Stephen Bates

Cai Zhou, Zijie Chen, Zian Li et al.

Many generative tasks in chemistry and science involve distributions invariant to group symmetries (e.g., permutation and rotation). A common strategy enforces invariance and equivariance through architectural constraints such as equivariant denoisers and invariant priors. In this paper, we challenge this tradition through the alternative canonicalization perspective: first map each sample to an orbit representative with a canonical pose or order, train an unconstrained (non-equivariant) diffusion or flow model on the canonical slice, and finally recover the invariant distribution by sampling a random symmetry transform at generation time. Building on a formal quotient-space perspective, our work provides a comprehensive theory of canonical diffusion by proving: (i) the correctness, universality and superior expressivity of canonical generative models over invariant targets; (ii) canonicalization accelerates training by removing diffusion score complexity induced by group mixtures and reducing conditional variance in flow matching. We then show that aligned priors and optimal transport act complementarily with canonicalization and further improves training efficiency. We instantiate the framework for molecular graph generation under $S_n \times SE(3)$ symmetries. By leveraging geometric spectra-based canonicalization and mild positional encodings, canonical diffusion significantly outperforms equivariant baselines in 3D molecule generation tasks, with similar or even less computation. Moreover, with a novel architecture Canon, CanonFlow achieves state-of-the-art performance on the challenging GEOM-DRUG dataset, and the advantage remains large in few-step generation.

Kerri Lu, Dan M. Kluger, Stephen Bates et al.

Current instance segmentation models achieve high performance on average predictions, but lack principled uncertainty quantification: their outputs are not calibrated, and there is no guarantee that a predicted mask is close to the ground truth. To address this limitation, we introduce a conformal prediction algorithm to generate adaptive confidence sets for instance segmentation. Given an image and a pixel coordinate query, our algorithm generates a confidence set of instance predictions for that pixel, with a provable guarantee for the probability that at least one of the predictions has high Intersection-Over-Union (IoU) with the true object instance mask. We apply our algorithm to instance segmentation examples in agricultural field delineation, cell segmentation, and vehicle detection. Empirically, we find that our prediction sets vary in size based on query difficulty and attain the target coverage, outperforming existing baselines such as Learn Then Test, Conformal Risk Control, and morphological dilation-based methods. We provide versions of the algorithm with asymptotic and finite sample guarantees.

Haichen Hu, Rui Ai, Stephen Bates et al.

Contextual sequential decision-making problems play a crucial role in machine learning, encompassing a wide range of downstream applications such as bandits, sequential hypothesis testing and online risk control. These applications often require different statistical measures, including expectation, variance and quantiles. In this paper, we provide a universal admissible algorithm framework for dealing with all kinds of contextual online decision-making problems that directly learns the whole underlying unknown distribution instead of focusing on individual statistics. This is much more difficult because the dimension of the regression is uncountably infinite, and any existing linear contextual bandits algorithm will result in infinite regret. To overcome this issue, we propose an efficient infinite-dimensional functional regression oracle for contextual cumulative distribution functions (CDFs), where each data point is modeled as a combination of context-dependent CDF basis functions. Our analysis reveals that the decay rate of the eigenvalue sequence of the design integral operator governs the regression error rate and, consequently, the utility regret rate. Specifically, when the eigenvalue sequence exhibits a polynomial decay of order $\frac{1}γ\ge 1$, the utility regret is bounded by $\tilde{\mathcal{O}}\Big(T^{\frac{3γ+2}{2(γ+2)}}\Big)$. By setting $γ=0$, this recovers the existing optimal regret rate for contextual bandits with finite-dimensional regression and is optimal under a stronger exponential decay assumption. Additionally, we provide a numerical method to compute the eigenvalue sequence of the integral operator, enabling the practical implementation of our framework.

Shai Feldman, Stephen Bates, Yaniv Romano

We introduce a framework for robust uncertainty quantification in situations where labeled training data are corrupted, through noisy or missing labels. We build on conformal prediction, a statistical tool for generating prediction sets that cover the test label with a pre-specified probability. The validity of conformal prediction, however, holds under the i.i.d assumption, which does not hold in our setting due to the corruptions in the data. To account for this distribution shift, the privileged conformal prediction (PCP) method proposed leveraging privileged information (PI) -- additional features available only during training -- to re-weight the data distribution, yielding valid prediction sets under the assumption that the weights are accurate. In this work, we analyze the robustness of PCP to inaccuracies in the weights. Our analysis indicates that PCP can still yield valid uncertainty estimates even when the weights are poorly estimated. Furthermore, we introduce uncertain imputation (UI), a new conformal method that does not rely on weight estimation. Instead, we impute corrupted labels in a way that preserves their uncertainty. Our approach is supported by theoretical guarantees and validated empirically on both synthetic and real benchmarks. Finally, we show that these techniques can be integrated into a triply robust framework, ensuring statistically valid predictions as long as at least one underlying method is valid.

