Related papers: Effective Multi-Task Learning for Biomedical Named…

Named entity recognition (NER) is a widely studied task in natural language processing. Recently, a growing number of studies have focused on the nested NER. The span-based methods, considering the entity recognition as a span…

Training a neural network-based biomedical named entity recognition (BioNER) model usually requires extensive and costly human annotations. While several studies have employed multi-task learning with multiple BioNER datasets to reduce…

Named entity recognition (NER) is the very first step in the linguistic processing of any new domain. It is currently a common process in BioNLP on English clinical text. However, it is still in its infancy in other major languages, as it…

The task of Named Entity Recognition (NER) is an important component of many natural language processing systems, such as relation extraction and knowledge graph construction. In this work, we present a simple and effective approach for…

Unlike widely used Named Entity Recognition (NER) data sets in generic domains, biomedical NER data sets often contain mentions consisting of discontinuous spans. Conventional sequence tagging techniques encode Markov assumptions that are…

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…

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…

Named entity recognition (NER) aims to identify mentions of named entities in an unstructured text and classify them into predefined named entity classes. While deep learning-based pre-trained language models help to achieve good predictive…

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…

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…

Named Entity Recognition (NER) or the extraction of concepts from clinical text is the task of identifying entities in text and slotting them into categories such as problems, treatments, tests, clinical departments, occurrences (such as…

The task of named entity recognition (NER) is normally divided into nested NER and flat NER depending on whether named entities are nested or not. Models are usually separately developed for the two tasks, since sequence labeling models,…

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…

In this paper, we study the named entity recognition (NER) problem under distant supervision. Due to the incompleteness of the external dictionaries and/or knowledge bases, such distantly annotated training data usually suffer from a high…

Background and Objective: Biomedical Named Entity Recognition (BioNER) is a foundational task in medical informatics, crucial for downstream applications like drug discovery and clinical trial matching. However, adapting general-domain…

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…

In this work, we explore the way to perform named entity recognition (NER) using only unlabeled data and named entity dictionaries. To this end, we formulate the task as a positive-unlabeled (PU) learning problem and accordingly propose a…

For languages with no annotated resources, transferring knowledge from rich-resource languages is an effective solution for named entity recognition (NER). While all existing methods directly transfer from source-learned model to a target…

We present a weakly-supervised data augmentation approach to improve Named Entity Recognition (NER) in a challenging domain: extracting biomedical entities (e.g., proteins) from the scientific literature. First, we train a neural NER (NNER)…

Named entity recognition (NER) and entity linking (EL) are two fundamentally related tasks, since in order to perform EL, first the mentions to entities have to be detected. However, most entity linking approaches disregard the mention…