T-187: Perturbation-count stopping rule#226
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ms609 merged 3 commits intocpp-searchfrom Mar 25, 2026
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Add perturbStopFactor parameter to SearchControl(): stop after nTip * K consecutive replicates that fail to improve the best score. Default 0 (disabled). Small values (1-3) are typical. Inspired by IQ-TREE's unsuccessful-perturbation stopping rule (Nguyen et al. 2015), adapted from per-perturbation to per-replicate granularity. Implemented in both serial (ts_driven.cpp) and parallel (ts_parallel.cpp) paths. The serial path tracks consecutive unsuccessful replicates directly; the parallel path monitors score improvement in the main thread's polling loop. Two new tests: verify the rule stops search early when enabled, and that it's a no-op when disabled (factor=0).
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Benchmarked perturbStopFactor across 10 morphobank/inapplicable datasets (23-213 tips). Key findings: - PSF=2 gives 2.4-6.9x speedup on converged searches with zero score loss - Complementary to targetHits: on hard landscapes where few replicates hit the best score, PSF fires first; on easy landscapes targetHits fires first (PSF is irrelevant) - PSF=5 provides smaller speedups and is too conservative for large trees Changed default from 0 (disabled) to 2 in SearchControl() and compat wrapper. Updated docs and fixed timeout test (needs PSF=0 to test the timeout path, not convergence).
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Agent D.
Adds
perturbStopFactorparameter toSearchControl(): stop afternTip * Kconsecutive replicates that fail to improve the best score. Default 0 (disabled).Inspired by IQ-TREE's unsuccessful-perturbation stopping rule (Nguyen et al. 2015), adapted from per-perturbation to per-replicate granularity.
Changes:
src/ts_driven.h: Newperturb_stop_factorfield inDrivenParamssrc/ts_driven.cpp: Counter tracking + stopping check (serial path)src/ts_parallel.cpp: Counter tracking + stopping check (parallel path)src/ts_rcpp.cpp: Wire through from RR/SearchControl.R: NewperturbStopFactorparam + docsR/ts-driven-compat.R: Backward-compat wrappertests/testthat/test-ts-driven.R: 2 new tests (enable/disable)Local test: 163/163 pass (test-ts-driven.R). GHA dispatched: 23546574279.