Contested result
CARP and Tranception: 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 CARP in 19 of 19 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks CARP above Tranception in 6 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 CARP above Tranception in 6 of their 25 comparisons and Tranception higher in 19. Of those papers, ProteinGym ranks Tranception higher on its own (19 of 19).
- Rank CARP higher (1): Livesey and Marsh 2025
- Rank Tranception higher (1): ProteinGym
- 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 CARP higher | Ranks Tranception higher | Ties |
|---|---|---|---|---|
| ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design and 6 more records · DOI | Agrees | 0 | 19 | 0 |
| Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) and 1 more record · DOI | Agrees | 6 | 0 | 0 |
Comparisons in ProteinGym (19)
| Protocol | Dataset | Metric | CARP | Tranception | 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 | 0.395 | 0.465 | 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 | 0.273 | 0.349 | Tranception |
| 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 | 0.397 | 0.45 | 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 | 0.424 | 0.471 | 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 | 0.417 | 0.455 | 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 | 0.331 | 0.421 | 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 | 0.374 | 0.443 | 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 | 0.366 | 0.435 | 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 | 0.395 | 0.497 | 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 | 0.381 | 0.414 | Tranception |
| 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 | 0.412 | 0.471 | 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 | 0.284 | 0.438 | 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 | 0.369 | 0.434 | 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 | 0.391 | 0.422 | 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 | 0.213 | 0.254 | 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 | 0.172 | 0.346 | 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 | 0.159 | 0.325 | 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 | 0.162 | 0.387 | Tranception |
| ProteinGym AMFR official zero-shot Spearman snapshot | ProteinGym AMFR 4G3O official snapshot cohort | Spearman, unitless | 0.165 | 0.356 | Tranception |
Comparisons in Livesey and Marsh 2025 (6)
| Protocol | Dataset | Metric | CARP | Tranception | 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 | 76.1 | 44.5 | CARP |
| 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 | 20 | 6.44 | CARP |
| 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 | 73 | 51.9 | CARP |
| 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 | 77.7 | 39.3 | CARP |
| 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 | 77.2 | 45.1 | CARP |
| 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 | 71.2 | 46.6 | CARP |
What disagrees
- studies
- 2
- Compared
- CARP, Tranception
- 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.
Finding discrepancy-3ed9b6f7dd01671f · All contested results · How findings are made and followed up