Yepeng

Discrepancies between using GoSearch and direct search on geneontology.org

1

Hi! Thanks for creating this wonderful library. I followed the instructions at https://github.com/tanghaibao/goatools/blob/main/notebooks/cell_cycle.ipynb to get GO-associated genes, but soon found out that there are some discrpancies between the results (in...

ENH: Adding back lookup or value setting by indices

2

### Feature Type - [X] Adding new functionality to pandas - [ ] Changing existing functionality in pandas - [ ] Removing existing functionality in pandas ### Problem Description As...

How are the methods implemented outside of the domain they are designed for?

1

For example, `DeepSynergy` and `MatchMaker` are requiring cell line information, and they are both implemented in the DrugBankDDI & TWOSIDES benchmarks where no cell line information is available at all...

Incorporate various dataset splits

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I also have one suggestion for future updates of this library perhaps. The current dataloaders, if I'm not mistaken, are not considering the different dataset split strategies. Recent works have...

Investigate using local server on remoteListenOnSocket

24

I was trying to get onto the second layer of an HPC after SSH-ing with some Slurm command (srun), as was generally described in #1722. I tried the newest `RemoteCommand`...

Hi! Thank you for creating this great library. For two GO terms, how can I derive the most recent common ancester term and their distance across that MRCA?

Hi! I finished writing this issue but did not submit it before I was able to resolve the issue. Thought it might still be helpful for people so I am...

Default node dimension changed from 66 to 67?

11

Hi! It looks like the `default` node featurizer now encodes molecules so that each node is of dimension 67. For compatibility purposes, could you kindly let me know which commit...

Any plans of implementing more models & releasing pretrained weights?

1

Hi! I wonder if you have any plans on implementing more state-of-the-art molecular representation learning models such as those in DeepChem. Others that haven't been incorporated into other libraries such...

Thanks for sharing the code of your enlightening work. I have a set of compounds that only have SMILES available. Would you recommend RDKit, Openbabel, or other tools for generating...