example with a chemical dataset

[thegodone]

In order to reproduce the work on Chemicals:

Can you share a example of data preparation ?

• with dummy 3D coordinate or rdkit 3D coordinate
• for one molecule

how look like your data preparation dataloader.

BR
Guillaume

[mokosaur]

@thegodone ,
thank you for your interest. We are going to upload a chemical example soon, probably by the end of this month.

[thegodone]

@mokosaur any update there ?

[mokosaur]

In the last update, I uploaded loaders for the chemical datasets. See the project README for a usage example. Thank you for your patience as it took a while to gather the code.

In the meantime, our efforts were focused on finishing our other work on another molecular prediction model which uses the Transformer architecture to extract information from molecular graphs. You can read more here: https://arxiv.org/abs/2002.08264.

[thegodone]

In your last preprint paper, Do you provide RMSE values at scaled range or at orignal data range ?

[mokosaur]

The RMSE is calculated for the standardized values. The datasets that we uploaded contain values that are already standardized. I think you can recover the RMSE of non-standard data by simply multiplying the RMSE by the standard deviation of the original data. However, these numbers still vary across different random data splits, and thus, unfortunately, they cannot be compared to other results in the literature.