Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2607.17345

A multiverse-consensus pipeline for reproducible feature selection in untargeted LC-MS metabolomics

Mohammed Saeed Al-Huraibi·Ihsan Yozgat·Ahmet Kaplan
View original source ↗Read source document ↗Export metadata ↓

Abstract

Background: Untargeted LC-MS metabolomics requires a long chain of preprocessing decisions, each with several equally defensible options. Analysts typically commit to one pipeline and report the resulting feature shortlist. How strongly that shortlist depends on choices that were never varied stays invisible. Results: We adapt multiverse analysis to untargeted metabolomics feature selection. We present an auditable, configuration-driven pipeline that (i) applies a ten-stage quality-control filter cascade in which every feature's fate is logged, and (ii) runs the downstream analysis as a multiverse over four contrasting preprocessing philosophies, each combined with four feature-ranking methods under bootstrap stability selection and label-permutation testing. Only features recurring across paths enter a tiered consensus. On a demonstration dataset of five breast-cancer cell lines (30,370 detected features), the four single pipelines individually returned shortlists of 4-20 features whose pairwise agreement was as low as Jaccard = 0.05. The multiverse consensus retained 15 features (>=2/4 paths), of which one recurred across all four, although two paths (sharing normalization and drift-correction methods) dominate the consensus. A pipeline-wide label-permutation test found no false discoveries in 50 null permutations. Conclusions: Reporting only preprocessing-robust features, with a complete kept/dropped audit trail, converts hidden analytical degrees of freedom into an explicit, inspectable output. We discuss scope and limitations, including single-batch design and the need for independent validation.

Explore related subjects

cs.LGq-bio.GN

Keep this discovery

BibTeXRIS

Mohammed Saeed Al-Huraibi, Ihsan Yozgat, Ahmet Kaplan. 2026-07-19. A multiverse-consensus pipeline for reproducible feature selection in untargeted LC-MS metabolomics. https://arxiv.org/abs/2607.17345

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

AUC Maximization from Biased Positive-unlabeled Data with Confidence

Maximizing the area under the receiver operating characteristic curve (AUC) is a standard approach to imbalanced binary classification. Although positive and negative data are required for maximizing the AUC, negative data are often difficult to collect in some real-world applications due to privacy concerns or the need for specialized expertise to annotate them. Thus, AUC maximization from positive and unlabeled (PU) data has been attracting attention. Existing methods assume that labeled positive data are unbiased samples from the true positive distribution. However, this ideal assumption is often violated in practice. In this paper, we propose a method to maximize the AUC from biased PU data. To address the bias, our key idea is to exploit {\it confidence}, i.e., the probability that an instance is positive, associated with the small number of labeled positive data. We derive an estimator of the AUC risk using biased PU data with confidence, enabling AUC maximization under such bias. We further show that the rewritten AUC risk induces a Bayes-optimal AUC ranking even when the available confidence is any strictly increasing transformation of the true posterior probability. We experimentally show the effectiveness of our method on eight real-world datasets.

cs.LG↗
arXiv2026

Measuring the Value of World-Model Updates: A Counterfactual Utility Protocol for Continual Adaptation

Continual world models must decide whether new data justify changing the model. Fixed replay schedules and prediction-error triggers specify when to update, but neither reveals the value of an individual update: one deployment run cannot show how the same model would have performed at that moment had it held its parameters. We introduce the fork ledger, which branches a deployment stream at pre-registered decision points into matched update and hold continuations under common random numbers. It evaluates both continuations on the same episodes and records $\Delta R = R_{\mathrm{update}} - R_{\mathrm{hold}}$. Always applying one fixed update mechanism lowers return on all three simulated control tasks: CartPole ($-144.0$; checkpoint-bootstrap $95\%$ CI $[-185.4,-116.1]$, against a converged return near $650$), Walker ($-82.8$; $[-101.1,-61.7]$) and Cheetah ($-18.6$; $[-29.0,-6.6]$). Divergence is an outcome of applying the update, so the estimand counts every attempted fork; restricted to the $693$ of $720$ that did not collapse, CartPole and Walker are unchanged in sign ($-113.4$ and $-82.1$) and Cheetah becomes unresolved ($-3.9$; $[-17.5,+13.0]$). The task is the unit of inference: each contributes $240$ attempted forks over five pretrained checkpoints crossed with two drift directions. The ledger makes counterfactual utility observable for a fixed mechanism, allowing triggers to be judged by the updates they select rather than by surprise detection alone.

cs.LG↗
arXiv2026

When More Is Not Better: Component Anti-Synergy in a P300 Speller

P300 brain-computer interface (BCI) spellers can provide hands-free communication for people with severe motor impairments. Modern pipelines combine multiple individually promising components, often assuming that 'more-is-better'. We tested this assumption using a four-component full-factorial experiment varying the inclusion of Euclidean Alignment (EA), xDAWN spatial filtering, subject calibration, and language model priors on a public P300 dataset. Performance was evaluated using accuracy, repetitions, and information transfer rate (ITR) with mixed-effects models. Results show that the value of components is conditional rather than additive. Calibration was the strongest singular contributor, while EA compensated for its absence in zero-calibration settings. Adding independently useful components could also reduce performance, revealing component anti-synergy. Contrary to conventional wisdom, LM support was not universally beneficial: its effect depends strongly on the strength of the underlying EEG pipeline, while results from a larger LM showed a similar pattern. Together, these findings challenge maximal 'all-on' pipeline design and highlight the value of selecting spatial and language-support components according to the quality of available EEG evidence.

cs.LG↗