You can deploy this model and start earning money today!

MasterYster/
yakRNA-Design

Views

No views yet

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:

bash

pip install huggingface_hub
huggingface-cli download MasterYster/yakRNA-Design yakRNA_110M.pt --local-dir checkpoints/

Python:

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

bash

# 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

Citation

bibtex

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

MasterYster/yakRNA-Design