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.