Active-set block skipping for label propagation rounds 2+#136
Open
Active-set block skipping for label propagation rounds 2+#136
Conversation
After each round's pointer jumping, track which positions changed labels in an AtomicBitVec. In subsequent rounds, skip blocks where no source or target endpoint position was in the changed set. This is correct because unchanged positions cannot benefit from re-hooking. Round 3+ skip 56-58M of 58M blocks (~1s per round vs ~8s without skip). Round 2 skips 1.5M blocks (most positions change after round 1). Total phase 2: ~50s vs ~62s. Output identical (2727 nodes, 52047bp).
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
After each round's pointer jumping, track which positions changed labels in an AtomicBitVec. In subsequent rounds, skip blocks where no source or target endpoint was in the changed set.
This is correct because unchanged positions cannot benefit from re-hooking — the label propagation only creates new connections when labels differ.
Results (466-seq MHC/C4, seqwish engine)
Total phase 2: ~50s vs ~62s without skip. Seqwish pipeline: 2m17s (vs 2m26s baseline on this branch).
Output identical: 2727 nodes, 52047bp, 3686 links.
Also adds
pointer_jump_tracking()andhook_range_tracking()to LabelProp.