| --- |
| 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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|
