arXiv subjects

Matteo Sesia

Publications and source records attributed to Matteo Sesia.

At least 37 records · Page 2Linked to original sources

arXiv2024

Random measure priors in Bayesian recovery from sketches

This paper introduces a Bayesian nonparametric approach to frequency recovery from lossy-compressed discrete data, leveraging all information contained in a sketch obtained through random hashing. By modeling the data points as random samples from an unknown discrete distribution endowed with a Poisson-Kingman prior, we derive the posterior distribution of a symbol's empirical frequency given the sketch. This leads to principled frequency estimates through mean functionals, e.g., the posterior mean, median and mode. We highlight applications of this general result to Dirichlet process and Pitman-Yor process priors. Notably, we prove that the former prior uniquely satisfies a sufficiency property that simplifies the posterior distribution, while the latter enables a convenient large-sample asymptotic approximation. Additionally, we extend our approach to the problem of cardinality recovery, estimating the number of distinct symbols in the sketched dataset. Our approach to frequency recovery also adapts to a more general ``traits'' setting, where each data point has integer levels of association with multiple symbols, typically referred to as ``traits''. By employing a generalized Indian buffet process, we compute the posterior distribution of a trait's frequency using both the Poisson and Bernoulli distributions for the trait association levels, respectively yielding exact and approximate posterior frequency distributions.

math.ST↗

arXiv2024

Conformalized Adaptive Forecasting of Heterogeneous Trajectories

This paper presents a new conformal method for generating simultaneous forecasting bands guaranteed to cover the entire path of a new random trajectory with sufficiently high probability. Prompted by the need for dependable uncertainty estimates in motion planning applications where the behavior of diverse objects may be more or less unpredictable, we blend different techniques from online conformal prediction of single and multiple time series, as well as ideas for addressing heteroscedasticity in regression. This solution is both principled, providing precise finite-sample guarantees, and effective, often leading to more informative predictions than prior methods.

stat.ML↗

arXiv2024

Adaptive conformal classification with noisy labels

This paper develops novel conformal prediction methods for classification tasks that can automatically adapt to random label contamination in the calibration sample, leading to more informative prediction sets with stronger coverage guarantees compared to state-of-the-art approaches. This is made possible by a precise characterization of the effective coverage inflation (or deflation) suffered by standard conformal inferences in the presence of label contamination, which is then made actionable through new calibration algorithms. Our solution is flexible and can leverage different modeling assumptions about the label contamination process, while requiring no knowledge of the underlying data distribution or of the inner workings of the machine-learning classifier. The advantages of the proposed methods are demonstrated through extensive simulations and an application to object classification with the CIFAR-10H image data set.

stat.ME↗

arXiv2023

Derandomized Novelty Detection with FDR Control via Conformal E-values

Conformal inference provides a general distribution-free method to rigorously calibrate the output of any machine learning algorithm for novelty detection. While this approach has many strengths, it has the limitation of being randomized, in the sense that it may lead to different results when analyzing twice the same data, and this can hinder the interpretation of any findings. We propose to make conformal inferences more stable by leveraging suitable conformal e-values instead of p-values to quantify statistical significance. This solution allows the evidence gathered from multiple analyses of the same data to be aggregated effectively while provably controlling the false discovery rate. Further, we show that the proposed method can reduce randomness without much loss of power compared to standard conformal inference, partly thanks to an innovative way of weighting conformal e-values based on additional side information carefully extracted from the same data. Simulations with synthetic and real data confirm this solution can be effective at eliminating random noise in the inferences obtained with state-of-the-art alternative techniques, sometimes also leading to higher power.

cs.LG↗

arXiv2023

Searching for subgroup-specific associations while controlling the false discovery rate

This paper introduces an innovative method for conducting conditional independence testing in high-dimensional data, facilitating the automated discovery of significant associations within distinct subgroups of a population, all while controlling the false discovery rate. This is achieved by expanding upon the model-X knockoff filter to provide more informative inferences. Our enhanced inferences can help explain sample heterogeneity and uncover interactions, making better use of the capabilities offered by modern machine learning models. Specifically, our method is able to leverage any model for the identification of data-driven hypotheses pertaining to interesting population subgroups. Then, it rigorously test these hypotheses without succumbing to selection bias. Importantly, our approach is efficient and does not require sample splitting. We demonstrate the effectiveness of our method through simulations and numerical experiments, using data derived from a randomized experiment featuring multiple treatment variables.

stat.ME↗

arXiv2023

Conformal Frequency Estimation using Discrete Sketched Data with Coverage for Distinct Queries

This paper develops conformal inference methods to construct a confidence interval for the frequency of a queried object in a very large discrete data set, based on a sketch with a lower memory footprint. This approach requires no knowledge of the data distribution and can be combined with any sketching algorithm, including but not limited to the renowned count-min sketch, the count-sketch, and variations thereof. After explaining how to achieve marginal coverage for exchangeable random queries, we extend our solution to provide stronger inferences that can account for the discreteness of the data and for heterogeneous query frequencies, increasing also robustness to possible distribution shifts. These results are facilitated by a novel conformal calibration technique that guarantees valid coverage for a large fraction of distinct random queries. Finally, we show our methods have improved empirical performance compared to existing frequentist and Bayesian alternatives in simulations as well as in examples of text and SARS-CoV-2 DNA data.

