BERTax taxonomic classification of genome fragments (Mock et al. 2022)
Superkingdom, phylum and genus assignment of 1,500-nt genome fragments, with every tool given the same reference or training data.
Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.
Overview
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Results on linked records
This benchmark has no results of its own in this release. 3 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- BERTax Closely related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022) Protocol · part of this benchmark · 9 evaluations · 54 results
- BERTax Distantly related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022) Protocol · part of this benchmark · 9 evaluations · 72 results
- BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022) Protocol · part of this benchmark · 9 evaluations · 27 results
Methods and evaluation design
Procedure, tasks and evaluated configurations
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 6 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- BERTax Closely related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022) · 0/2 roles measured
- BERTax Distantly related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022) · 0/2 roles measured
- BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022) · 0/2 roles measured
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks · Original source · PNAS 119(35):e2122636119, published 2022-08-26; PMC9436379 full-text XML
Technical metadata and extraction receipts
Stable ID: dna-pathogen-20261012-bertax-benchmark
- areas
- microbes-communities
- contexts
- research
- entity level
- suite
- version
- PNAS 2022, Table 1 and SI Tables S2 and S5
- task
- Assign a DNA fragment to its superkingdom, phylum or genus
- source locator
- Results 'Comparison to Other Classification Approaches'; Materials and Methods 'Three Evaluation Datasets', 'Comparison to Other Tools'
- scope note
- Architecture comparisons (SI Table S1), per-superkingdom AveP (S3), homology splits for BERTax only (S6) and ablations (S7) compare BERTax variants only and were not extracted. Figures and PR curves were not read.
- limitations
- Inputs are simulated 1,500-nt genome fragments, not sequencing reads or clinical specimens.; Database tools were given only the training partition as reference, not whole genomes; the authors call this a necessary deviation from their designed use.; Classification is at superkingdom, phylum and genus level, not species or strain.
- review
- method: source-hash-verification; scope-review; 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: c0bb2f1bba8680b300076292389b39346ae58bea4bdf28647dd9462333b3bcd7; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9436379/fullTextXML; note: Checked against the re-downloaded article XML (SHA-256 matches) and SI.
Related records
- subject: comparison_design: dna-pathogen-20261012-bertax-benchmark
- part of: BERTax Closely related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022)
- part of: BERTax Distantly related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022)
- part of: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)