MasterYster/yakRNA-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.

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Model Details

Architecture	ModernBERT-based discrete diffusion
Parameters	110M
Training data	Full Rfam database
Max sequence length	636 nt
Supported GO terms	280

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Quickstart

The easiest way to use yakRNA Design is via the Google Colab notebook — no setup required.

For local use, see the GitHub repository.

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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/")

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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

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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

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Links

• GitHub: YousufAKhan/yakRNA
• Colab:

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Citation

@software{yakrna2026,
  author = {Khan, Yousuf},
  title  = {yakRNA Design: A semantic multimodal RNA composer},
  year   = {2026},
  url    = {https://github.com/YousufAKhan/yakRNA}
}