The Benjamini-Hochberg (BH) procedure is widely used to control the false detection rate (FDR) in multiple testing.

The Benjamini-Hochberg (BH) procedure is widely used to control the false detection rate (FDR) in multiple testing.

Maximum Mean Discrepancy (MMD) is a widely used concept in machine learning research which has gained popularity in recent years as a highly effective tool for comparing (finite-dimensional) distributions. Since it is designed as a kernel-based method, the MMD can be extended to path space valued distributions using the signature kernel. The resulting signature MMD (sig-MMD) can be used to define a metric between distributions on path space. Similarly to the original use case of the MMD as a test statistic within a two-sample testing framework, the sig-MMD can be applied to determine if two sets of paths are drawn from the same stochastic process. This work is dedicated to understanding the possibilities and challenges associated with applying the sig-MMD as a statistical tool in practice. We introduce and explain the sig-MMD, and provide easily accessible and verifiable examples for its practical use. We present examples that can lead to Type 2 errors in the hypothesis test, falsely indicating that samples have been drawn from the same underlying process (which generally occurs in a limited data setting). We then present techniques to mitigate the occurrence of this type of error.

The Benjamini-Hochberg (BH) procedure is widely used to control the false detection rate (FDR) in multiple testing. Applications of this control abound in drug discovery, forensics, anomaly detection, and, in particular, machine learning, ranging from nonparametric outlier detection to out-of-distribution detection and one-class classification methods. Considering this control could be relied upon in critical safety/security contexts, we investigate its adversarial robustness. More precisely, we study under what conditions BH does and does not exhibit adversarial robustness, we present a class of simple and easily implementable adversarial test-perturbation algorithms, and we perform computational experiments. With our algorithms, we demonstrate that there are conditions under which BH's control can be significantly broken with relatively few (even just one) test score perturbation(s), and provide non-asymptotic guarantees on the expected adversarial-adjustment to FDR. Our technical analysis involves a combinatorial reframing of the BH procedure as a ``balls into bins'' process, and drawing a connection to generalized ballot problems to facilitate an information-theoretic approach for deriving non-asymptotic lower bounds.

We consider the problem of quantifying how an input perturbation impacts the outputs of large language models (LLMs), a fundamental task for model reliability and post-hoc interpretability. A key obstacle in this domain is disentangling the meaningful changes in model responses from the intrinsic stochasticity of LLM outputs. To overcome this, we introduce Distribution-Based Perturbation Analysis (DBPA), a framework that reformulates LLM perturbation analysis as a frequentist hypothesis testing problem. DBPA constructs empirical null and alternative output distributions within a low-dimensional semantic similarity space via Monte Carlo sampling. Comparisons of Monte Carlo estimates in the reduced dimensionality space enables tractable frequentist inference without relying on restrictive distributional assumptions. The framework is model-agnostic, supports the evaluation of arbitrary input perturbations on any black-box LLM, yields interpretable p-values, supports multiple perturbation testing via controlled error rates, and provides scalar effect sizes for any chosen similarity or distance metric. We demonstrate the effectiveness of DBPA in evaluating perturbation impacts, showing its versatility for perturbation analysis.

Given a default distribution $P$ and a set of test data $x^M=\{x_1,x_2,\ldots,x_M\}$ this paper seeks to answer the question if it was likely that $x^M$ was generated by $P$. For discrete distributions, the definitive answer is in principle given by Kolmogorov-Martin-L\"{o}f randomness. In this paper we seek to generalize this to continuous distributions. We consider a set of statistics $T_1(x^M),T_2(x^M),\ldots$. To each statistic we associate its maximum entropy distribution and with this a universal source coder. The maximum entropy distributions are subsequently combined to give a total codelength, which is compared with $-\log P(x^M)$. We show that this approach satisfied a number of theoretical properties. For real world data $P$ usually is unknown. We transform data into a standard distribution in the latent space using a bidirectional generate network and use maximum entropy coding there. We compare the resulting method to other methods that also used generative neural networks to detect anomalies. In most cases, our results show better performance.

There has been a recent explosion in research into machine-learning-based generative modeling to tackle computational challenges for simulations in high energy physics (HEP). In order to use such alternative simulators in practice, we need well-defined metrics to compare different generative models and evaluate their discrepancy from the true distributions. We present the first systematic review and investigation into evaluation metrics and their sensitivity to failure modes of generative models, using the framework of two-sample goodness-of-fit testing, and their relevance and viability for HEP. Inspired by previous work in both physics and computer vision, we propose two new metrics, the Fr\'echet and kernel physics distances (FPD and KPD, respectively), and perform a variety of experiments measuring their performance on simple Gaussian-distributed, and simulated high energy jet datasets. We find FPD, in particular, to be the most sensitive metric to all alternative jet distributions tested and recommend its adoption, along with the KPD and Wasserstein distances between individual feature distributions, for evaluating generative models in HEP. We finally demonstrate the efficacy of these proposed metrics in evaluating and comparing a novel attention-based generative adversarial particle transformer to the state-of-the-art message-passing generative adversarial network jet simulation model. The code for our proposed metrics is provided in the open source JetNet Python library.

Controlling false discovery rate (FDR) while leveraging the side information of multiple hypothesis testing is an emerging research topic in modern data science. Existing methods rely on the test-level covariates while ignoring possible hierarchy among the covariates. This strategy may not be optimal for complex large-scale problems, where hierarchical information often exists among those test-level covariates. We propose NeurT-FDR which boosts statistical power and controls FDR for multiple hypothesis testing while leveraging the hierarchy among test-level covariates. Our method parametrizes the test-level covariates as a neural network and adjusts the feature hierarchy through a regression framework, which enables flexible handling of high-dimensional features as well as efficient end-to-end optimization. We show that NeurT-FDR has strong FDR guarantees and makes substantially more discoveries in synthetic and real datasets compared to competitive baselines.

Analyzing large-scale, multi-experiment studies requires scientists to test each experimental outcome for statistical significance and then assess the results as a whole. We present Black Box FDR (BB-FDR), an empirical-Bayes method for analyzing multi-experiment studies when many covariates are gathered per experiment. BB-FDR learns a series of black box predictive models to boost power and control the false discovery rate (FDR) at two stages of study analysis. In Stage 1, it uses a deep neural network prior to report which experiments yielded significant outcomes. In Stage 2, a separate black box model of each covariate is used to select features that have significant predictive power across all experiments. In benchmarks, BB-FDR outperforms competing state-of-the-art methods in both stages of analysis. We apply BB-FDR to two real studies on cancer drug efficacy. For both studies, BB-FDR increases the proportion of significant outcomes discovered and selects variables that reveal key genomic drivers of drug sensitivity and resistance in cancer.