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Mol ID

A transformer encoder model pretrained on 50M ZINC SMILES string using flash attention 2

With modern hardware and software stacks, it only took me 6~7 hours to pretrain this 17M model on 50M molecules for 5 epochs

Hardware:

  • 4 cores cpu
  • 1 RTX 3090 gpu

Software:

  • flash attention 2
  • lightning for mixed precision (bf16-mixed)
  • wandb for logging
  • huggingface
    • tokenizers
    • datasets

github repo: link

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Dataset used to train blenderwang/mol_id