# Pre-trained Language Models in Biomedical Domain: A Systematic Survey

arXiv: https://arxiv.org/abs/2110.05006 · HTML: https://mlsanity.com/paper/2110.05006/

## Key facts

- Cited by 87 papers in the map (data through 14 Oct 2026).
- Builds on 187 of its 410 references that are in the map.
- First posted on arXiv 11 Oct 2021.

## Builds on (most cited first, 30 of 187)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [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)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [BERTScore: Evaluating Text Generation with BERT](https://mlsanity.com/paper/1904.09675/) (2019)
- [GLUE: A Multi-Task Benchmark and Analysis Platform for Natural Language Understanding](https://mlsanity.com/paper/1804.07461/) (2018)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [DistilBERT, a distilled version of BERT: smaller, faster, cheaper and lighter](https://mlsanity.com/paper/1910.01108/) (2019)
- [Zero-Shot Text-to-Image Generation](https://mlsanity.com/paper/2102.12092/) (2021)
- [SQuAD: 100,000+ Questions for Machine Comprehension of Text](https://mlsanity.com/paper/1606.05250/) (2016)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [XLNet: Generalized Autoregressive Pretraining for Language Understanding](https://mlsanity.com/paper/1906.08237/) (2019)
- [ALBERT: A Lite BERT for Self-supervised Learning of Language Representations](https://mlsanity.com/paper/1909.11942/) (2019)
- [A Broad-Coverage Challenge Corpus for Sentence Understanding through Inference](https://mlsanity.com/paper/1704.05426/) (2017)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [Deep contextualized word representations](https://mlsanity.com/paper/1802.05365/) (2018)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [HuggingFace's Transformers: State-of-the-art Natural Language Processing](https://mlsanity.com/paper/1910.03771/) (2019)
- [SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing](https://mlsanity.com/paper/1808.06226/) (2018)

## Built on by (most cited first, 30 of 87)

- [A Survey on the Memory Mechanism of Large Language Model based Agents](https://mlsanity.com/paper/2404.13501/) (2024)
- [Large-scale Multi-Modal Pre-trained Models: A Comprehensive Survey](https://mlsanity.com/paper/2302.10035/) (2023)
- [Arithmetic Control of LLMs for Diverse User Preferences: Directional Preference Alignment with Multi-Objective Rewards](https://mlsanity.com/paper/2402.18571/) (2024)
- [A Survey of Large Language Models in Medicine: Progress, Application, and Challenge](https://mlsanity.com/paper/2311.05112/) (2023)
- [A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery](https://mlsanity.com/paper/2406.10833/) (2024)
- [HuatuoGPT-II, One-stage Training for Medical Adaption of LLMs](https://mlsanity.com/paper/2311.09774/) (2023)
- [DISC-MedLLM: Bridging General Large Language Models and Real-World Medical Consultation](https://mlsanity.com/paper/2308.14346/) (2023)
- [Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions](https://mlsanity.com/paper/2404.03264/) (2024)
- [K2: A Foundation Language Model for Geoscience Knowledge Understanding and Utilization](https://mlsanity.com/paper/2306.05064/) (2023)
- [Fairness in Large Language Models: A Taxonomic Survey](https://mlsanity.com/paper/2404.01349/) (2024)
- [Generative Pre-trained Transformer: A Comprehensive Review on Enabling Technologies, Potential Applications, Emerging Challenges, and Future Directions](https://mlsanity.com/paper/2305.10435/) (2023)
- [A Comprehensive Survey of Large Language Models and Multimodal Large Language Models in Medicine](https://mlsanity.com/paper/2405.08603/) (2024)
- [A Comprehensive Evaluation of Large Language Models on Benchmark Biomedical Text Processing Tasks](https://mlsanity.com/paper/2310.04270/) (2023)
- [Position: Multimodal Large Language Models Can Significantly Advance Scientific Reasoning](https://mlsanity.com/paper/2502.02871/) (2025)
- [ClinicalBench: Can LLMs Beat Traditional ML Models in Clinical Prediction?](https://mlsanity.com/paper/2411.06469/) (2024)
- [Libra: Leveraging Temporal Images for Biomedical Radiology Analysis](https://mlsanity.com/paper/2411.19378/) (2024)
- [Demographic Bias of Expert-Level Vision-Language Foundation Models in Medical Imaging](https://mlsanity.com/paper/2402.14815/) (2024)
- [Transformer Uncertainty Estimation with Hierarchical Stochastic Attention](https://mlsanity.com/paper/2112.13776/) (2021)
- [Readability Controllable Biomedical Document Summarization](https://mlsanity.com/paper/2210.04705/) (2022)
- [Protein Large Language Models: A Comprehensive Survey](https://mlsanity.com/paper/2502.17504/) (2025)
- [Protein Language Models and Structure Prediction: Connection and Progression](https://mlsanity.com/paper/2211.16742/) (2022)
- [Transformers in Healthcare: A Survey](https://mlsanity.com/paper/2307.00067/) (2023)
- [In-BoXBART: Get Instructions into Biomedical Multi-Task Learning](https://mlsanity.com/paper/2204.07600/) (2022)
- [LingYi: Medical Conversational Question Answering System based on Multi-modal Knowledge Graphs](https://mlsanity.com/paper/2204.09220/) (2022)
- [Cross-Care: Assessing the Healthcare Implications of Pre-training Data on Language Model Bias](https://mlsanity.com/paper/2405.05506/) (2024)
- [PromptLink: Leveraging Large Language Models for Cross-Source Biomedical Concept Linking](https://mlsanity.com/paper/2405.07500/) (2024)
- [Towards Reliable Medical Question Answering: Techniques and Challenges in Mitigating Hallucinations in Language Models](https://mlsanity.com/paper/2408.13808/) (2024)
- [Clinical Concept and Relation Extraction Using Prompt-based Machine Reading Comprehension](https://mlsanity.com/paper/2303.08262/) (2023)
- [A dataset and benchmark for hospital course summarization with adapted large language models](https://mlsanity.com/paper/2403.05720/) (2024)
- [GRETEL: Graph Contrastive Topic Enhanced Language Model for Long Document Extractive Summarization](https://mlsanity.com/paper/2208.09982/) (2022)

## Abstract (arXiv)

Pre-trained language models (PLMs) have been the de facto paradigm for most natural language processing (NLP) tasks. This also benefits biomedical domain: researchers from informatics, medicine, and computer science (CS) communities propose various PLMs trained on biomedical datasets, e.g., biomedical text, electronic health records, protein, and DNA sequences for various biomedical tasks. However, the cross-discipline characteristics of biomedical PLMs hinder their spreading among communities; some existing works are isolated from each other without comprehensive comparison and discussions. It expects a survey that not only systematically reviews recent advances of biomedical PLMs and their applications but also standardizes terminology and benchmarks. In this paper, we summarize the recent progress of pre-trained language models in the biomedical domain and their applications in biomedical downstream tasks. Particularly, we discuss the motivations and propose a taxonomy of existing biomedical PLMs. Their applications in biomedical downstream tasks are exhaustively discussed. At last, we illustrate various limitations and future trends, which we hope can provide inspiration for the future research of the research community.