| --- |
| license: cc-by-4.0 |
| tags: |
| - rna |
| - rna-rna-interaction |
| - pytorch |
| --- |
| |
| # MARRI model checkpoints |
|
|
| Trained checkpoints for MARRI (mechanism-aware multimodal framework for RNA--RNA |
| interaction prediction). All checkpoints share the same architecture (RNA-FM + |
| RNet-2D dual-tower encoder, opening branch, hybridization-gain MLP, axial |
| cross-attention classifier) and the same backbone configuration -- RNA-FM |
| fine-tuned, RNet-2D frozen, epoch-wise dynamic negative resampling -- differing |
| only in random seed and/or training data split. |
|
|
| Code: https://github.com/GainGod-Xu/MARRI |
| Interpretability/attention export for the headline model: https://huggingface.co/datasets/Xu-AI4Science/MARRI-interpretability |
|
|
| Each `.pth` file is a raw `state_dict()` for the interaction model (not a full |
| training checkpoint with optimizer state), loadable via |
| `model.load_state_dict(torch.load(path, map_location=device))`. |
|
|
| ## Main-matrix checkpoints (N-clean dataset, random 8:1:1 split) |
|
|
| | File | Seed | Test ROC-AUC | Best epoch | Notes | |
| |---|---|---|---|---| |
| | `dyn_ft-rnafm_seed42/best_rna_physics_model.pth` | 42 | 0.7530 | 23 | **Headline model**, reported as the main MARRI result throughout the paper | |
| | `dyn_ft-rnafm_seed43/best_rna_physics_model.pth` | 43 | 0.7409 | 15 | Seed-repeat run, same recipe | |
| | `dyn_ft-rnafm_seed44/best_rna_physics_model.pth` | 44 | 0.7342 | 18 | Seed-repeat run, same recipe | |
|
|
| Mean +/- SD over these three seeds: ROC-AUC 0.7427 +/- 0.0095 (Table 1 in the paper). |
|
|
| ## Leakage-resistant held-out generalization checkpoints (seed 42, own data split each) |
|
|
| Same recipe, each retrained from scratch on its own leakage-resistant held-out |
| split (a separate positive/negative pool per split, not the main N-clean |
| dataset -- see Methods/Supplementary for split construction). |
|
|
| | File | Held-out split | Test ROC-AUC | Best epoch | |
| |---|---|---|---| |
| | `generalization_interaction_pair_seed42/best_rna_physics_model.pth` | Unseen RNA--RNA pair | 0.7422 | 14 | |
| | `generalization_transcript_seed42/best_rna_physics_model.pth` | Unseen RNA/gene (most stringent) | 0.6630 | 13 | |
| | `generalization_interaction_locus_seed42/best_rna_physics_model.pth` | Unseen local interaction locus | 0.7502 | 19 | |
|
|
| These three correspond to Table 4 ("Generalization under leakage-resistant |
| held-out splits") in the paper. |
|
|
