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Abstract Conformal prediction builds marginally valid prediction intervals that cover the unknown outcome of a randomly drawn test point with a prescribed probability. However, in practice, data-driven methods are often used to identify specific test unit(s) of interest, requiring uncertainty quantification tailored to these focal units. In such cases, marginally valid conformal prediction intervals may fail to provide valid coverage for the focal unit(s) due to selection bias. This article presents a general framework for constructing a prediction set with finite-sample exact coverage, conditional on the unit being selected by a given procedure. The general form of our method accommodates arbitrary selection rules that are invariant to the permutation of the calibration units and generalizes Mondrian Conformal Prediction to multiple test units and non-equivariant classifiers. We also work out computationally efficient implementation of our framework for a number of realistic selection rules, including top-K selection, optimization-based selection, selection based on conformal p-values, and selection based on properties of preliminary conformal prediction sets. The performance of our methods is demonstrated via applications in drug discovery and health risk prediction. 

Before deploying outputs from foundation models in high-stakes tasks, it is imperative to ensure that they align with human values. For instance, in radiology report generation, reports generated by a vision-language model must align with human evaluations before their use in medical decision-making. This paper presents Conformal Alignment, a general framework for identifying units whose outputs meet a user-specified alignment criterion. It is guaranteed that on average, a prescribed fraction of selected units indeed meet the alignment criterion, regardless of the foundation model or the data distribution. Given any pre-trained model and new units with model-generated outputs, Conformal Alignment leverages a set of reference data with ground-truth alignment status to train an alignment predictor. It then selects new units whose predicted alignment scores surpass a data-dependent threshold, certifying their corresponding outputs as trustworthy. Through applications to question answering and radiology report generation, we demonstrate that our method is able to accurately identify units with trustworthy outputs via lightweight training over a moderate amount of reference data. En route, we investigate the informativeness of various features in alignment prediction and combine them with standard models to construct the alignment predictor. 

Conformal prediction is a powerful tool for uncertainty quantification, but its application to time-series data is constrained by the violation of the exchangeability assumption. Current solutions for time-series prediction typically operate in the output space and rely on manually selected weights to address distribution drift, leading to overly conservative predictions. To enable dynamic weight learning in the semantically rich latent space, we introduce a novel approach called Conformalized Time Series with Semantic Features (CT-SSF). CT-SSF utilizes the inductive bias in deep representation learning to dynamically adjust weights, prioritizing semantic features relevant to the current prediction. Theoretically, we show that CT-SSF surpasses previous methods defined in the output space. Experiments on synthetic and benchmark datasets demonstrate that CT-SSF significantly outperforms existing state-of-the-art (SOTA) conformal prediction techniques in terms of prediction efficiency while maintaining a valid coverage guarantee. 

Summary This paper introduces an assumption-lean method that constructs valid and efficient lower predictive bounds for survival times with censored data. We build on recent work by Candès et al. (2023), whose approach first subsets the data to discard any data points with early censoring times and then uses a reweighting technique, namely, weighted conformal inference (Tibshirani et al., 2019), to correct for the distribution shift introduced by this subsetting procedure. For our new method, instead of constraining to a fixed threshold for the censoring time when subsetting the data, we allow for a covariate-dependent and data-adaptive subsetting step, which is better able to capture the heterogeneity of the censoring mechanism. As a result, our method can lead to lower predictive bounds that are less conservative and give more accurate information. We show that in the Type-I right-censoring setting, if either the censoring mechanism or the conditional quantile of the survival time is well estimated, our proposed procedure achieves nearly exact marginal coverage, where in the latter case we additionally have approximate conditional coverage. We evaluate the validity and efficiency of our proposed algorithm in numerical experiments, illustrating its advantage when compared with other competing methods. Finally, our method is applied to a real dataset to generate lower predictive bounds for users’ active times on a mobile app. 

Abstract In this paper, we develop an inferential method based on conformal prediction, which can wrap around any survival prediction algorithm to produce calibrated, covariate-dependent lower predictive bounds on survival times. In the Type I right-censoring setting, when the censoring times are completely exogenous, the lower predictive bounds have guaranteed coverage in finite samples without any assumptions other than that of operating on independent and identically distributed data points. Under a more general conditionally independent censoring assumption, the bounds satisfy a doubly robust property which states the following: marginal coverage is approximately guaranteed if either the censoring mechanism or the conditional survival function is estimated well. The validity and efficiency of our procedure are demonstrated on synthetic data and real COVID-19 data from the UK Biobank. 

We propose a model-free framework for sensitivity analysis of individual treatment effects (ITEs), building upon ideas from conformal inference. For any unit, our procedure reports the Γ-value, a number which quantifies the minimum strength of confounding needed to explain away the evidence for ITE. Our approach rests on the reliable predictive inference of counterfactuals and ITEs in situations where the training data are confounded. Under the marginal sensitivity model of [Z. Tan, J. Am. Stat. Assoc. 101, 1619-1637 (2006)], we characterize the shift between the distribution of the observations and that of the counterfactuals. We first develop a general method for predictive inference of test samples from a shifted distribution; we then leverage this to construct covariate-dependent prediction sets for counterfactuals. No matter the value of the shift, these prediction sets (resp. approximately) achieve marginal coverage if the propensity score is known exactly (resp. estimated). We describe a distinct procedure also attaining coverage, however, conditional on the training data. In the latter case, we prove a sharpness result showing that for certain classes of prediction problems, the prediction intervals cannot possibly be tightened. We verify the validity and performance of the methods via simulation studies and apply them to analyze real datasets. 

Abstract 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 associations in the data collected from minority populations, potentially opening the way to the development of more accurate polygenic risk scores.