Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Task
metagenomic genus classification
Genus classification compares sequence representations on separate simulated amplicon and shotgun datasets.
Sources
PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58At a glance
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.
| Property | Description and evidence |
|---|---|
| Datasets | Amplicon and shotgun collections derived from RDP version 11 update 5 (30 September 2016), with balanced taxonomic subsets and a separate unbalanced Qiita collection. The taxonomic label level and sequence-generation method must remain attached to each evaluation.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Results 3.1 Datasets |
| Splits | Ten-fold cross-validation is reported for the benchmark experiments.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Metrics | Classification accuracy at multiple ranks; the genus task must be distinguished from easier higher-rank outcomes.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Baselines | Conventional classifiers using PC-mer are compared with CNN/DBN approaches using alternative encodings.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Leakage controls | The study evaluates supervised classifiers with ten-fold cross-validation across the amplicon and shotgun collections. Sections 2.2 and 3.1–3.5 do not specify genome-, species- or homology-grouped fold assignment; ten-fold evaluation alone does not establish unseen-species generalization. · Not reported in inspected sourcesSourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods 2.2 Learning unit; Results 3.1 Datasets and 3.5.1 Training and testing procedure |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Entity type | Paper-specific computational evaluation protocol.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Organisms | Simulated microbial amplicon and shotgun communities.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Assays | Genus-level taxonomic labels.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Allowed inputs | Sequence-derived PC-mer or alternative feature encodings.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Adaptation | Supervised classifiers evaluated through ten-fold cross-validation.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
How it works
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58Evaluation methodology
Amplicon and shotgun collections derived from RDP version 11 update 5 (30 September 2016), with balanced taxonomic subsets and a separate unbalanced Qiita collection. The taxonomic label level and sequence-generation method must remain attached to each evaluation. Ten-fold cross-validation is reported for the benchmark experiments. Classification accuracy at multiple ranks; the genus task must be distinguished from easier higher-rank outcomes. Conventional classifiers using PC-mer are compared with CNN/DBN approaches using alternative encodings. The study evaluates supervised classifiers with ten-fold cross-validation across the amplicon and shotgun collections. Sections 2.2 and 3.1–3.5 do not specify genome-, species- or homology-grouped fold assignment; ten-fold evaluation alone does not establish unseen-species generalization.
Sources
PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Results 3.1 Datasets; Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58; Methods 2.2 Learning unit; Results 3.1 Datasets and 3.5.1 Training and testing procedureRecorded evaluations
Each evaluation records what was tested and under which conditions.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| PC-mer + LR: metagenomic genus classification k=8 PC-mer feature extraction with logistic regression on AMP genus-classification dataset Author-reported evaluation · Evaluation metadata: needs review | ||
| 96.95% accuracy Unit: percent · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Table 3, AMP section, PC-mer + LR k=8 row, Accuracy (%) column 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 resource | Version | Reference |
|---|---|---|
| PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification | version of record | Read source DOI: 10.1371/journal.pone.0307279 |
What is still missing
- Complete raw table acquired. Dataset and k-mer row spans must be propagated; CNN/DBN/RDP/PC-mer-LR/WalkIm rows retained. Structured extraction pending; do not infer equivalent preprocessing.
Search and extraction details
source found structured extraction pending
Searches
- PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification primary paper benchmark results
Evidence locations
- Table3 AMP/SG datasets and k-mer configurations
Strengths and limitations
Limitations and conditions
- Ten-fold classification is not evidence of unseen-genome or unseen-species generalization without grouped partition information. Hardware also differs across cited runtime comparisons.
Sources
PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Results 3.1 Datasets; Methods 2.2 Learning unit; Results 3.1 Datasets and 3.5.1 Training and testing procedure
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-4420dcdfe8338dEvidence 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
| 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 | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: Sequence-derived PC-mer or alternative feature encodings.","Evaluation: Ten-fold cross-validation is reported for the benchmark experiments.","Readout: Classification accuracy at multiple ranks; the genus task must be distinguished from easier higher-rank outcomes."] Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets Amplicon and shotgun collections derived from RDP version 11 update 5 (30 September 2016), with balanced taxonomic subsets and a separate unbalanced Qiita collection. The taxonomic label level and sequence-generation method must remain attached to each evaluation. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Results 3.1 Datasets Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Ten-fold cross-validation is reported for the benchmark experiments. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Supervised classifiers evaluated through ten-fold cross-validation. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Classification accuracy at multiple ranks; the genus task must be distinguished from easier higher-rank outcomes. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines Conventional classifiers using PC-mer are compared with CNN/DBN approaches using alternative encodings. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The study evaluates supervised classifiers with ten-fold cross-validation across the amplicon and shotgun collections. Sections 2.2 and 3.1–3.5 do not specify genome-, species- or homology-grouped fold assignment; ten-fold evaluation alone does not establish unseen-species generalization. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods 2.2 Learning unit; Results 3.1 Datasets and 3.5.1 Training and testing procedure Version: version of record | unreported automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | unreported automated source review · 2026-09-16 Audit detailsTargeted 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
2 source records and release history
- PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Original source · version of record
- PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Original source · version of record
Technical metadata and extraction receipts
Stable ID: reported-task-4420dcdfe8338d
- areas
- microbes-communities
- tasks
- metagenomic genus classification
- entity level
- task
- version
- Not reported
- task
- metagenomic genus classification
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: source_found_structured_extraction_pending; primary sources: evidence-expansion-p2-pc-mer-2024-0b0a225fa6f5; inspected locators: Table3 AMP/SG datasets and k-mer configurations; searched queries: PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification primary paper benchmark results; gaps: Complete raw table acquired. Dataset and k-mer row spans must be propagated; CNN/DBN/RDP/PC-mer-LR/WalkIm rows retained. Structured extraction pending; do not infer equivalent preprocessing.; 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
- 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: pc-mer-2024; source locator: Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58; 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: AMP
- benchmark: PC-mer + LR: metagenomic genus classification