# AMMU : A Survey of Transformer-based Biomedical Pretrained Language Models

arXiv: https://arxiv.org/abs/2105.00827 · HTML: https://mlsanity.com/paper/2105.00827/

## Key facts

- Cited by 32 papers in the map (data through 14 Oct 2026).
- Builds on 110 of its 221 references that are in the map.
- First posted on arXiv 16 Apr 2021.

## Builds on (most cited first, 30 of 110)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [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)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [GLUE: A Multi-Task Benchmark and Analysis Platform for Natural Language Understanding](https://mlsanity.com/paper/1804.07461/) (2018)
- [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)
- [Going Deeper with Convolutions](https://mlsanity.com/paper/1409.4842/) (2014)
- [Unsupervised Cross-lingual Representation Learning at Scale](https://mlsanity.com/paper/1911.02116/) (2019)
- [wav2vec 2.0: A Framework for Self-Supervised Learning of Speech Representations](https://mlsanity.com/paper/2006.11477/) (2020)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [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)
- [Deep contextualized word representations](https://mlsanity.com/paper/1802.05365/) (2018)
- [ViLBERT: Pretraining Task-Agnostic Visiolinguistic Representations for Vision-and-Language Tasks](https://mlsanity.com/paper/1908.02265/) (2019)
- [DeBERTa: Decoding-enhanced BERT with Disentangled Attention](https://mlsanity.com/paper/2006.03654/) (2020)
- [SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing](https://mlsanity.com/paper/1808.06226/) (2018)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Language Models as Knowledge Bases?](https://mlsanity.com/paper/1909.01066/) (2019)
- [A Survey on Bias and Fairness in Machine Learning](https://mlsanity.com/paper/1908.09635/) (2019)
- [A large annotated corpus for learning natural language inference](https://mlsanity.com/paper/1508.05326/) (2015)
- [SuperGLUE: A Stickier Benchmark for General-Purpose Language Understanding Systems](https://mlsanity.com/paper/1905.00537/) (2019)
- [Enriching Word Vectors with Subword Information](https://mlsanity.com/paper/1607.04606/) (2016)
- [Don't Stop Pretraining: Adapt Language Models to Domains and Tasks](https://mlsanity.com/paper/2004.10964/) (2020)
- [LXMERT: Learning Cross-Modality Encoder Representations from Transformers](https://mlsanity.com/paper/1908.07490/) (2019)
- [Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation](https://mlsanity.com/paper/1609.08144/) (2016)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)

