Vanessa Borst, Lukas Horn, Daniel Grillmeyer +2cs.CV cs.AI
Despite rapid advances in MIS, fair and reproducible comparisons of segmentation models remain challenging due to heterogeneous datasets, inconsistent evaluation protocols, and rapidly evolving architectures. In particular, comparisons often implicitly assume that model rankings are invariant to data partitioning, preprocessing, metric aggregation, uncertainty estimation, and computational constraints. The lack of extensible and unified evaluation frameworks further limits systematic investigation of new models, datasets, and training paradigms. We present MEDSEGBENCHMARKER (MSB), a configuration-driven framework for controlled benchmarking of 2D MIS. It integrates duplicate and near-duplicate image detection, group-aware data splitting, YAML study specifications, resumable training, hyperparameter optimization, cross-validation, and checkpoint-based evaluation. Rather than retaining only aggregate performance measures, MSB exports sample- and class-level pixel counts and predictions together with the evaluation context. These elementary artifacts enable post-hoc analyses without repeated inference. We demonstrate MSB in a case study involving three heterogeneous 2D datasets and multiple MIS and general-purpose vision models evaluated at 256- and 512-pixel input resolutions. Reaggregation of identical predictions changes the top-ranked architecture in three of six dataset-resolution settings, despite high rank correlations between aggregation strategies. Increasing input resolution produces model- and dataset-dependent performance gains and losses that must be considered alongside empirically measured inference complexity. These results show that seemingly minor choices in evaluation and experimental setup can affect benchmark conclusions. MSB, available at GitHub, provides a practical and extensible basis for making benchmark conditions and evaluation choices explicit and reproducible.
Recent work has argued normatively, on synthetic data, that evaluating survival models by discrimination alone (concordance index) yields systematically misleading model comparisons, because the metric ignores calibration and time-dependent accuracy. Whether this matters for real, published, non-clinical models has not been tested. We reproduce three published survival-ML models across three structurally distinct domains -- hard-drive failure prediction, peer-to-peer credit default, and user disengagement on digital platforms -- validate our instrument against the anchor paper's own synthetic experiment, and test five pre-registered hypotheses under a Holm-corrected family-wise error rate. Three of five reject (though one pre-registered threshold clears by a narrow margin). A model reproducing the published literature's discrimination almost exactly (C = 0.9595 vs. 0.958 reported) fails a formal calibration test at p < 0.001; a broad feature-ablation search finds no single attribute responsible for its discrimination, so the calibration failure is not a trivial shortcut artifact. A lender's estimated default risk is biased upward by roughly two percentage points, growing to nearly four in the riskiest segment, when loan prepayment is treated as non-informative censoring rather than a competing risk. A platform's churn model shows probability estimates that degrade with the horizon even as global discrimination stays within the pre-registered C-index band. A direct test of whether metric choice inverts model preference does not reject, though with limited power given two to three models per domain; the failure mode we document is better characterized as misplaced confidence in a chosen model than as choosing the wrong one. We release a pre-registered evaluation harness with full code and an annotated notebook, so these results can be verified independently and the audit extended.
Mohammed Saeed Al-Huraibi, Ihsan Yozgat, Ahmet Kaplancs.LG q-bio.GN
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.
Agentic artificial intelligence systems promise to accelerate scientific workflows, but neuroimaging poses unique challenges: heterogeneous modalities (sMRI, fMRI, dMRI, EEG), long multi-stage pipelines, and persistent reproducibility risks. To address this gap, we present NeuroClaw, a domain-specialized multi-agent research assistant for executable and reproducible neuroimaging research. NeuroClaw operates directly on raw neuroimaging data across formats and modalities, grounding decisions in dataset semantics and BIDS metadata so users need not prepare curated inputs or bespoke model code. The platform combines harness engineering with end-to-end environment management, including pinned Python environments, Docker support, automated installers for common neuroimaging tools, and GPU configuration. In practice, this layer emphasizes checkpointing, post-execution verification, structured audit traces, and controlled runtime setup, making toolchains more transparent while improving reproducibility and auditability. A three-tier skill/agent hierarchy separates user-facing interaction, high-level orchestration, and low-level tool skills to decompose complex workflows into safe, reusable units. Alongside the NeuroClaw framework, we introduce NeuroBench, a system-level benchmark for executability, artifact validity, and reproducibility readiness. Across multiple multimodal LLMs, NeuroClaw-enabled runs yield consistent and substantial score improvements compared with direct agent invocation. Project homepage: https://cuhk-aim-group.github.io/NeuroClaw/index.html