Permutation Testing

Modern deep generative models are primarily studied for their ability to generate realistic samples, yet the generative dynamics they learn can also serve as objects of statistical inference. We develop this idea for two-sample testing, the problem of deciding whether the same distribution generated two finite datasets. Using stochastic interpolants, we connect both distributions to a shared Gaussian bottleneck, so that each half of the resulting path is a Gaussian channel acting on a single population. We prove that the null hypothesis holds if and only if the population denoiser, or equivalently, the velocity fields of the two halves, coincide at any single noise level, which amounts to a reflection symmetry of the path about the bottleneck. Deviations from this symmetry yield a continuum of two-sample witnesses, which we estimate via held-out regression risks on learned denoisers and velocities and aggregate along the path; under an information-theoretic weighting, the aggregated discrepancy equals the Jeffreys divergence between the noise-smoothed distributions. Calibrating the resulting statistics by permutation yields tests that are valid in finite samples for any trained networks and consistent when the fields are learned accurately. On a synthetic benchmark and three image benchmarks, the proposed tests improve power over the strongest baseline by up to 33 percentage points at an equal total sample budget, with the best choice of regression representation and path weighting depending on the data modality. These results show that generative paths provide a principled representation for statistical testing, extending stochastic-interpolant models beyond generation.

Partial Least Squares (PLS) regression extracts a few outcome-aligned directions in a high-dimensional X and is widely used across applied science, but inference on the resulting fit is either expensive, biased and discouraged, or absent. We reduce inference to held-out OLS refits of the supervised subspace, a primitive shared by PLS, supervised PCA, and linear probes, and supply two tests using held-out correlations: a Nadeau-Bengio corrected asymptotic t-test as a fast approximation, and a permutation test with comparable power, finite-sample valid under outcome-predictor independence and iid rows. Held-out predictions are unchanged under any orthogonal rebasing of the supervised span, so an interpretable basis such as varimax inherits the joint claim but not a per-axis p-value; per-component claims come from a fixed-sequence test on the PLS extraction order. We validate on synthetic geometries, two NIR chemometric datasets, and cross-lingual word-embedding regressions; the exact test also transfers to supervised PCA and a ridge probe. The proposed tests have more power than CV-permutation-Q^2, at a fraction of its cost. A pre-run check on n and the spectrum of X says when the approximation is safe. We release a Rust library with Python, R, and Julia bindings, plus a Python text pipeline.

Memorization audits of generative models read similarity scores against thresholds, with no null distribution, and the conclusions they support can be wrong. By MemBench's rule, the benchmark's mitigations roughly halve Stable Diffusion's memorization; audited with false-discovery control, two thirds of the certified images are no longer detected under random prompt perturbations, five sixths under attention rescaling, and all of them under embedding optimization. The field's data-copying test, read against its own null, flags ten of twenty-four generators that reproduce nothing. We argue that for memorization the null is the hard part, and supply two. For a whole model, training and held-out images are exchangeable given its samples, and relabelling them is a permutation test, exact for any statistic when the held-out images are a random split; under it, a nearest-neighbour preference still fires on seven of those twenty-four, and a count restricted to the near-duplicate scale on none (McNemar p=0.016). For single images, the natural nulls fail twice, measurably: ranking an image among random images yields 596 false discoveries among 2,365 controls, and resampling independent generations makes the null three times too narrow. Calibrated against matched controls, the audit certifies 36 of 61 MemBench images at 5% false-discovery rate, held-out controls are certified in 0.01% of calibration splits, and on this benchmark two generations per image recover that count. A calibrated maximum, which reads occasional rather than typical copying, certifies 46. As the scale-restricted statistic we recommend the small-scale mass of the Intersection Euler Characteristic Profile, which also counts distinct images copied and tests whether two models copy the same ones.

Data-adaptive two-sample testing assesses if two samples come from the same distribution, using a discrepancy learned from the data (e.g., via kernel-based feature representations). Such methods typically rely on data splitting to decouple learning from testing and control type I error. However, this paradigm is ill-suited to few-shot settings with severe sample-size imbalance: abundant reference samples are available, while only a handful of query samples arrive. In this paper, we show how this imbalance can be leveraged constructively. Using abundant reference data, we learn reference-dependent representations that summarize salient structure of the reference distribution and provide informative signals for detecting departures. We incorporate a collection of representation families that capture both global and local structure, and adaptively weight them using only reference samples via an uncertainty-guided principle. Theoretically, we establish permutation-based type I error control and show consistency of the aggregated test: as the sample sizes grow, the test power converges to one whenever the representation set contains at least one consistent representation. Empirically, our aggregation achieves strong performance across a range of benchmarks while retaining type I error control.

