Commit ·
4bf8941
1
Parent(s): 5f6b4b5
Add concise model card with paper links
Browse files
README.md
ADDED
|
@@ -0,0 +1,75 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
tags:
|
| 3 |
+
- genomics
|
| 4 |
+
- gene-expression-prediction
|
| 5 |
+
- multimodal
|
| 6 |
+
- biology
|
| 7 |
+
- arxiv:2602.21550
|
| 8 |
+
library_name: pytorch
|
| 9 |
+
datasets:
|
| 10 |
+
- xingyusu/GeneExp
|
| 11 |
+
---
|
| 12 |
+
|
| 13 |
+
# Prism
|
| 14 |
+
|
| 15 |
+
Prism provides pretrained checkpoints for gene expression prediction by integrating genomic sequence and multimodal signals.
|
| 16 |
+
|
| 17 |
+
This repository is the model release for:
|
| 18 |
+
|
| 19 |
+
**Extending Sequence Length is Not All You Need: Effective Integration of Multimodal Signals for Gene Expression Prediction** (ICLR 2026)
|
| 20 |
+
|
| 21 |
+
## Paper
|
| 22 |
+
|
| 23 |
+
- [Hugging Face Paper Page](https://huggingface.co/papers/2602.21550)
|
| 24 |
+
- [arXiv: 2602.21550](https://arxiv.org/abs/2602.21550)
|
| 25 |
+
|
| 26 |
+
## Model Contents
|
| 27 |
+
|
| 28 |
+
- Pretrained checkpoints for `K562` and `GM12878`
|
| 29 |
+
- Five random seeds for each cell type: `2`, `22`, `222`, `2222`, `22222`
|
| 30 |
+
|
| 31 |
+
## Dataset
|
| 32 |
+
|
| 33 |
+
Prism follows the same dataset setting as Seq2Exp (`xingyusu/GeneExp`).
|
| 34 |
+
|
| 35 |
+
## Quick Start
|
| 36 |
+
|
| 37 |
+
Download checkpoints:
|
| 38 |
+
|
| 39 |
+
```bash
|
| 40 |
+
pip install huggingface_hub
|
| 41 |
+
python -c "from huggingface_hub import snapshot_download; snapshot_download(repo_id='yangyz1230/Prism', repo_type='model', local_dir='./ckpt')"
|
| 42 |
+
```
|
| 43 |
+
|
| 44 |
+
Run inference with the official code:
|
| 45 |
+
|
| 46 |
+
```bash
|
| 47 |
+
git clone https://github.com/yangzhao1230/Prism
|
| 48 |
+
cd Prism
|
| 49 |
+
pip install -r requirements.txt
|
| 50 |
+
DATA_ROOT=/path/to/data
|
| 51 |
+
bash test.sh $DATA_ROOT ./ckpt
|
| 52 |
+
```
|
| 53 |
+
|
| 54 |
+
## Limitations
|
| 55 |
+
|
| 56 |
+
- Research use only
|
| 57 |
+
- Performance may vary across preprocessing settings and seeds
|
| 58 |
+
- Not intended for clinical or diagnostic use
|
| 59 |
+
|
| 60 |
+
## Citation
|
| 61 |
+
|
| 62 |
+
```bibtex
|
| 63 |
+
@inproceedings{
|
| 64 |
+
yang2026extending,
|
| 65 |
+
title={Extending Sequence Length is Not All You Need: Effective Integration of Multimodal Signals for Gene Expression Prediction},
|
| 66 |
+
author={Zhao Yang and Yi Duan and Jiwei Zhu and Ying Ba and Chuan Cao and Bing Su},
|
| 67 |
+
booktitle={The Fourteenth International Conference on Learning Representations},
|
| 68 |
+
year={2026}
|
| 69 |
+
}
|
| 70 |
+
```
|
| 71 |
+
|
| 72 |
+
## Links
|
| 73 |
+
|
| 74 |
+
- Code: https://github.com/yangzhao1230/Prism
|
| 75 |
+
- Model: https://huggingface.co/yangyz1230/Prism
|