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.