Generative surveying -- where collections of LLM-based personas provide feedback on messages -- has emerged as a cheap and scalable alternative to traditional market research. However, LLMs are sensitive to small variations in prompt design and conclusions drawn from generative surveys may depend on arbitrary phrasing choices. Controlling for this sensitivity requires including semantically equivalent perturbations in the analysis. In this paper, we show that standard hypothesis tests, including the sign test and Wilcoxon signed-rank test, are invalid under a statistical model for generative surveying that includes realistic perturbation structure. We propose a permutation test that is valid under this model and formally characterize the conditions under which standard tests fail. Applying our framework to a simple generative surveying problem, we estimate relevant parameters, characterize the power of the permutation test under realistic conditions, and provide practical guidance on budget allocation across personas, perturbations, and replicates. Finally, we show that both the magnitude and direction of the estimated effect are sensitive to the choice of model, even within the same model family.

Validating interpretable surrogate models for ensemble learners requires measuring agreement between the ensemble's internal representation and its surrogate approximation, rather than mere association. Correlation-based approaches are scale-invariant and fail to detect systematic discrepancies in co-occurrence structure. We propose a statistical framework grounded in the agreement-association distinction, centered on the normalized Loss of Interpretability (nLoI). Rooted in the Cressie-Read power divergence family with lambda equal to 2, the nLoI admits a closed-form decomposition into within-node and between-node components, providing a unique diagnostic capability to identify precisely where and why reconstruction fails. The framework incorporates four complementary measures capturing distinct structural facets of approximation quality. A unified permutation testing procedure delivers valid inference for all measures within a single resampling pass. Theoretical properties, including boundedness and symmetry, are established for each metric. Monte Carlo simulations and empirical evaluations confirm exact Type I error control and demonstrate that these measures detect reconstruction fidelity gradients invisible to correlation-based alternatives. The framework is developed and illustrated in the context of Explainable Ensemble Trees (E2Tree), and empirical evaluation on three benchmark datasets illustrates the practical utility of the framework.

Measuring the breadth of a word's meaning, or its spread across contexts, has become feasible with contextualized token embeddings. A word type can be represented as a cloud of token vectors, with dispersion-based statistics serving as proxies for contextual diversity (Nagata and Tanaka-Ishii, ACL2025). These measurements are useful for deciding appropriate sense distinctions when constructing thesauri and domain-specific dictionaries. However, when comparing the breadth of two word types, naive hypothesis testing on dispersion can be misleading: differences in semantic direction can masquerade as dispersion differences, inflating Type-I error and yielding "statistically significant" outcomes even when there is no true breadth difference. This is problematic because significance testing should distinguish genuine effects from incidental fluctuations in small-difference regimes. We propose a Householder-aligned permutation test to isolate dispersion differences from directional differences. Our method applies a single Householder reflection to align the mean directions of the two word types and then performs a permutation test on the aligned token clouds, yielding calibrated, non-parametric p-values. For practicality, we introduce a GPU-oriented implementation that batches permutations and linear algebra operations. Empirically, our alignment reduced Type-I error by 32.5% while preserving sensitivity to genuine breadth differences, and achieved a 23x speedup over the CPU baseline.

The standard constraint-based paradigm for causal discovery with incomplete data -- impute first, test second -- is frequently miscalibrated: any consistent conditional independence (CI) test rejects a true null with probability approaching 1 when imputation error induces spurious conditional dependence. We introduce PAIR-CI, a nonparametric CI test that restores calibration by integrating multiple imputation directly into the inferential procedure via a paired permutation design. PAIR-CI compares cross-validated models that include and exclude the candidate variable while receiving the same imputed conditioning set, forcing imputation error to cancel in their loss difference rather than contaminate the test statistic. A provably consistent variance estimator jointly accounts for uncertainty arising from cross-validation and multiple imputation -- to our knowledge, the first formal unification of these two inferential frameworks. In simulations, existing imputation-based CI tests exhibit false positive rates of 28--45% when data are missing not at random (MNAR), whereas PAIR-CI averages below the nominal 5% level across data-generating processes and missingness mechanisms. These gains are largest in nonlinear settings and grow with causal graph size: when integrated into the PC algorithm, PAIR-CI reduces structural Hamming distance by 8% on 10-variable nonlinear graphs, 15% on 30-variable equivalents, and up to 44% on the 56-variable HAILFINDER network, with stable performance in all settings.

