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Protocol

Protective-antigen classification feature comparison (vaccine-antigen candidate prediction)

Protective-antigen classification feature comparison · Table 1.. Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.

SourcesEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1.: Val Accuracy, Protective-antigen classification feature comparison

3 evaluations · 21 metric rows

At a glance

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
PropertyDescription and evidence
DatasetsNot extracted or verified for this record.
OrganismsNot extracted or verified for this record.
AssaysNot extracted or verified for this record.
SplitsNot extracted or verified for this record.
Allowed inputsNot extracted or verified for this record.
AdaptationNot extracted or verified for this record.
MetricsNot extracted or verified for this record.
BaselinesNot extracted or verified for this record.

How it works

Evaluation in this paper

Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.

SourcesEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1.: Val Accuracy, Protective-antigen classification feature comparison

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

Protective-antigen classification feature comparison · Table 1.

Val Accuracy (fraction) · Higher values are better for this metric.

Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.

Evaluation protocol · Protective-antigen classification feature comparison

  1. Original · Configuration · Author-reported evaluation0.96 ± 0.008
  2. ESM Only · Configuration · Author-reported evaluation0.96 ± 0.005
  3. Combined · Configuration · Author-reported evaluation0.97 ± 0.004

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1.: Val Accuracy, Protective-antigen classification feature comparison
Values, uncertainty and evidence
Val Accuracy: original source values
Tested entityPrinted valueUncertaintyEvidence
Original · Configuration0.96 ± 0.008 fractiontype: reported_plus_minus_type_unresolved; value: 0.008Author-reported evaluation · source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Original, column Val Accuracy; XML row2 column2
ESM Only · Configuration0.96 ± 0.005 fractiontype: reported_plus_minus_type_unresolved; value: 0.005Author-reported evaluation · source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row ESM Only, column Val Accuracy; XML row3 column2
Combined · Configuration0.97 ± 0.004 fractiontype: reported_plus_minus_type_unresolved; value: 0.004Author-reported evaluation · source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Combined, column Val Accuracy; XML row4 column2
Scope and limitations
  • Reported± values preserved; uncertainty type and resampling denominator not established in inspected methods.
  • Published prose states specificity equal but table contains differences; table values retained.
  • No interval assigned unless printed in source cell.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 3 evaluations · 21 metric rows. Different protocols are not a single leaderboard.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
ESM Only: Protective-antigen classification feature comparison

Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.

Author-reported evaluation · Evaluation metadata: needs review

0.85 ± 0.036 AUPRC

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.036

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row ESM Only, column AUPRC; XML row3 column7

Source checking is not independent reproduction.

0.98 ± 0.004 Specificity

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.004

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row ESM Only, column Specificity; XML row3 column4

Source checking is not independent reproduction.

0.75 ± 0.063 Sensitivity

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.063

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row ESM Only, column Sensitivity; XML row3 column3

Source checking is not independent reproduction.

0.96 ± 0.005 Val Accuracy

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.005

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row ESM Only, column Val Accuracy; XML row3 column2

Source checking is not independent reproduction.

0.77 ± 0.043 MCC

Unit: dimensionless · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.043

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row ESM Only, column MCC; XML row3 column6

Source checking is not independent reproduction.

0.94 AUROC

Unit: fraction · Direction: higher

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row ESM Only, column AUROC; XML row3 column8

Source checking is not independent reproduction.

0.96 ± 0.007 Weighted F1

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.007

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row ESM Only, column Weighted F1; XML row3 column5

Source checking is not independent reproduction.

Combined: Protective-antigen classification feature comparison

Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.

Author-reported evaluation · Evaluation metadata: needs review

0.85 ± 0.021 MCC

Unit: dimensionless · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.021

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Combined, column MCC; XML row4 column6

Source checking is not independent reproduction.

0.99 ± 0.004 Specificity

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.004

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Combined, column Specificity; XML row4 column4

Source checking is not independent reproduction.

0.97 ± 0.004 Weighted F1

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.004

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Combined, column Weighted F1; XML row4 column5

Source checking is not independent reproduction.

0.97 ± 0.004 Val Accuracy

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.004

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Combined, column Val Accuracy; XML row4 column2

Source checking is not independent reproduction.

0.92 ± 0.013 AUPRC

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.013

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Combined, column AUPRC; XML row4 column7

Source checking is not independent reproduction.

0.83 ± 0.045 Sensitivity

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.045

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Combined, column Sensitivity; XML row4 column3

Source checking is not independent reproduction.

0.97 AUROC

Unit: fraction · Direction: higher

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Combined, column AUROC; XML row4 column8

Source checking is not independent reproduction.

