| --- |
| license: mit |
|
|
| tags: |
| - chemistry |
| - flow matching |
| - proteins |
| - generative modelling |
| - mars-fm |
| - biology |
| - molecular-dynamics |
| - pytorch |
| --- |
| |
| # MarS-FM (MD-CATH) Model Checkpoint |
|
|
| This repository contains the PyTorch model weights for **MarS-FM** (Markov Space Flow Matching) trained on the **MD-CATH** dataset. This model was introduced in the ICLR 2026 paper: [*MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models*](https://arxiv.org/abs/2509.24779). |
|
|
| ## 🔗 Links and Resources |
| * **Official GitHub Repository:** [valence-labs/mars-fm](https://github.com/valence-labs/mars-fm) |
| * **Paper:** [arXiv:2509.24779](https://arxiv.org/abs/2509.24779) |
| * **Dataset:** [compsciencelab/mdCATH](https://huggingface.co/datasets/compsciencelab/mdCATH) |
|
|
| ## ⚙️ Model Configuration |
| * **Dataset:** MD-CATH (`--mdcath`) |
| * **Temperature:** 450K (`--temp 450`) |
| * **MSM States (`--msm_num_states`):** 10 |
| * **MSM Lag Time (`--msm_lagtime`):** 50 |
| |
| ## 💻 How to Use |
| For full instructions on how to set up the environment, load this checkpoint, and run generation sampling, please follow the documentation in the **[official GitHub repository](https://github.com/valence-labs/mars-fm)**. |
| |
| ## 📝 Citation |
| If you use these weights, please cite the original authors: |
| |
| ```bibtex |
| @article{kapusniak2025mars, |
| title={MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models}, |
| author={Kapu{\'s}niak, Kacper and Gabellini, Cristian and Bronstein, Michael and Tossou, Prudencio and Di Giovanni, Francesco}, |
| journal={arXiv preprint arXiv:2509.24779}, |
| year={2025} |
| } |
| ``` |
