| Configuration: BERTax (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 66.9% Macro average precision (genus rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBERTax on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "BERTax", column group "Final", column "Genus" (PNAS PDF page 4) |
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| Configuration: BERTax (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 95.1% Macro average precision (phylum rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBERTax on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "BERTax", column group "Final", column "Phyl." (PNAS PDF page 4) |
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| Configuration: BERTax (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 98.6% Macro average precision (superkingdom rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBERTax on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "BERTax", column group "Final", column "Supk." (PNAS PDF page 4) |
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| Configuration: DeepMicrobes (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 66.4% Macro average precision (genus rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDeepMicrobes on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "DeepMicrobes", column group "Final", column "Genus" (PNAS PDF page 4) |
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| Configuration: DeepMicrobes (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 92.1% Macro average precision (phylum rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDeepMicrobes on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "DeepMicrobes", column group "Final", column "Phyl." (PNAS PDF page 4) |
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| Configuration: DeepMicrobes (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 98.1% Macro average precision (superkingdom rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDeepMicrobes on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "DeepMicrobes", column group "Final", column "Supk." (PNAS PDF page 4) |
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| Configuration: Kraken2 (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 70.6% Macro average precision (genus rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceKraken2 on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "Kraken2", column group "Final", column "Genus" (PNAS PDF page 4) |
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| Configuration: Kraken2 (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 87.1% Macro average precision (phylum rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceKraken2 on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "Kraken2", column group "Final", column "Phyl." (PNAS PDF page 4) |
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| Configuration: Kraken2 (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 93.7% Macro average precision (superkingdom rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceKraken2 on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "Kraken2", column group "Final", column "Supk." (PNAS PDF page 4) |
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| Configuration: minimap2 (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 66.7% Macro average precision (genus rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "minimap2", column group "Final", column "Genus" (PNAS PDF page 4) |
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| Configuration: minimap2 (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 86.7% Macro average precision (phylum rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "minimap2", column group "Final", column "Phyl." (PNAS PDF page 4) |
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| Configuration: minimap2 (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 93.5% Macro average precision (superkingdom rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceminimap2 on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "minimap2", column group "Final", column "Supk." (PNAS PDF page 4) |
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| Configuration: MMseqs2 + BERTax (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 79.3% Macro average precision (genus rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 + BERTax on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2+ BERTax", column group "Final", column "Genus" (PNAS PDF page 4) |
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| Configuration: MMseqs2 + BERTax (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 97.8% Macro average precision (phylum rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 + BERTax on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2+ BERTax", column group "Final", column "Phyl." (PNAS PDF page 4) |
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| Configuration: MMseqs2 + BERTax (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 99.8% Macro average precision (superkingdom rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 + BERTax on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2+ BERTax", column group "Final", column "Supk." (PNAS PDF page 4) |
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| Configuration: MMseqs2 + DeepMicrobes (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 77.8% Macro average precision (genus rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 + DeepMicrobes on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2+ DeepMicrobes", column group "Final", column "Genus" (PNAS PDF page 4) |
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| Configuration: MMseqs2 + DeepMicrobes (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 93.2% Macro average precision (phylum rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 + DeepMicrobes on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2+ DeepMicrobes", column group "Final", column "Phyl." (PNAS PDF page 4) |
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| Configuration: MMseqs2 + DeepMicrobes (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 97.2% Macro average precision (superkingdom rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 + DeepMicrobes on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2+ DeepMicrobes", column group "Final", column "Supk." (PNAS PDF page 4) |
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| Configuration: MMseqs2 (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 74.8% Macro average precision (genus rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2", column group "Final", column "Genus" (PNAS PDF page 4) |
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| Configuration: MMseqs2 (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 92.9% Macro average precision (phylum rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2", column group "Final", column "Phyl." (PNAS PDF page 4) |
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| Configuration: MMseqs2 (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 96.9% Macro average precision (superkingdom rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2", column group "Final", column "Supk." (PNAS PDF page 4) |
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| Configuration: MMseqs2 taxonomy* (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 75.1% Macro average precision (genus rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 taxonomy* on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2 tax. ∗", column group "Final", column "Genus" (PNAS PDF page 4) |
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| Configuration: MMseqs2 taxonomy* (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 93.5% Macro average precision (phylum rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 taxonomy* on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2 tax. ∗", column group "Final", column "Phyl." (PNAS PDF page 4) |
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| Configuration: MMseqs2 taxonomy* (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 98.1% Macro average precision (superkingdom rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMMseqs2 taxonomy* on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "MMseqs2 tax. ∗", column group "Final", column "Supk." (PNAS PDF page 4) |
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| Configuration: sourmash (Final model dataset, Mock et al. 2022) | Protocol: BERTax Final model dataset: taxonomic classification at superkingdom and phylum, and genus (Mock et al. 2022)
Dataset: BERTax Final model dataset (Mock et al. 2022) | 3.07% Macro average precision (genus rank; macro average over classes; unclassified samples treated as random guesses) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcesourmash on the BERTax final model dataset dna-pathogen-20261012-bertax-protocol-final Aggregation: Not reported Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks (PNAS PDF) · Table 1, row "sourmash", column group "Final", column "Genus" (PNAS PDF page 4) |
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