| --- |
| license: cc-by-4.0 |
| task_categories: |
| - fill-mask |
| language: |
| - en |
| tags: |
| - chemistry |
| - molecules |
| - selfies |
| - chembl |
| - pre-training |
| --- |
| |
| # ChEMBL 36 SELFIES |
|
|
| Pre-training dataset for [ModernMolBERT](https://github.com/HauserGroup/ModernMolBERT). Contains ~2.4M drug-like small molecules from ChEMBL 36 represented as [SELFIES](https://github.com/aspuru-guzik-group/selfies) strings. |
|
|
| ## Dataset details |
|
|
| | field | value | |
| |-------|-------| |
| | source | [lukaskim/ChEMBL-36](https://huggingface.co/datasets/lukaskim/ChEMBL-36) | |
| | representation | SELFIES | |
| | train rows | 2,390,314 | |
| | validation rows | 24,228 | |
| | total rows | 2,414,542 | |
| | min heavy atoms | 3 | |
| | max heavy atoms | 100 | |
| | max MW | 1000.0 | |
| | deduplicated by | InChIKey | |
| | split method | deterministic hash on InChIKey | |
| | valid fraction | 0.01 | |
|
|
| ## Preparation stats |
|
|
| - Input rows: 2,854,815 |
| - After deduplication: 2,854,815 |
| - Valid SELFIES conversions: 2,854,762 |
| - After physicochemical filters: 2,414,542 |
| - Dropped (invalid or filtered): 440,273 |
|
|
| ## Columns |
|
|
| | column | description | |
| |--------|-------------| |
| | `selfies` | SELFIES string (primary pre-training input) | |
| | `canonical_smiles` | original ChEMBL SMILES | |
| | `smiles_canonical_clean` | RDKit-canonicalized SMILES | |
| | `standard_inchi_key` | InChIKey used for deduplication and splitting | |
| | `chembl_id` | ChEMBL compound identifier | |
| | `qed_weighted` | QED drug-likeness score | |
| | `heavy_atoms`, `mw_freebase`, `alogp`, ... | Physicochemical descriptors from ChEMBL | |
|
|
| ## Usage |
|
|
| ```python |
| from datasets import load_dataset |
| |
| ds = load_dataset('HauserGroup/ChEMBL36-SELFIES') |
| print(ds['train'][0]['selfies']) |
| ``` |
|
|
| ## Versions |
|
|
| - datasets: 4.8.5 |
| - rdkit: 2026.03.1 |
| - selfies: 2.1.1 |
| - pandas: 3.0.3 |
| - pyarrow: 24.0.0 |
|
|
| ## License |
|
|
| ChEMBL data is released under [CC BY-SA 3.0](https://creativecommons.org/licenses/by-sa/3.0/). The prepared dataset files in this repository are released under CC BY 4.0. |
|
|
