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Molenet dataset - #48

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aditya0by0 wants to merge 65 commits into

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feature/molenet_dataset

Open

Molenet dataset #48
aditya0by0 wants to merge 65 commits into
devfrom
feature/molenet_dataset

Commits on Aug 8, 2026
- chebi aug variant with all props except node level
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Commits on Aug 10, 2026
- allow adding new tokens through augmented class for atom specific props
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- BACE dataset tokens
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Commits on Aug 11, 2026
- check len of base_df after merge, to avoid memory blow due to duplicated entries leading to cross merge
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Commits on Aug 12, 2026
- BBBP tokens
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- hiv tokens
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- clintox tokens
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- sider tokens
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- HIV tokens
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Commits on Aug 13, 2026
- muv tokens
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- Merge branch 'feature/molenet_dataset' of https://github.com/ChEB-AI/python-chebai-graph into feature/molenet_dataset
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Commits on Aug 14, 2026
- pcba tokens
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- Merge branch 'feature/molenet_dataset' of https://github.com/ChEB-AI/python-chebai-graph into feature/molenet_dataset
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Commits on Aug 15, 2026
Commits on Aug 18, 2026
- add baseline to aug-ablation script too
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Commits on Aug 19, 2026
- aug props for gnwa_wfga_wfge
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Commits on Aug 20, 2026
Commits on Aug 24, 2026
- aug ablation study for tox21, toxcast
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- add tox ablation classes to configs
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Commits on Sep 5, 2026
- add aug ablation scripts
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Commits on Sep 6, 2026
- rectify script
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  e1e1d77
- update chebi aug ablation script
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Commits on Sep 9, 2026
- final aug chang to gnwa_fgwa_wfge
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Commits on Sep 10, 2026
- update molenet final config to gnwa_fgwa_wfge config
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- enable seperate learning rate for gnn and final classification layer
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Commits on Oct 7, 2026
- allow pretrained weights with mismatchning edges
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Commits on Oct 9, 2026
- update aug ablation script for tox
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Commits on Oct 11, 2026
- himol msp pretraining
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- zinc pretraining dataset
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- Revert "Separate Token files based on data type (#47)"
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- delete data type based tokens
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- fixes
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Commits on Oct 14, 2026
- use existing vocab for msp
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Commits on Oct 16, 2026
- Reapply "Separate Token files based on data type (#47)"
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- commit tokens of all dataset and _shared
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Commits on Oct 18, 2026
- zinc15 250K samples tokens
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- change data_type -> tokens_directory
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- for msp loss set tokens dir to shared
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- fix permanenet del of of custom data for collator: for remaining epochs
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- print for loaded pretrained ckpt
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Commits on Oct 20, 2026
- update visualization script
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  8af009e
- fix prediction pipeline issue for graph
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Commits on Oct 24, 2026
- molnet final script
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Commits on Oct 25, 2026
- add molnet script to run all classif dataset and report avg test scores for each
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Commits on Oct 26, 2026
- update changes
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  b47a2dc
- update changes
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Commits on Oct 27, 2026
- pre-commit fix
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- pre-commit fix
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- Merge branch 'dev' into feature/molenet_dataset
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- remove duplicates introduced in https://github.com/ChEB-AI/python-chebai-graph/pull/51
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- pretraining scripts for zinc_msp_pretraining and final-chebi.sh have been added. The .gitignore file has been updated to include the new pretraining scripts.
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- update readme
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- update model hyperparams section
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- update augmented
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- other info
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- Replace image in README with new graph illustration
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Commits on Oct 28, 2026
- add batch norm param
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  4759b2d
- Merge branch 'feature/molenet_dataset' of https://github.com/ChEB-AI/python-chebai-graph into feature/molenet_dataset
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Commits on Nov 2, 2026
- script for amg analysis
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  399bade

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Commits on Nov 2, 2026