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Current statistical methods in differential proteomics analysis generally leave aside several challenges, such as missing values, correlations between peptide intensities and uncertainty quantification. Moreover, they provide point estimates, such as the mean intensity for a given peptide or protein in a given condition. The decision of whether an analyte should be considered as differential is then based on comparing the p-value to a significance threshold, usually 5%. In the state-of-the-art limma approach, a hierarchical model is used to deduce the posterior distribution of the variance estimator for each analyte. The expectation of this distribution is then used as a moderated estimation of variance and is injected directly into the expression of the t-statistic. However, instead of merely relying on the moderated estimates, we could provide more powerful and intuitive results by leveraging a fully Bayesian approach and hence allow the quantification of uncertainty. The present work introduces this idea by taking advantage of standard results from Bayesian inference with conjugate priors in hierarchical models to derive a methodology tailored to handle multiple imputation contexts. Furthermore, we aim to tackle a more general problem of multivariate differential analysis, to account for possible inter-peptide correlations. By defining a hierarchical model with prior distributions on both mean and variance parameters, we achieve a global quantification of uncertainty for differential analysis. The inference is thus performed by computing the posterior distribution for the difference in mean peptide intensities between two experimental conditions. In contrast to more flexible models that can be achieved with hierarchical structures, our choice of conjugate priors maintains analytical expressions for direct sampling from posterior distributions without requiring expensive MCMC methods.

Causal phenomena associated with rare events occur across a wide range of engineering problems, such as risk-sensitive safety analysis, accident analysis and prevention, and extreme value theory. However, current methods for causal discovery are often unable to uncover causal links, between random variables in a dynamic setting, that manifest only when the variables first experience low-probability realizations. To address this issue, we introduce a novel statistical independence test on data collected from time-invariant dynamical systems in which rare but consequential events occur. In particular, we exploit the time-invariance of the underlying data to construct a superimposed dataset of the system state before rare events happen at different timesteps. We then design a conditional independence test on the reorganized data. We provide non-asymptotic sample complexity bounds for the consistency of our method, and validate its performance across various simulated and real-world datasets, including incident data collected from the Caltrans Performance Measurement System (PeMS). Code containing the datasets and experiments is publicly available.

Developing and deploying machine learning models safely depends on the ability to characterize and compare their abilities to generalize to new environments. Although recent work has proposed a variety of methods that can directly predict or theoretically bound the generalization capacity of a model, they rely on strong assumptions such as matching train/test distributions and access to model gradients. In order to characterize generalization when these assumptions are not satisfied, we propose neighborhood invariance, a measure of a classifier's output invariance in a local transformation neighborhood. Specifically, we sample a set of transformations and given an input test point, calculate the invariance as the largest fraction of transformed points classified into the same class. Crucially, our measure is simple to calculate, does not depend on the test point's true label, makes no assumptions about the data distribution or model, and can be applied even in out-of-domain (OOD) settings where existing methods cannot, requiring only selecting a set of appropriate data transformations. In experiments on robustness benchmarks in image classification, sentiment analysis, and natural language inference, we demonstrate a strong and robust correlation between our neighborhood invariance measure and actual OOD generalization on over 4,600 models evaluated on over 100 unique train/test domain pairs.

We show how to find all $k$ marked elements in a list of size $N$ using the optimal number $O(\sqrt{N k})$ of quantum queries and only a polylogarithmic overhead in the gate complexity, in the setting where one has a small quantum memory. Previous algorithms either incurred a factor $k$ overhead in the gate complexity, or had an extra factor $\log(k)$ in the query complexity. We then consider the problem of finding a multiplicative $\delta$-approximation of $s = \sum_{i=1}^N v_i$ where $v=(v_i) \in [0,1]^N$, given quantum query access to a binary description of $v$. We give an algorithm that does so, with probability at least $1-\rho$, using $O(\sqrt{N \log(1/\rho) / \delta})$ quantum queries (under mild assumptions on $\rho$). This quadratically improves the dependence on $1/\delta$ and $\log(1/\rho)$ compared to a straightforward application of amplitude estimation. To obtain the improved $\log(1/\rho)$ dependence we use the first result.

Randomized trials balance all covariates on average and provide the gold standard for estimating treatment effects. Chance imbalances nevertheless exist more or less in realized treatment allocations and intrigue an important question: what should we do in case the treatment groups differ with respect to some important baseline characteristics? A common strategy is to conduct a {\it preliminary test} of the balance of baseline covariates after randomization, and invoke covariate adjustment for subsequent inference if and only if the realized allocation fails some prespecified criterion. Although such practice is intuitive and popular among practitioners, the existing literature has so far only evaluated its properties under strong parametric model assumptions in theory and simulation, yielding results of limited generality. To fill this gap, we examine two strategies for conducting preliminary test-based covariate adjustment by regression, and evaluate the validity and efficiency of the resulting inferences from the randomization-based perspective. As it turns out, the preliminary-test estimator based on the analysis of covariance can be even less efficient than the unadjusted difference in means, and risks anticonservative confidence intervals based on normal approximation even with the robust standard error. The preliminary-test estimator based on the fully interacted specification is on the other hand less efficient than its counterpart under the {\it always-adjust} strategy, and yields overconservative confidence intervals based on normal approximation. Based on theory and simulation, we echo the existing literature and do not recommend the preliminary-test procedure for covariate adjustment in randomized trials.

