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New regression and classification datasets for ontology pre-training - #130

Merged

sfluegel05 merged 61 commits into

ChEB-AI:devfrom

schnamo:dev

Dec 15, 2025

Commits on Jun 6, 2024
- create new class for solubility data
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- adjusting new class
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- add solubility yml file
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Commits on Jun 7, 2024
- adjusting solubility class to correctly download solubility data
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- make it compatible with classification problem
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Commits on Jul 4, 2024
- onehotencoding for solubility labels
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Commits on Jul 17, 2024
- adjust to regression, add yml files for regression
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- adjust prediction to regression
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Commits on Jul 23, 2024
- refactor code
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Commits on Jul 25, 2024
- regression fix, yml files for mae loss
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- take out kinect dataset
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- adjust learning rate
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Commits on Dec 12, 2024
- adjustments for new solu dataset
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- Merge branch 'dev' of https://github.com/schnamo/python-chebai into solubility
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Commits on Dec 19, 2024
- working on evaluation script, addded a bunch of things earlier for solubility regression
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Commits on Dec 20, 2024
- further adjusting evaluation function for regression
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- regression adjustments
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Commits on Jan 8, 2025
- fix union expression
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  fa97f45
- fix tuple issue to make it backwards compatible
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Commits on Jan 13, 2025
- wandb
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Commits on Jan 16, 2025
- fix issue with solubility dataset read in
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Commits on Jan 17, 2025
- Fix missing label handling
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- add more datasets
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- Merge commit 'b537b7fd776e6afc535e05a111a0bc6a493ec8e9' of https://github.com/schnamo/python-chebai into sol_new_fix
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- merge branches part 2
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Commits on Jan 18, 2025
- add more datasets
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  326e9a2
- adjust metrics for classifications, add BBBP
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  c272f45
Commits on Jan 19, 2025
- more datasets
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Commits on Jan 20, 2025
- bug fixes and different loss and electra params
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Commits on Jan 21, 2025
- changes to missing labels: negate labels as well as logits, add them to eval fct
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Commits on Feb 13, 2025
- try different splits, remove debugging comments
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Commits on Feb 20, 2025
- Merge branch 'dev' of https://github.com/schnamo/python-chebai into sol_new_fix
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  baa085f
Commits on Mar 12, 2025
- fix issue with input args
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  ba01607
Commits on Mar 19, 2025
- add missing configs
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Commits on Apr 4, 2025
- add HIV dataset handling
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- dd MUV dataset
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Commits on Apr 18, 2025
- debugging
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Commits on Jul 1, 2025
- final updates
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  ebe049e
Commits on Sep 29, 2025
- add focal loss
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- add focal loss
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- format for lint
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- lint fix
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- lint fix
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- add regression to readme
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- fix union expression
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- fix tuple issue to make it backwards compatible
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Commits on Oct 23, 2025
- Merge branch 'sol_final' into dev and adjustments to new logic, adjustments for regression tasks and classification tasks
  
  Charlotte Tumescheit
  authored and
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  committed
  af7df07
Commits on Oct 29, 2025
- adjust to current dev branch
  
  Charlotte Tumescheit
  authored and
  Charlotte Tumescheit
  committed
  ed1d4b4
- adjust all regression tasks to new logic
  
  Charlotte Tumescheit
  authored and
  Charlotte Tumescheit
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  dca60a3
- adjust classification tasks for new logic
  
  Charlotte Tumescheit
  authored and
  Charlotte Tumescheit
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  b6f0d23
- lightning cli issue
  
  Charlotte Tumescheit
  authored and
  Charlotte Tumescheit
  committed
  9b29411
- black-lint fix
  schnamo
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  d56e226
Commits on Nov 3, 2025
- fix load from checkpoint issues for pretrained models
  schnamo
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  fc444e0
Commits on Nov 11, 2025
- adding decoding of encoded tokens function
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  5304b3e
- remove print statements from debugging
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  426f1b0
Commits on Nov 13, 2025
- Merge branch 'dev' of https://github.com/ChEB-AI/python-chebai into dev
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  b0b3113
- lint fixes
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  fb6fdb7
- ruff fixes
  schnamo
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  81f8025
- black fixes
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Commits on Dec 11, 2025
- lint fixes
  schnamo
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  e67e4eb
Commits on Dec 15, 2025
- adjust unit tests for missing labels in tox21
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Commits on Dec 15, 2025