracy of medical image segmentation methods. Medical image segmentation involves segmenting specific organs (e.g., the pancreas, liver, and bladder), determining certain functional parts of an organ (e.g., cardiac segmentation and retinal vessel segmentation), and identifying tumors in the organs. Medical images can generally be categorized according to the imaging technology and data form. Imaging technology includes X-ray photos, computed tomography, magnetic resonance imaging (MRI), and ultrasound imaging. Raw measurements are transformed into pixelated imaging data as part of the standard process. Although the original data are mostly three-dimensional images, two-dimensional slices are often created according to clinical procedure protocols that target specific applications. Most medical image segmentation methods are designed for two-dimensional slices.

Objective: Medical relations are the core components of medical knowledge graphs that are needed for healthcare artificial intelligence. However, the requirement of expert annotation by conventional algorithm development processes creates a major bottleneck for mining new relations. In this paper, we present Hi-RES, a framework for high-throughput relation extraction algorithm development. We also show that combining knowledge articles with electronic health records (EHRs) significantly increases the classification accuracy. Methods: We use relation triplets obtained from structured databases and semistructured webpages to label sentences from target corpora as positive training samples. Two methods are also provided for creating improved negative samples by combining positive samples with na\"ive negative samples. We propose a common model that summarizes sentence information using large-scale pretrained language models and multi-instance attention, which then joins with the concept embeddings trained from the EHRs for relation prediction. Results: We apply the Hi-RES framework to develop classification algorithms for disorder-disorder relations and disorder-location relations. Millions of sentences are created as training data. Using pretrained language models and EHR-based embeddings individually provides considerable accuracy increases over those of previous models. Joining them together further tremendously increases the accuracy to 0.947 and 0.998 for the two sets of relations, respectively, which are 10-17 percentage points higher than those of previous models. Conclusion: Hi-RES is an efficient framework for achieving high-throughput and accurate relation extraction algorithm development.