This paper addresses structured out-of-distribution (OOD) testing in high-stakes machine learning applications. Traditional conformal methods rely on joint exchangeability, making it difficult to incorporate auxiliary information such as spatiotemporal or grouping structures. To overcome this limitation, we propose the structure-adaptive conformal q-value (SCQ), a significance index that integrates individual test evidence with structural patterns. We also develop pseudo-score-guided transductive automated model selection (P-TAMS), which adapts conformalized model selection to structured OOD testing across a toolbox of candidate models. Together, SCQ and P-TAMS form a unified framework under pairwise exchangeability, providing finite-sample error-rate control, improved power, and enhanced interpretability. Experiments on simulated and real data demonstrate that the proposed approach controls the false discovery rate and performs well across diverse settings.

We study distribution-free root cause analysis in multi-stream data, where an evolving underlying system is observed through multiple data streams that may each undergo distributional changes at unknown timepoints. In such settings, the stream exhibiting the earliest change provides a natural starting point for investigating the underlying cause, which we refer to as the root-cause index. Leveraging conformal $p$-values, we propose a novel framework, Conformal Root Cause Analysis (CROC), which constructs finite-sample valid confidence sets for the root-cause index under minimal assumptions: the data streams are independent, and within each stream the pre- and post-change observations are sampled exchangeably from arbitrary and unknown distributions. We further establish a universality property, showing that any distribution-free method for root cause localization can be represented within the CROC framework. In addition, under mild regularity conditions and principled score design, our method yields asymptotically sharp confidence sets that efficiently isolate the root cause. We further extend CROC to efficiently handle cross-stream dependence when present. Extensive simulations demonstrate accurate localization of the root stream, supporting our theoretical guarantees.

The Benjamini-Hochberg (BH) procedure is widely used to control the false detection rate (FDR) in multiple testing.

Instead, we apply powerful machine learning models for one-class (Moya et al., 1993) or

We propose a sequential test for detecting arbitrary distribution shifts that allows conformal test martingales (CTMs) to work under a fixed, reference-conditional setting. Existing CTM detectors construct test martingales by continually growing a reference set with each incoming sample, using it to assess how atypical the new sample is relative to past observations. While this design yields anytime-valid type-I error control, it suffers from test-time contamination: after a change, post-shift observations enter the reference set and dilute the evidence for distribution shift, increasing detection delay and reducing power. In contrast, our method avoids contamination by design by comparing each new sample to a fixed null reference dataset. Our main technical contribution is a robust martingale construction that remains valid conditional on the null reference data, achieved by explicitly accounting for the estimation error in the reference distribution induced by the finite reference set. This yields anytime-valid type-I error control together with guarantees of asymptotic power one and bounded expected detection delay. Empirically, our method detects shifts faster than standard CTMs, providing a powerful and reliable distribution-shift detector.

We study the problem of offline changepoint localization in a distribution-free setting. One observes a vector of data with a single changepoint, assuming that the data before and after the changepoint are iid (or more generally exchangeable) from arbitrary and unknown distributions. The goal is to produce a finite-sample confidence set for the index at which the change occurs without making any other assumptions. Existing methods often rely on parametric assumptions, tail conditions, or asymptotic approximations, or only produce point estimates. In contrast, our distribution-free algorithm, CONformal CHangepoint localization (CONCH), only leverages exchangeability arguments to construct confidence sets with finite sample coverage. By proving a conformal Neyman-Pearson lemma, we derive principled score functions that yield informative (small) sets. Moreover, with such score functions, the normalized length of the confidence set shrinks to zero under weak assumptions. We also establish a universality result showing that any distribution-free changepoint localization method must be an instance of CONCH. Experiments suggest that CONCH delivers precise confidence sets even in challenging settings involving images or text.

Conformal novelty detection is a classical machine learning task for which uncertainty quantification is essential for providing reliable results. Recent work has shown that the BH procedure applied to conformal p-values controls the false discovery rate (FDR). Unfortunately, the BH procedure can lead to over-optimistic assessments near the rejection threshold, with an increase of false discoveries at the margin as pointed out by Soloff et al. (2024). This issue is solved therein by the support line (SL) correction, which is proven to control the boundary false discovery rate (bFDR) in the independent, non-conformal setting. The present work extends the SL method to the conformal setting: first, we show that the SL procedure can violate the bFDR control in this specific setting. Second, we propose several alternatives that provably control the bFDR in the conformal setting. Finally, numerical experiments with both synthetic and real data support our theoretical findings and show the relevance of the new proposed procedures.

Detecting chemical modifications on RNA molecules remains a key challenge in epitranscriptomics. Traditional reverse transcription-based sequencing methods introduce enzyme- and sequence-dependent biases and fragment RNA molecules, confounding the accurate mapping of modifications across the transcriptome. Nanopore direct RNA sequencing offers a powerful alternative by preserving native RNA molecules, enabling the detection of modifications at single-molecule resolution. However, current computational tools can identify only a limited subset of modification types within well-characterized sequence contexts for which ample training data exists. Here, we introduce a model-free computational method that reframes modification detection as an anomaly detection problem, requiring only canonical (unmodified) RNA reads without any other annotated data. For each nanopore read, our approach extracts robust, modification-sensitive features from the raw ionic current signal at a site using the signature transform, then computes an anomaly score by comparing the resulting feature vector to its nearest neighbors in an unmodified reference dataset. We convert anomaly scores into statistical p-values to enable anomaly detection at both individual read and site levels. Validation on densely-modified \textit{E. coli} rRNA demonstrates that our approach detects known sites harboring diverse modification types, without prior training on these modifications. We further applyied this framework to dengue virus (DENV) transcripts and mammalian mRNAs. For DENV sfRNA, it led to revealing a novel 2'-O-methylated site, which we validate orthogonally by qRT-PCR assays. These results demonstrate that our model-free approach operates robustly across different types of RNAs and datasets generated with different nanopore sequencing chemistries.