BERTax (Distantly related dataset, Mock et al. 2022)
Configuration of BERTax: All-in-one architecture: 12 transformer blocks, 5 attention heads, embedding dimension 250, fine-tuned for at most 16 epochs with early stopping and class weights.
Overview
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Evaluations and results
1 evaluation · 12 results. Different protocols are not a single leaderboard.
Protocol: BERTax Distantly related dataset: taxonomic classification at superkingdom and phylum (Mock et al. 2022) · Dataset: BERTax Distantly related dataset (Mock et al. 2022)
Sorted by Accuracy (phylum rank; among the samples the tool classified; SI Table S2 'acc.') (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Accuracy (phylum rank; among the samples the tool classified; SI Table S2 'acc.') | Accuracy (phylum rank; among the samples the tool classified; SI Table S5; all distantly related test sequences) | Accuracy (phylum rank; among the samples the tool classified; SI Table S5; test sequences with at least one megablast hit to the training partition (removed by the filter)) | Accuracy (phylum rank; among the samples the tool classified; SI Table S5; test sequences without a megablast hit to the training partition) | Accuracy (superkingdom rank; among the samples the tool classified; SI Table S2 'acc.') | Accuracy (superkingdom rank; among the samples the tool classified; SI Table S5; all distantly related test sequences) | Accuracy (superkingdom rank; among the samples the tool classified; SI Table S5; test sequences with at least one megablast hit to the training partition (removed by the filter)) | Accuracy (superkingdom rank; among the samples the tool classified; SI Table S5; test sequences without a megablast hit to the training partition) | Macro average precision (phylum rank; macro average over classes; unclassified samples treated as random guesses) | Macro average precision (superkingdom rank; macro average over classes; unclassified samples treated as random guesses) | Proportion (phylum rank; share of test samples the tool returned a prediction for) | Proportion (superkingdom rank; share of test samples the tool returned a prediction for) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BERTax (Distantly related dataset, Mock et al. 2022)Evaluation | 60.1% | 60.1% | 63.5% | 59.1% | 89% | 89% | 93.5% | 88.3% | 54.1% | 90.1% | 100% | 100% |
All 12 result rows with coverage, uncertainty and sources
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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-config-bertax-distantly
- areas
- microbes-communities
- contexts
- research
- method types
- supervised_machine_learning
- reported name
- BERTax
- foundation model eligible
- false
- parameters
- All-in-one architecture: 12 transformer blocks, 5 attention heads, embedding dimension 250, fine-tuned for at most 16 epochs with early stopping and class weights
- source locator
- Materials and Methods 'Comparison to Other Tools' paragraphs 1-2; Results 'Comparison to Other Classification Approaches' paragraphs 1 and 3
- access reuse
- Tool run by the article's authors; trained models and reference builds are not released except the downloadable final BERTax model
- missing metadata
- version: reason: unreported; note: Tool versions are not stated in the article or SI, except MMseqs2-linclust 11.e1a1c used for dataset clustering
- 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.
- provenance note
- BERTax as run by the BERTax authors with the distantly related dataset's training partition as reference or training data.
Related records
- configuration of: BERTax
- system: BERTax on the BERTax distantly related dataset