Recall (genus level; mean across all 81 isolates (species in and out of the database)) of MMseqs2 (main database, Peres da Silva et al. 2024) on ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024)
0.81 Recall (genus level; mean across all 81 isolates (species in and out of the database))
Methods
- Tested configuration
- MMseqs2 (main database, Peres da Silva et al. 2024)
- Protocol
- Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- Dataset
- ONT reads from 81 bacterial isolates (Peres da Silva et al. 2024)
- Procedure
- Genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- Evaluation
- MMseqs2 on genus-level read classification of ONT bacterial isolates, main database (Peres da Silva et al. 2024)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source: Figure 3 shows standard-deviation error bars; no value is printed in the text
- Evidence
- Author-reported evaluation · source checkedMetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Results 'Results for all genomes' paragraph 1, sentence 4 (values shown in Fig. 3a)
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Test sets 'Species in the database' (47 isolates) and 'Species out of the database' (34 isolates)
- Adaptation
- All tools use the 516-genome main database
- Scoring implementation
- For each taxon, sensitivity is the proportion of its reads classified as such and precision the proportion of correctly classified reads; F1 is their harmonic mean. Averages are across bacterial isolates; Wilcoxon rank-sum tests compare MetageNN with each tool.
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.81 Individual claims | MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes Results 'Results for all genomes' paragraph 1, sentence 4 (values shown in Fig. 3a) Version: BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML | source checked ["source-hash-verification","independent-cell-check"] · 2026-10-12 author reported Audit detailsRe-downloaded the Europe PMC full-text XML and matched its SHA-256; compared the value with a separate parser of the Table 1 table-wrap and of the Results sentences written for this review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes · Original source · BMC Bioinformatics 25:153, published 2024-04-16; PMC11022314 full-text XML
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261012-metagenn-result-mmseqs2-isolates-all-recall
- metric
- recall
- metric direction
- higher
- unit
- fraction
- printed value
- 0.81
- metric qualifier
- genus level; mean across all 81 isolates (species in and out of the database)
- source locator
- Results 'Results for all genomes' paragraph 1, sentence 4 (values shown in Fig. 3a)
- missing metadata
- uncertainty: reason: unreported; note: Figure 3 shows standard-deviation error bars; no value is printed in the text
- review
- method: source-hash-verification; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent (rev-mlvb), independent of the extracting agent; no human review claimed; date: 2026-10-12; artifact sha256: ac4b137508d295d5e04e9be263bef40bdcf2c494e096407e5896611194f14e12; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11022314/fullTextXML; method note: Transcribed from a Results sentence of the pinned XML; extract/extract_metagenn.py asserts the exact sentence before writing the value.; note: Re-downloaded the Europe PMC full-text XML and matched its SHA-256; compared the value with a separate parser of the Table 1 table-wrap and of the Results sentences written for this review.
- numeric value
- 0.81