jonghyunlee/DrugLikeMoleculeBERT

Model description

This model is BERT-based architecture with 8 layers. The detailed config is summarized as follows. The drug-like molecule BERT is inspired by "Self-Attention Based Molecule Representation for Predicting Drug-Target Interaction". We modified several points of training procedures.

config = BertConfig(
    vocab_size=vocab_size,
    hidden_size=128,
    num_hidden_layers=8,
    num_attention_heads=8,
    intermediate_size=512,
    hidden_act="gelu",
    hidden_dropout_prob=0.1,
    attention_probs_dropout_prob=0.1,
    max_position_embeddings=max_seq_len + 2,
    type_vocab_size=1,
    pad_token_id=0,
    position_embedding_type="absolute"
)

Training and evaluation data

It's trained on drug-like molecules on the PubChem database. The PubChem database contains more than 100 M molecules, therefore, we filtered drug-like molecules using the quality of drug-likeliness score (QED). The 4.1 M molecules were filtered and the QED score threshold was set to 0.7.

Tokenizer

We utilize a character-level tokenizer. The special tokens are "[SOS]", "[EOS]", "[PAD]", "[UNK]".

Training hyperparameters

The following hyperparameters were used during training:

• Adam optimizer, learning_rate: 5e-4, scheduler: cosine annealing
• Batch size: 2048
• Training steps: 24 K
• Training_precision: FP16
• Loss function: cross-entropy loss
• Training masking rate: 30 %
• Testing masking rate: 15 % (original molecule BERT utilized 15 % of masking rate)
• NSP task: None

Performance

• Accuracy: 94.02 %