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I've noticed that BatchSize even it is there for Fine Tuning it is always 1 to make sure it functions properly. If one wants to set it bigger than 1, then it triggers an error due to a fact that self.…
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[97320630003100S1_2.pdf](https://github.com/Global-Chem/global-chem/files/12805267/97320630003100S1_2.pdf)
Here's the paper and we need to abstract table 2 I believe.
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SMARTS are already in many chemistry frameworks, such as CDK, babel, chemaxon etc.
Instead of SIMILES use SMARTS.
Example:
https://github.com/openbabel/openbabel/blob/master/data/SMARTS_InteLigan…
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When we are training a million molecules should we keep the limit_data as 5000 or we change ? What are the parameters affecting in training a set of 1 million ?
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Hi,
I wanted to try the Retip package, but running your example it made R crash when it wants to compute the chemical descriptors.
In Rstudio I get this output:
```
[1] "Computing Chemical Des…
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"metabolite_quantified": should be the ChemicalEntity object
"$ref": "#/definitions/ChemicalEntity",
"MetaboliteQuantification": {:
"additionalProperties": false,
"descriptio…
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When I run the command with a data-set specified in exp.json it trains the model, but does not return a file with the final encoded representation of the smiles. How can I change that?
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Dear,
Sorry to bother, i am curious about the input format for this model, if I would like to use the pre-trained model to predict the liver injury. Like gene profiles? Drug smiles?
Sorry for …
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Dear Sir,
I could not understand how the SMILES format is converted to ECFP to feed in the input layer of the model. Moreover, I could not understand how you have calculated the known binding affinit…
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A feature that I have not seen commonplace in any MS software is the support for modifications that might fragment due to the presence of peptide bonds.
For example,
![image](https://github.com/l…