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Stephen Bates

Stephen Bates contributes to research discovery and scholarly infrastructure.

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Published work

8 published item(s)

preprint2026arXiv

Causal Inference with Categorical Unobserved Confounder via Mixture Learning

Unobserved confounding is a fundamental challenge for estimating causal effects. To address unobserved confounding, recent literature has turned to two different approaches -- proxy variables and the use of multiple treatments. The first approach, commonly referred to as proximal causal inference, requires proxies to be assigned to specific asymmetric roles: treatment-inducing proxies (negative control exposures), variables that act as common causes of the treatment and outcome, and outcome-inducing proxies (negative control outcomes). In practice, however, identifying variables that satisfy these asymmetric roles can be difficult depending on the application domain. The second approach, commonly referred to as the ``Deconfounder," deals with multiple conditionally independent treatments. There has been limited progress towards developing a consistent estimation method for this setting. As the primary contribution of this work, we establish that causal effects are identifiable in both settings when the unobserved confounder is categorical under suitable conditions. Our approach builds on a mixture learning perspective: we show that the underlying confounding structure can be recovered by identifying the corresponding mixture distribution. We propose an estimation procedure based on tensor decomposition, which allows consistent recovery of the latent structure and comes with non-asymptotic guarantees. Simulation studies and real data experiments demonstrate that the proposed method performs well even with limited data.

preprint2026arXiv

Isotonic Survival Regression: Calibrated Survival Distributions from Deep Cox Models

Time-to-event data is widespread across the life sciences and engineering, but it is typically encountered together with censoring, which complicates the application of standard machine learning methods. Deep Cox models have emerged as a popular method for analyzing time-to-event data because they gracefully handle censoring and can be used with unstructured data such as clinical text reports, genomic sequences, and pathology images. However, their predicted survival probabilities are often poorly calibrated, thus limiting their practical utility. In this paper, we propose a novel post hoc calibration method for Deep Cox models that uses isotonic regression to refine predicted survival probabilities without affecting discriminative power. We establish favorable theoretical guarantees, including a double-robustness property and asymptotic calibration. Experiments on synthetic and real-world clinical data demonstrate the empirical effectiveness of our method.

preprint2022arXiv

Confidence Intervals for the Generalisation Error of Random Forests

Out-of-bag error is commonly used as an estimate of generalisation error in ensemble-based learning models such as random forests. We present confidence intervals for this quantity using the delta-method-after-bootstrap and the jackknife-after-bootstrap techniques. These methods do not require growing any additional trees. We show that these new confidence intervals have improved coverage properties over the naive confidence interval, in real and simulated examples.

preprint2022arXiv

Image-to-Image Regression with Distribution-Free Uncertainty Quantification and Applications in Imaging

Image-to-image regression is an important learning task, used frequently in biological imaging. Current algorithms, however, do not generally offer statistical guarantees that protect against a model's mistakes and hallucinations. To address this, we develop uncertainty quantification techniques with rigorous statistical guarantees for image-to-image regression problems. In particular, we show how to derive uncertainty intervals around each pixel that are guaranteed to contain the true value with a user-specified confidence probability. Our methods work in conjunction with any base machine learning model, such as a neural network, and endow it with formal mathematical guarantees -- regardless of the true unknown data distribution or choice of model. Furthermore, they are simple to implement and computationally inexpensive. We evaluate our procedure on three image-to-image regression tasks: quantitative phase microscopy, accelerated magnetic resonance imaging, and super-resolution transmission electron microscopy of a Drosophila melanogaster brain.

preprint2022arXiv

Recommendation Systems with Distribution-Free Reliability Guarantees

When building recommendation systems, we seek to output a helpful set of items to the user. Under the hood, a ranking model predicts which of two candidate items is better, and we must distill these pairwise comparisons into the user-facing output. However, a learned ranking model is never perfect, so taking its predictions at face value gives no guarantee that the user-facing output is reliable. Building from a pre-trained ranking model, we show how to return a set of items that is rigorously guaranteed to contain mostly good items. Our procedure endows any ranking model with rigorous finite-sample control of the false discovery rate (FDR), regardless of the (unknown) data distribution. Moreover, our calibration algorithm enables the easy and principled integration of multiple objectives in recommender systems. As an example, we show how to optimize for recommendation diversity subject to a user-specified level of FDR control, circumventing the need to specify ad hoc weights of a diversity loss against an accuracy loss. Throughout, we focus on the problem of learning to rank a set of possible recommendations, evaluating our methods on the Yahoo! Learning to Rank and MSMarco datasets.

preprint2022arXiv

Robust Calibration with Multi-domain Temperature Scaling

Uncertainty quantification is essential for the reliable deployment of machine learning models to high-stakes application domains. Uncertainty quantification is all the more challenging when training distribution and test distribution are different, even the distribution shifts are mild. Despite the ubiquity of distribution shifts in real-world applications, existing uncertainty quantification approaches mainly study the in-distribution setting where the train and test distributions are the same. In this paper, we develop a systematic calibration model to handle distribution shifts by leveraging data from multiple domains. Our proposed method -- multi-domain temperature scaling -- uses the heterogeneity in the domains to improve calibration robustness under distribution shift. Through experiments on three benchmark data sets, we find our proposed method outperforms existing methods as measured on both in-distribution and out-of-distribution test sets.

preprint2022arXiv

Uncertainty Sets for Image Classifiers using Conformal Prediction

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.

preprint2020arXiv

Achieving Equalized Odds by Resampling Sensitive Attributes

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.