When to Call an Apple Red: Humans Follow Introspective Rules, VLMs Don’t

arXiv:2604.06422v1 Announce Type: cross Abstract: Understanding when Vision-Language Models (VLMs) will behave unexpectedly, whether models can reliably predict their own behavior, and if models adhere

Bi-Level Optimization for Single Domain Generalization

arXiv:2604.06349v1 Announce Type: cross Abstract: Generalizing from a single labeled source domain to unseen target domains, without access to any target data during training, remains

Uncertainty Estimation for Deep Reconstruction in Actuatic Disaster Scenarios with Autonomous Vehicles

arXiv:2604.06387v1 Announce Type: cross Abstract: Accurate reconstruction of environmental scalar fields from sparse onboard observations is essential for autonomous vehicles engaged in aquatic monitoring. Beyond

$S^3$: Stratified Scaling Search for Test-Time in Diffusion Language Models

arXiv:2604.06260v1 Announce Type: cross Abstract: Test-time scaling investigates whether a fixed diffusion language model (DLM) can generate better outputs when given more inference compute, without

Harnessing Hyperbolic Geometry for Harmful Prompt Detection and Sanitization

arXiv:2604.06285v1 Announce Type: cross Abstract: Vision-Language Models (VLMs) have become essential for tasks such as image synthesis, captioning, and retrieval by aligning textual and visual

Benchmarking Heritability Estimation Strategies Across 86 Configurations and Their Downstream Effect on Polygenic Risk Score Performance

April 6, 2026

arXiv:2604.02394v1 Announce Type: new
Abstract: Objective: SNP heritability estimates vary substantially across estimation strategies, yet the downstream consequences for polygenic risk score (PRS) construction remain poorly characterised. We systematically benchmarked heritability estimation configurations and assessed their propagation into downstream PRS performance.
Methods: We benchmarked 86 heritability-estimation configurations spanning six tool families (GEMMA, GCTA, LDAK, DPR, LDSC, and SumHer) and ten method groups across 10 UK Biobank phenotypes, yielding 844 configuration-level estimates. Each estimate was propagated into GCTA-SBLUP and LDpred2-lassosum2 PRS frameworks and evaluated across five cross-validation folds using null, PRS-only, and full models. Eleven binary analytical contrasts were tested using Mann-Whitney U tests to identify drivers of heritability variability.
Results: Heritability ranged from -0.862 to 2.735 (mean = 0.134, SD = 0.284), with 133 of 844 estimates (15.8%) being negative and concentrated in unconstrained estimation regimes. Ten of eleven analytical contrasts significantly affected heritability magnitude, with algorithm choice and GRM standardisation showing the largest effects. Despite this upstream variability, downstream PRS test performance was only weakly coupled to heritability magnitude: pooled Pearson correlations between h^2 and test AUC were r = -0.023 for GCTA-SBLUP and r = +0.014 for LDpred2-lassosum2, with both being non-significant.
Conclusion: SNP heritability is best interpreted as a configuration-sensitive modelling parameter rather than a universally stable scalar input. Heritability estimates should always be reported alongside their full estimation specification, and downstream PRS performance is comparatively robust to moderate variation in the heritability input.

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