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This paper proposes a medical literature summary generation method based on the BERT model to address the challenges brought by the current explosion of medical information. By fine-tuning and optimizing the BERT model, we develop an…

The unstructured nature of clinical notes within electronic health records often conceals vital patient-related information, making it challenging to access or interpret. To uncover this hidden information, specialized Natural Language…

The extraction and analysis of insights from medical data, primarily stored in free-text formats by healthcare workers, presents significant challenges due to its unstructured nature. Medical coding, a crucial process in healthcare, remains…

Extracting structured clinical information from radiology reports is challenging, especially in low-resource languages. This is pronounced in Crohn's disease, with sparsely represented multi-organ findings. We developed Hierarchical…

The automatic generation of radiology reports has emerged as a promising solution to reduce a time-consuming task and accurately capture critical disease-relevant findings in X-ray images. Previous approaches for radiology report generation…

In recent years, the number of biomedical publications has steadfastly grown, resulting in a rich source of untapped new knowledge. Most biomedical facts are however not readily available, but buried in the form of unstructured text, and…

Retrieval-augmented learning based on radiology reports has emerged as a promising direction to improve performance on long-tail medical imaging tasks, such as rare disease detection in chest X-rays. Most existing methods rely on comparing…

Constructing large-scaled medical knowledge graphs can significantly boost healthcare applications for medical surveillance, bring much attention from recent research. An essential step in constructing large-scale MKG is extracting…

Extracting structured clinical information from free-text radiology reports can enable the use of radiology report information for a variety of critical healthcare applications. In our work, we present RadGraph, a dataset of entities and…

Recently we proposed the Span Attribute Tagging (SAT) Model (Du et al., 2019) to infer clinical entities (e.g., symptoms) and their properties (e.g., duration). It tackles the challenge of large label space and limited training data using a…

Utilizing clinical texts in survival analysis is difficult because they are largely unstructured. Current automatic extraction models fail to capture textual information comprehensively since their labels are limited in scope. Furthermore,…

This paper explores methods for extracting information from radiology reports that generalize across exam modalities to reduce requirements for annotated data. We demonstrate that multi-pass T5-based text-to-text generative models exhibit…

Dense retrieval has shown promise in the first-stage retrieval process when trained on in-domain labeled datasets. However, previous studies have found that dense retrieval is hard to generalize to unseen domains due to its weak modeling of…

Modern epidemiology integrates knowledge from heterogeneous collections of data consisting of numerical, descriptive and imaging. Large-scale epidemiological studies use sophisticated statistical analysis, mathematical models using…

This study explores three approaches to processing table data in scientific papers to enhance extractive question answering and develop a software tool for the systematic review process. The methods evaluated include: (1) Optical Character…

Multi-modal data abounds in biomedicine, such as radiology images and reports. Interpreting this data at scale is essential for improving clinical care and accelerating clinical research. Biomedical text with its complex semantics poses…

Medical imaging plays a critical role in the diagnosis and treatment planning of various medical conditions, with radiology and pathology heavily reliant on precise image segmentation. The Segment Anything Model (SAM) has emerged as a…

The surging amount of biomedical literature & digital clinical records presents a growing need for text mining techniques that can not only identify but also semantically relate entities in unstructured data. In this paper we propose a text…

Biomedical information is growing rapidly in the recent years and retrieving useful data through information extraction system is getting more attention. In the current research, we focus on different aspects of relation extraction…

Objective: The generalizability of clinical large language models is usually ignored during the model development process. This study evaluated the generalizability of BERT-based clinical NLP models across different clinical settings…