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license: mit
language:
- en
tags:
- chemistry
- molecule-representation
- rmmol
- molecular-property-prediction
- qm9
- tox21
- sider
pretty_name: RMMol
---
# RMMol
This bundle contains standardized CSV files and a Jupyter sample notebook for RMMol frozen-embedding examples across Biophysics, Physiological, Physical Chemistry, and Quantum Mechanics.
## Contents
- `dataset/biophysics/`: BBBP full CSV and HIV train/val/test splits.
- `dataset/physiological/`: BACE, ClinTox FDA-approved, Tox21 single-label splits, and SIDER single-label splits.
- `dataset/physical_chemistry/`: ESOL, FreeSolv, and Lipophilicity splits.
- `dataset/quantum_mechanics/`: QM9 splits.
- `examples/RMMol_sample.ipynb`: RMMol-only sample notebook with the selected downstream-head settings.
- `examples/RMMol_lipid_conformation_distance.ipynb`: RMMol-only LNPDB heldout IL_SMILES workflow for embedding distance versus RDKit USR conformation distance.
- `MANIFEST.csv`: file-level provenance, row counts, columns, and checksums.
## Naming convention
Each split follows `<dataset>_<split>.csv` for split datasets and `<dataset>_<task>_<split>.csv` for Tox21/SIDER single-task files. BBBP is stored as `bbbp.csv` because its protocol uses five-fold cross-validation over the full BBBP table. The validation split is standardized to `val`.
## Evaluation protocol
All tasks use frozen embeddings. Classification tasks report ROC-AUC; Physical Chemistry reports RMSE; QM9 reports MAE. The notebook records the selected RMMol downstream-head settings without storing local output tables in the package.
## Hardware note
The current inference and downstream-probe reproduction was run on the Spark workstation. RMMol pretraining used 8 x A800 40G GPUs.
## Weights
The RMMol model weights are intended to be distributed from the Hugging Face model repository: `https://huggingface.co/Creeperbbs/RMMol`.
## Provenance
The CSV files were standardized from the local GraphWorld/MoleculeNet data tree, the HIV split, and the split Tox21/SIDER archives. This bundle was generated on 2026-09-15.
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