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BPNet (X-large), trained from scratch (NT benchmark)

BPNet (X-large), trained from scratch: trained from scratch.

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

19 evaluations · 19 results. Different protocols are not a single leaderboard.

Sorted by MCC (median over 10 cross-validation folds) (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	Protocol and dataset	MCC (median over 10 cross-validation folds)	MCC (mean over three task categories of median cross-validation MCC)
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark Splice site all, probing, NT benchmark Splice site all	0.745 (± 0.016) (best in column)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark Splice acceptor, probing, NT benchmark Splice acceptor	0.744 (± 0.01)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark Splice donor, probing, NT benchmark Splice donor	0.706 (± 0.009)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark Promoter non-TATA, probing, NT benchmark Promoter non-TATA	0.608 (± 0.061)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark Promoter TATA, probing, NT benchmark Promoter TATA	0.607 (± 0.064)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark Promoter all, probing, NT benchmark Promoter all	0.579 (± 0.087)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H3K36me3, probing, NT benchmark H3K36me3	0.562 (± 0.011)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H3K27me3, probing, NT benchmark H3K27me3	0.542 (± 0.009)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark Enhancer, probing, NT benchmark Enhancer	0.501 (± 0.013)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H2AFZ, probing, NT benchmark H2AFZ	0.475 (± 0.011)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H3K4me1, probing, NT benchmark H3K4me1	0.457 (± 0.013)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark Enhancer types, probing, NT benchmark Enhancer types	0.455 (± 0.012)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H4K20me1, probing, NT benchmark H4K20me1	0.411 (± 0.054)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H3K4me2, probing, NT benchmark H3K4me2	0.341 (± 0.038)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H3K4me3, probing, NT benchmark H3K4me3	0.338 (± 0.076)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H3K9ac, probing, NT benchmark H3K9ac	0.235 (± 0.06)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H3K9me3, probing, NT benchmark H3K9me3	0.216 (± 0.085)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark H3K27ac, probing, NT benchmark H3K27ac	0.16 (± 0.042)	Not reported
BPNet (X-large), trained from scratch (NT benchmark)Evaluation	NT benchmark normalised summed performance (Supplementary Table 9), NT benchmark, all 18 tasks	Not reported	0.566

