RosettaCommons / RosettaCommons/foundry

[BUG] RFD3 is missing training data artifacts

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@r-krishna is already working on this.

Since May 8, 2026.

bug
Dominant language
Python
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Merged PRs (30d)
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Description

Describe the bug
RFD3's training resources contain most of the required materials for others to reproduce its results. However, a few key data artifacts are currently missing, which makes exact reproducibility unattainable for the time being.

Expected behavior
In no particular order, the following data artifacts (i.e., data files or datasets) should be publicly available for download, to make RFD3's training fully reproducible.

  1. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/train/pdb/na_complex_distillation.yaml#L12
  2. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/train/rfd3_monomer_distillation.yaml#L21
  3. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/val_examples/bcov_ppi_easy_medium_with_ori.yaml#L4-L151
  4. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/dna_binder_design5.yaml#L7
  5. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/dna_binder_long.yaml#L7
  6. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/dna_binder_short.yaml#L7
  7. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/indexed.yaml#L7
  8. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/mcsa_41_short_rigid.yaml#L9
  9. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/mcsa_41.yaml#L7
  10. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/sm_binder_hbonds_short.yaml#L7
  11. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/sm_binder_hbonds.yaml#L6
  12. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/unconditional_deep.yaml#L7
  13. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/unconditional.yaml#L6
  14. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/datasets/val/unindexed.yaml#L7
  15. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/paths/data/default.yaml#L6-L7
  16. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/paths/data/default.yaml#L12-L13
  17. https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/paths/data/default.yaml#L18
  18. (Probably optional): https://github.com/RosettaCommons/foundry/blob/cee116dc5598d2c0c6087701914c5185aac98b48/models/rfd3/configs/paths/data/default.yaml#L16
    Additional context
    Thank you for open-sourcing RFD3's code and configs! These are significant resources from which the research community has already begun benefitting.

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