metadata
license: mit
language:
- en
tags:
- rna
- biology
- diffusion
- generative
- sequence-design
yakRNA Design: A semantic multimodal RNA composer
yakRNA Design is a 110M-parameter discrete diffusion language model for conditional RNA sequence design. It can generate RNA sequences conditioned on any combination of secondary structure, consensus sequence, and Gene Ontology (GO) terms — or unconditionally from a target length.
Model Details
| Architecture | ModernBERT-based discrete diffusion |
| Parameters | 110M |
| Training data | Full Rfam database |
| Max sequence length | 636 nt |
| Supported GO terms | 280 |
Quickstart
The easiest way to use yakRNA Design is via the Google Colab notebook — no setup required.
For local use, see the GitHub repository.
Download the Weights
CLI:
pip install huggingface_hub
huggingface-cli download MasterYster/yakRNA-Design yakRNA_110M.pt --local-dir checkpoints/
Python:
from huggingface_hub import hf_hub_download
hf_hub_download(repo_id="MasterYster/yakRNA-Design", filename="yakRNA_110M.pt", local_dir="checkpoints/")
Generation Modes
| Mode | Description |
|---|---|
| Unconditional | Generate from a target length |
| Structure-conditioned | Dot-bracket secondary structure |
| Consensus-conditioned | Mixed-case IUPAC consensus |
| GO term-conditioned | Up to 12 GO terms |
| Sequence infilling | Fixed positions + * masks |
| Multimodal | Any combination of the above |
Example Usage
# Install
git clone https://github.com/YousufAKhan/yakRNA.git
cd yakRNA
pip install -r requirements.txt
# Generate 5 sequences conditioned on a hairpin structure
python inference/rna_sequence_generator.py \
--config configs/inference.yaml \
--checkpoint checkpoints/yakRNA_110M.pt \
--secondary_structure "((((....))))" \
--num_sequences 5
# Generate with all three modalities
python inference/rna_sequence_generator.py \
--config configs/inference.yaml \
--checkpoint checkpoints/yakRNA_110M.pt \
--secondary_structure ":::::::<<<<<<<<<-:::--[[[[[-->>>>>>>>><<<<<<<<<<_________>>>->>>>>>>::::]]]]]::::" \
--consensus "GAGUaaGGGGuuCuAGU...gcaGCcCgcCUaGaaCCCUGcgacacuGGuucuaaaaCagAugucgUuuuaAGgGCuUUUG" \
--go_terms "GO:0075523" \
--num_sequences 5
Links
- GitHub: YousufAKhan/yakRNA
- Colab:
Citation
@software{yakrna2026,
author = {Khan, Yousuf},
title = {yakRNA Design: A semantic multimodal RNA composer},
year = {2026},
url = {https://github.com/YousufAKhan/yakRNA}
}