arXiv preprints from January 1, 2026 through July 20, 2026 — 07:33:25 EST
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...
Single-cell and spatial foundation models promise transferable biological representations, yet their generality remains largely untested across modalities, biological domains and analytical tasks. We benchmarked six representative models, Nicheformer, CellPLM, scGPT-spatial, GenePT, scELMo and Novae, using a harmonised framework...
Part of the excitation energy transfer (EET) characteristics of the photosystem II (PSII) comes from the interconnection between pigments. To understand the correlation between the EET and the pigments' interaction structure, we construct a network from the EET rates, which are related to both the distance between the pigments...
Gene expression is a stochastic process that gives rise to large fluctuations in protein levels leading to phenotypic heterogeneity in clonal cell populations; post-transcriptional regulation plays a crucial role in controlling the level of phenotypic variability within a population, which is directly tied to cell-fate decisions. As...
Accurate kidney failure risk assessment is critical to timely intervention in chronic kidney disease (CKD). Existing equations (e.g. Kidney Failure Risk Equation; KFRE) rely on single laboratory measurements to estimate short- and long-term kidney failure risk, leaving longitudinal laboratory patterns unused. Here we introduce Clalit...
The public goods game serves as a significant paradigm for investigating the emergence and maintenance of cooperation in conflicting situations. In the traditional public goods game, the multiplication factor characterizing the synergy effect of common efforts is typically assumed to be constant. In real-world scenarios, however,...
A fundamental challenge in the science of consciousness is the lack of a universal, predictive framework for motivated behavior. While existing theories excel at describing specific mechanisms, from neural pathways to computational models, they do not provide a foundational principle that explains the consistent direction of conscious...
OBJECTIVES: Vision-language models are increasingly used to interpret medical and everyday images through consumer chat interfaces, yet their ability to read orientation - the single perceptual operation tested by the tumbling-E acuity optotype - is poorly characterized on the surfaces through which they are actually used. METHODS: We...
Many dynamical systems exhibit diverse modes of behavior. In biology, such modes can represent individual or cell fates. While the emergence of multimodality is commonly studied, transient bimodality is much less well understood. Under transient bimodality, a system moving from a well-defined initial to a final state transiently...
Neural activity is widely held to organize on low-dimensional structure embedded in a high-dimensional state space. Persistent homology reads such structure directly from the pattern of pairwise correlations, without assuming in advance which variables are relevant. We apply persistent homology to microelectrode-array (MEA) recordings...
We consider a supercritical two-type continuous-time linear birth-death process with mutation and selection, in which wild-type individuals give rise to mutant offspring with a larger net growth rate. In this setting, we investigate the ``driver'' site frequency spectrum (SFS), or the random measure that records mutant allelic...
Understanding how cooperation persists despite the advantage of selfish behavior remains a central challenge in evolutionary dynamics. Classical models of public goods dilemmas predict dominance of defectors, yet natural and social systems often sustain cooperation. We study an eco-evolutionary public goods game on complex networks...
Fair clustering aims to make cluster assignments independent of sensitive attributes, but this goal becomes challenging when multiple sensitive attributes jointly define many subgroups. In such settings, directly extending existing fair clustering algorithms is computationally expensive or numerically unstable, especially when the...
A simple alternative to the binomial distribution that places more probability weight on the tails is considered. Its derivation only requires the weighted arithmetic mean of two discrete probability mass functions, one being the binomial itself and the other being the bi-uniform introduced here. Some properties are derived, and an...
A Bayesian network framework is proposed for modelling unit-bounded continuous variables using conditional beta-distributed nodes within a fully Bayesian inference setting. The model captures conditional dependencies and propagates uncertainty through the network, with inference performed via Markov Chain Monte Carlo methods...
Statistical modeling for goals scored in football is typically achieved using the Poisson distribution and its variants. Here we propose a Bayesian framework for modeling under- and over-dispersion in count data by combining the Conway-Maxwell-Poisson (CMP) likelihood with a spikeand-slab (SAS) prior on unit-specific dispersion...
TabPFN is a transformer-based foundation model for tabular prediction that performs inference without task-specific training by conditioning on a support set and query inputs. Despite its strong empirical performance, its internal behavior on structurally difficult tabular geometries remains poorly understood. We study this behavior...
Electronic health record (EHR) networks provide unprecedented opportunities to study treatment mechanisms at scale, but mediation analyses across institutions are often hindered by privacy and governance constraints that restrict sharing of patient-level data. We developed a privacy-preserving federated mediation framework that...
Importance splitting (ISPLIT) evaluates the probabilities of rare events in non-Markovian models. It requires a heuristic importance function (IFUN) that estimates the distance to the target. While including timer evaluations in the IFUN can substantially improve the effectiveness of ISPLIT, the existing time-sensitive IFUNs evaluate...
High-stakes decisions in oncology clinical trials must often be made while survival data remains immature: progression-free survival (PFS) and overall survival (OS) are heavily censored, few events have accumulated, and the primary endpoint may be months or years from reading out. What is available at interim data cut-offs is...
Many prediction and decision-making problems in operations research involve path-valued covariates -- data that evolve over time -- for which path signatures have become a canonical feature representation. Their use is justified by a universal approximation theorem, but this is an existence result: it guarantees that a finite-level...
The conditional randomization test (CRT) provides a principled approach to conditional independence (CI) testing, guaranteeing exact type-I error control when the true conditional distribution is known. In practice, however, this distribution must be estimated, and estimation errors can inflate type-I errors, while high dimensionality...
Nonlinear state estimation under structural model uncertainty remains a central challenge in autonomous Guidance, Navigation, and Control (GNC) systems. Classical estimators propagate states using assumed dynamics and incorporate measurements through posterior correction, which under mismatch leads to biased innovations, estimator...
Missing data and confounding are common in real-world statistical applications, yet few studies have examined how imputation methods perform under time-varying confounding in binary variables, or how missingness mechanism, missing rate, missingness location and sample size jointly affect performance and the underlying identifiability...
Network meta-regression (NMR) extends network meta-analysis (NMA) by synthesizing evidence on multiple treatments while adjusting for potential effect modifiers. By accounting for effect modification, NMR can reduce between-study heterogeneity and improve the validity of relative treatment effects, providing insight regarding...