Related papers: Partial Annotation Learning for Biomedical Entity …

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…

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)…

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 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…

Objective: Extracting PICO elements -- Participants, Intervention, Comparison, and Outcomes -- from clinical trial literature is essential for clinical evidence retrieval, appraisal, and synthesis. Existing approaches do not distinguish the…

We study learning named entity recognizers in the presence of missing entity annotations. We approach this setting as tagging with latent variables and propose a novel loss, the Expected Entity Ratio, to learn models in the presence of…

Biomedical named entity recognition (NER) is a critial task that aims to identify structured information in clinical text, which is often replete with complex, technical terms and a high degree of variability. Accurate and reliable NER can…

Biomedical named entity recognition (BNER) serves as the foundation for numerous biomedical text mining tasks. Unlike general NER, BNER require a comprehensive grasp of the domain, and incorporating external knowledge beyond training data…

In many scenarios, named entity recognition (NER) models severely suffer from unlabeled entity problem, where the entities of a sentence may not be fully annotated. Through empirical studies performed on synthetic datasets, we find two…

Accurate recognition of biomedical named entities is critical for medical information extraction and knowledge discovery. However, existing methods often struggle with nested entities, entity boundary ambiguity, and cross-lingual…

This study evaluated the effect of BioBERT in medical text processing for the task of medical named entity recognition. Through comparative experiments with models such as BERT, ClinicalBERT, SciBERT, and BlueBERT, the results showed that…

Named-entity recognition (NER) is fundamental to extracting structured information from the >80% of healthcare data that resides in unstructured clinical notes and biomedical literature. Despite recent advances with large language models,…

Nested named entity recognition identifies entities contained within other entities, but requires expensive multi-level annotation. While flat NER corpora exist abundantly, nested resources remain scarce. We investigate whether models can…

Existing models for named entity recognition (NER) are mainly based on large-scale labeled datasets, which always obtain using crowdsourcing. However, it is hard to obtain a unified and correct label via majority voting from multiple…

Named entity recognition (NER) is a vital task in spoken language understanding, which aims to identify mentions of named entities in text e.g., from transcribed speech. Existing neural models for NER rely mostly on dedicated word-level…

While typical named entity recognition (NER) models require the training set to be annotated with all target types, each available datasets may only cover a part of them. Instead of relying on fully-typed NER datasets, many efforts have…

Developing high-performance entity normalization algorithms that can alleviate the term variation problem is of great interest to the biomedical community. Although deep learning-based methods have been successfully applied to biomedical…

Prion diseases are rare, rapidly progressive, and fatal neurodegenerative disorders that remain difficult to diagnose, particularly in their early stages because of nonspecific clinical presentations. However, to our knowledge, there is no…

Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. However, it is a common scenario that only entities within a…

Background: Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and showed promising…