stat.ME↗

arXiv2023

Conformal inference is (almost) free for neural networks trained with early stopping

Early stopping based on hold-out data is a popular regularization technique designed to mitigate overfitting and increase the predictive accuracy of neural networks. Models trained with early stopping often provide relatively accurate predictions, but they generally still lack precise statistical guarantees unless they are further calibrated using independent hold-out data. This paper addresses the above limitation with conformalized early stopping: a novel method that combines early stopping with conformal calibration while efficiently recycling the same hold-out data. This leads to models that are both accurate and able to provide exact predictive inferences without multiple data splits nor overly conservative adjustments. Practical implementations are developed for different learning tasks -- outlier detection, multi-class classification, regression -- and their competitive performance is demonstrated on real data.

stat.ML↗

arXiv2022

Conformal Frequency Estimation with Sketched Data

A flexible conformal inference method is developed to construct confidence intervals for the frequencies of queried objects in very large data sets, based on a much smaller sketch of those data. The approach is data-adaptive and requires no knowledge of the data distribution or of the details of the sketching algorithm; instead, it constructs provably valid frequentist confidence intervals under the sole assumption of data exchangeability. Although our solution is broadly applicable, this paper focuses on applications involving the count-min sketch algorithm and a non-linear variation thereof. The performance is compared to that of frequentist and Bayesian alternatives through simulations and experiments with data sets of SARS-CoV-2 DNA sequences and classic English literature.

stat.ME↗

arXiv2022

Training Uncertainty-Aware Classifiers with Conformalized Deep Learning

Deep neural networks are powerful tools to detect hidden patterns in data and leverage them to make predictions, but they are not designed to understand uncertainty and estimate reliable probabilities. In particular, they tend to be overconfident. We begin to address this problem in the context of multi-class classification by developing a novel training algorithm producing models with more dependable uncertainty estimates, without sacrificing predictive power. The idea is to mitigate overconfidence by minimizing a loss function, inspired by advances in conformal inference, that quantifies model uncertainty by carefully leveraging hold-out data. Experiments with synthetic and real data demonstrate this method can lead to smaller conformal prediction sets with higher conditional coverage, after exact calibration with hold-out data, compared to state-of-the-art alternatives.

stat.ML↗

arXiv2022

Bayesian nonparametric estimation of coverage probabilities and distinct counts from sketched data

The estimation of coverage probabilities, and in particular of the missing mass, is a classical statistical problem with applications in numerous scientific fields. In this paper, we study this problem in relation to randomized data compression, or sketching. This is a novel but practically relevant perspective, and it refers to situations in which coverage probabilities must be estimated based on a compressed and imperfect summary, or sketch, of the true data, because neither the full data nor the empirical frequencies of distinct symbols can be observed directly. Our contribution is a Bayesian nonparametric methodology to estimate coverage probabilities from data sketched through random hashing, which also solves the challenging problems of recovering the numbers of distinct counts in the true data and of distinct counts with a specified empirical frequency of interest. The proposed Bayesian estimators are shown to be easily applicable to large-scale analyses in combination with a Dirichlet process prior, although they involve some open computational challenges under the more general Pitman-Yor process prior. The empirical effectiveness of our methodology is demonstrated through numerical experiments and applications to real data sets of Covid DNA sequences, classic English literature, and IP addresses.

stat.ME↗

arXiv2022

Integrative conformal p-values for powerful out-of-distribution testing with labeled outliers

This paper develops novel conformal methods to test whether a new observation was sampled from the same distribution as a reference set. Blending inductive and transductive conformal inference in an innovative way, the described methods can re-weight standard conformal p-values based on dependent side information from known out-of-distribution data in a principled way, and can automatically take advantage of the most powerful model from any collection of one-class and binary classifiers. The solution can be implemented either through sample splitting or via a novel transductive cross-validation+ scheme which may also be useful in other applications of conformal inference, due to tighter guarantees compared to existing cross-validation approaches. After studying false discovery rate control and power within a multiple testing framework with several possible outliers, the proposed solution is shown to outperform standard conformal p-values through simulations as well as applications to image recognition and tabular data.

stat.ME↗

arXiv2022

Coordinated Double Machine Learning

Double machine learning is a statistical method for leveraging complex black-box models to construct approximately unbiased treatment effect estimates given observational data with high-dimensional covariates, under the assumption of a partially linear model. The idea is to first fit on a subset of the samples two non-linear predictive models, one for the continuous outcome of interest and one for the observed treatment, and then to estimate a linear coefficient for the treatment using the remaining samples through a simple orthogonalized regression. While this methodology is flexible and can accommodate arbitrary predictive models, typically trained independently of one another, this paper argues that a carefully coordinated learning algorithm for deep neural networks may reduce the estimation bias. The improved empirical performance of the proposed method is demonstrated through numerical experiments on both simulated and real data.

