| --- |
| library_name: pytorch |
| license: apache-2.0 |
| tags: |
| - polymers |
| - molecular-optimization |
| - transformer |
| - polyedit |
| --- |
| |
| # PolyEdit Molecular Optimization Transformer (polymer-retrained) |
|
|
| This checkpoint adapts MolecularAI's released Molecular Optimization Transformer to |
| two-anchor PSMILES and the eight PolyEdit DFT properties. It is not directly comparable |
| to the authors' original LogD/Solubility/Clint model without this adaptation. |
|
|
| The original transformer body is retained: 6 encoder/decoder layers, hidden size 256, |
| 8 heads, and feed-forward size 2,048. All 258 shape-compatible upstream tensors were |
| loaded. Four vocabulary-dependent embedding/generator tensors were initialized for a |
| new vocabulary in which padding and the `*` polymer anchor have distinct IDs. Training |
| used 152,036 component-held-out examples; the best validation checkpoint was epoch 7 |
| of 10. |
|
|
| On the balanced 8,176-request test set, the checkpoint obtains 99.217% RDKit+TDC |
| validity, 99.168% two-anchor polymer validity, 99.083% changed outputs, 8.892% strict |
| MIPS-retrained full-edit hits, and 10.127% strict DFT full-edit hits at 95.034% DFT |
| coverage. Only 383 unique raw outputs were generated, so the strong validity comes with |
| substantial mode collapse and must not be reported without the diversity result. |
|
|
| Upstream code: <https://github.com/MolecularAI/deep-molecular-optimization> |
|
|
| Upstream checkpoint: <https://doi.org/10.5281/zenodo.5571965> |
|
|
| PolyEdit implementation and record-level evaluation: <https://github.com/promotion-kim/POLYEDIT/tree/tsyou/balanced-polymer-baseline-eval> |
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