CHARTER: Auditing Reference Substitution in Hierarchical Compact-Evidence Evaluation for Computational Pathology

Foundation Models (FMs) have recently redefined the state-of-the-art in histopathology by providing robust representations for whole-slide image (WSI) analysis. However, selecting the optimal foundation model (FM) for a specific clinical cohort currently requires multiple preprocessing steps, followed by computationally expensive feature extraction and the training of a Multiple Instance Learning (MIL) aggregator for every model. In this work, we investigate whether efficient tile-level linear probing can serve as a reliable proxy for slide-level performance, reducing the need to run full slide-level pipelines for every candidate encoder. We benchmark 19 state-of-the-art FMs on 42 slide-level and 16 tile-level tasks, comparing tile probing metrics against slide-level outcomes using ABMIL and Mean Pooling aggregations. We observe a high correlation between tile and slide performance across varying task difficulties, indicating that encoder representation quality is the primary determinant of WSI success. Sensitivity analyses show that transferability is stable across models and is more influenced by cohort sizes and numbers of tiles per slide than by average task difficulty. We also measure the agreement in best performing models between tile and slide-level tasks, showing tile benchmarks reliably shortlist strong candidates. Overall, our study indicates that tile-level benchmarking provides an efficient and practical first step for narrowing down candidate models, while slide-level evaluation remains essential for final validation on clinical tasks.

Background and Objective: Quality control is a prerequisite for whole-slide image analysis, yet the benchmarks on which quality-control methods are compared share four properties that make their reported differences hard to interpret: few independent slides, annotation concentrated in a minority of them, pooled ratio metrics with no closed-form standard error, and a single inherited train/test partition. We propose a reliability protocol for such benchmarks. Methods: The protocol quantifies four sources of variability - test-set sampling, training stochasticity, partition composition, and undocumented preprocessing - a claim is reportable only if it survives all four; three of the four cost minutes of compute. We apply it to an independent reconstruction of a published diffusion-based artifact detector, evaluated on the original 24-slide partition and against a supervised baseline. Results: The method's central mechanism reproduces: the auxiliary contrastive term improves pooled F1 from 0.673 to 0.688 and replicates under a second seed (+0.0156, p = 0.031; +0.0190, p = 0.005), although it acts on pen marking rather than the artifact types cited to motivate it. Its comparative claims do not: differences between design variants, and against the supervised baseline, fall inside the uncertainty of the evaluation. Four of 24 slides carry 70% of scored annotated pixels, giving an effective sample size of 6.2, and the inherited partition sits at the 7th percentile. An unreported tissue-restriction step excludes 41.4% of out-of-focus annotation against 2.6% of air bubble; such a gate is confounded with blur by construction. Conclusions: Small-cohort benchmarks support far weaker conclusions than current reporting implies. The four checks are cheap enough to accompany any evaluation on such a resource and separate reproducible effects from differences the evaluation cannot resolve.

Search-agent rewards mix answer quality, citation grounding, tool cost, and anti-hacking terms; a high score therefore need not imply that cited evidence was retrieved, and added penalties can cancel. We introduce HERALD, an offline audit that applies exact same-question interventions, separates candidate-visible from oracle information, and enumerates detector contracts before policy optimization. On four Qwen3-8B pools from HotpotQA, 2WikiMultiHopQA, and MuSiQue, $R_0$ rejects search deletion and fake IDs, but a label-free citation-laundering attack succeeds. A complete $2^3$ ablation identifies targeted strengthening of $L$---citing a corpus passage absent from the retrieved evidence---as the observed inclusion-minimal repair: $R[L]$ has zero empirical ASR with a 0.50% one-sided cluster upper bound. The gap persists across pool rules, a visible BM25 attacker, and four models; broader hardening remains vulnerable when the attack removes an oracle support-ID penalty. Under strict 5M-token matched training evaluated on 256 paired questions per benchmark, $R[L]$ meets the EM non-inferiority gate on HotpotQA and 2Wiki but not MuSiQue. Equal-suite citation precision and support recall improve by 2.02 and 1.46 points, unsupported citations fall by 1.69, and laundering attackability falls on 2Wiki and MuSiQue. Natural $L$ is not reduced, and the detector appears in only 18 of 58,368 training trajectories. HERALD thus separates robust scoring, sparse learning signal, and policy transfer.