Related papers: BioNerFlair: biomedical named entity recognition u…

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…

Named Entity Recognition (NER) is an essential precursor task for many natural language applications, such as relation extraction or event extraction. Much of the NER research has been done on datasets with few classes of entity types (e.g.…

Open Named Entity Recognition (NER), which involves identifying arbitrary types of entities from arbitrary domains, remains challenging for Large Language Models (LLMs). Recent studies suggest that fine-tuning LLMs on extensive NER data can…

Biomedical named entity recognition (NER) and entity linking (EL) strongly depend on annotated corpora, but the utility of these resources for benchmarking is often assumed rather than characterized. We present a corpus-centric framework…

Medical named entity recognition (NER) has wide applications in intelligent healthcare. Sufficient labeled data is critical for training accurate medical NER model. However, the labeled data in a single medical platform is usually limited.…

We present SwellShark, a framework for building biomedical named entity recognition (NER) systems quickly and without hand-labeled data. Our approach views biomedical resources like lexicons as function primitives for autogenerating weak…

Fine-grained Entity Recognition (FgER) is the task of detecting and classifying entity mentions to a large set of types spanning diverse domains such as biomedical, finance and sports. We observe that when the type set spans several…

Named entity recognition (NER) is a popular domain of natural language processing. For this reason, many tools exist to perform this task. Amongst other points, they differ in the processing method they rely upon, the entity types they can…

This work investigates multiple approaches to Named Entity Recognition (NER) for text in Electronic Health Record (EHR) data. In particular, we look into the application of (i) rule-based, (ii) deep learning and (iii) transfer learning…

Term clustering is important in biomedical knowledge graph construction. Using similarities between terms embedding is helpful for term clustering. State-of-the-art term embeddings leverage pretrained language models to encode terms, and…

When an entity name contains other names within it, the identification of all combinations of names can become difficult and expensive. We propose a new method to recognize not only outermost named entities but also inner nested ones. We…

This paper presents an iterative approach to performing Scientific Named Entity Recognition (SciNER) using BERT-based models. We leverage transfer learning to fine-tune pretrained models with a small but high-quality set of manually…

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 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…

Embedding models have become essential for retrieval-augmented generation (RAG) tasks, semantic clustering, and text re-ranking. But despite their growing use, many of these come with notable limitations. For example, Jina fails to capture…

The practice of fine-tuning Pre-trained Language Models (PLMs) from general or domain-specific data to a specific task with limited resources, has gained popularity within the field of natural language processing (NLP). In this work, we…

In recent years, Deep Learning (DL) models are becoming important due to their demonstrated success at overcoming complex learning problems. DL models have been applied effectively for different Natural Language Processing (NLP) tasks such…

We compare three simple and popular approaches for NER: 1) SEQ (sequence-labeling with a linear token classifier) 2) SeqCRF (sequence-labeling with Conditional Random Fields), and 3) SpanPred (span-prediction with boundary token…

In the domain of Natural Language Processing (NLP), Named Entity Recognition (NER) stands out as a pivotal mechanism for extracting structured insights from unstructured text. This manuscript offers an exhaustive exploration into the…

Named-entity recognition (NER) aims at identifying entities of interest in a text. Artificial neural networks (ANNs) have recently been shown to outperform existing NER systems. However, ANNs remain challenging to use for non-expert users.…