Contested result
Tranception and VESPAl: ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design and Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) disagree
- Low severity
- Not yet reviewed
- two-study-conflict
- different-task
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks Tranception above VESPAl in 17 of 18 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks VESPAl above Tranception in 6 of 7 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 Tranception above VESPAl in 18 of their 26 comparisons and VESPAl higher in 7; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks VESPAl higher on its own (6 of 7).
- Rank Tranception higher (1): ProteinGym
- Rank VESPAl higher (1): Livesey and Marsh 2025
- 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 Tranception higher | Ranks VESPAl higher | Ties |
|---|---|---|---|---|
| ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design and 6 more records · DOI | Agrees | 17 | 1 | 1 |
| Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) and 1 more record · DOI | Agrees | 1 | 6 | 0 |
Comparisons in ProteinGym (19)
| Protocol | Dataset | Metric | Tranception | VESPAl | Higher |
|---|---|---|---|---|---|
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Activity assays: mean over proteins of assay-level Spearman), unitless | 0.465 | 0.429 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Binding assays: mean over proteins of assay-level Spearman), unitless | 0.349 | 0.347 | Tie |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Expression assays: mean over proteins of assay-level Spearman), unitless | 0.45 | 0.326 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, High MSA depth proteins: mean over proteins of assay-level Spearman), unitless | 0.471 | 0.449 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Human proteins: mean over proteins of assay-level Spearman), unitless | 0.455 | 0.394 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Low MSA depth proteins: mean over proteins of assay-level Spearman), unitless | 0.421 | 0.377 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Medium MSA depth proteins: mean over proteins of assay-level Spearman), unitless | 0.443 | 0.411 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Organismal fitness assays: mean over proteins of assay-level Spearman), unitless | 0.435 | 0.403 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Other eukaryote proteins: mean over proteins of assay-level Spearman), unitless | 0.497 | 0.472 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Prokaryote proteins: mean over proteins of assay-level Spearman), unitless | 0.414 | 0.434 | VESPAl |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Stability assays: mean over proteins of assay-level Spearman), unitless | 0.471 | 0.461 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, Virus proteins: mean over proteins of assay-level Spearman), unitless | 0.438 | 0.403 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, mean over selection types of the per-type mean over proteins of assay-level Spearman (all 217 assays)), unitless | 0.434 | 0.393 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 1 substitution: mean over protein and selection-type groups of assay-level Spearman), unitless | 0.422 | 0.386 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 2 substitutions: mean over protein and selection-type groups of assay-level Spearman), unitless | 0.254 | 0.141 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 3 substitutions: mean over protein and selection-type groups of assay-level Spearman), unitless | 0.346 | 0.321 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 4 substitutions: mean over protein and selection-type groups of assay-level Spearman), unitless | 0.325 | 0.282 | Tranception |
| ProteinGym v1.3 zero-shot DMS substitutions | ProteinGym DMS substitution assays at commit 144fe22 (217 assays) | Spearman (ProteinGym zero-shot DMS substitutions, variants with 5 or more substitutions: mean over protein and selection-type groups of assay-level Spearman), unitless | 0.387 | 0.32 | Tranception |
| ProteinGym AMFR official zero-shot Spearman snapshot | ProteinGym AMFR 4G3O official snapshot cohort | Spearman, unitless | 0.356 | 0.228 | Tranception |
Comparisons in Livesey and Marsh 2025 (7)
| Protocol | Dataset | Metric | Tranception | VESPAl | Higher |
|---|---|---|---|---|---|
| Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense | Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins) | Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each), percent | 39.7 | 55.2 | VESPAl |
| 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 | 44.5 | 53.5 | VESPAl |
| 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 | 6.44 | 10.9 | VESPAl |
| 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 | 51.9 | 48.8 | Tranception |
| 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 | 39.3 | 56.6 | VESPAl |
| 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 | 45.1 | 51.6 | VESPAl |
| 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 | 46.6 | 52.5 | VESPAl |
What disagrees
- studies
- 2
- Compared
- Tranception, VESPAl
- Study that disagrees
- Other studies
- Rule
- two-study-conflict; different-task
- 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.
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