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Validation plus experiments - #4
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jeromekelleher merged 4 commits intoOct 16, 2026
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A node can only be copied from one site to the next without a recombination if it is in the tree over the whole interval between them, which is what the engine does. The dense reference allowed copying across trees with no sites in which the node is absent. Add a hand-built example with such a gap, and vectorise CompressedMatrix.decode.
verification/verification.py runs empirical validations of tsls on msprime-simulated ARGs and writes plots, in the style of msprime's verification.py: posterior calibration under the model, threading a held-out sample, and numerical behaviour (likelihood threshold, normalisation, agreement with the dense reference, weight_by_n).
AncestorMatcher gains pruning=("relative", f), which prunes nodes with
values below f times the maximum, and pruning=("top_n", n), which
prunes all but the n largest values. Pruned nodes get the value
likelihood_threshold. count_distinct=True records the mean number of
distinct likelihood values per site in Viterbi. make_matcher in the
verification suite passes these options through.
experiments/thresholding compares floor, relative and top_n pruning and the lossless Viterbi floor on held-out threading, model calibration and sc2ts sub-ARGs, with findings from a quick run in the README.
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