feat: resolve reversion-driven polytomies in the optimize loop - #947
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ivan-aksamentov merged 4 commits intoSep 3, 2026
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- Add a reversion-driven hoist: when a child edge reverts a substitution on the parent edge, insert a node grouping the child with its sibling subtree and lift the non-reverted substitutions above it, removing one mutation per reversion and adding none. Branch lengths split proportionally to preserve root-to-node distances; indels use an all-or-nothing distance-preserving rule. - Fold the shared-mutation merge, the hoist, and helper-node retirement into a single per-polytomy routine driven to a fixpoint by a monotone (mutation count, node count) potential. Run it every loop iteration, independent of the zero-optimal collapse, so reversions in the input and in polytomies formed by earlier iterations are resolved. - Relocate the two moved edges with reparent_edge to keep their keys and partition state; register the fresh node and edge in dense partitions.
- Require the polytomy node to keep at least two children before hoisting: moving the reverting child under the new node must leave a sibling behind, or the node becomes a childless stub (a spurious leaf). A node whose children all revert the same position merges to a single reverting child and is now left with its residual reversion rather than dissolved.
- Unit-test the hoist move on constructed trees: the untouched substitutions land once above the new node without duplication, chained positions compose onto both output edges, pure reversions drop one mutation, distances are preserved, and per-partition splits are independent. - Unit-test the indel rule for the cancelling, overlapping-fallback, and clean-hoist cases. - Integration-test the merge -> hoist -> retire routine end to end: the worked example reaches the parsimony optimum, incompatible splits stop at the greedy bound, helper retirement spares pre-existing internal nodes, and the root and reversion-free polytomies are left untouched. - Add a loop test proving the hoist fires through prune_and_merge_in_loop with no zero-optimal collapse. - Property-test that the potential never rises and strictly falls on any change, and that leaves, non-negative branch lengths, and the single-root tree shape are preserved. The committed regression seed pins the all-children-revert degenerate case.
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September 3, 2026 06:28
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A polytomy resolution can place a substitution on a parent edge and revert it on a child -- two mutations where one suffices. These reversions persisted. This adds a reversion hoist that removes them, run together with merge and helper-node cleanup as one fixpoint routine every iteration.
Work items
reparent_edge[src]merge_single_polytomytopub(crate)for reuse by the routine [src]Possible improvements