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datasets/raw/sw480_compounds.csv

#2
by AdamSulek - opened
base: refs/heads/main
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from: refs/pr/2
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  1. .gitattributes +3 -0
  2. checkpoints/rmat/README.md +23 -0
  3. checkpoints/{xgb_full_release/mcf10a/kfold/fold_3/metrics.json β†’ rmat/mcf10a/fold_0.pt} +2 -2
  4. checkpoints/rmat/mcf10a/fold_1.pt +3 -0
  5. checkpoints/rmat/mcf10a/fold_2.pt +3 -0
  6. checkpoints/rmat/mcf10a/fold_3.pt +3 -0
  7. checkpoints/rmat/mcf10a/fold_4.pt +3 -0
  8. checkpoints/rmat/mcf10a/fold_5.pt +3 -0
  9. checkpoints/rmat/mcf10a/fold_6.pt +3 -0
  10. checkpoints/rmat/mcf10a/fold_7.pt +3 -0
  11. checkpoints/rmat/mcf10a/fold_8.pt +3 -0
  12. checkpoints/rmat/mcf10a/fold_9.pt +3 -0
  13. checkpoints/rmat/mcf10a/scaffold.pt +3 -0
  14. checkpoints/rmat/sw480/fold_0.pt +3 -0
  15. checkpoints/rmat/sw480/fold_1.pt +3 -0
  16. checkpoints/rmat/sw480/fold_2.pt +3 -0
  17. checkpoints/rmat/sw480/fold_3.pt +3 -0
  18. checkpoints/rmat/sw480/fold_4.pt +3 -0
  19. checkpoints/rmat/sw480/fold_5.pt +3 -0
  20. checkpoints/rmat/sw480/fold_6.pt +3 -0
  21. checkpoints/rmat/sw480/fold_7.pt +3 -0
  22. checkpoints/rmat/sw480/fold_8.pt +3 -0
  23. checkpoints/rmat/sw480/fold_9.pt +3 -0
  24. checkpoints/rmat/sw480/scaffold.pt +3 -0
  25. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_0/model.json +0 -0
  26. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_1/model.json +0 -0
  27. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_2/model.json +0 -0
  28. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_3/model.json +0 -0
  29. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_4/model.json +0 -0
  30. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_5/model.json +0 -0
  31. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_6/model.json +0 -0
  32. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_7/model.json +0 -0
  33. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_8/model.json +0 -0
  34. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_9/model.json +0 -0
  35. checkpoints/{xgb_full_release β†’ xgb}/mcf10a/scaffold/model.json +0 -0
  36. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_0/model.json +0 -0
  37. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_1/model.json +0 -0
  38. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_2/model.json +0 -0
  39. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_3/model.json +0 -0
  40. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_4/model.json +0 -0
  41. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_5/model.json +0 -0
  42. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_6/model.json +0 -0
  43. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_7/model.json +0 -0
  44. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_8/model.json +0 -0
  45. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_9/model.json +0 -0
  46. checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/scaffold/model.json +0 -0
  47. checkpoints/xgb_full_release/mcf10a/kfold/fold_0/predictions.csv +0 -0
  48. checkpoints/xgb_full_release/mcf10a/kfold/fold_1/predictions.csv +0 -0
  49. checkpoints/xgb_full_release/mcf10a/kfold/fold_2/predictions.csv +0 -0
  50. checkpoints/xgb_full_release/mcf10a/kfold/fold_3/predictions.csv +0 -0
.gitattributes CHANGED
@@ -59,3 +59,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.json filter=lfs diff=lfs merge=lfs -text
 
 
 
 
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  *.webm filter=lfs diff=lfs merge=lfs -text
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  *.json filter=lfs diff=lfs merge=lfs -text
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+ raw/mcf10a_compounds.csv filter=lfs diff=lfs merge=lfs -text
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+ *.p filter=lfs diff=lfs merge=lfs -text
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+ raw/sw480_compounds.csv filter=lfs diff=lfs merge=lfs -text
checkpoints/rmat/README.md ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ # R-MAT checkpoints
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+
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+ All checkpoints in this directory were selected by the lowest validation loss
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+ (`best_val_loss`).
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+
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+ ## Layout
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+
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+ - `mcf10a/fold_0.pt` ... `mcf10a/fold_9.pt`: MCF10A 10-fold CV models
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+ - `mcf10a/scaffold.pt`: MCF10A scaffold-split model
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+ - `sw480/fold_0.pt` ... `sw480/fold_9.pt`: SW480-clean 10-fold CV models
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+ - `sw480/scaffold.pt`: SW480-clean scaffold-split model
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+
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+ ## Training settings
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+
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+ | Dataset | Split | Loss | Learning rate | Seed |
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+ |---|---|---|---:|---:|
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+ | MCF10A | 10-fold | BCE | 2.5e-5 | 42 |
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+ | MCF10A | scaffold | BCE | 2.5e-5 | 42 |
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+ | SW480-clean | 10-fold | BCE | 5e-5 | 42 |
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+ | SW480-clean | scaffold | BCE | 5e-5 | 42 |
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+
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+ The directory name `sw480` is the release name for checkpoints trained on the
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+ cleaned dataset identified as `sw480_clean` in the training artifacts.
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checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_0/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_1/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_4/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_5/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_6/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_7/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_8/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/mcf10a/kfold/fold_9/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/mcf10a/scaffold/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_0/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_1/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_2/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_3/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_4/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_5/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_6/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_7/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_8/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/kfold/fold_9/model.json RENAMED
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checkpoints/{xgb_full_release β†’ xgb}/sw480_clean/scaffold/model.json RENAMED
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