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feat(environments): Release all model checkpoints
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kmaziarz committed Aug 15, 2023
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Expand Up @@ -23,9 +23,27 @@ If you want to use a different one, make sure to edit these two files accordingl
The GLN model is not compatible with the others, currently requiring a specialized environment creation which includes building `rdkit` from source.
We packaged all the necessary steps into a Docker environment defined in `gln/Dockerfile`.

## Model checkpoints

See table below for links to model checkpoints trained on USPTO-50K alongside with information on how these checkpoints were obtained.
Note that all checkpoints were produced in a way that involved external model repositories, hence may be affected by the exact license each model was released with.
For more details about a particular model see the top of the corresponding model wrapper file in `reaction_prediction/inference/`.


| Model checkpoint link | Source |
|----------------------------------------------------------------|--------|
| [Chemformer](https://figshare.com/ndownloader/files/42009888) | finetuned by us starting from checkpoint released by authors |
| [GLN](https://figshare.com/ndownloader/files/42012720) | released by authors |
| [LocalRetro](https://figshare.com/ndownloader/files/42012729) | trained by us |
| [MEGAN](https://figshare.com/ndownloader/files/42012732) | trained by us |
| [MHNreact](https://figshare.com/ndownloader/files/42012777) | trained by us |
| [RetroKNN](https://figshare.com/ndownloader/files/42012786) | trained by us |
| [RootAligned](https://figshare.com/ndownloader/files/42012792) | released by authors |

## Back-translation

In `reaction_prediction/cli/eval.py` a forward model may be used for computing back-translation (round-trip) accuracy.
Currently, Chemformer is the only supported forward model.

To evaluate a particular model with back-translation computed using Chemformer, simply set up an environment for that model and then run `setup_chemformer.sh` on top.
See [here](https://figshare.com/ndownloader/files/42012708) for a Chemformer checkpoint finetuned for forward prediction on USPTO-50K. As for the backward direction, pretrained weights released by original authors were used as a starting point.

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