# Utilizing Large Language Models for Named Entity Recognition in Traditional Chinese Medicine against COVID-19 Literature: Comparative Study

arXiv: https://arxiv.org/abs/2408.13501 · HTML: https://mlsanity.com/paper/2408.13501/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 27 of its 49 references that are in the map.
- First posted on arXiv 24 Aug 2024.

## Builds on (most cited first, 27 of 27)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [SQuAD: 100,000+ Questions for Machine Comprehension of Text](https://mlsanity.com/paper/1606.05250/) (2016)
- [Know What You Don't Know: Unanswerable Questions for SQuAD](https://mlsanity.com/paper/1806.03822/) (2018)
- [MiniLM: Deep Self-Attention Distillation for Task-Agnostic Compression of Pre-Trained Transformers](https://mlsanity.com/paper/2002.10957/) (2020)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [ChatGPT Outperforms Crowd-Workers for Text-Annotation Tasks](https://mlsanity.com/paper/2303.15056/) (2023)
- [Is ChatGPT a General-Purpose Natural Language Processing Task Solver?](https://mlsanity.com/paper/2302.06476/) (2023)
- [ChatIE: Zero-Shot Information Extraction via Chatting with ChatGPT](https://mlsanity.com/paper/2302.10205/) (2023)
- [CORD-19: The COVID-19 Open Research Dataset](https://mlsanity.com/paper/2004.10706/) (2020)
- [Does Synthetic Data Generation of LLMs Help Clinical Text Mining?](https://mlsanity.com/paper/2303.04360/) (2023)
- [Evaluating ChatGPT's Information Extraction Capabilities: An Assessment of Performance, Explainability, Calibration, and Faithfulness](https://mlsanity.com/paper/2304.11633/) (2023)
- [Exploring the Feasibility of ChatGPT for Event Extraction](https://mlsanity.com/paper/2303.03836/) (2023)
- [Testing the Reliability of ChatGPT for Text Annotation and Classification: A Cautionary Remark](https://mlsanity.com/paper/2304.11085/) (2023)
- [An Empirical Study on Information Extraction using Large Language Models](https://mlsanity.com/paper/2305.14450/) (2023)
- [Evaluation of ChatGPT Family of Models for Biomedical Reasoning and Classification](https://mlsanity.com/paper/2304.02496/) (2023)
- [QaNER: Prompting Question Answering Models for Few-shot Named Entity Recognition](https://mlsanity.com/paper/2203.01543/) (2022)
- [GSAP-NER: A Novel Task, Corpus, and Baseline for Scholarly Entity Extraction Focused on Machine Learning Models and Datasets](https://mlsanity.com/paper/2311.09860/) (2023)
- [VicunaNER: Zero/Few-shot Named Entity Recognition using Vicuna](https://mlsanity.com/paper/2305.03253/) (2023)
- [Product Information Extraction using ChatGPT](https://mlsanity.com/paper/2306.14921/) (2023)
- [A Sui Generis QA Approach using RoBERTa for Adverse Drug Event Identification](https://mlsanity.com/paper/2011.00057/) (2020)
- [Evaluating ChatGPT text-mining of clinical records for obesity monitoring](https://mlsanity.com/paper/2308.01666/) (2023)

## Built on by (most cited first, 1 of 1)

- [Chatting with Papers: A Hybrid Approach Using LLMs and Knowledge Graphs](https://mlsanity.com/paper/2505.11633/) (2025)

## Abstract (arXiv)

Objective: To explore and compare the performance of ChatGPT and other state-of-the-art LLMs on domain-specific NER tasks covering different entity types and domains in TCM against COVID-19 literature. Methods: We established a dataset of 389 articles on TCM against COVID-19, and manually annotated 48 of them with 6 types of entities belonging to 3 domains as the ground truth, against which the NER performance of LLMs can be assessed. We then performed NER tasks for the 6 entity types using ChatGPT (GPT-3.5 and GPT-4) and 4 state-of-the-art BERT-based question-answering (QA) models (RoBERTa, MiniLM, PubMedBERT and SciBERT) without prior training on the specific task. A domain fine-tuned model (GSAP-NER) was also applied for a comprehensive comparison. Results: The overall performance of LLMs varied significantly in exact match and fuzzy match. In the fuzzy match, ChatGPT surpassed BERT-based QA models in 5 out of 6 tasks, while in exact match, BERT-based QA models outperformed ChatGPT in 5 out of 6 tasks but with a smaller F-1 difference. GPT-4 showed a significant advantage over other models in fuzzy match, especially on the entity type of TCM formula and the Chinese patent drug (TFD) and ingredient (IG). Although GPT-4 outperformed BERT-based models on entity type of herb, target, and research method, none of the F-1 scores exceeded 0.5. GSAP-NER, outperformed GPT-4 in terms of F-1 by a slight margin on RM. ChatGPT achieved considerably higher recalls than precisions, particularly in the fuzzy match. Conclusions: The NER performance of LLMs is highly dependent on the entity type, and their performance varies across application scenarios. ChatGPT could be a good choice for scenarios where high recall is favored. However, for knowledge acquisition in rigorous scenarios, neither ChatGPT nor BERT-based QA models are off-the-shelf tools for professional practitioners.