Early stopping based on unique generated SMILES#324
Open
NicklasOsterbacka wants to merge 5 commits intoMolecularAI:mainfrom
Open
Early stopping based on unique generated SMILES#324NicklasOsterbacka wants to merge 5 commits intoMolecularAI:mainfrom
NicklasOsterbacka wants to merge 5 commits intoMolecularAI:mainfrom
Conversation
Contributor
Author
|
I have additionally added a new terminator that stops execution after the top-k scores no longer improve after N epochs. This is primarily meant for the Practical Molecular Optimization benchmark in conjunction with unique SMILES-based early stopping, but might be interesting as a general alternative to checking mean scores as well. I refactored the convergence check in learning.py to accommodate this change; it should in principle be a bit easier to extend it with more terminators, if need be. I also added two new stage parameters, |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This PR adds a new stage parameter (
max_smiles) that stops generation once the number of canonicalized generated SMILES reachesmax_smiles. This also changes the behaviour oflearning.pyto add only valid SMILES tosmiles_memory.This allows for the running of the Practical Molecular Optimization benchmark through REINVENT4 by setting
max_smilesto 10000.