Task

vaccine-antigen candidate prediction

Vaccine-antigen classification tests transfer by withholding one organism’s labeled protein examples.

Sources

4 evaluations · 22 results

Overview

Datasets

Previously curated vaccine-antigen positive/negative datasets used by Vaxign-ML and Vaxign-DL.

Metrics

Accuracy, sensitivity, specificity, weighted F1, MCC, AUROC and AUPRC.

Allowed inputs

Protein sequence representations.

Sources

Evaluation procedure diagram

How it worksComputational evaluation flow

Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.

Sources

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

Evaluation scope and datasetMetric and reported setup

Protective-antigen classification feature comparison · Table 1.

Val Accuracy (fraction) · Higher values are better.

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

Evidence origin: Author-reported evaluation.

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

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.

Comparison details and limitations

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

No interval assigned unless printed in source cell.

Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

Find a tested model or method

Showing 3 of 3 matching rows.

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Tested configuration

00.250.50.751

Reported score

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Evaluation methodology

Previously curated vaccine-antigen positive/negative datasets used by Vaxign-ML and Vaxign-DL. Leave-one-pathogen-out evaluation trains on the remaining organisms and predicts the withheld organism’s labels. Accuracy, sensitivity, specificity, weighted F1, MCC, AUROC and AUPRC. Vaxign-ML and Vaxign-DL are the referenced baseline datasets/methods. Dataset curation removes positive-protein homologs above 30% sequence similarity and selects negative proteins below 30% similarity to positives. The LOPOV experiment additionally withholds one of ten pathogens. These controls do not establish that sequences were absent from ESM-1b pretraining.

Sources

Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39; Methods: Collection of Positive and Negative protein sequences; Leave-one-pathogen-out validation

Evaluation design

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

Protocols

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

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

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Vaxign-DL + ESM: vaccine-antigen candidate prediction

Run this benchmark

Choose a concrete protocol before running an evaluation. Its inputs, split and scoring rules determine which results can be compared.

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

Run instructions

No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

Long proteins may be omitted or truncated, changing evaluation coverage.
Sources
Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39

Profile review details

Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change.

Stable record: reported-task-47465954d606e6

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Datasets	Previously curated vaccine-antigen positive/negative datasets used by Vaxign-ML and Vaxign-DL. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39
Splits	Leave-one-pathogen-out evaluation trains on the remaining organisms and predicts the withheld organism’s labels. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39
Metrics	Accuracy, sensitivity, specificity, weighted F1, MCC, AUROC and AUPRC. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39
Baselines	Vaxign-ML and Vaxign-DL are the referenced baseline datasets/methods. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39
Leakage controls	Dataset curation removes positive-protein homologs above 30% sequence similarity and selects negative proteins below 30% similarity to positives. The LOPOV experiment additionally withholds one of ten pathogens. These controls do not establish that sequences were absent from ESM-1b pretraining. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: Collection of Positive and Negative protein sequences; Leave-one-pathogen-out validation
Uncertainty	Tables 1–3 include ± terms for most metrics but not AUROC. Their captions and the Deep learning pipeline section do not define whether those terms are standard deviations, standard errors or confidence intervals, or specify their repetition count. · Not reported in inspected sources Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: Deep learning pipeline; Tables 1–3
Entity type	Paper-specific computational evaluation protocol. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39
Organisms	Multiple pathogen species in the curated antigen evaluation. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39
Assays	Vaccine-antigen positive/negative annotations. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39
Allowed inputs	Protein sequence representations. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39
Adaptation	Supervised candidate classification with leave-one-pathogen-out evaluation. Sources Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39

Evidence

Source checking verifies the cited claim or transcription. It does not establish 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 resource	Version	Reference
Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features	preprint version in PMC	Read source DOI: 10.1101/2024.09.04.611295

Historical gaps recorded on 2026-09-17

The catalogue now holds 22 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.

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

Tables1–2; Performance analysis and feature sets

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.

17 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39 Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps Input: Protein sequence representations. Evaluation: Leave-one-pathogen-out evaluation trains on the remaining organisms and predicts the withheld organism’s labels. Readout: Accuracy, sensitivity, specificity, weighted F1, MCC, AUROC and AUPRC. Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39 Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Computational evaluation flow Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39 Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Datasets Previously curated vaccine-antigen positive/negative datasets used by Vaxign-ML and Vaxign-DL. Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39 Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Splits Leave-one-pathogen-out evaluation trains on the remaining organisms and predicts the withheld organism’s labels. Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39 Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Adaptation Supervised candidate classification with leave-one-pathogen-out evaluation. Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39 Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Metrics Accuracy, sensitivity, specificity, weighted F1, MCC, AUROC and AUPRC. Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39 Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Baselines Vaxign-ML and Vaxign-DL are the referenced baseline datasets/methods. Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39 Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Leakage controls Dataset curation removes positive-protein homologs above 30% sequence similarity and selects negative proteins below 30% similarity to positives. The LOPOV experiment additionally withholds one of ten pathogens. These controls do not establish that sequences were absent from ESM-1b pretraining. Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: Collection of Positive and Negative protein sequences; Leave-one-pathogen-out validation Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Uncertainty Tables 1–3 include ± terms for most metrics but not AUROC. Their captions and the Deep learning pipeline section do not define whether those terms are standard deviations, standard errors or confidence intervals, or specify their repetition count. Individual claims	Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features Original source ↗ Methods: Deep learning pipeline; Tables 1–3 Version: preprint version in PMC Retrieved: 2026-09-16T10:41:06Z	unreported automated source review · 2026-09-16 Audit details Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `b76fff917addd0e9ff8a2fc843496132ecf832d3ceef248e3edf2dbc78baab5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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2 source records and release history

Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Original source · preprint version in PMC
Enhancing Vaxign-DL for Vaccine Candidate Prediction with added ESM-Generated Features · Original source · preprint version in PMC

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Technical metadata and extraction receipts

Stable ID: reported-task-47465954d606e6

areas: proteins-complexes
tasks: vaccine-antigen candidate prediction
entity level: task
version: Not reported
task: vaccine-antigen candidate prediction
scope note: Paper-specific evaluation task; protocol completeness requires further extraction.
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: Tables1–2; Performance analysis and feature sets; 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.
historical missing metadata: protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: vaxign-esm-2024; source locator: Methods: leave-one-pathogen-out validation; Performance evaluation; Results: long-protein coverage; cached text lines 18, 25–26, 39; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.

Related records

dataset: vaccine candidate validation
benchmark: Vaxign-DL + ESM: vaccine-antigen candidate prediction
evaluates task: Protective-antigen classification feature comparison (vaccine-antigen candidate prediction)

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