Related papers: Extracting UMLS Concepts from Medical Text Using G…

In this paper, we report a knowledge-based method for Word Sense Disambiguation in the domains of biomedical and clinical text. We combine word representations created on large corpora with a small number of definitions from the UMLS to…

We analyze the extent to which internal representations of language models (LMs) identify and distinguish mentions of named entities, focusing on the many-to-many correspondence between entities and their mentions. We first formulate two…

In NLP, fine-tuning LLMs is effective for various applications but requires high-quality annotated data. However, manual annotation of data is labor-intensive, time-consuming, and costly. Therefore, LLMs are increasingly used to automate…

Medical Entity Recognition (MedER) is an essential NLP task for extracting meaningful entities from the medical corpus. Nowadays, MedER-based research outcomes can remarkably contribute to the development of automated systems in the medical…

This paper shines a light on the potential of definition-based semantic models for detecting idiomatic and semi-idiomatic multiword expressions (MWEs) in clinical terminology. Our study focuses on biomedical entities defined in the UMLS…

Named entity recognition (NER) and relation extraction (RE) are two important tasks in information extraction and retrieval (IE \& IR). Recent work has demonstrated that it is beneficial to learn these tasks jointly, which avoids the…

Mining relationships between treatment(s) and medical problem(s) is vital in the biomedical domain. This helps in various applications, such as decision support system, safety surveillance, and new treatment discovery. We propose a deep…

Tasks, Datasets and Evaluation Metrics are important concepts for understanding experimental scientific papers. However, most previous work on information extraction for scientific literature mainly focuses on the abstracts only, and does…

Unstructured information comprises a valuable source of data in clinical records. For text mining in clinical records, concept extraction is the first step in finding assertions and relationships. This study presents a system developed for…

Developing conversational agents to interact with patients and provide primary clinical advice has attracted increasing attention due to its huge application potential, especially in the time of COVID-19 Pandemic. However, the training of…

This survey presents a comprehensive description of recent neural entity linking (EL) systems developed since 2015 as a result of the "deep learning revolution" in natural language processing. Its goal is to systemize design features of…

In the rapidly evolving field of healthcare and beyond, the integration of generative AI in Electronic Health Records (EHRs) represents a pivotal advancement, addressing a critical gap in current information extraction techniques. This…

Recently, the performance of Pre-trained Language Models (PLMs) has been significantly improved by injecting knowledge facts to enhance their abilities of language understanding. For medical domains, the background knowledge sources are…

Accurate recognition of biomedical named entities is critical for medical information extraction and knowledge discovery. However, existing methods often struggle with nested entities, entity boundary ambiguity, and cross-lingual…

Entities, as important carriers of real-world knowledge, play a key role in many NLP tasks. We focus on incorporating entity knowledge into an encoder-decoder framework for informative text generation. Existing approaches tried to index,…

Most existing methods for biomedical entity recognition task rely on explicit feature engineering where many features either are specific to a particular task or depends on output of other existing NLP tools. Neural architectures have been…

Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting…

Although deep learning models like CNNs have achieved great success in medical image analysis, the small size of medical datasets remains a major bottleneck in this area. To address this problem, researchers have started looking for…

Extracting relations across large text spans has been relatively underexplored in NLP, but it is particularly important for high-value domains such as biomedicine, where obtaining high recall of the latest findings is crucial for practical…

Distributed representations of medical concepts have been used to support downstream clinical tasks recently. Electronic Health Records (EHR) capture different aspects of patients' hospital encounters and serve as a rich source for…