Related papers: Ontology-Driven and Weakly Supervised Rare Disease…
Background: Common data models solve many challenges of standardizing electronic health record (EHR) data, but are unable to semantically integrate all the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO)…
Weak labeling is a popular weak supervision strategy for Named Entity Recognition (NER) tasks, with the goal of reducing the necessity for hand-crafted annotations. Although there are numerous remarkable annotation tools for NER labeling,…
Clinical studies often require understanding elements of a patient's narrative that exist only in free text clinical notes. To transform notes into structured data for downstream use, these elements are commonly extracted and normalized to…
Knowledge discovery is hindered by the increasing volume of publications and the scarcity of extensive annotated data. To tackle the challenge of information overload, it is essential to employ automated methods for knowledge extraction and…
Eye gaze that reveals human observational patterns has increasingly been incorporated into solutions for vision tasks. Despite recent explorations on leveraging gaze to aid deep networks, few studies exploit gaze as an efficient annotation…
Fine-grained glomerular subtyping is central to kidney biopsy interpretation, but clinically valuable labels are scarce and difficult to obtain. Existing computational pathology approaches instead tend to evaluate coarse diseased…
The emergence of generative Large Language Models (LLMs) emphasizes the need for accurate and efficient prompting approaches. LLMs are often applied in Few-Shot Learning (FSL) contexts, where tasks are executed with minimal training data.…
Dense annotations, such as segmentation masks, are expensive and time-consuming to obtain, especially for 3D medical images where expert voxel-wise labeling is required. Weakly supervised approaches aim to address this limitation, but often…
Medical entity linking is the task of identifying and standardizing medical concepts referred to in an unstructured text. Most of the existing methods adopt a three-step approach of (1) detecting mentions, (2) generating a list of candidate…
Recently, there has been a growing interest in Multimodal Large Language Models (MLLMs) due to their remarkable potential in various tasks integrating different modalities, such as image and text, as well as applications such as image…
Leveraging knowledge from electronic health records (EHRs) to predict a patient's condition is essential to the effective delivery of appropriate care. Clinical notes of patient EHRs contain valuable information from healthcare…
Novel contexts may often arise in complex querying scenarios such as in evidence-based medicine (EBM) involving biomedical literature, that may not explicitly refer to entities or canonical concept forms occurring in any fact- or rule-based…
Clinical notes in Electronic Health Records (EHR) present rich documented information of patients to inference phenotype for disease diagnosis and study patient characteristics for cohort selection. Unsupervised user embedding aims to…
Many ways of annotating a dataset for machine learning classification tasks that go beyond the usual class labels exist in practice. These are of interest as they can simplify or facilitate the collection of annotations, while not greatly…
Document clustering is a text mining technique used to provide better document search and browsing in digital libraries or online corpora. A lot of research has been done on biomedical document clustering that is based on using existing…
Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model…
Ontology can be used for the interpretation of natural language. To construct an anti-infective drug ontology, one needs to design and deploy a methodological step to carry out the entity discovery and linking. Medical synonym resources…
Weak supervision has shown promising results in many natural language processing tasks, such as Named Entity Recognition (NER). Existing work mainly focuses on learning deep NER models only with weak supervision, i.e., without any human…
Medical information extraction consists of a group of natural language processing (NLP) tasks, which collaboratively convert clinical text to pre-defined structured formats. Current state-of-the-art (SOTA) NLP models are highly integrated…
Accurate segmentation of organelle instances from electron microscopy (EM) images plays an essential role in many neuroscience researches. However, practical scenarios usually suffer from high annotation costs, label scarcity, and large…