ApeTokenizer-SELFIES

ApeTokenizer-SELFIES is the Atom Pair Encoding (APE) tokenizer used by ModernMolBERT — a family of compact encoder-only transformer models for small-molecule representation learning pre-trained on SELFIES strings from ChEMBL 36.

APE is a byte-pair-style merging scheme applied directly to SELFIES bracket tokens, so every token boundary aligns with a chemically valid SELFIES primitive. The vocabulary is derived from ~2M unique SELFIES strings from ChEMBL 36.

Tokenizer Details

• Developed by: Hauser Group, Department of Drug Design and Pharmacology, University of Copenhagen
• Input representation: SELFIES (convert SMILES first; see below)
• Algorithm: Atom Pair Encoding (APE) — pair merging over SELFIES bracket tokens
• Vocabulary size: 631
• Max merge pieces: 2
• Min merge frequency: 3000
• Training corpus size: 2M unique SELFIES (ChEMBL 36)
• License: MIT
• Repository: https://github.com/HauserGroup/ModernMolBERT

special token	id
<s> (BOS)	0
<pad>	1
</s> (EOS)	2
<unk>	3
<mask>	4

How to Get Started

from transformers import AutoTokenizer

tokenizer = AutoTokenizer.from_pretrained(
    "HauserGroup/ApeTokenizer-SELFIES",
    trust_remote_code=True,
    use_fast=False,
)

# A SELFIES string — here aspirin.
selfies = "[C][C][=Branch1][C][=O][O][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=Branch1][C][=O][O]"

tokens = tokenizer.tokenize(selfies)
print(tokens)
# ['[C][C]', '[=Branch1][C]', '[=O][O]', '[C][=C]', '[C][=C]', '[C][=C]', '[Ring1][=Branch1]', '[C][=Branch1]', '[C][=O]', '[O]']

inputs = tokenizer(selfies, return_tensors="pt")
print(inputs["input_ids"])
# tensor([[  0, 334, 335, 370, 333, 333, 333, 338, 377, 511,   6,   2]])

If you start from SMILES, convert first:

import selfies
smi = "CC(=O)Oc1ccccc1C(=O)O"
sf = selfies.encoder(smi)   # '[C][C][=Branch1][C][=O][O][C]...'
inputs = tokenizer(sf, return_tensors="pt")

Using with ModernMolBERT models

This tokenizer is shared by all four ModernMolBERT checkpoints. Load it from the model repo using subfolder="ape_tokenizer" to avoid routing AutoTokenizer to the built-in fast ModernBERT tokenizer:

from transformers import AutoTokenizer

tokenizer = AutoTokenizer.from_pretrained(
    "HauserGroup/ModernMolBERT-small",
    subfolder="ape_tokenizer",
    trust_remote_code=True,
    use_fast=False,
)

Or load this standalone repo directly as shown above — both produce identical tokenizations.

Citation

@article{madsen_modernmolbert,
  title  = {ModernMolBERT: A ModernBERT Encoder Family for SELFIES Molecular Language Modeling},
  author = {Madsen, Jakob S. and Angelucci, Sara and Hauser, Alexander S.},
  year   = {2026}
}

The APE algorithm follows Leon et al., Comparing SMILES and SELFIES tokenization for enhanced chemical language modeling, Sci. Rep. 14, 25016 (2024).