Beyond Agreement: Scoring Panel-Surfaced Biomedical Entity Candidates for Curator Triage

Biomedical named entity recognition (NER) and entity linking (EL) strongly depend on annotated corpora, but the utility of these resources for benchmarking is often assumed rather than characterized. We present a corpus-centric framework for diagnosing benchmark-relevant properties directly from corpus annotations, concept links, train-test splits, document metadata, and terminology mappings. The framework organizes standardized statistics into five families: (1) scale, density and label distribution, (2) lexical and conceptual structure, (3) train-test overlap, (4) metadata composition, and (5) terminology coverage where applicable. Applying the framework to nine corpora spanning diseases, chemicals, and cell types, we find that corpus properties can differ substantially, even when they address the same apparent task. We find differences in the evaluation signal they provide, the generalization demands they impose, the degree of train-test reuse they permit, and the regions of biomedical literature and concept space they represent. These differences suggest that commonly reported corpus statistics can be insufficient to characterize what biomedical NER and EL benchmarks evaluate. We argue that corpus-centric diagnostics provide a practical framework for analyzing corpora beyond surface descriptors such as corpus size and entity type, for identifying potential transfer risks, and for interpreting the scope of benchmarking conclusions. We release the framework as open-source code with an interactive dashboard to support reproducing our analyses and characterizing additional corpora.

Validating an LLM judge against human annotations usually means reporting several agreement statistics: accuracy, precision, recall, $F_1$, Cohen's $κ$, and one or more rank correlations. A survey of 24 recent LLM-as-judge papers finds metric choice entangled with the judgment scale, tie handling, invalid outputs, and abstention handling, and those choices rarely stated. For binary criteria -- the common case in rubric-based evaluation, where each criterion is graded MET or UNMET -- most of the reported numbers are redundant: Pearson's $r$, Spearman's $ρ$, Kendall's $τ_b$, the phi coefficient $φ$, and the Matthews Correlation Coefficient all reduce to a single number on non-degenerate binary data, so reporting several of them only creates an illusion of corroborating evidence. Cohen's $κ$ is the one agreement coefficient that adds information: it shares $φ$'s numerator but normalizes differently, and the gap between them measures how far the judge's positive-label rate has drifted from the human's. We then trace what changes when a judge may abstain with a CANNOT_ASSESS verdict: the three common ways of handling abstentions are not interchangeable preprocessing choices but answer different questions, and they break the binary equivalences. The same equivalences reappear, up to a negligible finite-sample correction, for multi-judge ensembles scored with Fleiss' $κ$ or Krippendorff's $α$. We close with a reporting checklist that names the judgment scale, the abstention and tie handling mode, coverage, the confusion matrix, and the aggregation level alongside any scalar agreement coefficient.

Biomedical findings often seem to conflict across studies, but many of these differences are context-dependent rather than true contradictions. Variations in cohort, geography, assay protocol, disease subtype, and clinical setting can make both claims locally valid. Existing NLI and scientific claim-verification benchmarks reduce such cases to entailment, contradiction, or neutral, failing to capture the contextual structure behind divergence. To address this, we introduce BioDivergence, an evaluation framework with a six-class conflict taxonomy, a 13-axis divergence ontology, and four structured outputs per claim pair: conflict type, divergence axes, dominant confounder, and reconciliation explanation. We release BioDivergence-Silver-v1.0, an article-disjoint silver benchmark of 11,865 claim pairs across five biomedical domains, alongside a legacy deduplicated variant for comparison. Results show notable ranking differences between the two variants, with the fine-tuned reference model dropping about 12 points under the article-disjoint setting, while Mistral-7B-Instruct-v0.3 achieves 0.5523 accuracy and 0.3894 contextual-F1 on the 842-example primary test set. BioDivergence offers a more faithful way to distinguish contextual divergence from direct contradiction and to separate article-level memorization from genuine task learning.