David R. Burt, Renato Berlinghieri, Stephen Bates et al.

Estimating associations between spatial covariates and responses - rather than merely predicting responses - is central to environmental science, epidemiology, and economics. For instance, public health officials might be interested in whether air pollution has a strictly positive association with a health outcome, and the magnitude of any effect. Standard machine learning methods often provide accurate predictions but offer limited insight into covariate-response relationships. And we show that existing methods for constructing confidence (or credible) intervals for associations can fail to provide nominal coverage in the face of model misspecification and nonrandom locations - despite both being essentially always present in spatial problems. We introduce a method that constructs valid frequentist confidence intervals for associations in spatial settings. Our method requires minimal assumptions beyond a form of spatial smoothness and a homoskedastic Gaussian error assumption. In particular, we do not require model correctness or covariate overlap between training and target locations. Our approach is the first to guarantee nominal coverage in this setting and outperforms existing techniques in both real and simulated experiments. Our confidence intervals are valid in finite samples when the noise of the Gaussian error is known, and we provide an asymptotically consistent estimation procedure for this noise variance when it is unknown.

Menghua Wu, Cai Zhou, Stephen Bates et al.

Reasoning large language models achieve impressive test-time scaling by thinking for longer, but this performance gain comes at significant compute cost. Directly limiting test-time budget hurts overall performance, but not all problems are equally difficult. We propose thought calibration to decide dynamically when thinking can be terminated. To calibrate our decision rule, we view a language model's growing body of thoughts as a nested sequence of reasoning trees, where the goal is to identify the point at which novel reasoning plateaus. We realize this framework through lightweight probes that operate on top of the language model's hidden representations, which are informative of both the reasoning structure and overall consistency of response. Based on three reasoning language models and four datasets, thought calibration preserves model performance with up to a 60% reduction in thinking tokens on in-distribution data, and up to 20% in out-of-distribution data.

Anastasios N. Angelopoulos, Stephen Bates, Emmanuel J. Candès et al.

We introduce a framework for calibrating machine learning models so that their predictions satisfy explicit, finite-sample statistical guarantees. Our calibration algorithms work with any underlying model and (unknown) data-generating distribution and do not require model refitting. The framework addresses, among other examples, false discovery rate control in multi-label classification, intersection-over-union control in instance segmentation, and the simultaneous control of the type-1 error of outlier detection and confidence set coverage in classification or regression. Our main insight is to reframe the risk-control problem as multiple hypothesis testing, enabling techniques and mathematical arguments different from those in the previous literature. We use the framework to provide new calibration methods for several core machine learning tasks, with detailed worked examples in computer vision and tabular medical data.

Anastasios N. Angelopoulos, Stephen Bates

Black-box machine learning models are now routinely used in high-risk settings, like medical diagnostics, which demand uncertainty quantification to avoid consequential model failures. Conformal prediction is a user-friendly paradigm for creating statistically rigorous uncertainty sets/intervals for the predictions of such models. Critically, the sets are valid in a distribution-free sense: they possess explicit, non-asymptotic guarantees even without distributional assumptions or model assumptions. One can use conformal prediction with any pre-trained model, such as a neural network, to produce sets that are guaranteed to contain the ground truth with a user-specified probability, such as 90%. It is easy-to-understand, easy-to-use, and general, applying naturally to problems arising in the fields of computer vision, natural language processing, deep reinforcement learning, and so on. This hands-on introduction is aimed to provide the reader a working understanding of conformal prediction and related distribution-free uncertainty quantification techniques with one self-contained document. We lead the reader through practical theory for and examples of conformal prediction and describe its extensions to complex machine learning tasks involving structured outputs, distribution shift, time-series, outliers, models that abstain, and more. Throughout, there are many explanatory illustrations, examples, and code samples in Python. With each code sample comes a Jupyter notebook implementing the method on a real-data example; the notebooks can be accessed and easily run using our codebase.

Celestine Mendler-Dünner, Wenshuo Guo, Stephen Bates et al.

An increasingly common setting in machine learning involves multiple parties, each with their own data, who want to jointly make predictions on future test points. Agents wish to benefit from the collective expertise of the full set of agents to make better predictions than they would individually, but may not be willing to release their data or model parameters. In this work, we explore a decentralized mechanism to make collective predictions at test time, leveraging each agent's pre-trained model without relying on external validation, model retraining, or data pooling. Our approach takes inspiration from the literature in social science on human consensus-making. We analyze our mechanism theoretically, showing that it converges to inverse meansquared-error (MSE) weighting in the large-sample limit. To compute error bars on the collective predictions we propose a decentralized Jackknife procedure that evaluates the sensitivity of our mechanism to a single agent's prediction. Empirically, we demonstrate that our scheme effectively combines models with differing quality across the input space. The proposed consensus prediction achieves significant gains over classical model averaging, and even outperforms weighted averaging schemes that have access to additional validation data.