Original: Protective-antigen classification feature comparison

Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.

Author-reported evaluation · Evaluation metadata: needs review

0.94 AUROC

Unit: fraction · Direction: higher

Uncertainty: unreported

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Original, column AUROC; XML row2 column8

Source checking is not independent reproduction.

0.96 ± 0.008 Weighted F1

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.008

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Original, column Weighted F1; XML row2 column5

Source checking is not independent reproduction.

0.78 ± 0.046 MCC

Unit: dimensionless · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.046

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Original, column MCC; XML row2 column6

Source checking is not independent reproduction.

0.84 ± 0.049 AUPRC

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.049

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Original, column AUPRC; XML row2 column7

Source checking is not independent reproduction.

0.74 ± 0.071 Sensitivity

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.071

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Original, column Sensitivity; XML row2 column3

Source checking is not independent reproduction.

0.96 ± 0.008 Val Accuracy

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.008

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Original, column Val Accuracy; XML row2 column2

Source checking is not independent reproduction.

0.99 ± 0.004 Specificity

Unit: fraction · Direction: higher

Uncertainty: type: reported plus minus type unresolved; value: 0.004

Scored: Not reported · Eligible: Not reported

source checkedEnhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Table 1., row Original, column Specificity; XML row2 column4

Source checking is not independent reproduction.

Papers and result coverage

Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.

Paper or primary resourceVersionReference
Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Featurespreprint version in PMCRead source
DOI: 10.1101/2024.09.04.611295

What is still missing

  • Independent batch review before import; preserve existing observation identities.
Search and extraction details

complete comparison tables extracted pending publication review

Searches

  • Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features primary paper benchmark results

Evidence locations

  • Table 1.: Val Accuracy, Protective-antigen classification feature comparison

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

No source-reviewed explanatory claims are recorded here yet.

Profile review details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Stable record: paper-protocol-a7bf3c8f6b432c3093

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

3 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statementOriginal source and locationReview and provenance
Evaluation in this paper

Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.

Individual claims
Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features

Original source ↗

Table 1.: Val Accuracy, Protective-antigen classification feature comparison

Version: preprint version in PMC
Retrieved: 2026-09-17T07:56:15.123850+00:00

source checked

automated source review · 2026-09-17

Audit details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Field: attributes.profile.sections.0.body

Source artifact SHA-256: b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Introduction

Protective-antigen classification feature comparison · Table 1.. Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.

Individual claims
Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features

Original source ↗

Table 1.: Val Accuracy, Protective-antigen classification feature comparison

Version: preprint version in PMC
Retrieved: 2026-09-17T07:56:15.123850+00:00

source checked

automated source review · 2026-09-17

Audit details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Field: attributes.profile.summary

Source artifact SHA-256: b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: evaluates task

reported-task-47465954d606e6

Individual claims
Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features

Original source ↗

Table 1.: Val Accuracy, Protective-antigen classification feature comparison

Version: preprint version in PMC
Retrieved: 2026-09-17T07:56:15.123850+00:00

source checked

automated source review · 2026-09-17

Audit details

Field: links:evaluates_task:reported-task-47465954d606e6

Claim: paper-claim-6875cf87327d9dc4af

Source artifact SHA-256: b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: paper-protocol-a7bf3c8f6b432c3093

