metadata
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. Contains ~2.4M drug-like small molecules from ChEMBL 36 represented as SELFIES strings.
Dataset details
| field | value |
|---|---|
| source | 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
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. The prepared dataset files in this repository are released under CC BY 4.0.