| ---
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| license: mit
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| language:
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| - en
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| tags:
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| - rna
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| - biology
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| - diffusion
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| - generative
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| - sequence-design
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| ---
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|
|
| # yakRNA Design: A semantic multimodal RNA composer
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|
|
| <p align="center">
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| <img src="https://raw.githubusercontent.com/YousufAKhan/yakRNA/main/mascot.png" width="160"/>
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| </p>
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|
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| **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
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|
|
| | | |
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| |---|---|
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| | **Architecture** | ModernBERT-based discrete diffusion |
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| | **Parameters** | 110M |
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| | **Training data** | Full Rfam database |
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| | **Max sequence length** | 636 nt |
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| | **Supported GO terms** | 280 |
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|
|
| ---
|
|
|
| ## Quickstart
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|
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| The easiest way to use yakRNA Design is via the **[Google Colab notebook](https://colab.research.google.com/github/YousufAKhan/yakRNA/blob/main/yakRNA_colab.ipynb)** — no setup required.
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|
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| For local use, see the **[GitHub repository](https://github.com/YousufAKhan/yakRNA)**.
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|
|
| ---
|
|
|
| ## Download the Weights
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|
|
| **CLI:**
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| ```bash
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| pip install huggingface_hub
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| huggingface-cli download MasterYster/yakRNA-Design yakRNA_110M.pt --local-dir checkpoints/
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| ```
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|
|
| **Python:**
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| ```python
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| from huggingface_hub import hf_hub_download
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| hf_hub_download(repo_id="MasterYster/yakRNA-Design", filename="yakRNA_110M.pt", local_dir="checkpoints/")
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| ```
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|
|
| ---
|
|
|
| ## Generation Modes
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|
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| | Mode | Description |
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| |------|-------------|
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| | Unconditional | Generate from a target length |
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| | Structure-conditioned | Dot-bracket secondary structure |
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| | Consensus-conditioned | Mixed-case IUPAC consensus |
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| | GO term-conditioned | Up to 12 GO terms |
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| | Sequence infilling | Fixed positions + `*` masks |
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| | Multimodal | Any combination of the above |
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|
|
| ---
|
|
|
| ## Example Usage
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|
|
| ```bash
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| # Install
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| git clone https://github.com/YousufAKhan/yakRNA.git
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| cd yakRNA
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| pip install -r requirements.txt
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|
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| # Generate 5 sequences conditioned on a hairpin structure
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| python inference/rna_sequence_generator.py \
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| --config configs/inference.yaml \
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| --checkpoint checkpoints/yakRNA_110M.pt \
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| --secondary_structure "((((....))))" \
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| --num_sequences 5
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|
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| # Generate with all three modalities
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| python inference/rna_sequence_generator.py \
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| --config configs/inference.yaml \
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| --checkpoint checkpoints/yakRNA_110M.pt \
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| --secondary_structure ":::::::<<<<<<<<<-:::--[[[[[-->>>>>>>>><<<<<<<<<<_________>>>->>>>>>>::::]]]]]::::" \
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| --consensus "GAGUaaGGGGuuCuAGU...gcaGCcCgcCUaGaaCCCUGcgacacuGGuucuaaaaCagAugucgUuuuaAGgGCuUUUG" \
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| --go_terms "GO:0075523" \
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| --num_sequences 5
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| ```
|
|
|
| ---
|
|
|
| ## Links
|
|
|
| - **GitHub**: [YousufAKhan/yakRNA](https://github.com/YousufAKhan/yakRNA)
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| - **Colab**: [](https://colab.research.google.com/github/YousufAKhan/yakRNA/blob/main/yakRNA_colab.ipynb)
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|
|
| ---
|
|
|
| ## Citation
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|
|
| ```bibtex
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| @software{yakrna2026,
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| author = {Khan, Yousuf},
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| title = {yakRNA Design: A semantic multimodal RNA composer},
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| year = {2026},
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| url = {https://github.com/YousufAKhan/yakRNA}
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| }
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| ```
|
|
|
