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HauserGroup/ChEMBL36-SELFIES

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… See the full description on the dataset page: https://huggingface.co/datasets/HauserGroup/ChEMBL36-SELFIES.

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ChEMBL 36 SELFIES

Pre-training dataset for ModernMolBERT. Contains ~2.4M drug-like small molecules from ChEMBL 36 represented as SELFIES strings.

Dataset details

fieldvalue
sourcelukaskim/ChEMBL-36
representationSELFIES
train rows2,390,314
validation rows24,228
total rows2,414,542
min heavy atoms3
max heavy atoms100
max MW1000.0
deduplicated byInChIKey
split methoddeterministic hash on InChIKey
valid fraction0.01

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

columndescription
selfiesSELFIES string (primary pre-training input)
canonical_smilesoriginal ChEMBL SMILES
smiles_canonical_cleanRDKit-canonicalized SMILES
standard_inchi_keyInChIKey used for deduplication and splitting
chembl_idChEMBL compound identifier
qed_weightedQED 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. The prepared dataset files in this repository are released under CC BY 4.0.