Task

pathogen detection

The source reports a separate metagenomic taxon-detection comparison, but its executable evaluation protocol remains incomplete.

Sources

Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133

1 evaluation · 1 result

Overview

Datasets

MetaHIT and iHMP shotgun-sequencing cohorts; the source describes expert annotations or high-confidence reference calls as ground truth without resolving their construction here.

Metrics

Precision, recall, F1 and ROC-AUC for the genomic comparison.

Allowed inputs

Metagenomic sequencing data and model-specific representations.

Sources

Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133

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

Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133

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

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

1 evaluation · 1 result. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Pipeline: TCINet + HTRS	Task: pathogen detection Dataset: MetaHIT	0.84 F1 fraction · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons The paper reports a MetaHIT/iHMP sequencing experiment in Section 4.3 and Table 3, but that section does not identify exact samples, split manifests or construction of its taxonomic reference labels. The five-fold procedure in Section 4.2 is described for different text/image datasets and cannot safely be assigned to this result. The printed score is retained; protocol identity remains unresolved and the row is excluded from comparisons.Enhancing pathogen identification through AI-assisted metagenomic sequencing · Section 4.2 Experimental details versus the additional metagenomic experiment in Section 4.3 and Table 3 Methods, coverage and source TCINet + HTRS: pathogen detection Taxonomy-constrained inference network with hierarchical taxonomy representation Aggregation: Not reported Enhancing pathogen identification through AI-assisted metagenomic sequencing · Table 3, MetaHIT dataset section, TCINet + HTRS (Ours) row, F1-score column

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Evaluation methodology

MetaHIT and iHMP shotgun-sequencing cohorts; the source describes expert annotations or high-confidence reference calls as ground truth without resolving their construction here. The genomic experiment in §4.3 does not specify a sample/split manifest. The five-fold procedure in §4.2 concerns other datasets and cannot supply this missing genomic protocol. Precision, recall, F1 and ROC-AUC for the genomic comparison. Kraken2 and MetaPhlAn3. The genomic experiment in §4.3 does not establish independence of the expert/reference-derived labels from the compared prediction systems.

Sources

Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133

Recorded evaluations

Each evaluation records what was tested and under which conditions.

TCINet + HTRS: pathogen detection

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

Section 4.3 reports a sequencing experiment, but does not fix sample accessions, split membership, genomic fitting or reference-label construction. The unrelated five-fold setup in §4.2 does not resolve these protocol gaps.
Sources
Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133

What remains unknown

Splits: The genomic experiment in §4.3 does not specify a sample/split manifest. The five-fold procedure in §4.2 concerns other datasets and cannot supply this missing genomic protocol.
Leakage controls: The genomic experiment in §4.3 does not establish independence of the expert/reference-derived labels from the compared prediction systems.
Uncertainty: MetaHIT/iHMP Table 3 gives point precision, recall, F1 and AUC values without a replicate count or confidence-interval procedure. The ± values and five-fold evaluation elsewhere concern other datasets and cannot supply uncertainty for this sequencing comparison.
Adaptation: Section 4.3 says the model is applied directly to preprocessed sequencing reads but does not specify its genomic fitting partition, checkpoint or whether MetaHIT/iHMP labels were available during fitting. The five-fold setup in §4.2 is attached to other datasets.

Profile review details

Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.

Stable record: reported-task-d3fd502fdc2b38

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	MetaHIT and iHMP shotgun-sequencing cohorts; the source describes expert annotations or high-confidence reference calls as ground truth without resolving their construction here. Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133
Splits	The genomic experiment in §4.3 does not specify a sample/split manifest. The five-fold procedure in §4.2 concerns other datasets and cannot supply this missing genomic protocol. · Not reported in inspected sources Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133
Metrics	Precision, recall, F1 and ROC-AUC for the genomic comparison. Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133
Baselines	Kraken2 and MetaPhlAn3. Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133
Leakage controls	The genomic experiment in §4.3 does not establish independence of the expert/reference-derived labels from the compared prediction systems. · Not reported in inspected sources Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133
Uncertainty	MetaHIT/iHMP Table 3 gives point precision, recall, F1 and AUC values without a replicate count or confidence-interval procedure. The ± values and five-fold evaluation elsewhere concern other datasets and cannot supply uncertainty for this sequencing comparison. · Not reported in inspected sources Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · §4.3, MetaHIT/iHMP experiment paragraph and Table 3; contrast §4.2 and Table 2
Entity type	Paper-specific computational evaluation protocol. Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133
Organisms	Human-cohort microbial communities in MetaHIT and iHMP. Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133
Assays	Shotgun sequencing; expert/reference-derived labels whose construction remains insufficiently specified. Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133
Allowed inputs	Metagenomic sequencing data and model-specific representations. Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133
Adaptation	Section 4.3 says the model is applied directly to preprocessed sequencing reads but does not specify its genomic fitting partition, checkpoint or whether MetaHIT/iHMP labels were available during fitting. The five-fold setup in §4.2 is attached to other datasets. · Not reported in inspected sources Sources Enhancing pathogen identification through AI-assisted metagenomic sequencing · §4.2–4.3, genomic sequencing experiment immediately preceding Table 3

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-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.

