Related papers: Improving Biomedical Entity Linking with Retrieval…

The growth rate in the amount of biomedical documents is staggering. Unlocking information trapped in these documents can enable researchers and practitioners to operate confidently in the information world. Biomedical NER, the task of…

Although deep learning techniques have shown significant achievements, they frequently depend on extensive amounts of hand-labeled data and tend to perform inadequately in few-shot scenarios. The objective of this study is to devise a…

Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate…

As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful…

Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity…

In recent years, there has been substantial progress in using pretrained Language Models (LMs) on a range of tasks aimed at improving the understanding of biomedical texts. Nonetheless, existing biomedical LLMs show limited comprehension of…

Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models have achieved…

Information extraction techniques, including named entity recognition (NER) and relation extraction (RE), are crucial in many domains to support making sense of vast amounts of unstructured text data by identifying and connecting relevant…

In recent years, there has been an increasing number of frameworks developed for biomedical entity and relation extraction. This research effort aims to address the accelerating growth in biomedical publications and the intricate nature of…

Despite their strong linguistic capabilities, Large Language Models (LLMs) are computationally demanding and require substantial resources for fine-tuning, which is unadapted to privacy and budget constraints of many healthcare settings. To…

Contextualized word embeddings derived from pre-trained language models (LMs) show significant improvements on downstream NLP tasks. Pre-training on domain-specific corpora, such as biomedical articles, further improves their performance.…

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…

In recent years, with the growing amount of biomedical documents, coupled with advancement in natural language processing algorithms, the research on biomedical named entity recognition (BioNER) has increased exponentially. However, BioNER…

Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and…

Entity Alignment (EA) is essential for knowledge graph (KG) fusion, but existing benchmarks often allow models to exploit name overlap rather than relational structure. This makes it difficult to evaluate whether models can reject same-name…

Pre-trained models such as BERT are widely used in NLP tasks and are fine-tuned to improve the performance of various NLP tasks consistently. Nevertheless, the fine-tuned BERT model trained on our protocol corpus still has a weak…

We present SynCABEL (Synthetic Contextualized Augmentation for Biomedical Entity Linking), a framework that addresses a central bottleneck in supervised biomedical entity linking (BEL): the scarcity of expert-annotated training data.…

Biomedical Named Entity Recognition (BioNER) is a crucial step for analyzing Biomedical texts, which aims at extracting biomedical named entities from a given text. Different supervised machine learning algorithms have been applied for…

We introduce BioCoM, a contrastive learning framework for biomedical entity linking that uses only two resources: a small-sized dictionary and a large number of raw biomedical articles. Specifically, we build the training instances from raw…

Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important…