CountsDiff: A Diffusion Model on the Natural Numbers for Generation and Imputation of Count-Based Data

Diffusion models have excelled at generative tasks for both continuous and token-based domains, but their application to discrete ordinal data remains underdeveloped. We present CountsDiff, a diffusion framework designed to natively model distributions on the natural numbers. CountsDiff extends the Blackout diffusion framework by simplifying its formulation through a direct parameterization in terms of a survival probability schedule and an explicit loss weighting. This introduces flexibility through design parameters with direct analogues in existing diffusion modeling frameworks. Beyond this reparameterization, CountsDiff introduces features from modern diffusion models, previously absent in counts-based domains, including continuous-time training, classifier-free guidance, and churn/remasking reverse dynamics that allow non-monotone reverse trajectories. We propose an initial instantiation of CountsDiff and validate it on natural image datasets (CIFAR-10, CelebA), exploring the effects of varying the introduced design parameters in a complex, well-studied, and interpretable data domain. We then highlight biological count assays as a natural use case, evaluating CountsDiff on single-cell RNA-seq imputation in a fetal cell and heart cell atlas. Remarkably, we find that even this simple instantiation matches or surpasses the performance of a state-of-the-art discrete generative model and leading RNA-seq imputation methods, while leaving substantial headroom for further gains through optimized design choices in future work.

Online Reasoning Calibration: Test-Time Training Enables Generalizable Conformal LLM Reasoning

While test-time scaling has enabled large language models to solve highly difficult tasks, state-of-the-art results come at exorbitant compute costs. These inefficiencies can be attributed to the miscalibration of post-trained language models, and the lack of calibration in popular sampling techniques. Here, we present Online Reasoning Calibration (ORCA), a framework for calibrating the sampling process that draws upon conformal prediction and test-time training. Specifically, we introduce a meta-learning procedure that updates the calibration module for each input. This allows us to provide valid confidence estimates under distributional shift, e.g. in thought patterns that occur across different stages of reasoning, or in prompt distributions between model development and deployment. ORCA not only provides theoretical guarantees on conformal risks, but also empirically shows higher efficiency and generalization across different reasoning tasks. At risk level $δ=0.1$, ORCA improves Qwen2.5-32B efficiency on in-distribution tasks with savings up to 47.5% with supervised labels and 40.7% with self-consistency labels. Under zero-shot out-of-domain settings, it improves MATH-500 savings from 24.8% of the static calibration baseline to 67.0% while maintaining a low empirical error rate, and the same trend holds across model families and downstream benchmarks. Our code is publicly available at https://github.com/wzekai99/ORCA.

Multiple-Prediction-Powered Inference

Statistical estimation often involves tradeoffs between expensive, high-quality measurements and a variety of lower-quality proxies. We introduce Multiple-Prediction-Powered Inference (MultiPPI): a general framework for constructing statistically efficient estimates by optimally allocating resources across these diverse data sources. This work provides theoretical guarantees about the minimax optimality, finite-sample performance, and asymptotic normality of the MultiPPI estimator. Through experiments across three diverse large language model (LLM) evaluation scenarios, we show that MultiPPI consistently achieves lower estimation error than existing baselines. This advantage stems from its budget-adaptive allocation strategy, which strategically combines subsets of models by learning their complex cost and correlation structures.

M-estimation under Two-Phase Multiwave Sampling with Applications to Prediction-Powered Inference

In two-phase multiwave sampling, inexpensive measurements are collected on a large sample and expensive, more informative measurements are adaptively obtained on subsets of units across multiple waves. Adaptively collecting the expensive measurements can increase efficiency but complicates statistical inference. We give valid estimators and confidence intervals for M-estimation under adaptive two-phase multiwave sampling. We focus on the case where proxies for the expensive variables -- such as predictions from pretrained machine learning models -- are available for all units and propose a Multiwave Predict-Then-Debias estimator that combines proxy information with the expensive, higher-quality measurements to improve efficiency while removing bias. We establish asymptotic linearity and normality and propose asymptotically valid confidence intervals. We also develop an approximately greedy sampling strategy that improves efficiency relative to uniform sampling. Data-based simulation studies support the theoretical results and demonstrate efficiency gains.

Rethinking Diffusion Models with Symmetries through Canonicalization with Applications to Molecular Graph Generation

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.

Conformal Prediction Sets for Instance Segmentation

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.

Conformal Prediction for Generative Models via Adaptive Cluster-Based Density Estimation

Conditional generative models map input variables to complex, high-dimensional distributions, enabling realistic sample generation in a diverse set of domains. A critical challenge with these models is the absence of calibrated uncertainty, which undermines trust in individual outputs for high-stakes applications. To address this issue, we propose a systematic conformal prediction approach tailored to conditional generative models, leveraging density estimation on model-generated samples. We introduce a novel method called CP4Gen, which utilizes clustering-based density estimation to construct prediction sets that are less sensitive to outliers, more interpretable, and of lower structural complexity than existing methods. Extensive experiments on synthetic datasets and real-world applications, including climate emulation tasks, demonstrate that CP4Gen consistently achieves superior performance in terms of prediction set volume and structural simplicity. Our approach offers practitioners a powerful tool for uncertainty estimation associated with conditional generative models, particularly in scenarios demanding rigorous and interpretable prediction sets.

Thought calibration: Efficient and confident test-time scaling

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.

Conformal Prediction with Corrupted Labels: Uncertain Imputation and Robust Re-weighting

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.

Lipschitz-Driven Inference: Bias-corrected Confidence Intervals for Spatial Linear Models

Linear models remain ubiquitous in modern spatial applications - including climate science, public health, and economics - due to their interpretability, speed, and reproducibility. While practitioners generally report a form of uncertainty, popular spatial uncertainty quantification methods do not jointly handle model misspecification and distribution shift - despite both being essentially always present in spatial problems. In the present paper, we show that existing methods for constructing confidence (or credible) intervals in spatial linear models fail to provide correct coverage due to unaccounted-for bias. In contrast to classical methods that rely on an i.i.d. assumption that is inappropriate in spatial problems, in the present work we instead make a spatial smoothness (Lipschitz) assumption. We are then able to propose a new confidence-interval construction that accounts for bias in the estimation procedure. We demonstrate that our new method achieves nominal coverage via both theory and experiments. Code to reproduce experiments is available at https://github.com/DavidRBurt/Lipschitz-Driven-Inference.