stat.ML↗

arXiv2022

Testing for Outliers with Conformal p-values

This paper studies the construction of p-values for nonparametric outlier detection, taking a multiple-testing perspective. The goal is to test whether new independent samples belong to the same distribution as a reference data set or are outliers. We propose a solution based on conformal inference, a broadly applicable framework which yields p-values that are marginally valid but mutually dependent for different test points. We prove these p-values are positively dependent and enable exact false discovery rate control, although in a relatively weak marginal sense. We then introduce a new method to compute p-values that are both valid conditionally on the training data and independent of each other for different test points; this paves the way to stronger type-I error guarantees. Our results depart from classical conformal inference as we leverage concentration inequalities rather than combinatorial arguments to establish our finite-sample guarantees. Furthermore, our techniques also yield a uniform confidence bound for the false positive rate of any outlier detection algorithm, as a function of the threshold applied to its raw statistics. Finally, the relevance of our results is demonstrated by numerical experiments on real and simulated data.

stat.ME↗

arXiv2021

Conformal Prediction using Conditional Histograms

This paper develops a conformal method to compute prediction intervals for non-parametric regression that can automatically adapt to skewed data. Leveraging black-box machine learning algorithms to estimate the conditional distribution of the outcome using histograms, it translates their output into the shortest prediction intervals with approximate conditional coverage. The resulting prediction intervals provably have marginal coverage in finite samples, while asymptotically achieving conditional coverage and optimal length if the black-box model is consistent. Numerical experiments with simulated and real data demonstrate improved performance compared to state-of-the-art alternatives, including conformalized quantile regression and other distributional conformal prediction approaches.

stat.ME↗

arXiv2021

Transfer learning in genome-wide association studies with knockoffs

This paper presents and compares alternative transfer learning methods that can increase the power of conditional testing via knockoffs by leveraging prior information in external data sets collected from different populations or measuring related outcomes. The relevance of this methodology is explored in particular within the context of genome-wide association studies, where it can be helpful to address the pressing need for principled ways to suitably account for, and efficiently learn from the genetic variation associated to diverse ancestries. Finally, we apply these methods to analyze several phenotypes in the UK Biobank data set, demonstrating that transfer learning helps knockoffs discover more numerous associations in the data collected from minority populations, potentially opening the way to the development of more accurate polygenic risk scores.

stat.AP↗

arXiv2021

Searching for consistent associations with a multi-environment knockoff filter

This paper develops a method based on model-X knockoffs to find conditional associations that are consistent across diverse environments, controlling the false discovery rate. The motivation for this problem is that large data sets may contain numerous associations that are statistically significant and yet misleading, as they are induced by confounders or sampling imperfections. However, associations consistently replicated under different conditions may be more interesting. In fact, consistency sometimes provably leads to valid causal inferences even if conditional associations do not. While the proposed method is flexible and can be deployed in a wide range of applications, this paper highlights its relevance to genome-wide association studies, in which consistency across populations with diverse ancestries mitigates confounding due to unmeasured variants. The effectiveness of this approach is demonstrated by simulations and applications to the UK Biobank data.

stat.ME↗

arXiv2021

Interpretable Classification of Bacterial Raman Spectra with Knockoff Wavelets

Deep neural networks and other sophisticated machine learning models are widely applied to biomedical signal data because they can detect complex patterns and compute accurate predictions. However, the difficulty of interpreting such models is a limitation, especially for applications involving high-stakes decision, including the identification of bacterial infections. In this paper, we consider fast Raman spectroscopy data and demonstrate that a logistic regression model with carefully selected features achieves accuracy comparable to that of neural networks, while being much simpler and more transparent. Our analysis leverages wavelet features with intuitive chemical interpretations, and performs controlled variable selection with knockoffs to ensure the predictors are relevant and non-redundant. Although we focus on a particular data set, the proposed approach is broadly applicable to other types of signal data for which interpretability may be important.

eess.SP↗

arXiv2020

Classification with Valid and Adaptive Coverage

Conformal inference, cross-validation+, and the jackknife+ are hold-out methods that can be combined with virtually any machine learning algorithm to construct prediction sets with guaranteed marginal coverage. In this paper, we develop specialized versions of these techniques for categorical and unordered response labels that, in addition to providing marginal coverage, are also fully adaptive to complex data distributions, in the sense that they perform favorably in terms of approximate conditional coverage compared to alternative methods. The heart of our contribution is a novel conformity score, which we explicitly demonstrate to be powerful and intuitive for classification problems, but whose underlying principle is potentially far more general. Experiments on synthetic and real data demonstrate the practical value of our theoretical guarantees, as well as the statistical advantages of the proposed methods over the existing alternatives.

stat.ME↗