Contested result

ProGen2 and Tranception: ProteinGym AMFR assay-level Spearman comparison reverses the order

Low severity
Not yet reviewed
Ordering reversal
Different tasks across studies

ProteinGym AMFR assay-level Spearman comparison ranks Tranception above ProGen2 in 18 of 18 comparisons; other studies rank ProGen2 above Tranception in 6 of 6.

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

Livesey and Marsh 2025 ranks ProGen2 above Tranception in all 6 of its comparisons. ProteinGym AMFR assay-level Spearman… ranks Tranception above ProGen2 in all 18 comparisons that are not ties (2 are ties).

Rank ProGen2 higher (1): Livesey and Marsh 2025
Rank Tranception higher (1): ProteinGym AMFR assay-level Spearman… (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.

ProGen2 higherTieTranception higherNumbers are counts of comparisons; the outlined bar is the paper that disagrees.

Papers compared (2)
Paper	Role	Ranks ProGen2 higher	Ranks Tranception higher	Ties
ProteinGym AMFR assay-level Spearman comparison and 4 more records · Repository	Disagrees	0	18	2
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 AMFR assay-level Spearman… (20)

Protocol	Dataset	Metric	ProGen2	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	0.406	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	0.302	0.372	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	0.437	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	0.442	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	0.422	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	0.339	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	0.412	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	0.387	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	0.458	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	0.418	0.414	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	0.445	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	0.402	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	0.391	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	0.384	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	0.182	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	0.271	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	0.234	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	0.28	0.387	Tranception
ProteinGym AMFR official zero-shot Spearman snapshot	ProteinGym AMFR 4G3O official snapshot cohort	Spearman, unitless	0.056	0.402	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	0.851	0.852	Tie

Comparisons in Livesey and Marsh 2025 (6)

Protocol	Dataset	Metric	ProGen2	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	56.7	44.5	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	8.89	6.44	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	61	51.9	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	53.1	39.3	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	56.5	45.1	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	58.6	46.6	ProGen2

What disagrees

Other studies: rank ProGen2 above Tranception in 6 of 6 comparisons
This study: ranks Tranception above ProGen2 in 18 of 18 comparisons

Compared: ProGen2, Tranception
Study that disagrees: 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
Other studies: Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML), Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8)
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.

In the study that disagrees (36)
Study	Tool	Protocol or benchmark	Metric	Value
ProteinGym AMFR assay-level Spearman comparison; Protocol metadata evidence: proteingym-reference_files-DMS_substitutions.csv	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym AMFR official zero-shot Spearman snapshot	Spearman	0.056
ProteinGym AMFR assay-level Spearman comparison; Protocol metadata evidence: proteingym-reference_files-DMS_substitutions.csv	Tranception M [ProteinGym 144fe22b snapshot]	ProteinGym AMFR official zero-shot Spearman snapshot	Spearman	0.402
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 Base [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Expression assays: mean over proteins of assay-level Spearman)	0.437
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 Base [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Human proteins: mean over proteins of assay-level Spearman)	0.422
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Activity assays: mean over proteins of assay-level Spearman)	0.406
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Low MSA depth proteins: mean over proteins of assay-level Spearman)	0.339
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, mean over selection types of the per-type mean over proteins of assay-level Spearman (all 217 assays))	0.391
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 1 substitution: mean over protein and selection-type groups of assay-level Spearman)	0.384
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 2 substitutions: mean over protein and selection-type groups of assay-level Spearman)	0.182
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 3 substitutions: mean over protein and selection-type groups of assay-level Spearman)	0.271
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 4 substitutions: mean over protein and selection-type groups of assay-level Spearman)	0.234
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 5 or more substitutions: mean over protein and selection-type groups of assay-level Spearman)	0.28
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Binding assays: mean over proteins of assay-level Spearman)	0.302
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Organismal fitness assays: mean over proteins of assay-level Spearman)	0.387
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Stability assays: mean over proteins of assay-level Spearman)	0.445
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, High MSA depth proteins: mean over proteins of assay-level Spearman)	0.442
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Medium MSA depth proteins: mean over proteins of assay-level Spearman)	0.412
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Other eukaryote proteins: mean over proteins of assay-level Spearman)	0.458
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Progen2 XL [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Virus proteins: mean over proteins of assay-level Spearman)	0.402
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, mean over selection types of the per-type mean over proteins of assay-level Spearman (all 217 assays))	0.434
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 1 substitution: mean over protein and selection-type groups of assay-level Spearman)	0.422
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 2 substitutions: mean over protein and selection-type groups of assay-level Spearman)	0.254
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 3 substitutions: mean over protein and selection-type groups of assay-level Spearman)	0.346
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 4 substitutions: mean over protein and selection-type groups of assay-level Spearman)	0.325
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, variants with 5 or more substitutions: mean over protein and selection-type groups of assay-level Spearman)	0.387
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Activity assays: mean over proteins of assay-level Spearman)	0.465
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Expression assays: mean over proteins of assay-level Spearman)	0.45
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Organismal fitness assays: mean over proteins of assay-level Spearman)	0.435
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Stability assays: mean over proteins of assay-level Spearman)	0.471
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, High MSA depth proteins: mean over proteins of assay-level Spearman)	0.471
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Low MSA depth proteins: mean over proteins of assay-level Spearman)	0.421
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Medium MSA depth proteins: mean over proteins of assay-level Spearman)	0.443
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Human proteins: mean over proteins of assay-level Spearman)	0.455
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Other eukaryote proteins: mean over proteins of assay-level Spearman)	0.497
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception L [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Virus proteins: mean over proteins of assay-level Spearman)	0.438
ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22; Protocol metadata evidence: proteingym-proteingym-performance_DMS_benchmarks.py	Tranception S [ProteinGym 144fe22b snapshot]	ProteinGym v1.3 zero-shot DMS substitutions	Spearman (ProteinGym zero-shot DMS substitutions, Binding assays: mean over proteins of assay-level Spearman)	0.372

In the other studies (12)
Study	Tool	Protocol or benchmark	Metric	Value
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ProGen2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets)	56.7
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ProGen2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	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)	8.89
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	Tranception (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets)	44.5
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	Tranception (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	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)	6.44
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ProGen2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, direct assays only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, direct DMS assays only)	61
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	Tranception (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, direct assays only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, direct DMS assays only)	51.9
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ProGen2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, indirect assays only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, indirect DMS assays only)	53.1
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	Tranception (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, indirect assays only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, indirect DMS assays only)	39.3
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ProGen2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions with gaps filled	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)	58.6
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	Tranception (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions with gaps filled	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)	46.6
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ProGen2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, SNV-accessible substitutions only)	56.5
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	Tranception (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, SNV-accessible substitutions only)	45.1

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-9cbc05f4ed8c7e40 · All contested results · How findings are made and followed up