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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…

We study clinical Named Entity Recognition (NER) on the CADEC corpus and compare three families of approaches: (i) BERT-style encoders (BERT Base, BioClinicalBERT, RoBERTa-large), (ii) GPT-4o used with few-shot in-context learning (ICL)…

This paper presents a comprehensive study to efficiently build named entity recognition (NER) systems when a small number of in-domain labeled data is available. Based upon recent Transformer-based self-supervised pre-trained language…

The rapidly increasing volume of electronic health record (EHR) data underscores a pressing need to unlock biomedical knowledge from unstructured clinical texts to support advancements in data-driven clinical systems, including patient…

With the growing interest in large language models, the need for evaluating the quality of machine text compared to reference (typically human-generated) text has become focal attention. Most recent works focus either on task-specific…

The automatic generation of brain CT reports has gained widespread attention, given its potential to assist radiologists in diagnosing cranial diseases. However, brain CT scans involve extensive medical entities, such as diverse anatomy…

Named Entity Recognition (NER) is a key information extraction task with a long-standing tradition. While recent studies address and aim to correct annotation errors via re-labeling efforts, little is known about the sources of human label…

Negative sampling is highly effective in handling missing annotations for named entity recognition (NER). One of our contributions is an analysis on how it makes sense through introducing two insightful concepts: missampling and…

Named Entity Recognition (NER) is a fundamental problem in natural language processing (NLP). However, the task of extracting longer entity spans (e.g., awards) from extended texts (e.g., homepages) is barely explored. Current NER methods…

In biomedical fields, one named entity may consist of a series of non-adjacent tokens and overlap with other entities. Previous methods recognize discontinuous entities by connecting entity fragments or internal tokens, which face…

Cross-domain NER is a practical yet challenging problem since the data scarcity in the real-world scenario. A common practice is first to learn a NER model in a rich-resource general domain and then adapt the model to specific domains. Due…

This technical report introduces a Named Clinical Entity Recognition Benchmark for evaluating language models in healthcare, addressing the crucial natural language processing (NLP) task of extracting structured information from clinical…

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,…

Recent advancements in language models (LMs) have led to the emergence of powerful models such as Small LMs (e.g., T5) and Large LMs (e.g., GPT-4). These models have demonstrated exceptional capabilities across a wide range of tasks, such…

Building an accurate computer-aided diagnosis system based on data-driven approaches requires a large amount of high-quality labeled data. In medical imaging analysis, multiple expert annotators often produce subjective estimates about…

We consider the problem of Named Entity Recognition (NER) on biomedical scientific literature, and more specifically the genomic variants recognition in this work. Significant success has been achieved for NER on canonical tasks in recent…

Named entity recognition (NER) is usually developed and tested on text from well-written sources. However, in intelligent voice assistants, where NER is an important component, input to NER may be noisy because of user or speech recognition…

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…

Background: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP…

Sequential labeling is a task predicting labels for each token in a sequence, such as Named Entity Recognition (NER). NER tasks aim to extract entities and predict their labels given a text, which is important in information extraction.…