# Recent advances in deep learning and language models for studying the microbiome

arXiv: https://arxiv.org/abs/2409.10579 · HTML: https://mlsanity.com/paper/2409.10579/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 61 references that are in the map.
- First posted on arXiv 15 Sep 2024.

## Builds on (most cited first, 16 of 16)

- [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)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [A Survey on Evaluation of Large Language Models](https://mlsanity.com/paper/2307.03109/) (2023)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Unifying Large Language Models and Knowledge Graphs: A Roadmap](https://mlsanity.com/paper/2306.08302/) (2023)
- [Retrieval-Augmented Generation for AI-Generated Content: A Survey](https://mlsanity.com/paper/2402.19473/) (2024)
- [ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing](https://mlsanity.com/paper/2007.06225/) (2020)
- [ProGen2: Exploring the Boundaries of Protein Language Models](https://mlsanity.com/paper/2206.13517/) (2022)
- [Summary of ChatGPT-Related Research and Perspective Towards the Future of Large Language Models](https://mlsanity.com/paper/2304.01852/) (2023)
- [A Comprehensive Review of Multimodal Large Language Models: Performance and Challenges Across Different Tasks](https://mlsanity.com/paper/2408.01319/) (2024)
- [BEND: Benchmarking DNA Language Models on biologically meaningful tasks](https://mlsanity.com/paper/2311.12570/) (2023)
- [ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction](https://mlsanity.com/paper/2405.06649/) (2024)
- [FGBERT: Function-Driven Pre-trained Gene Language Model for Metagenomics](https://mlsanity.com/paper/2402.16901/) (2024)

## Abstract (arXiv)

Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.