Evidence and investigation

Contested results

Where one study disagrees with what other studies report for the same models, and what we are doing to resolve each case.

These are automatic leads, not findings of error. Each release, a check compares how every study ranks the models it shares with other studies. It flags a study that reverses the order the others agree on, or whose gap to a shared reference model lies well outside theirs. Different tasks, populations or metrics often explain a flag.

A flag never hides a result. Flagged results stay in every table, page and download, marked Contested. A result is withheld only when a reviewer marks it disputed.

How the check works, and how each follow-up is recorded: discrepancies between studies.

In this release

121open
5settled
7resolved
1medium severity
132low severity

Release 2026-11-02-a7f03c9e55a5 · 133 findings in all · rules version 4

Findings

Status: All · Open · Settled · Resolved

Severity: All · Medium · Low

State: All · Not yet reviewed · Under investigation · Explained · Confirmed error · Not a real disagreement

Showing findings that compare PhyloGPN. All models

1 finding matches, most severe first.

DNABERT-2 and PhyloGPN: GUANinE v1.1 reveals complementarity of supervised and genomic language models and Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) disagree

Low severity
Not yet reviewed
two-study-conflict
unknown

GUANinE v1.1 reveals complementarity of supervised and genomic language models ranks DNABERT-2 above PhyloGPN in 6 of 6 comparisons; Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) ranks PhyloGPN above DNABERT-2 in 14 of 14 comparisons. No other study gives a verdict, so neither is the outlier.

2 papers rank DNABERT-2 above PhyloGPN in 6 of their 20 comparisons and PhyloGPN higher in 14. Of those papers, Genomic heterogeneity inflates… ranks PhyloGPN higher on its own (14 of 14).

DNABERT-2 higherTiePhyloGPN higher

Compared: DNABERT-2, PhyloGPN

Not reviewed yet.