Reporting guidance for information-theoretic measures is rarely tested against ground truth. We test one guardrail in two multi-agent reinforcement learning games, a social dilemma and a coordination race, where directed influence between selected agent pairs is zero by construction, over 100 seeds. Omitting one precondition, exclusion of the non-stationary training transient, gives false-positive rates of 100.00% and 99.95%: agents annealing exploration independently, in runs that never met, are flagged as influencing one another. Excluding the transient reaches 3.0% in the social dilemma but 11.8% in the coordination game, which stationarity tests explain: 95.7% of social-dilemma series are stationary afterwards against 56.8% of coordination series. So the non-stationarity must be treated, and exclusion is neither the only way nor sufficient. What we recommend instead changes the null model rather than the data: permuting the source within blocks of training time reaches 5.25% and 5.50%, the only one of four constructions at the size of the test in both games, leaving series, statistic and estimand untouched. Titrating injected links of known strength in both games shows it is also the most sensitive of the three, detecting 89.0% in the coordination game where conditioning detects 61.0% on identical pairs, while the ablated test reports 100% with or without a link, so its apparent sensitivity is uninformative. The block count is not critical: every setting from 16 to 256 lands in the nominal region, and a partition derived from the stationarity test removes the parameter, though less sensitively. Code and data are released.

The King Wen sequence of the I-Ching (c. 1000 BC) orders 64 hexagrams -- states of a six-dimensional binary space -- in a pattern that has puzzled scholars for three millennia. We present a rigorous statistical characterization of this ordering using Monte Carlo permutation analysis against 100,000 random baselines. We find that the sequence has four statistically significant properties: higher-than-random transition distance (98.2nd percentile), negative lag-1 autocorrelation (p=0.037), yang-balanced groups of four (p=0.002), and asymmetric within-pair vs. between-pair distances (99.2nd percentile). These properties superficially resemble principles from curriculum learning and curiosity-driven exploration, motivating the hypothesis that they might benefit neural network training. We test this hypothesis through three experiments: learning rate schedule modulation, curriculum ordering, and seed sensitivity analysis, conducted across two hardware platforms (NVIDIA RTX 2060 with PyTorch and Apple Silicon with MLX). The results are uniformly negative. King Wen LR modulation degrades performance at all tested amplitudes. As curriculum ordering, King Wen is the worst non-sequential ordering on one platform and within noise on the other. A 30-seed sweep confirms that only King Wen's degradation exceeds natural seed variance. We explain why: the sequence's high variance -- the very property that makes it statistically distinctive -- destabilizes gradient-based optimization. Anti-habituation in a fixed combinatorial sequence is not the same as effective training dynamics.

Modeling of longitudinal cohort data typically involves complex temporal dependencies between multiple variables. There, the transformer architecture, which has been highly successful in language and vision applications, allows us to account for the fact that the most recently observed time points in an individual's history may not always be the most important for the immediate future. This is achieved by assigning attention weights to observations of an individual based on a transformation of their values. One reason why these ideas have not yet been fully leveraged for longitudinal cohort data is that typically, large datasets are required. Therefore, we present a simplified transformer architecture that retains the core attention mechanism while reducing the number of parameters to be estimated, to be more suitable for small datasets with few time points. Guided by a statistical perspective on transformers, we use an autoregressive model as a starting point and incorporate attention as a kernel-based operation with temporal decay, where aggregation of multiple transformer heads, i.e. different candidate weighting schemes, is expressed as accumulating evidence on different types of underlying characteristics of individuals. This also enables a permutation-based statistical testing procedure for identifying contextual patterns. In a simulation study, the approach is shown to recover contextual dependencies even with a small number of individuals and time points. In an application to data from a resilience study, we identify temporal patterns in the dynamics of stress and mental health. This indicates that properly adapted transformers can not only achieve competitive predictive performance, but also uncover complex context dependencies in small data settings.

The Platonic Representation Hypothesis suggests that representations from neural networks are converging to a common statistical model of reality. We show that the existing metrics used to measure representational similarity are confounded by network scale: increasing model depth or width can systematically inflate representational similarity scores. To correct these effects, we introduce a permutation-based null-calibration framework that transforms any representational similarity metric into a calibrated score with statistical guarantees. We revisit the Platonic Representation Hypothesis with our calibration framework, which reveals a nuanced picture: the apparent convergence reported by global spectral measures largely disappears after calibration, while local neighborhood similarity, but not local distances, retains significant agreement across different modalities. Based on these findings, we propose the Aristotelian Representation Hypothesis: representations in neural networks are converging to shared local neighborhood relationships.