Evaluation

Prot-T5-XL on DeepProtein Subcellular localization (PEER) (Averaged F1 ↑)

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Evaluation results

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Subcellular localization (PEER): Averaged F1 ↑ Dataset: Subcellular localization (PEER)	69.86 ± 0.39% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.39 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 Prot-T5-XL on DeepProtein Subcellular localization (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-subcellular-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑'

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Evaluation procedure

DeepProtein Subcellular localization (PEER): Averaged F1 ↑

Configuration: Prot-T5-XL (DeepProtein benchmark)
Protocol: DeepProtein Subcellular localization (PEER): Averaged F1 ↑
Dataset: Subcellular localization (PEER)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: lit-protein-20261011-deepprotein-protocol-subcellular-avg-f1
dataset version: Not reported
split: 8945/2248/2768
population: train/valid/test 8945/2248/2768
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: averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale
aggregation: Mean over five random seeds
budget: Not reported

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

Reproduction

Split: 8945/2248/2768
Adaptation: Trained on the task's training split with the DeepProtein default configuration
Scoring implementation: averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale

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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 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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 averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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 8945/2248/2768 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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-subcellular-avg-f1 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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 8945/2248/2768 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Table 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑' 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-subcellular-avg-f1-prot-t5-xl

areas: protein-function
contexts: research
origin: author_reported
protocol: lit-protein-20261011-deepprotein-protocol-subcellular-avg-f1
version: Primary source as retrieved 2026-10-11
comparison: protocol id: lit-protein-20261011-deepprotein-protocol-subcellular-avg-f1; dataset version: Not reported; split: 8945/2248/2768; population: train/valid/test 8945/2248/2768; 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: averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale; aggregation: Mean over five random seeds; budget: Not reported
source locator: Table 3. row 'Prot-T5-XL', column group 'Subcellular', column 'Averaged F1 ↑'
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: Prot-T5-XL (DeepProtein benchmark)
assessment: DeepProtein Subcellular localization (PEER): Averaged F1 ↑
data: Subcellular localization (PEER)
evaluation: Prot-T5-XL Subcellular localization (PEER) Averaged F1 ↑

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