Related papers: Generative Biomedical Entity Linking via Knowledge…

Pretrained language models have shown success in many natural language processing tasks. Many works explore incorporating knowledge into language models. In the biomedical domain, experts have taken decades of effort on building large-scale…

Biomedical named entity recognition is one of the core tasks in biomedical natural language processing (BioNLP). To tackle this task, numerous supervised/distantly supervised approaches have been proposed. Despite their remarkable success,…

Pre-trained language models (PLMs) were considered to be able to store relational knowledge present in the training data. However, some relational knowledge seems to be discarded unsafely in PLMs due to \textbf{report bias}: low-frequency…

Generative approaches powered by large language models (LLMs) have demonstrated emergent abilities in tasks that require complex reasoning abilities. Yet the generative nature still makes the generated content suffer from hallucinations,…

Entity linking (EL) is the process of linking entity mentions appearing in web text with their corresponding entities in a knowledge base. EL plays an important role in the fields of knowledge engineering and data mining, underlying a…

We introduce GENomic Encoding REpresentation with Language Model (GENEREL), a framework designed to bridge genetic and biomedical knowledge bases. What sets GENEREL apart is its ability to fine-tune language models to infuse biological…

Entity Linking (EL) is the gateway into Knowledge Bases. Recent advances in EL utilize dense retrieval approaches for Candidate Generation, which addresses some of the shortcomings of the Lookup based approach of matching NER mentions…

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…

Generative approaches have been recently shown to be effective for both Entity Disambiguation and Entity Linking (i.e., joint mention detection and disambiguation). However, the previously proposed autoregressive formulation for EL suffers…

Biomedical knowledge graphs (KGs) hold rich information on entities such as diseases, drugs, and genes. Predicting missing links in these graphs can boost many important applications, such as drug design and repurposing. Recent work has…

Entity linking (EL) aligns textual mentions with their corresponding entities in a knowledge base, facilitating various applications such as semantic search and question answering. Recent advances in multimodal entity linking (MEL) have…

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…

Biomedical Named Entity Recognition (NER) is a fundamental task of Biomedical Natural Language Processing for extracting relevant information from biomedical texts, such as clinical records, scientific publications, and electronic health…

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.…

Medical knowledge bases (KBs), distilled from biomedical literature and regulatory actions, are expected to provide high-quality information to facilitate clinical decision making. Entity disambiguation (also referred to as entity linking)…

Progress in biomedical Named Entity Recognition (NER) and Entity Linking (EL) is currently hindered by a fragmented data landscape, a lack of resources for building explainable models, and the limitations of semantically-blind evaluation…

Entity linking (EL) is the task of automatically identifying entity mentions in text and resolving them to a corresponding entity in a reference knowledge base like Wikipedia. Throughout the past decade, a plethora of EL systems and…

We propose a Bayesian generative model for incorporating prior domain knowledge into hierarchical topic modeling. Although embedded topic models (ETMs) and its variants have gained promising performance in text analysis, they mainly focus…

Biomedical entity linking and event extraction are two crucial tasks to support text understanding and retrieval in the biomedical domain. These two tasks intrinsically benefit each other: entity linking disambiguates the biomedical…

Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a…