Related papers: Clinical Named Entity Recognition using Contextual…

Biomedical named entity recognition is one of the core tasks in biomedical natural language processing (BioNLP). To tackle this task, numerous supervised/distantly supervised approaches have been proposed. Despite their remarkable success,…

Named Entity Disambiguation (NED) refers to the task of resolving multiple named entity mentions in a document to their correct references in a knowledge base (KB) (e.g., Wikipedia). In this paper, we propose a novel embedding method…

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…

Clinical trials (CTs) often fail due to inadequate patient recruitment. This paper tackles the challenges of CT retrieval by presenting an approach that addresses the patient-to-trials paradigm. Our approach involves two key components in a…

Current state-of-the-art approaches for named entity recognition (NER) typically consider text at the sentence-level and thus do not model information that crosses sentence boundaries. However, the use of transformer-based models for NER…

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…

This study introduces a novel knowledge enhanced tokenisation mechanism, K-Tokeniser, for clinical text processing. Technically, at initialisation stage, K-Tokeniser populates global representations of tokens based on semantic types of…

Named Entity Recognition (NER) in historical texts presents unique challenges due to non-standardized language, archaic orthography, and nested or overlapping entities. This study benchmarks a diverse set of NER approaches, ranging from…

We propose yet another entity linking model (YELM) which links words to entities instead of spans. This overcomes any difficulties associated with the selection of good candidate mention spans and makes the joint training of mention…

The widespread availability of electronic health records (EHRs) promises to usher in the era of personalized medicine. However, the problem of extracting useful clinical representations from longitudinal EHR data remains challenging. In…

We compare the use of LSTM-based and CNN-based character-level word embeddings in BiLSTM-CRF models to approach chemical and disease named entity recognition (NER) tasks. Empirical results over the BioCreative V CDR corpus show that the use…

Traditional information retrieval treats named entity recognition as a pre-indexing corpus annotation task, allowing entity tags to be indexed and used during search. Named entity taggers themselves are typically trained on thousands or…

Embeddings of medical concepts such as medication, procedure and diagnosis codes in Electronic Medical Records (EMRs) are central to healthcare analytics. Previous work on medical concept embedding takes medical concepts and EMRs as words…

Cross-lingual named entity recognition (CrossNER) faces challenges stemming from uneven performance due to the scarcity of multilingual corpora, especially for non-English data. While prior efforts mainly focus on data-driven transfer…

Entity recognition is a critical first step to a number of clinical NLP applications, such as entity linking and relation extraction. We present the first attempt to apply state-of-the-art entity recognition approaches on a newly released…

Natural language processing techniques are being applied to increasingly diverse types of electronic health records, and can benefit from in-depth understanding of the distinguishing characteristics of medical document types. We present a…

Contextual embeddings represent a new generation of semantic representations learned from Neural Language Modelling (NLM) that addresses the issue of meaning conflation hampering traditional word embeddings. In this work, we show that…

Recent advances in deep neural models allow us to build reliable named entity recognition (NER) systems without handcrafting features. However, such methods require large amounts of manually-labeled training data. There have been efforts on…

Concept normalization in free-form texts is a crucial step in every text-mining pipeline. Neural architectures based on Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art results in the biomedical…

Named Entity Recognition (NER) is the task of identifying and classifying named entities in unstructured text. In the legal domain, named entities of interest may include the case parties, judges, names of courts, case numbers, references…