Shai Feldman, Stephen Bates, Yaniv Romano

We develop a method to generate prediction intervals that have a user-specified coverage level across all regions of feature-space, a property called conditional coverage. A typical approach to this task is to estimate the conditional quantiles with quantile regression -- it is well-known that this leads to correct coverage in the large-sample limit, although it may not be accurate in finite samples. We find in experiments that traditional quantile regression can have poor conditional coverage. To remedy this, we modify the loss function to promote independence between the size of the intervals and the indicator of a miscoverage event. For the true conditional quantiles, these two quantities are independent (orthogonal), so the modified loss function continues to be valid. Moreover, we empirically show that the modified loss function leads to improved conditional coverage, as evaluated by several metrics. We also introduce two new metrics that check conditional coverage by looking at the strength of the dependence between the interval size and the indicator of miscoverage.

Stephen Bates, Trevor Hastie, Robert Tibshirani

Cross-validation is a widely-used technique to estimate prediction error, but its behavior is complex and not fully understood. Ideally, one would like to think that cross-validation estimates the prediction error for the model at hand, fit to the training data. We prove that this is not the case for the linear model fit by ordinary least squares; rather it estimates the average prediction error of models fit on other unseen training sets drawn from the same population. We further show that this phenomenon occurs for most popular estimates of prediction error, including data splitting, bootstrapping, and Mallow's Cp. Next, the standard confidence intervals for prediction error derived from cross-validation may have coverage far below the desired level. Because each data point is used for both training and testing, there are correlations among the measured accuracies for each fold, and so the usual estimate of variance is too small. We introduce a nested cross-validation scheme to estimate this variance more accurately, and we show empirically that this modification leads to intervals with approximately correct coverage in many examples where traditional cross-validation intervals fail.

Stephen Bates, Anastasios Angelopoulos, Lihua Lei et al.

While improving prediction accuracy has been the focus of machine learning in recent years, this alone does not suffice for reliable decision-making. Deploying learning systems in consequential settings also requires calibrating and communicating the uncertainty of predictions. To convey instance-wise uncertainty for prediction tasks, we show how to generate set-valued predictions from a black-box predictor that control the expected loss on future test points at a user-specified level. Our approach provides explicit finite-sample guarantees for any dataset by using a holdout set to calibrate the size of the prediction sets. This framework enables simple, distribution-free, rigorous error control for many tasks, and we demonstrate it in five large-scale machine learning problems: (1) classification problems where some mistakes are more costly than others; (2) multi-label classification, where each observation has multiple associated labels; (3) classification problems where the labels have a hierarchical structure; (4) image segmentation, where we wish to predict a set of pixels containing an object of interest; and (5) protein structure prediction. Lastly, we discuss extensions to uncertainty quantification for ranking, metric learning and distributionally robust learning.

Anastasios Angelopoulos, Stephen Bates, Jitendra Malik et al.

Convolutional image classifiers can achieve high predictive accuracy, but quantifying their uncertainty remains an unresolved challenge, hindering their deployment in consequential settings. Existing uncertainty quantification techniques, such as Platt scaling, attempt to calibrate the network's probability estimates, but they do not have formal guarantees. We present an algorithm that modifies any classifier to output a predictive set containing the true label with a user-specified probability, such as 90%. The algorithm is simple and fast like Platt scaling, but provides a formal finite-sample coverage guarantee for every model and dataset. Our method modifies an existing conformal prediction algorithm to give more stable predictive sets by regularizing the small scores of unlikely classes after Platt scaling. In experiments on both Imagenet and Imagenet-V2 with ResNet-152 and other classifiers, our scheme outperforms existing approaches, achieving coverage with sets that are often factors of 5 to 10 smaller than a stand-alone Platt scaling baseline.

Yaniv Romano, Stephen Bates, Emmanuel J. Candès

We present a flexible framework for learning predictive models that approximately satisfy the equalized odds notion of fairness. This is achieved by introducing a general discrepancy functional that rigorously quantifies violations of this criterion. This differentiable functional is used as a penalty driving the model parameters towards equalized odds. To rigorously evaluate fitted models, we develop a formal hypothesis test to detect whether a prediction rule violates this property, the first such test in the literature. Both the model fitting and hypothesis testing leverage a resampled version of the sensitive attribute obeying equalized odds, by construction. We demonstrate the applicability and validity of the proposed framework both in regression and multi-class classification problems, reporting improved performance over state-of-the-art methods. Lastly, we show how to incorporate techniques for equitable uncertainty quantification---unbiased for each group under study---to communicate the results of the data analysis in exact terms.