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Paired Bootstrap Resampling for Hypothesis Testing
The paired bootstrap is a hypothesis-testing and confidence-interval procedure for comparing two procedures (or systems) and evaluated on the same items. Let be the per-item paired difference of a performance metric , with observed mean . For replicates (with typically in the thousands), draw a bootstrap index set of size with replacement and recompute the paired statistic on the same resampled items for both systems, e.g. The empirical distribution approximates the sampling distribution of the paired difference, from which a percentile confidence interval is read off and a two-sided p-value can be derived (e.g., as the bootstrap probability that the difference reverses sign). Resampling item indices rather than the two systems independently preserves the pairing structure, which removes between-item variance and gives more power than an unpaired test.
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