Evaluation

Graphormer on DeepProtein beta-lactamase (PEER) (ρ ↑)

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Graphormer (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): ρ ↑ Dataset: beta-lactamase (PEER)	0.067±0.046 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.046 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Graphormer on DeepProtein beta-lactamase (PEER) (ρ ↑) lit-protein-20261011-deepprotein-protocol-beta-lactamase-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑'

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

DeepProtein beta-lactamase (PEER): ρ ↑

Configuration: Graphormer (DeepProtein benchmark)
Protocol: DeepProtein beta-lactamase (PEER): ρ ↑
Dataset: beta-lactamase (PEER)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: lit-protein-20261011-deepprotein-protocol-beta-lactamase-rho
dataset version: Not reported
split: 4158/520/520
population: train/valid/test 4158/520/520
inputs: Amino-acid sequence (graph models also take the protein graph)
adaptation: Trained on the task's training split with the DeepProtein default configuration
metric implementation: Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split
aggregation: Mean over five random seeds
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: 4158/520/520
Adaptation: Trained on the task's training split with the DeepProtein default configuration
Scoring implementation: Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split

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Evidence

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Evidence table

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20 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation Trained on the task's training split with the DeepProtein default configuration Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Mean over five random seeds Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	missing or unspecified No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version Not reported Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	missing or unspecified No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs Amino-acid sequence (graph models also take the protein graph) Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: metric implementation Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: population train/valid/test 4158/520/520 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: protocol id lit-protein-20261011-deepprotein-protocol-beta-lactamase-rho Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: split 4158/520/520 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
N runs 5 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑' Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded author reported Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.n_runs` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

DeepProtein: deep learning library and benchmark for protein sequence learning · Original source · Version of record, Bioinformatics 2025 (PMC12553333 JATS full text)

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Technical metadata and extraction receipts

Stable ID: lit-protein-20261011-deepprotein-eval-beta-lactamase-rho-graphormer

areas: protein-function
contexts: research
origin: author_reported
protocol: lit-protein-20261011-deepprotein-protocol-beta-lactamase-rho
version: Primary source as retrieved 2026-10-11
comparison: protocol id: lit-protein-20261011-deepprotein-protocol-beta-lactamase-rho; dataset version: Not reported; split: 4158/520/520; population: train/valid/test 4158/520/520; inputs: Amino-acid sequence (graph models also take the protein graph); adaptation: Trained on the task's training split with the DeepProtein default configuration; metric implementation: Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split; aggregation: Mean over five random seeds; budget: Not reported
source locator: Table 2. row 'Graphormer', column group 'β-lactamase', column 'ρ ↑'
missing metadata: comparison.budget: reason: unreported; comparison.dataset version: reason: unreported
n runs: 5
seeds: Five random seeds (table footnote a: 'we used five different random seeds to perform independent runs, reporting the average results along with their standard deviations')

Related records

system: Graphormer (DeepProtein benchmark)
assessment: DeepProtein beta-lactamase (PEER): ρ ↑
data: beta-lactamase (PEER)
evaluation: Graphormer beta-lactamase (PEER) ρ ↑

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