rewirebio.iobenchmarks
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 SiPhy. All models

2 findings match, most severe first.

SiPhy and phyloP: Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods reverses the order

  • Low severity
  • Not yet reviewed
  • Ordering reversal
  • Same task, different protocols

Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks SiPhy above phyloP in 3 of 4 comparisons; 2 of 2 other studies rank phyloP above SiPhy.

2 papers rank phyloP above SiPhy in all 13 of their comparisons. Brandes et al. 2023 ranks SiPhy above phyloP in 3 of its 4 comparisons and phyloP higher in 1.

Comparisons in which each paper scores phyloP or SiPhy higher2 other papers: phyloP higher in 13, SiPhy higher in 0, 0 ties. Brandes et al. 2023 (disagrees): phyloP higher in 1, SiPhy higher in 3, 0 ties.2 other papers13 phyloP higher13Disagrees: Brandes et al. 2023Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods1 phyloP higher13 SiPhy higher3
phyloP higherTieSiPhy higher
Compared
SiPhy, phyloP

Not reviewed yet.

SiPhy and GERP: Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods reverses the order

  • Low severity
  • Not yet reviewed
  • Ordering reversal
  • Same task, different protocols

Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks SiPhy above GERP in 4 of 4 comparisons; 2 of 2 other studies rank GERP above SiPhy.

2 papers rank GERP above SiPhy in 11 of their 13 comparisons and SiPhy higher in 1; 1 is a tie. Brandes et al. 2023 ranks SiPhy above GERP in all 4 of its comparisons.

Comparisons in which each paper scores GERP or SiPhy higher2 other papers: GERP higher in 11, SiPhy higher in 1, 1 tie. Brandes et al. 2023 (disagrees): GERP higher in 0, SiPhy higher in 4, 0 ties.2 other papers11 GERP higher111 tie1 SiPhy higherDisagrees: Brandes et al. 2023Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods4 SiPhy higher4
GERP higherTieSiPhy higher
Compared
SiPhy, GERP

Not reviewed yet.