Related papers: Biomedical Named Entity Recognition via Reference-…

In this work, we propose a two-stage method for named entity recognition (NER), especially for nested NER. We borrowed the idea from the two-stage Object Detection in computer vision and the way how they construct the loss function. First,…

A challenge for named entity disambiguation (NED), the task of mapping textual mentions to entities in a knowledge base, is how to disambiguate entities that appear rarely in the training data, termed tail entities. Humans use subtle…

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…

Few-shot Named Entity Recognition (NER) is imperative for entity tagging in limited resource domains and thus received proper attention in recent years. Existing approaches for few-shot NER are evaluated mainly under in-domain settings. In…

Biomedical Named Entity Recognition (BioNER), task6 in BioASQ (A challenge in large-scale biomedical semantic indexing and question answering), is crucial for extracting information from scientific literature but faces hurdles such as…

Cross-domain named entity recognition (NER) models are able to cope with the scarcity issue of NER samples in target domains. However, most of the existing NER benchmarks lack domain-specialized entity types or do not focus on a certain…

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…

Despite impressive results of language models for named entity recognition (NER), their generalization to varied textual genres, a growing entity type set, and new entities remains a challenge. Collecting thousands of annotations in each…

Precision is of utmost importance in the realm of clinical entity extraction from clinical notes and reports. Encoder Models fine-tuned for Named Entity Recognition (NER) are an efficient choice for this purpose, as they don't hallucinate.…

Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on…

Named Entity Recognition (NER) is a low-level task often used as a foundation for solving higher level NLP problems. In the context of character detection in novels, NER false negatives can be an issue as they possibly imply missing certain…

Named Entity Recognition (NER) encounters the challenge of unbalanced labels, where certain entity types are overrepresented while others are underrepresented in real-world datasets. This imbalance can lead to biased models that perform…

Incorporating external knowledge into Named Entity Recognition (NER) systems has been widely studied in the generic domain. In this paper, we focus on clinical domain where only limited data is accessible and interpretability is important.…

Recurrent Neural Network models are the state-of-the-art for Named Entity Recognition (NER). We present two innovations to improve the performance of these models. The first innovation is the introduction of residual connections between the…

The Biocreative VII Track-2 challenge consists of named entity recognition, entity-linking (or entity-normalization), and topic indexing tasks -- with entities and topics limited to chemicals for this challenge. Named entity recognition is…

Named entity recognition (NER) is one of the tasks in natural language processing that can greatly benefit from the use of external knowledge sources. We propose a named entity recognition framework composed of knowledge-based feature…

Named Entity Linking (NEL) is a core component of biomedical Information Extraction (IE) pipelines, yet assessing its quality at scale is challenging due to the high cost of expert annotations and the large size of corpora. In this paper,…

In this paper, we present our system for the BioNNE English track, which aims to extract 8 types of biomedical nested named entities from biomedical text. We use a large language model (Mixtral 8x7B instruct) and ScispaCy NER model to…

We cast nested named entity recognition (NNER) as a sequence labeling task by leveraging prior work that linearizes constituency structures, effectively reducing the complexity of this structured prediction problem to straightforward token…

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.…