0.948 recall
hall2024-sim-illumina-minimap2-mtb recall (per read, M. tuberculosis)
- Tested configuration
- minimap2 MTB (Hall and Coin 2024)
- Protocol
- M. tuberculosis read classification, simulated Illumina (Hall and Coin 2024 Table 7)
- Dataset
- Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)
- Procedure
- dna-pathogen-20261009-protocol-hall2024-mtb-reads-sim-illumina
- Evaluation
- minimap2 MTB on Simulated sputum-like Illumina metagenome, non-human reads (Hall and Coin 2024)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- 95% CI 0.9467 to 0.9482. Wilson score interval (table footnote)
- Evidence
- Author-reported evaluation · source checkedPangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Table 7, row 'minimap2 MTB', column 'Sensitivity (95% CI)'
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
- Single dataset
- Adaptation
- Database as stated per configuration
- Scoring implementation
- Per-read confusion counts against known read origin
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 0.9475 Individual claims | Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data Table 7, row 'minimap2 MTB', column 'Sensitivity (95% CI)' Version: GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 author reported Audit detailsExtracted by deterministic parse of the pinned Europe PMC full-text XML (extract/extract_pathogen.py), with every row and column label asserted. printed_value is the table cell text exactly as in the XML. Pending independent review. Independent review 2026-10-09: value and identity match the source. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
1 source records and release history
- Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data · Original source · GigaScience 13:giae010, published online 2024-04-04; PMC10993716 full-text XML
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261009-result-hall2024-sim-illumina-minimap2-mtb-sensitivity
- metric
- recall
- metric direction
- higher
- unit
- fraction
- printed value
- 0.9475
- numeric value
- 0.9475
- source locator
- Table 7, row 'minimap2 MTB', column 'Sensitivity (95% CI)'
- metric qualifier
- per read, M. tuberculosis
- uncertainty
- type: confidence_interval; printed: (0.9467–0.9482); lower: 0.9467; upper: 0.9482; level: 0.95; method: analytic; note: Wilson score interval (table footnote)
- printed source cell
- 0.9475 (0.9467–0.9482)
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: ea3c34a01222d5c5203c52a85a700b7dae5cccd6f48e6d50808d5abbd6385554; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10993716/fullTextXML; method note: Re-downloaded the article XML and matched its SHA-256. Read Hall Tables 5-8 with a separate parser written for this review (row and column spans expanded; the extractor's script was not run). Checked printed and numeric value, locator, metric, qualifier, unit and direction from the headers, and the evaluation's configuration, protocol and dataset. Checked the interval bounds, level and Wilson method against the cell and table footnote.; note: Extracted by deterministic parse of the pinned Europe PMC full-text XML (extract/extract_pathogen.py), with every row and column label asserted. printed_value is the table cell text exactly as in the XML. Pending independent review. Independent review 2026-10-09: value and identity match the source.