# Large Language Models for Bioinformatics

arXiv: https://arxiv.org/abs/2501.06271 · HTML: https://mlsanity.com/paper/2501.06271/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 129 of its 391 references that are in the map.
- First posted on arXiv 10 Jan 2025.

## Builds on (most cited first, 30 of 129)

- [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)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Proximal Policy Optimization Algorithms](https://mlsanity.com/paper/1707.06347/) (2017)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [Direct Preference Optimization: Your Language Model is Secretly a Reward Model](https://mlsanity.com/paper/2305.18290/) (2023)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [Deep reinforcement learning from human preferences](https://mlsanity.com/paper/1706.03741/) (2017)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [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)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Concrete Problems in AI Safety](https://mlsanity.com/paper/1606.06565/) (2016)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation](https://mlsanity.com/paper/2108.12409/) (2021)
- [SpanBERT: Improving Pre-training by Representing and Predicting Spans](https://mlsanity.com/paper/1907.10529/) (2019)
- [Distilling Step-by-Step! Outperforming Larger Language Models with Less Training Data and Smaller Model Sizes](https://mlsanity.com/paper/2305.02301/) (2023)
- [Subword Regularization: Improving Neural Network Translation Models with Multiple Subword Candidates](https://mlsanity.com/paper/1804.10959/) (2018)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [MIMIC-CXR-JPG, a large publicly available database of labeled chest radiographs](https://mlsanity.com/paper/1901.07042/) (2019)
- [MedMCQA : A Large-scale Multi-Subject Multi-Choice Dataset for Medical domain Question Answering](https://mlsanity.com/paper/2203.14371/) (2022)
- [Generalizing from a Few Examples: A Survey on Few-Shot Learning](https://mlsanity.com/paper/1904.05046/) (2019)
- [Hyena Hierarchy: Towards Larger Convolutional Language Models](https://mlsanity.com/paper/2302.10866/) (2023)
- [Pre-Trained Models: Past, Present and Future](https://mlsanity.com/paper/2106.07139/) (2021)
- [A Structured Self-attentive Sentence Embedding](https://mlsanity.com/paper/1703.03130/) (2017)

## Built on by (most cited first, 3 of 3)

- [A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers](https://mlsanity.com/paper/2508.21148/) (2025)
- [MechPert: Mechanistic Consensus as an Inductive Bias for Unseen Perturbation Prediction](https://mlsanity.com/paper/2602.13791/) (2026)
- [Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances](https://mlsanity.com/paper/2511.03354/) (2025)

## Abstract (arXiv)

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.