README.md

---
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.