Contested result
ProGen2 and Tranception: Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) reverses the order
- Low severity
- Not yet reviewed
- Ordering reversal
- Different tasks across studies
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ProGen2 above Tranception in 6 of 6 comparisons; other studies rank Tranception above ProGen2 in 18 of 18.
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
ProteinGym AMFR assay-level Spearman… ranks Tranception above ProGen2 in all 18 comparisons that are not ties (2 are ties). Livesey and Marsh 2025 ranks ProGen2 above Tranception in all 6 of its comparisons.
- Rank Tranception higher (1): ProteinGym AMFR assay-level Spearman…
- Rank ProGen2 higher (1): Livesey and Marsh 2025 (disagrees)
- 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 ProGen2 higher | Ties |
|---|---|---|---|---|
| Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) and 1 more record · DOI | Disagrees | 0 | 6 | 0 |
| ProteinGym AMFR assay-level Spearman comparison and 4 more records · Repository | Agrees | 18 | 0 | 2 |
Comparisons in Livesey and Marsh 2025 (6)
| Protocol | Dataset | Metric | Tranception | ProGen2 | 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 | 44.5 | 56.7 | ProGen2 |
| 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 | 8.89 | ProGen2 |
| 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 | 61 | ProGen2 |
| 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 | 53.1 | ProGen2 |
| 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 | 56.5 | ProGen2 |
| 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 | 58.6 | ProGen2 |
Comparisons in ProteinGym AMFR assay-level Spearman… (20)
| Protocol | Dataset | Metric | Tranception | ProGen2 | 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 | 0.406 | 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 | 0.372 | 0.302 | 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 | 0.45 | 0.437 | 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 | 0.442 | 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 | 0.422 | 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 | 0.339 | 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 | 0.412 | 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 | 0.387 | 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 | 0.458 | 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 | 0.418 | Tie |
| 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 | 0.445 | 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 | 0.402 | 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 | 0.391 | 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 | 0.384 | 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 | 0.182 | 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 | 0.271 | 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 | 0.234 | 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 | 0.28 | Tranception |
| ProteinGym AMFR official zero-shot Spearman snapshot | ProteinGym AMFR 4G3O official snapshot cohort | Spearman, unitless | 0.402 | 0.056 | Tranception |
| ProteinGym clinical indels, zero-shot, average AUC (commit 144fe22) | ProteinGym clinical indel benchmark at commit 144fe22 | AUROC (ProteinGym clinical indels, zero-shot, Average_AUC over proteins), unitless | 0.852 | 0.851 | Tie |
What disagrees
- Other studies
- rank Tranception above ProGen2 in 18 of 18 comparisons
- This study
- ranks ProGen2 above Tranception in 6 of 6 comparisons
- Compared
- ProGen2, Tranception
- Study that disagrees
- Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML), Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8)
- Other studies
- ProteinGym AMFR assay-level Spearman comparison, ProteinGym clinical supervised substitutions AUC summary at commit 144fe22, ProteinGym clinical zero-shot indels AUC summary at commit 144fe22, ProteinGym clinical zero-shot substitutions AUC summary at commit 144fe22, ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22
- Rule
- Ordering reversal; different tasks across studies
- Model identity
- Matched across studies partly through links not yet reviewed
The compared numbers
Each value links to its result record and source. Compare values within one protocol; the rule compares rankings, not raw values across protocols.
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-94e49bc95a0c9f73 · All contested results · How findings are made and followed up