AME Benchmark Clarification

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Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
python
Domain
machine-learning

Research direction

Start at rf_diffusion/dev/benchmark.py line 1158 and compare its AME benchmark RMSD alignment with section 3 of the RFdiffusion2 preprint and Figure 3B. Confirm which alignment was used for the figure and document or reconcile the discrepancy so the benchmark and published description agree.

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Description

The github currently has the AME benchmark defaulted to an all-atom aligned RMSD here, but the RFDiffusion2 preprint section 3 states that the data in Figure 3B are for backbone aligned RMSD.

Could you please clarify which was used for Figure 3B? Thanks!

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