Related papers: BELB: a Biomedical Entity Linking Benchmark

Entities can be expressed in diverse formats, such as texts, images, or column names and cell values in tables. While existing entity linking (EL) models work well on per modality configuration, such as text-only EL, visual grounding, or…

Entity matching (EM) is the most critical step for entity resolution (ER). While current deep learningbased methods achieve very impressive performance on standard EM benchmarks, their realworld application performance is much frustrating.…

Entity Linking (EL) is the process of associating ambiguous textual mentions to specific entities in a knowledge base. Traditional EL methods heavily rely on large datasets to enhance their performance, a dependency that becomes problematic…

Entity summarization is the problem of computing an optimal compact summary for an entity by selecting a size-constrained subset of triples from RDF data. Entity summarization supports a multiplicity of applications and has led to fruitful…

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…

Biomedical text mining and question-answering are essential yet highly demanding tasks, particularly in the face of the exponential growth of biomedical literature. In this work, we present our participation in the 13th edition of the…

Entity linking (EL) is the task of disambiguating mentions in text by associating them with entries in a predefined database of mentions (persons, organizations, etc). Most previous EL research has focused mainly on one language, English,…

Recent advances in large language models (LLMs) and biomedical foundation models (BioFMs) have achieved strong results in biological text reasoning, molecular modeling, and single-cell analysis, yet they remain siloed in disjoint embedding…

In this work, we formulate the NER task as a multi-answer knowledge guided QA task (KGQA) which helps to predict entities only by assigning B, I and O tags without associating entity types with the tags. We provide different knowledge…

Specialized entity linking (EL) models are well-trained at mapping mentions to unique knowledge base (KB) entities according to a given context. However, specialized EL models struggle to disambiguate long-tail entities due to their limited…

We propose Medical Entity Definition-based Sentence Embedding (MED-SE), a novel unsupervised contrastive learning framework designed for clinical texts, which exploits the definitions of medical entities. To this end, we conduct an…

Entity Linking (EL) is an essential and challenging task in natural language processing that seeks to link some text representing an entity within a document or sentence with its corresponding entry in a dictionary or knowledge base. Most…

The overwhelming amount of biomedical scientific texts calls for the development of effective language models able to tackle a wide range of biomedical natural language processing (NLP) tasks. The most recent dominant approaches are…

Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the…

Multimodal entity linking (MEL), a task aimed at linking mentions within multimodal contexts to their corresponding entities in a knowledge base (KB), has attracted much attention due to its wide applications in recent years. However,…

The goal of entity matching is to find the corresponding records representing the same real-world entity from different data sources. At present, in the mainstream methods, rule-based entity matching methods need tremendous domain…

Knowledge graphs have emerged as an important model for studying complex multi-relational data. This has given rise to the construction of numerous large scale but incomplete knowledge graphs encoding information extracted from various…

External knowledge,e.g., entities and entity descriptions, can help humans understand texts. Many works have been explored to include external knowledge in the pre-trained models. These methods, generally, design pre-training tasks and…

Named entity disambiguation (NED), which involves mapping textual mentions to structured entities, is particularly challenging in the medical domain due to the presence of rare entities. Existing approaches are limited by the presence of…

Recognizing spans of biomedical concepts and their types (e.g., drug or gene) in free text, often called biomedical named entity recognition (NER), is a basic component of information extraction (IE) pipelines. Without a strong NER…