With the increasing availability of datasets, developing data fusion methods to leverage the strengths of different datasets to draw causal effects is of great practical importance to many scientific fields. In this paper, we consider estimating the quantile treatment effects using small validation data with fully-observed confounders and large auxiliary data with unmeasured confounders. We propose a Fused Quantile Treatment effects Estimator (FQTE) by integrating the information from two datasets based on doubly robust estimating functions. We allow for the misspecification of the models on the dataset with unmeasured confounders. Under mild conditions, we show that the proposed FQTE is asymptotically normal and more efficient than the initial QTE estimator using the validation data solely. By establishing the asymptotic linear forms of related estimators, convenient methods for covariance estimation are provided. Simulation studies demonstrate the empirical validity and improved efficiency of our fused estimators. We illustrate the proposed method with an application.

The criticality problem in nuclear engineering asks for the principal eigen-pair of a Boltzmann operator describing neutron transport in a reactor core. Being able to reliably design, and control such reactors requires assessing these quantities within quantifiable accuracy tolerances. In this paper we propose a paradigm that deviates from the common practice of approximately solving the corresponding spectral problem with a fixed, presumably sufficiently fine discretization. Instead, the present approach is based on first contriving iterative schemes, formulated in function space, that are shown to converge at a quantitative rate without assuming any a priori excess regularity properties, and that exploit only properties of the optical parameters in the underlying radiative transfer model. We develop the analytical and numerical tools for approximately realizing each iteration step withing judiciously chosen accuracy tolerances, verified by a posteriori estimates, so as to still warrant quantifiable convergence to the exact eigen-pair. This is carried out in full first for a Newton scheme. Since this is only locally convergent we analyze in addition the convergence of a power iteration in function space to produce sufficiently accurate initial guesses. Here we have to deal with intrinsic difficulties posed by compact but unsymmetric operators preventing standard arguments used in the finite dimensional case. Our main point is that we can avoid any condition on an initial guess to be already in a small neighborhood of the exact solution. We close with a discussion of remaining intrinsic obstructions to a certifiable numerical implementation, mainly related to not knowing the gap between the principal eigenvalue and the next smaller one in modulus.

The Shapley value is arguably the most popular approach for assigning a meaningful contribution value to players in a cooperative game, which has recently been used intensively in explainable artificial intelligence. The meaningfulness is due to axiomatic properties that only the Shapley value satisfies, which, however, comes at the expense of an exact computation growing exponentially with the number of agents. Accordingly, a number of works are devoted to the efficient approximation of the Shapley values, most of them revolve around the notion of an agent's marginal contribution. In this paper, we propose with SVARM and Stratified SVARM two parameter-free and domain-independent approximation algorithms based on a representation of the Shapley value detached from the notion of marginal contributions. We prove unmatched theoretical guarantees regarding their approximation quality and provide empirical results including synthetic games as well as common explainability use cases comparing ourselves with state-of-the-art methods.

The goal of explainable Artificial Intelligence (XAI) is to generate human-interpretable explanations, but there are no computationally precise theories of how humans interpret AI generated explanations. The lack of theory means that validation of XAI must be done empirically, on a case-by-case basis, which prevents systematic theory-building in XAI. We propose a psychological theory of how humans draw conclusions from saliency maps, the most common form of XAI explanation, which for the first time allows for precise prediction of explainee inference conditioned on explanation. Our theory posits that absent explanation humans expect the AI to make similar decisions to themselves, and that they interpret an explanation by comparison to the explanations they themselves would give. Comparison is formalized via Shepard's universal law of generalization in a similarity space, a classic theory from cognitive science. A pre-registered user study on AI image classifications with saliency map explanations demonstrate that our theory quantitatively matches participants' predictions of the AI.

This paper focuses on the expected difference in borrower's repayment when there is a change in the lender's credit decisions. Classical estimators overlook the confounding effects and hence the estimation error can be magnificent. As such, we propose another approach to construct the estimators such that the error can be greatly reduced. The proposed estimators are shown to be unbiased, consistent, and robust through a combination of theoretical analysis and numerical testing. Moreover, we compare the power of estimating the causal quantities between the classical estimators and the proposed estimators. The comparison is tested across a wide range of models, including linear regression models, tree-based models, and neural network-based models, under different simulated datasets that exhibit different levels of causality, different degrees of nonlinearity, and different distributional properties. Most importantly, we apply our approaches to a large observational dataset provided by a global technology firm that operates in both the e-commerce and the lending business. We find that the relative reduction of estimation error is strikingly substantial if the causal effects are accounted for correctly.