MutFormer and PolyPhen-2: Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) and An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers disagree
- Low severity
- Not yet reviewed
- two-study-conflict
- unknown
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above PolyPhen-2 in 6 of 6 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks PolyPhen-2 above MutFormer in 5 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
An automatic lead, not a finding of error. The results below are shown as published, everywhere on the site, until a reviewer decides otherwise.
Which studies agree
2 papers rank MutFormer above PolyPhen-2 in 7 of their 12 comparisons and PolyPhen-2 higher in 5. Of those papers, An openly licensed benchmark… ranks PolyPhen-2 higher on its own (5 of 6).
- Rank MutFormer higher (1): Livesey and Marsh 2025
- Rank PolyPhen-2 higher (1): An openly licensed benchmark…
- Mixed (0): none
Each paper sits where at least two thirds of its comparisons point; Mixed means neither model reaches two thirds. The larger, outlined dot is the paper that disagrees.
| Paper | Role | Ranks MutFormer higher | Ranks PolyPhen-2 higher | Ties |
|---|---|---|---|---|
| Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) and 1 more record · DOI | Agrees | 6 | 0 | 0 |
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers and 1 more record · DOI | Agrees | 1 | 5 | 0 |
Comparisons in Livesey and Marsh 2025 (6)
| Protocol | Dataset | Metric | MutFormer | PolyPhen-2 | Higher |
|---|---|---|---|---|---|
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS sets | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, 36 human DMS sets), percent | 71.4 | 42.4 | MutFormer |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS sets | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), |Spearman| with DMS on shared variants, 36 human DMS sets), percent | 17.2 | 6.76 | MutFormer |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, direct assays only | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, direct DMS assays only), percent | 74.7 | 41.5 | MutFormer |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, indirect assays only | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, indirect DMS assays only), percent | 68.9 | 43.1 | MutFormer |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions only | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, SNV-accessible substitutions only), percent | 71.4 | 42.4 | MutFormer |
| Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions with gaps filled | Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS, SNV-accessible substitutions, missing predictions filled with the VEP's most benign score), percent | 70.5 | 44.1 | MutFormer |
Comparisons in An openly licensed benchmark… (6)
What disagrees
- studies
- 2
- Compared
- MutFormer, PolyPhen-2
- Study that disagrees
- Other studies
- Rule
- two-study-conflict; unknown
- Model identity
- Matched across studies partly through links not yet reviewed
Follow-up
Current state: Not yet reviewed.
No one has reviewed this finding yet.
How to help resolve this
If you know why these studies disagree, for example a different population, metric or preprocessing step, or you have a corrected value, tell us through the contribution form. A reviewer checks every submission against its source before anything changes, and the step is added to the follow-up above.
Finding discrepancy-42f49d4564b65f62 · All contested results · How findings are made and followed up