# Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics

arXiv: https://arxiv.org/abs/2506.02212 · HTML: https://mlsanity.com/paper/2506.02212/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 37 of its 157 references that are in the map.
- First posted on arXiv 2 Jun 2025.

## Builds on (most cited first, 30 of 37)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [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)
- [FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning](https://mlsanity.com/paper/2307.08691/) (2023)
- [Deep contextualized word representations](https://mlsanity.com/paper/1802.05365/) (2018)
- [Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention](https://mlsanity.com/paper/2006.16236/) (2020)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Reformer: The Efficient Transformer](https://mlsanity.com/paper/2001.04451/) (2020)
- [Rethinking Attention with Performers](https://mlsanity.com/paper/2009.14794/) (2020)
- [Enriching Word Vectors with Subword Information](https://mlsanity.com/paper/1607.04606/) (2016)
- [Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation](https://mlsanity.com/paper/1609.08144/) (2016)
- [Distributed Representations of Sentences and Documents](https://mlsanity.com/paper/1405.4053/) (2014)
- [Subword Regularization: Improving Neural Network Translation Models with Multiple Subword Candidates](https://mlsanity.com/paper/1804.10959/) (2018)
- [Combining Recurrent, Convolutional, and Continuous-time Models with Linear State-Space Layers](https://mlsanity.com/paper/2110.13985/) (2021)
- [FlashAttention-3: Fast and Accurate Attention with Asynchrony and Low-precision](https://mlsanity.com/paper/2407.08608/) (2024)
- [Hyena Hierarchy: Towards Larger Convolutional Language Models](https://mlsanity.com/paper/2302.10866/) (2023)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [ProGen: Language Modeling for Protein Generation](https://mlsanity.com/paper/2004.03497/) (2020)
- [BERTology Meets Biology: Interpreting Attention in Protein Language Models](https://mlsanity.com/paper/2006.15222/) (2020)
- [Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval](https://mlsanity.com/paper/2205.13760/) (2022)
- [A Comprehensive Survey on Applications of Transformers for Deep Learning Tasks](https://mlsanity.com/paper/2306.07303/) (2023)
- [Learning protein sequence embeddings using information from structure](https://mlsanity.com/paper/1902.08661/) (2019)
- [Information Retrieval: Recent Advances and Beyond](https://mlsanity.com/paper/2301.08801/) (2023)
- [RITA: a Study on Scaling Up Generative Protein Sequence Models](https://mlsanity.com/paper/2205.05789/) (2022)

## Abstract (arXiv)

Natural Language Processing (NLP) has transformed various fields beyond linguistics by applying techniques originally developed for human language to the analysis of biological sequences. This review explores the application of NLP methods to biological sequence data, focusing on genomics, transcriptomics, and proteomics. We examine how various NLP methods, from classic approaches like word2vec to advanced models employing transformers and hyena operators, are being adapted to analyze DNA, RNA, protein sequences, and entire genomes. The review also examines tokenization strategies and model architectures, evaluating their strengths, limitations, and suitability for different biological tasks. We further cover recent advances in NLP applications for biological data, such as structure prediction, gene expression, and evolutionary analysis, highlighting the potential of these methods for extracting meaningful insights from large-scale genomic data. As language models continue to advance, their integration into bioinformatics holds immense promise for advancing our understanding of biological processes in all domains of life.