# Multi-level biomedical NER through multi-granularity embeddings and enhanced labeling

arXiv: https://arxiv.org/abs/2312.15550 · HTML: https://mlsanity.com/paper/2312.15550/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 56 references that are in the map.
- First posted on arXiv 24 Dec 2023.

## Builds on (most cited first, 18 of 18)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [ALBERT: A Lite BERT for Self-supervised Learning of Language Representations](https://mlsanity.com/paper/1909.11942/) (2019)
- [Deep contextualized word representations](https://mlsanity.com/paper/1802.05365/) (2018)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Enriching Word Vectors with Subword Information](https://mlsanity.com/paper/1607.04606/) (2016)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Convolutional Neural Networks for Sentence Classification](https://mlsanity.com/paper/1408.5882/) (2014)
- [Neural Architectures for Named Entity Recognition](https://mlsanity.com/paper/1603.01360/) (2016)
- [Bidirectional LSTM-CRF Models for Sequence Tagging](https://mlsanity.com/paper/1508.01991/) (2015)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets](https://mlsanity.com/paper/1906.05474/) (2019)
- [Named Entity Recognition with Bidirectional LSTM-CNNs](https://mlsanity.com/paper/1511.08308/) (2015)
- [Enhancing Clinical Concept Extraction with Contextual Embeddings](https://mlsanity.com/paper/1902.08691/) (2019)
- [Few-shot Learning for Named Entity Recognition in Medical Text](https://mlsanity.com/paper/1811.05468/) (2018)
- [Investigation of BERT Model on Biomedical Relation Extraction Based on Revised Fine-tuning Mechanism](https://mlsanity.com/paper/2011.00398/) (2020)
- [NEAR: Named Entity and Attribute Recognition of clinical concepts](https://mlsanity.com/paper/2208.13949/) (2022)
- [BIOptimus: Pre-training an Optimal Biomedical Language Model with Curriculum Learning for Named Entity Recognition](https://mlsanity.com/paper/2308.08625/) (2023)

## Abstract (arXiv)

Biomedical Named Entity Recognition (NER) is a fundamental task of Biomedical Natural Language Processing for extracting relevant information from biomedical texts, such as clinical records, scientific publications, and electronic health records. The conventional approaches for biomedical NER mainly use traditional machine learning techniques, such as Conditional Random Fields and Support Vector Machines or deep learning-based models like Recurrent Neural Networks and Convolutional Neural Networks. Recently, Transformer-based models, including BERT, have been used in the domain of biomedical NER and have demonstrated remarkable results. However, these models are often based on word-level embeddings, limiting their ability to capture character-level information, which is effective in biomedical NER due to the high variability and complexity of biomedical texts. To address these limitations, this paper proposes a hybrid approach that integrates the strengths of multiple models. In this paper, we proposed an approach that leverages fine-tuned BERT to provide contextualized word embeddings, a pre-trained multi-channel CNN for character-level information capture, and following by a BiLSTM + CRF for sequence labelling and modelling dependencies between the words in the text. In addition, also we propose an enhanced labelling method as part of pre-processing to enhance the identification of the entity's beginning word and thus improve the identification of multi-word entities, a common challenge in biomedical NER. By integrating these models and the pre-processing method, our proposed model effectively captures both contextual information and detailed character-level information. We evaluated our model on the benchmark i2b2/2010 dataset, achieving an F1-score of 90.11. These results illustrate the proficiency of our proposed model in performing biomedical Named Entity Recognition.