yuyangw / MolCLR

Implementation of MolCLR: "Molecular Contrastive Learning of Representations via Graph Neural Networks" in PyG.
MIT License
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Cannot reproduce the results on serveral datasets shown in the paper. #28

Open zhangtia16 opened 6 months ago

zhangtia16 commented 6 months ago

Thank you for your work. However, I have found that I am unable to reproduce the results on many datasets as presented in the paper. I have the following questions:

  1. Is the best result for each dataset achieved under the SAME hyperparameter configuration of the pre-trained mode? (i.e., the pre-training results provided in the ckpt file) I noticed in Table 6 that there is mention of parameter search during the fine-tuning stage, but it's not clear whether different datasets shared the pretrained model under the same hyperparameter configuration.

  2. I noticed that in Table 6 of the supplementary material, the parameter search range for the fine-tuning stage is provided. However, I still encountered difficulties during the replication stage for some datasets. I was wondering if you could please provide the exact hyperparameter configurations for the best result of each dataset rather than the search range? Since I've noticed that others have also raised issues regarding replication problem. Thus, this would help reproducers save time. Thank you!