metadata
license: mit
tags:
- PubChem
- chemistry
A machine learning dataset based on SMILES strings from PubChem. This dataset is unlabeled and intended for self-supervised learning tasks. It contains 123,860,695 SMILES strings and that have been canonicalized with RDKit and tokenized for a Transformer model.
The dataset has been generated with the ChEB-AI library (v1.3.0).
Dataset structure
Pubchem/
├── raw/full/
│ ├── smiles.txt # Full list of SMILES from the [PubChem FTP server, May 2026](https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Monthly/)
│
└── processed/full/
│
├── data.pkl # molecule table as a pandas DataFrame (parsed SMILES strings)
├── splits.csv # ID-split pairs with 1,000,000 train samples and 100,000 validation / test samples each. All other IDs are train samples.
│
└── static_smiles/ # Tokenized SMILES strings ([Tokenizer implementation](https://github.com/ChEB-AI/python-chebai/blob/dev/chebai/preprocessing/smiles_tokenizer.py))
│
├── train_{i}.pt # i=0..123, blocks of 1,000,000 train samples (excluding parsing errors)
├── validation.pt # 100,000 validation samples (excluding parsing errors)
├── test.pt # 100,000 test samples (excluding parsing errors)
Usage
This dataset can be used to train ELECTRA transformer models with the ChEB-AI library. For usage examples, see the README. A model trained on this dataset is available here.