# Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models

arXiv: https://arxiv.org/abs/2509.12266 · HTML: https://mlsanity.com/paper/2509.12266/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 47 references that are in the map.
- First posted on arXiv 13 Sep 2025.

## Builds on (most cited first, 19 of 19)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Judging LLM-as-a-Judge with MT-Bench and Chatbot Arena](https://mlsanity.com/paper/2306.05685/) (2023)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Gemini 2.5: Pushing the Frontier with Advanced Reasoning, Multimodality, Long Context, and Next Generation Agentic Capabilities](https://mlsanity.com/paper/2507.06261/) (2025)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [LlamaFactory: Unified Efficient Fine-Tuning of 100+ Language Models](https://mlsanity.com/paper/2403.13372/) (2024)
- [LLaMA-Adapter: Efficient Fine-tuning of Language Models with Zero-init Attention](https://mlsanity.com/paper/2303.16199/) (2023)
- [An Introduction to Convolutional Neural Networks](https://mlsanity.com/paper/1511.08458/) (2015)
- [How Far Can Camels Go? Exploring the State of Instruction Tuning on Open Resources](https://mlsanity.com/paper/2306.04751/) (2023)
- [Extreme Compression of Large Language Models via Additive Quantization](https://mlsanity.com/paper/2401.06118/) (2024)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [Gradio: Hassle-Free Sharing and Testing of ML Models in the Wild](https://mlsanity.com/paper/1906.02569/) (2019)
- [On the Effectiveness of Adapter-based Tuning for Pretrained Language Model Adaptation](https://mlsanity.com/paper/2106.03164/) (2021)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [Liger Kernel: Efficient Triton Kernels for LLM Training](https://mlsanity.com/paper/2410.10989/) (2024)
- [Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling](https://mlsanity.com/paper/2403.03234/) (2024)
- [Colossal-AI: A Unified Deep Learning System For Large-Scale Parallel Training](https://mlsanity.com/paper/2110.14883/) (2021)
- [LMFlow: An Extensible Toolkit for Finetuning and Inference of Large Foundation Models](https://mlsanity.com/paper/2306.12420/) (2023)
- [NeurIPS 2023 LLM Efficiency Fine-tuning Competition](https://mlsanity.com/paper/2503.13507/) (2025)

## Built on by (most cited first, 1 of 1)

- [D-DOIT: Training-free Adaptation of Discrete Diffusion via Doob's h-Transform](https://mlsanity.com/paper/2610.04938/) (2026)

## Abstract (arXiv)

We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify the workflow for genomic model development: data collection, model tuning, inference, benchmarking, and interpretability. For data collection, Genome-Factory offers an automated pipeline to download genomic sequences and preprocess them. For model tuning, Genome-Factory supports both full and parameter-efficient fine-tuning across diverse genomic models. For inference, Genome-Factory enables both embedding extraction and DNA sequence generation. For benchmarking, we include two existing benchmarks and provide a flexible interface to incorporate additional benchmarks. For interpretability, Genome-Factory introduces an open-source biological interpreter based on a sparse auto-encoder. We validate the utility of Genome-Factory across three dimensions: (i) Compatibility with diverse models and fine-tuning methods; (ii) Benchmarking downstream performance using two open-source benchmarks; (iii) Biological interpretation of learned representations with DNABERT-2. These results highlight its practical value for real-world genomic analysis. GitHub: https://github.com/WeiminWu2000/Genome_Factory.