Repository navigation
Audit cluster mates of flagged leaders together; expose max_rounds - #39
Merged
Merged
Conversation
The structural audit loop audits one leader per cluster per round and, when that leader is related (TM >= .45), promotes the next member. A large cluster that is structurally related to a query but carries no shared Rfam family or clan therefore advanced one member per round: the NuFold predicted-database fit at --audit-ceiling 100 still had 5 unaudited leaders after 70 of its 75 rounds (about 13 minutes each). When a leader is flagged, also audit every unaudited, scored, eligible mate in its cluster with E0 <= ceiling. Mates score no higher than the eligible leader, so these are the audits later rounds would request; a mate with TM < .45 stays in the background exactly as an unaudited one. On NuFold the loop now settles in 2 rounds at ceiling 100 and in 5 at ceiling 400 (212,859 -> 3,726 -> 57 -> 2 -> 0 pairs). The predicted fit takes max_rounds like the experimental one (default 75, as before) and both report the round limit when the audit does not settle.
DylanYang
added a commit
that referenced
this pull request
Nov 10, 2026
README: cluster-mate auditing is merged (#39)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The structural audit loop audits one leader per cluster per round and, when that leader is related (TM >= .45), promotes the next member. A large cluster that is structurally related to a query but carries no shared Rfam family or clan therefore advanced one member per round: the NuFold predicted-database fit at --audit-ceiling 100 still had 5 unaudited leaders after 70 of its 75 rounds (about 13 minutes each).
When a leader is flagged, also audit every unaudited, scored, eligible mate in its cluster with E0 <= ceiling. Mates score no higher than the eligible leader, so these are the audits later rounds would request; a mate with TM < .45 stays in the background exactly as an unaudited one. On NuFold the loop now settles in 2 rounds at ceiling 100 and in 5 at ceiling 400 (212,859 -> 3,726 -> 57 -> 2 -> 0 pairs).
The predicted fit takes max_rounds like the experimental one (default 75, as before) and both report the round limit when the audit does not settle.