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View Code? Open in Web Editor NEWGT4SD, an open-source library to accelerate hypothesis generation in the scientific discovery process.
Home Page: https://gt4sd.github.io/gt4sd-core/
License: MIT License
GT4SD, an open-source library to accelerate hypothesis generation in the scientific discovery process.
Home Page: https://gt4sd.github.io/gt4sd-core/
License: MIT License
If something is wrong in the GT4SDConfiguration (host name, secure setup) the Client enters in a loop and tries to re-connect for a long time without any error/log message. Maybe we should have a smaller max number of trials (~10/100) or a log message every time the client has to re-connect.
All PaccMann based models, e.g. proteomic and omics based generator should be retrained using the pypi-distribution of pytoda. This will enable all paccmann-related repos in vcs_requirements.txt
to be pip installable and could free us almost entirely from the vcs requirements. This will affect inference of PaccMannRLProteinBasedGenerator
and PaccMannRLOmicBasedGenerator
I accept and sign the CLA to contribute to GT4SD.
I accept the CLA and I would like to sign it to contribute to GT4SD.
Is your feature request related to a problem? Please describe.
Unify interface for prediction algorithm making use of the property predictor.
Describe alternatives you've considered
gt4sd.properties
in gt4sd.algorithms.prediction
(preferable even in case we go for namespace packaging)gt4sd.algorithms.prediction
in gt4sd.properties
Hey @C-nit I tried merging the PR for the bdist_wheel building and it fails with the error below.
Could you take a look? Maybe wheel is missing from the image running the action.
Instead of using https://github.com/GT4SD/reinvent_models (tracked contribution here MolecularAI/Reinvent#41).
We should directly open the fork on the public repo: https://github.com/MolecularAI/reinvent-models (most likely not available at the time we went live)
Involving @Ashish13898 mostly for feedback on what is needed to implement this.
I accept the CLA and I would like to sign it to contribute to GT4SD.
I accept and sign the CLA to contribute to GT4SD.
I accept and sign the CLA to contribute to GT4SD.
I accept and sign the CLA to contribute to GT4SD.
I accept and sign the CLA to contribute to GT4SD.
The new multiprocess library version (0.70.13
) gives problems when installing gt4sd-core
using the development mode. I had to set multiprocess==0.70.12.2
to install the library.
I accept and sign the CLA to contribute to GT4SD.
Currently, the RT supports only plain inference with user provided masked inputs like:
<QED>0.123|[C][MASK][C][O]
which is prohibitive, especially since we use SELFIES. Til now, scaffold decoration was impossible with selfies since smiles-selfies conversion mappings could not be retrieveid. This is fixed in SELFIES >=2.1.0, for details see aspuru-guzik-group/selfies#75.
Bumping selfies to >=2.1.0 requires an update of PaccMann models, so this issue is sequential to #38.
Is your feature request related to a problem? Please describe.
No problem, just an update of MoLeR dependency: https://github.com/microsoft/molecule-generation/releases/tag/v0.2.0.
Currently, our TorchDrug interface does support property optimization conceptually.
However, most runs will fail due to an underlying bug in TorchDrug that raises whenever there is only invalid SMILES in a batch, see DeepGraphLearning/torchdrug#83
Once this is fixed in torchdrug and a new version is released on conda, we can enable our unittests (already written): https://github.com/gt4sd/gt4sd-core/blob/master/src/gt4sd/training_pipelines/tests/test_training_torchdrug_gcpn.py#L76
Currently predictive models such as PaccMann, adhere to the GenerativeAlgorithm interface. This is not an ideal fit, we should consider adding a dedicated interface.
Currently on pypi we only publish a source distribution, and it's not containing the package_data. It's there when building a wheel, e.g. with python setup.py bdist_wheel
.
While building a wheel is something we should anyway do, we also need to add a MANIFEST.in file.
Edit: it should be possible without MANIFEST.in
I accept the CLA and I would like to sign it to contribute to GT4SD.
CLA signing should be automatically committed via github actions, but the workflow fails to clone the repo it seems:
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