Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Task
CAMI II phylum read classification
CAMI II read classification evaluates a computationally limited subsample, with taxonomic-rank-specific interpretation.
Sources
Normalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116At 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 | A 10,000-read subset of CAMI II Sample_0 from the human-microbiome collection.SourcesNormalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 |
| Splits | Queries are classified against the paper’s separately assembled metagenomic reference/training data.SourcesNormalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 |
| Metrics | Macro-F1 is the arithmetic mean of classwise F1; only classes present in the evaluated subset enter the macro calculation.SourcesNormalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 |
| Baselines | NCD-gzip and Kraken2.SourcesNormalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 |
| Leakage controls | The CAMI II test uses 10,000 reads from Sample_0 and the paper’s RefSeq metagenomic training collection. A disjoint genome split is described for the separate simulated RefSeq experiment; the CAMI passage does not establish reference-genome or homology exclusion against this external sample. · Not reported in inspected sourcesSourcesNormalized compression distance for DNA classification · Methods: Datasets/Metagenomic reads; Results: CAMI dataset |
| Uncertainty | Table 5 describes a single 10,000-read CAMI II subsample. It does not provide confidence intervals, repeated-subsample variation or random-seed uncertainty for the phylum metrics. · Not reported in inspected sourcesSourcesNormalized compression distance for DNA classification · Results: CAMI dataset; Table 5 |
| Entity type | Paper-specific computational evaluation protocol.SourcesNormalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 |
| Organisms | CAMI II human-microbiome community taxa.SourcesNormalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 |
| Assays | Read-origin taxonomy at the selected evaluation rank.SourcesNormalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 |
| Allowed inputs | DNA reads and a separately assembled reference/training collection.SourcesNormalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 |
| Adaptation | Reference-based classification using NCD-gzip or Kraken2.SourcesNormalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 |
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
Normalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116Evaluation methodology
A 10,000-read subset of CAMI II Sample_0 from the human-microbiome collection. Queries are classified against the paper’s separately assembled metagenomic reference/training data. Macro-F1 is the arithmetic mean of classwise F1; only classes present in the evaluated subset enter the macro calculation. NCD-gzip and Kraken2. The CAMI II test uses 10,000 reads from Sample_0 and the paper’s RefSeq metagenomic training collection. A disjoint genome split is described for the separate simulated RefSeq experiment; the CAMI passage does not establish reference-genome or homology exclusion against this external sample.
Sources
Normalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116; Methods: Datasets/Metagenomic reads; Results: CAMI datasetRecorded 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 |
|---|---|---|
| NCD-gzip: CAMI II phylum read classification Configuration: NCD-gzipTask: CAMI II phylum read classificationDataset: CAMI II Sample_0 10,000-read subsample Phylum-level macro-averaged F1; distinct taxonomic rank from the other row. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.1263 Macro F1 Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedNormalized compression distance for DNA classification · Table 5, NCD Phylum row, F1 column Source checking is not 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 |
|---|---|---|
| Normalized compression distance for DNA classification | version of record | Read source DOI: 10.7717/peerj.20677 |
What is still missing
- Table 5 prints NCD only. Narrative compares Kraken2 but supplies no paired numerical Kraken2 row; do not manufacture a two-model chart.
- Do not attach five-fold Human DNA results from Table 3 to CAMI II.
Search and extraction details
primary comparison table screened
Searches
- "Normalized compression distance for DNA classification"
Evidence locations
- Table 5
- Results: CAMI analysis
- Methods: Metagenomic reads and Genome fragmentation
Strengths and limitations
Limitations and conditions
- The subsample contains only Bacteria at superkingdom level, so that result does not establish broad multiclass discrimination. Phylum and superkingdom are separate catalogue outcomes.
Sources
Normalized compression distance for DNA classification · Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116
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-45105e1c486251Evidence 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 | Normalized compression distance for DNA classification Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 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: DNA reads and a separately assembled reference/training collection.","Evaluation: Queries are classified against the paper’s separately assembled metagenomic reference/training data.","Readout: Macro-F1 is the arithmetic mean of classwise F1; only classes present in the evaluated subset enter the macro calculation."] Individual claims | Normalized compression distance for DNA classification Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 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 | Normalized compression distance for DNA classification Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 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 A 10,000-read subset of CAMI II Sample_0 from the human-microbiome collection. Individual claims | Normalized compression distance for DNA classification Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 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 Queries are classified against the paper’s separately assembled metagenomic reference/training data. Individual claims | Normalized compression distance for DNA classification Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 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 Reference-based classification using NCD-gzip or Kraken2. Individual claims | Normalized compression distance for DNA classification Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 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 Macro-F1 is the arithmetic mean of classwise F1; only classes present in the evaluated subset enter the macro calculation. Individual claims | Normalized compression distance for DNA classification Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 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 NCD-gzip and Kraken2. Individual claims | Normalized compression distance for DNA classification Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116 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 CAMI II test uses 10,000 reads from Sample_0 and the paper’s RefSeq metagenomic training collection. A disjoint genome split is described for the separate simulated RefSeq experiment; the CAMI passage does not establish reference-genome or homology exclusion against this external sample. Individual claims | Normalized compression distance for DNA classification Methods: Datasets/Metagenomic reads; Results: CAMI dataset 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 Table 5 describes a single 10,000-read CAMI II subsample. It does not provide confidence intervals, repeated-subsample variation or random-seed uncertainty for the phylum metrics. Individual claims | Normalized compression distance for DNA classification Results: CAMI dataset; Table 5 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
- Normalized compression distance for DNA classification · Original source · version of record
- Normalized compression distance for DNA classification · Original source · version of record
Technical metadata and extraction receipts
Stable ID: reported-task-45105e1c486251
- areas
- microbes-communities
- tasks
- CAMI II phylum read classification
- entity level
- task
- version
- Not reported
- task
- CAMI II phylum read classification
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_table_screened; primary sources: expansion-p3-ncd-metagenomics-2026; inspected locators: Table 5; Results: CAMI analysis; Methods: Metagenomic reads and Genome fragmentation; searched queries: "Normalized compression distance for DNA classification"; gaps: Table 5 prints NCD only. Narrative compares Kraken2 but supplies no paired numerical Kraken2 row; do not manufacture a two-model chart.; Do not attach five-fold Human DNA results from Table 3 to CAMI II.; 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: ncd-metagenomics-2026; source locator: Methods: Evaluation protocol; Results: CAMI II; cached text lines 67–68, 113–116; 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.