areas
proteins-complexes
tasks
vaccine-antigen candidate prediction
entity level
protocol
protocol
Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.
comparison panels
id: part2-vaxign-esm-2024-T1-1dcdb2e905; title: Protective-antigen classification feature comparison · Table 1.; protocol id: paper-protocol-a7bf3c8f6b432c3093; dataset id: paper-dataset-c1edd1f6f7e93d9f6e; metric: Val Accuracy; unit: fraction; direction: higher; result ids: paper-result-cff4683107e593c8b4; paper-result-6884d284eba92a5c06; paper-result-7af576f4ade426848e; source ids: part2-vaxign-esm-2024; source locator: Table 1.: Val Accuracy, Protective-antigen classification feature comparison; context: Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.; caveats: Reported± values preserved; uncertainty type and resampling denominator not established in inspected methods.; Published prose states specificity equal but table contains differences; table values retained.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-vaxign-esm-2024-T1-aaa5cd1083; title: Protective-antigen classification feature comparison · Table 1.; protocol id: paper-protocol-a7bf3c8f6b432c3093; dataset id: paper-dataset-c1edd1f6f7e93d9f6e; metric: Sensitivity; unit: fraction; direction: higher; result ids: paper-result-c8bfac2d90d81feeb3; paper-result-5b5f63e259d93937fa; paper-result-e97d7b6a6ecb22428f; source ids: part2-vaxign-esm-2024; source locator: Table 1.: Sensitivity, Protective-antigen classification feature comparison; context: Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.; caveats: Reported± values preserved; uncertainty type and resampling denominator not established in inspected methods.; Published prose states specificity equal but table contains differences; table values retained.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-vaxign-esm-2024-T1-a4c286072e; title: Protective-antigen classification feature comparison · Table 1.; protocol id: paper-protocol-a7bf3c8f6b432c3093; dataset id: paper-dataset-c1edd1f6f7e93d9f6e; metric: Specificity; unit: fraction; direction: higher; result ids: paper-result-ef311f3bd240402622; paper-result-368137517fff441366; paper-result-4fbe5feb8bf19db3cf; source ids: part2-vaxign-esm-2024; source locator: Table 1.: Specificity, Protective-antigen classification feature comparison; context: Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.; caveats: Reported± values preserved; uncertainty type and resampling denominator not established in inspected methods.; Published prose states specificity equal but table contains differences; table values retained.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-vaxign-esm-2024-T1-7185c1558b; title: Protective-antigen classification feature comparison · Table 1.; protocol id: paper-protocol-a7bf3c8f6b432c3093; dataset id: paper-dataset-c1edd1f6f7e93d9f6e; metric: Weighted F1; unit: fraction; direction: higher; result ids: paper-result-651ddc5c811de9e8bb; paper-result-f4fc84c79d3f4a5dd2; paper-result-6314ca1ea38e3cc0b5; source ids: part2-vaxign-esm-2024; source locator: Table 1.: Weighted F1, Protective-antigen classification feature comparison; context: Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.; caveats: Reported± values preserved; uncertainty type and resampling denominator not established in inspected methods.; Published prose states specificity equal but table contains differences; table values retained.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-vaxign-esm-2024-T1-e43ff059cc; title: Protective-antigen classification feature comparison · Table 1.; protocol id: paper-protocol-a7bf3c8f6b432c3093; dataset id: paper-dataset-c1edd1f6f7e93d9f6e; metric: MCC; unit: dimensionless; direction: higher; result ids: paper-result-774bc1695cb59c05ac; paper-result-bc30cb500a5d4c0a21; paper-result-0588c3eaf97f2abf9e; source ids: part2-vaxign-esm-2024; source locator: Table 1.: MCC, Protective-antigen classification feature comparison; context: Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.; caveats: Reported± values preserved; uncertainty type and resampling denominator not established in inspected methods.; Published prose states specificity equal but table contains differences; table values retained.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-vaxign-esm-2024-T1-6ed0c48e92; title: Protective-antigen classification feature comparison · Table 1.; protocol id: paper-protocol-a7bf3c8f6b432c3093; dataset id: paper-dataset-c1edd1f6f7e93d9f6e; metric: AUPRC; unit: fraction; direction: higher; result ids: paper-result-7b567777b97aa43653; paper-result-04617e3534e8f83c6d; paper-result-b0ccdc4a3d8bbe1ae7; source ids: part2-vaxign-esm-2024; source locator: Table 1.: AUPRC, Protective-antigen classification feature comparison; context: Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.; caveats: Reported± values preserved; uncertainty type and resampling denominator not established in inspected methods.; Published prose states specificity equal but table contains differences; table values retained.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-vaxign-esm-2024-T1-0189da3e2b; title: Protective-antigen classification feature comparison · Table 1.; protocol id: paper-protocol-a7bf3c8f6b432c3093; dataset id: paper-dataset-c1edd1f6f7e93d9f6e; metric: AUROC; unit: fraction; direction: higher; result ids: paper-result-11bf48c7b68484cc04; paper-result-d002da139f31ba9e3f; paper-result-ff4ba6f92feb183bff; source ids: part2-vaxign-esm-2024; source locator: Table 1.: AUROC, Protective-antigen classification feature comparison; context: Original 509 features vs ESM 1,280 features vs combined 1,789 features. 372 protection-positive and 3,720 protection-negative samples.; caveats: Reported± values preserved; uncertainty type and resampling denominator not established in inspected methods.; Published prose states specificity equal but table contains differences; table values retained.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17
benchmark research
review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-vaxign-esm-2024; inspected locators: Table 1.: Val Accuracy, Protective-antigen classification feature comparison; searched queries: Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features primary paper benchmark results; gaps: Independent batch review before import; preserve existing observation identities.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
legacy kinds
benchmark
entity classification
review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-vaxign-esm-2024; source locator: Table 1.: Val Accuracy, Protective-antigen classification feature comparison; ambiguities: None recorded
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