sokrypton / sokrypton/ColabFold
How is ESMFold PAE output?
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Description
Hi,
I am working with ESMFold and do not understand something. In the dictionary of the output, before parse_output function, there is a predicted_aligned_error key, which I thought would the PAE. HOwever, I see in the notebook, that PAE is ectracted from an other element:
pae = (output["aligned_confidence_probs"][0] * np.arange(64)).mean(-1) * 31
Why is this done this way?
Thank you for the clarification!
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
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Research direction
Start with the notebook code around parse_output, predicted_aligned_error, and aligned_confidence_probs. Trace how each output is produced and document why the PAE is calculated from the confidence probabilities; the work is done when the relationship between the two keys and the formula is clear.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, numpy
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100