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HyenaDNA

By Stanford University (Hazy Research) →

Long-range genomic foundation model handling context lengths up to 1 million base pairs

HyenaDNA uses sub-quadratic Hyena operators to process up to 1 million base pairs at single-nucleotide resolution, unlocking long-range regulatory element and chromatin interaction modeling.

Sub-quadratic scaling allowing context lengths up to 1,000,000 base pairsSingle-nucleotide resolution without k-mer tokenization artifactsTrained on the human reference genome (T2T-CHM13)State-of-the-art benchmarks across the Genomic Benchmarks suite
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Overview

HyenaDNA uses sub-quadratic Hyena operators to process up to 1 million base pairs at single-nucleotide resolution, unlocking long-range regulatory element and chromatin interaction modeling.

Information checked against an official source; not a hands-on test. Source · Last reviewed: 20/09/2026, 11:09:40

Key Features

  • Sub-quadratic scaling allowing context lengths up to 1,000,000 base pairs
  • Single-nucleotide resolution without k-mer tokenization artifacts
  • Trained on the human reference genome (T2T-CHM13)
  • State-of-the-art benchmarks across the Genomic Benchmarks suite

Academic Context & Research Evidence

Biological & Workflow Fit

Biological Application
Enhancer-promoter interaction prediction, chromatin profile modeling, and splicing regulation
Research Workflow
Input long DNA sequence -> predict regulatory activity, chromatin marks, and variant effects
Compute & Hardware
1x GPU (A100 or H100 recommended for 1M context)
Licensing & Academic Use
Apache 2.0
Documented Evidence
View validation publication / source ↗

Cite this Tool

Use this citation format when referencing HyenaDNA in scientific publications and benchmark papers.

@software{hyenadna_2026,
  title = {{HyenaDNA}},
  author = {{Stanford University (Hazy Research)}},
  year = {2026},
  url = {https://github.com/HazyResearch/hyena-dna},
  note = {Indexed on aibioatlas - AI for Biology and Drug Discovery}
}

Peer-Reviewed Literature & Preprints

Live scientific citations streamed from Europe PMC and PubMed for HyenaDNA.

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Technical / Product Information

Missing values mean the catalog has no recorded information. They do not mean a feature is absent.

Entry typeAI Model
Access modeOpen Source
AI roleLong-Range Sequence Modeling
Input dataNot recorded
Output dataNot recorded
Licence conditionsApache 2.0
Commercial eligibilityOpen source release
Compute requirements1x GPU (A100 or H100 recommended for 1M context)
ValidationNot recorded
TypeLong-context genomic foundation model
Intended useNot recorded
CompatibilityNot recorded
ManufacturerStanford University
Biological applicationEnhancer-promoter interaction prediction, chromatin profile modeling, and splicing regulation
Research workflowInput long DNA sequence -> predict regulatory activity, chromatin marks, and variant effects
Evidence levelPeer-reviewed research (NeurIPS 2023)
Integration evidencehttps://github.com/HazyResearch/hyena-dna
Laboratory handoffIdentifies candidate non-coding regulatory elements for CRISPR perturbation validation
AvailabilityAvailable on GitHub and Hugging Face
Price / accessFree Open Source

Research fit & compatibility

No software–hardware integration has been verified for this entry yet. Explore documented research workflows.

Gallery & resources

No licensed product photograph recorded for HyenaDNA yet. Visit the official resource below for manufacturer imagery.

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FAQ

Where is this product available?

Available on GitHub and Hugging Face

How is pricing handled?

Prices reflect the source at its last check. Confirm current pricing and regional availability on the official site.

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Peer Reviews & Community Ratings

Feedback from researchers and computational biologists evaluating HyenaDNA.

5.0
★★★★★Based on 0 researcher evaluations
Biological Accuracy
4.8/5
Ease of Installation
4.3/5
Documentation & Code
4.6/5