Clay Kosonocky issues

Results 7 issues of


                                            Clay Kosonocky

Link to moleculenet.ai should be moleculenet.org

Title

Question about chirality and model results from paper

Hi, ChemBERTa was trained on achiral canonicalized molecules, as evidenced by the achiral canonicalized dataset. The MoleculeNet fine-tuning datasets in the paper contain chiral molecules. How was this addressed? Did...

What does the TTA stand for in RoseTTAFold?

Is it "three-track attention"? Just curious.

Preprocess dataset doesn't work because the paths aren't correct

Hi, I followed the instructions for preprocessing the datasets as per the readme. However, I get errors. The --root command does work at first to specify the path that is...

Any way to open in Hugging Face Transformers library?

Apologies if this is obvious / impossible, but is there any way to open the pre-trained models using the huggingface transformers library? Looking to use this model in a paper...

When loading BART via fairseq, which dict.txt should be in the model directory?

Hi, I am loading this model via fairseq in python, and am more or less copying the code in compute_score.py, line 79-81: `bart = BARTModel.from_pretrained(model, checkpoint_file = chkpt_path, bpe="sentencepiece", sentencepiece_model=f"{root}/BARTSmiles/chemical/tokenizer/chem.model")...

How do I actually run this locally?

I don't have much web dev background. How do I run this locally? I'm confused where the js code goes that is on the readme. And how to actually start...