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Matteo Sesia

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14 papers

2 author rows

ICML Conference 2025 Conference Paper

Doubly Robust Conformalized Survival Analysis with Right-Censored Data

Matteo Sesia
Vladimir Svetnik

We present a conformal inference method for constructing lower prediction bounds for survival times from right-censored data, extending recent approaches designed for more restrictive type-I censoring scenarios. The proposed method imputes unobserved censoring times using a machine learning model, and then analyzes the imputed data using a survival model calibrated via weighted conformal inference. This approach is theoretically supported by an asymptotic double robustness property. Empirical studies on simulated and real data demonstrate that our method leads to relatively informative predictive inferences and is especially robust in challenging settings where the survival model may be inaccurate.

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ICML Conference 2025 Conference Paper

Robust Conformal Outlier Detection under Contaminated Reference Data

Meshi Bashari
Matteo Sesia
Yaniv Romano

Conformal prediction is a flexible framework for calibrating machine learning predictions, providing distribution-free statistical guarantees. In outlier detection, this calibration relies on a reference set of labeled inlier data to control the type-I error rate. However, obtaining a perfectly labeled inlier reference set is often unrealistic, and a more practical scenario involves access to a contaminated reference set containing a small fraction of outliers. This paper analyzes the impact of such contamination on the validity of conformal methods. We prove that under realistic, non-adversarial settings, calibration on contaminated data yields conservative type-I error control, shedding light on the inherent robustness of conformal methods. This conservativeness, however, typically results in a loss of power. To alleviate this limitation, we propose a novel, active data-cleaning framework that leverages a limited labeling budget and an outlier detection model to selectively annotate data points in the contaminated reference set that are suspected as outliers. By removing only the annotated outliers in this “suspicious” subset, we can effectively enhance power while mitigating the risk of inflating the type-I error rate, as supported by our theoretical analysis. Experiments on real datasets validate the conservative behavior of conformal methods under contamination and show that the proposed data-cleaning strategy improves power without sacrificing validity.

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NeurIPS Conference 2024 Conference Paper

Conformal Classification with Equalized Coverage for Adaptively Selected Groups

Yanfei Zhou
Matteo Sesia

This paper introduces a conformal inference method to evaluate uncertainty in classification by generating prediction sets with valid coverage conditional on adaptively chosen features. These features are carefully selected to reflect potential model limitations or biases. This can be useful to find a practical compromise between efficiency---by providing informative predictions---and algorithmic fairness---by ensuring equalized coverage for the most sensitive groups. We demonstrate the validity and effectiveness of this method on simulated and real data sets.

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ICML Conference 2024 Conference Paper

Conformalized Adaptive Forecasting of Heterogeneous Trajectories

Yanfei Zhou
Lars Lindemann
Matteo Sesia

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.

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JMLR Journal 2024 Journal Article

Random measure priors in Bayesian recovery from sketches

Mario Beraha
Stefano Favaro
Matteo Sesia

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. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2024. ( edit, beta )

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JMLR Journal 2023 Journal Article

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

Matteo Sesia
Stefano Favaro
Edgar Dobriban

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. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2023. ( edit, beta )

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ICML Conference 2023 Conference Paper

Conformal Inference is (almost) Free for Neural Networks Trained with Early Stopping

Ziyi Liang
Yanfei Zhou
Matteo Sesia

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.

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NeurIPS Conference 2023 Conference Paper

Derandomized novelty detection with FDR control via conformal e-values

Meshi Bashari
Amir Epstein
Yaniv Romano
Matteo Sesia

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.

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NeurIPS Conference 2022 Conference Paper

Conformal Frequency Estimation with Sketched Data

Matteo Sesia
Stefano Favaro

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.

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ICML Conference 2022 Conference Paper

Coordinated Double Machine Learning

Nitai Fingerhut
Matteo Sesia
Yaniv Romano

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.

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JBHI Journal 2022 Journal Article

Interpretable Classification of Bacterial Raman Spectra With Knockoff Wavelets

Charmaine Chia
Matteo Sesia
Chi-Sing Ho
Stefanie S. Jeffrey
Jennifer Dionne
Emmanuel J. Candes
Roger T. Howe

Deep neural networks and other 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. This paper considers fast Raman spectroscopy data and demonstrates 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.

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NeurIPS Conference 2022 Conference Paper

Training Uncertainty-Aware Classifiers with Conformalized Deep Learning

Bat-Sheva Einbinder
Yaniv Romano
Matteo Sesia
Yanfei Zhou

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.

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NeurIPS Conference 2021 Conference Paper

Conformal Prediction using Conditional Histograms

Matteo Sesia
Yaniv Romano

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.

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NeurIPS Conference 2020 Conference Paper

Classification with Valid and Adaptive Coverage

Yaniv Romano
Matteo Sesia
Emmanuel Candes

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.

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