## Built on by (most cited first, 30 of 32)

- [Knowledge Editing for Large Language Models: A Survey](https://mlsanity.com/paper/2310.16218/) (2023)
- [A Survey of Large Language Models for Healthcare: from Data, Technology, and Applications to Accountability and Ethics](https://mlsanity.com/paper/2310.05694/) (2023)
- [Pre-trained Language Models in Biomedical Domain: A Systematic Survey](https://mlsanity.com/paper/2110.05006/) (2021)
- [A Survey of GPT-3 Family Large Language Models Including ChatGPT and GPT-4](https://mlsanity.com/paper/2310.12321/) (2023)
- [A Comprehensive Survey on Applications of Transformers for Deep Learning Tasks](https://mlsanity.com/paper/2306.07303/) (2023)
- [Generative Pre-trained Transformer: A Comprehensive Review on Enabling Technologies, Potential Applications, Emerging Challenges, and Future Directions](https://mlsanity.com/paper/2305.10435/) (2023)
- [Evaluating Large Language Models on a Highly-specialized Topic, Radiation Oncology Physics](https://mlsanity.com/paper/2304.01938/) (2023)
- [A Comprehensive Evaluation of Large Language Models on Benchmark Biomedical Text Processing Tasks](https://mlsanity.com/paper/2310.04270/) (2023)
- [Spatial Transformer Network on Skeleton-based Gait Recognition](https://mlsanity.com/paper/2204.03873/) (2022)
- [TIP: Tabular-Image Pre-training for Multimodal Classification with Incomplete Data](https://mlsanity.com/paper/2407.07582/) (2024)
- [Multimodality Representation Learning: A Survey on Evolution, Pretraining and Its Applications](https://mlsanity.com/paper/2302.00389/) (2023)
- [Evaluation of ChatGPT on Biomedical Tasks: A Zero-Shot Comparison with Fine-Tuned Generative Transformers](https://mlsanity.com/paper/2306.04504/) (2023)
- [Emergency Department Decision Support using Clinical Pseudo-notes](https://mlsanity.com/paper/2402.00160/) (2024)
- [Benchmarking for Biomedical Natural Language Processing Tasks with a Domain Specific ALBERT](https://mlsanity.com/paper/2107.04374/) (2021)
- [ExBEHRT: Extended Transformer for Electronic Health Records to Predict Disease Subtypes & Progressions](https://mlsanity.com/paper/2303.12364/) (2023)
- [Open Challenges and Opportunities in Federated Foundation Models Towards Biomedical Healthcare](https://mlsanity.com/paper/2405.06784/) (2024)
- [Biomedical and Clinical Language Models for Spanish: On the Benefits of Domain-Specific Pretraining in a Mid-Resource Scenario](https://mlsanity.com/paper/2109.03570/) (2021)
- [Exploring the In-context Learning Ability of Large Language Model for Biomedical Concept Linking](https://mlsanity.com/paper/2307.01137/) (2023)
- [Fairness Definitions in Language Models Explained](https://mlsanity.com/paper/2407.18454/) (2024)
- [Transformer-based Generative Adversarial Networks in Computer Vision: A Comprehensive Survey](https://mlsanity.com/paper/2302.08641/) (2023)
- [Performance of Recent Large Language Models for a Low-Resourced Language](https://mlsanity.com/paper/2407.21330/) (2024)
- [A Comparative Evaluation Of Transformer Models For De-Identification Of Clinical Text Data](https://mlsanity.com/paper/2204.07056/) (2022)
- [A Comprehensive Review and a Taxonomy of Edge Machine Learning: Requirements, Paradigms, and Techniques](https://mlsanity.com/paper/2302.08571/) (2023)
- [A Lightweight Transformer for Faster and Robust EBSD Data Collection](https://mlsanity.com/paper/2308.09693/) (2023)
- [Towards Transparent AI: A Survey on Explainable Language Models](https://mlsanity.com/paper/2509.21631/) (2025)
- [Multilingual Multiword Expression Identification Using Lateral Inhibition and Domain Adaptation](https://mlsanity.com/paper/2306.10419/) (2023)
- [A Semantic and Motion-Aware Spatiotemporal Transformer Network for Action Detection](https://mlsanity.com/paper/2405.08204/) (2024)
- [Enhancing Natural Language Inference Performance with Knowledge Graph for COVID-19 Automated Fact-Checking in Indonesian Language](https://mlsanity.com/paper/2409.00061/) (2024)
- [COVIDHealth: A Benchmark Twitter Dataset and Machine Learning based Web Application for Classifying COVID-19 Discussions](https://mlsanity.com/paper/2402.09897/) (2024)
- [Language modelling techniques for analysing the impact of human genetic variation](https://mlsanity.com/paper/2503.10655/) (2025)

## Abstract (arXiv)

Transformer-based pretrained language models (PLMs) have started a new era in modern natural language processing (NLP). These models combine the power of transformers, transfer learning, and self-supervised learning (SSL). Following the success of these models in the general domain, the biomedical research community has developed various in-domain PLMs starting from BioBERT to the latest BioELECTRA and BioALBERT models. We strongly believe there is a need for a survey paper that can provide a comprehensive survey of various transformer-based biomedical pretrained language models (BPLMs). In this survey, we start with a brief overview of foundational concepts like self-supervised learning, embedding layer and transformer encoder layers. We discuss core concepts of transformer-based PLMs like pretraining methods, pretraining tasks, fine-tuning methods, and various embedding types specific to biomedical domain. We introduce a taxonomy for transformer-based BPLMs and then discuss all the models. We discuss various challenges and present possible solutions. We conclude by highlighting some of the open issues which will drive the research community to further improve transformer-based BPLMs.