Understanding how pretraining in SMILES lead good performance in predicting molecular propeties

by Xiaoyan Bai2 months ago
1

MOLFormer, from this paper: Large-scale chemical language representations, first pre-trained on larger SMILES data and then fine-tuned on other tasks. It can achieve better performance. I wonder if we can use mechanistic interpretability method to understand what information it learned during pretraining is useful for later inference time task. Here is what the paper claims: specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. Here is the model: https://github.com/IBM/molformer

If you are inspired by this idea, you can reach out to the authors for collaboration or cite it:

@misc{bai-understanding-how-pretraining-2026,
  author = {Bai, Xiaoyan},
  title = {Understanding how pretraining in SMILES lead good performance in predicting molecular propeties},
  year = {2026},
  url = {https://hypogenic.ai/ideahub/idea/4HqgJfOfmUcRVn3FM04A}
}

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