Paper or primary resource	Version	Reference
Enhancing pathogen identification through AI-assisted metagenomic sequencing	version of record	Read source DOI: 10.3389/fmicb.2025.1634194

Historical gaps recorded on 2026-09-17

The catalogue now holds 1 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.

Comparison blocked: Section 4.3 lacks exact sample/split manifest and reference-label construction.
Section 4.2 five-fold procedure concerns other datasets and cannot be assigned to Table 3.
Do not claim the genomic experiment is absent: Section 4.3 explicitly describes it.

Search and extraction details

source concern comparison blocked

Searches

"PMC12493982"

Evidence locations

Section 4.3
Table 3

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 pathogen identification through AI-assisted metagenomic sequencing Original source ↗ Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133 Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps Input: Metagenomic sequencing data and model-specific representations. Task: The source reports a separate metagenomic taxon-detection comparison, but its executable evaluation protocol remains incomplete. Individual claims	Enhancing pathogen identification through AI-assisted metagenomic sequencing Original source ↗ Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133 Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Computational evaluation flow Individual claims	Enhancing pathogen identification through AI-assisted metagenomic sequencing Original source ↗ Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133 Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Datasets MetaHIT and iHMP shotgun-sequencing cohorts; the source describes expert annotations or high-confidence reference calls as ground truth without resolving their construction here. Individual claims	Enhancing pathogen identification through AI-assisted metagenomic sequencing Original source ↗ Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133 Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Splits The genomic experiment in §4.3 does not specify a sample/split manifest. The five-fold procedure in §4.2 concerns other datasets and cannot supply this missing genomic protocol. Individual claims	Enhancing pathogen identification through AI-assisted metagenomic sequencing Original source ↗ Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133 Version: version of record Retrieved: 2026-09-16T10:41:06Z	unreported automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Adaptation Section 4.3 says the model is applied directly to preprocessed sequencing reads but does not specify its genomic fitting partition, checkpoint or whether MetaHIT/iHMP labels were available during fitting. The five-fold setup in §4.2 is attached to other datasets. Individual claims	Enhancing pathogen identification through AI-assisted metagenomic sequencing Original source ↗ §4.2–4.3, genomic sequencing experiment immediately preceding Table 3 Version: version of record Retrieved: 2026-09-16T10:41:06Z	unreported automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Metrics Precision, recall, F1 and ROC-AUC for the genomic comparison. Individual claims	Enhancing pathogen identification through AI-assisted metagenomic sequencing Original source ↗ Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133 Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Baselines Kraken2 and MetaPhlAn3. Individual claims	Enhancing pathogen identification through AI-assisted metagenomic sequencing Original source ↗ Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133 Version: version of record Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Leakage controls The genomic experiment in §4.3 does not establish independence of the expert/reference-derived labels from the compared prediction systems. Individual claims	Enhancing pathogen identification through AI-assisted metagenomic sequencing Original source ↗ Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133 Version: version of record Retrieved: 2026-09-16T10:41:06Z	unreported automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Uncertainty MetaHIT/iHMP Table 3 gives point precision, recall, F1 and AUC values without a replicate count or confidence-interval procedure. The ± values and five-fold evaluation elsewhere concern other datasets and cannot supply uncertainty for this sequencing comparison. Individual claims	Enhancing pathogen identification through AI-assisted metagenomic sequencing Original source ↗ §4.3, MetaHIT/iHMP experiment paragraph and Table 3; contrast §4.2 and Table 2 Version: version of record Retrieved: 2026-09-16T10:41:06Z	unreported automated source review · 2026-09-16 Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `aa88de1b0f0fd7ba1fedc1074bba9ba6ce199a0b723072a04d531db4585ae77c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: needs review

2 source records and release history

Enhancing pathogen identification through AI-assisted metagenomic sequencing · Original source · version of record
Enhancing pathogen identification through AI-assisted metagenomic sequencing · Original source · version of record

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Technical metadata and extraction receipts

Stable ID: reported-task-d3fd502fdc2b38

areas: microbes-communities
tasks: pathogen detection
entity level: task
version: Not reported
task: pathogen detection
scope note: Paper-specific evaluation task; protocol completeness requires further extraction.
benchmark research: review date: 2026-09-17; status: source_concern_comparison_blocked; primary sources: expansion-p3-metagenomic-pathogens-2025; inspected locators: Section 4.3; Table 3; searched queries: "PMC12493982"; gaps: Comparison blocked: Section 4.3 lacks exact sample/split manifest and reference-label construction.; Section 4.2 five-fold procedure concerns other datasets and cannot be assigned to Table 3.; Do not claim the genomic experiment is absent: Section 4.3 explicitly describes it.; claim scope: Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
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: metagenomic-pathogens-2025; source locator: Methods §§4.1–4.2; Results §4.3, Table 3 and preceding paragraph; cached text lines 118–133; 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: MetaHIT
benchmark: TCINet + HTRS: pathogen detection

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