Niek de Jonge

In another project I did write SpectrumSet classes. This was mostly to make it easier to work on a molecule/inchikey level. For me it resolved: - Molecular fingerprints. These don't...

@zhanghailiangcsu Thank you for looking into this and sorry for the inconvenience. We discovered the same issue recently, there was a bug in the training algorithm that went unnoticed for...

Hi @AharoniLab, This was a mistake on our end, thanks for notifying us! We forgot updating the version of MS2Deepscore before training that model, which results in this warning. However,...

Hi @AharoniLab Sorry I missed this question before. This new model is indeed not designed to be used with MonteCarlo dropout. In principle a new one could be trained to...

Hi asmirn1 we updated our code quite a bit recently, but we did not have the time yet to update this. We should remove or update this tutorial. The readme...

Ah yes, you are right, that is missing. Below the code to create embedding/vector representations. ```python model = load_model(model_file_name) ms2ds_model = MS2DeepScore(model) ms2ds_embeddings = ms2ds_model.get_embedding_array(spectra_cleaned_for_ms2deepscore) ``` I recently gave a...

@asmirn1 The issue you have here is that your spectra don't have the ionmode specified. Since MS2Deepscore 2.0 uses the ionmode to make a prediciton the model will not run....

The readme and tutorial are up to date again (the tutorial is based on the workshop). Feel free to create a new issue if anything is still unclear.