All 19 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark normalised summed performance (Supplementary Table 9) Dataset: NT benchmark, all 18 tasks	0.566 MCC (mean over three task categories of median cross-validation MCC) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) (control) NT benchmark normalised summed performance lit-genomics-20261011-ntbench-protocol-normalised-summed-performance Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 9, row 'BPNet (X-large)', approach 'control', column 'Average performance'
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark Enhancer, probing Dataset: NT benchmark Enhancer	0.501 (± 0.013) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.013 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark Enhancer (probing) lit-genomics-20261011-ntbench-protocol-enhancer-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Enhancer'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark Enhancer types, probing Dataset: NT benchmark Enhancer types	0.455 (± 0.012) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.012 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark Enhancer types (probing) lit-genomics-20261011-ntbench-protocol-enhancer-types-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Enhancer types'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H2AFZ, probing Dataset: NT benchmark H2AFZ	0.475 (± 0.011) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.011 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H2AFZ (probing) lit-genomics-20261011-ntbench-protocol-h2afz-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H2AFZ'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H3K27ac, probing Dataset: NT benchmark H3K27ac	0.16 (± 0.042) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.042 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H3K27ac (probing) lit-genomics-20261011-ntbench-protocol-h3k27ac-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H3K27ac'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H3K27me3, probing Dataset: NT benchmark H3K27me3	0.542 (± 0.009) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H3K27me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k27me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H3K27me3'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H3K36me3, probing Dataset: NT benchmark H3K36me3	0.562 (± 0.011) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.011 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H3K36me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k36me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H3K36me3'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H3K4me1, probing Dataset: NT benchmark H3K4me1	0.457 (± 0.013) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.013 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H3K4me1 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me1-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H3K4me1'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H3K4me2, probing Dataset: NT benchmark H3K4me2	0.341 (± 0.038) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.038 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H3K4me2 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me2-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H3K4me2'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H3K4me3, probing Dataset: NT benchmark H3K4me3	0.338 (± 0.076) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.076 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H3K4me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k4me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H3K4me3'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H3K9ac, probing Dataset: NT benchmark H3K9ac	0.235 (± 0.06) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.06 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H3K9ac (probing) lit-genomics-20261011-ntbench-protocol-h3k9ac-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H3K9ac'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H3K9me3, probing Dataset: NT benchmark H3K9me3	0.216 (± 0.085) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.085 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H3K9me3 (probing) lit-genomics-20261011-ntbench-protocol-h3k9me3-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H3K9me3'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark H4K20me1, probing Dataset: NT benchmark H4K20me1	0.411 (± 0.054) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.054 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark H4K20me1 (probing) lit-genomics-20261011-ntbench-protocol-h4k20me1-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'H4K20me1'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark Promoter all, probing Dataset: NT benchmark Promoter all	0.579 (± 0.087) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.087 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark Promoter all (probing) lit-genomics-20261011-ntbench-protocol-promoter-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Promoter all'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark Promoter non-TATA, probing Dataset: NT benchmark Promoter non-TATA	0.608 (± 0.061) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.061 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark Promoter non-TATA (probing) lit-genomics-20261011-ntbench-protocol-promoter-non-tata-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Promoter non-TATA'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark Promoter TATA, probing Dataset: NT benchmark Promoter TATA	0.607 (± 0.064) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.064 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark Promoter TATA (probing) lit-genomics-20261011-ntbench-protocol-promoter-tata-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Promoter TATA'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark Splice acceptor, probing Dataset: NT benchmark Splice acceptor	0.744 (± 0.01) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark Splice acceptor (probing) lit-genomics-20261011-ntbench-protocol-splice-acceptor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Splice acceptor'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark Splice donor, probing Dataset: NT benchmark Splice donor	0.706 (± 0.009) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark Splice donor (probing) lit-genomics-20261011-ntbench-protocol-splice-donor-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Splice donor'; printed identically in Supplementary Table 7
Configuration: BPNet (X-large), trained from scratch (NT benchmark)	Protocol: NT benchmark Splice site all, probing Dataset: NT benchmark Splice site all	0.745 (± 0.016) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.016 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source BPNet (X-large) on NT benchmark Splice site all (probing) lit-genomics-20261011-ntbench-protocol-splice-site-all-probing Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 6, row 'BPNet (X-large)', column 'Splice site all'; printed identically in Supplementary Table 7

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Original source · Nature Methods 22, 287-297 (published online 2024-11-28); Supplementary Information PDF (MOESM1, 25 pages)

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-ntbench-config-bpnet-x-large-trained-from-scratch

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: BPNet (X-large)
foundation model eligible: false
parameters: trained from scratch; hyperparameters in Supplementary Tables 1 and 8
access reuse: Not stated in the tables
source locator: Supplementary Tables 6, 7 and 9 row labels
missing metadata: version: reason: unreported; note: Row label gives training data and parameter count only
provenance note: BPNet (X-large) as evaluated in the NT benchmark, trained from scratch.

Related records

configuration of: BPNet
system: BPNet (X-large) (control) NT benchmark normalised summed performance
system: BPNet (X-large) on NT benchmark Enhancer (probing)
system: BPNet (X-large) on NT benchmark Enhancer types (probing)
system: BPNet (X-large) on NT benchmark H2AFZ (probing)
system: BPNet (X-large) on NT benchmark H3K27ac (probing)
system: BPNet (X-large) on NT benchmark H3K27me3 (probing)
system: BPNet (X-large) on NT benchmark H3K36me3 (probing)
system: BPNet (X-large) on NT benchmark H3K4me1 (probing)
system: BPNet (X-large) on NT benchmark H3K4me2 (probing)
system: BPNet (X-large) on NT benchmark H3K4me3 (probing)
system: BPNet (X-large) on NT benchmark H3K9ac (probing)
system: BPNet (X-large) on NT benchmark H3K9me3 (probing)
system: BPNet (X-large) on NT benchmark H4K20me1 (probing)
system: BPNet (X-large) on NT benchmark Promoter all (probing)
system: BPNet (X-large) on NT benchmark Promoter non-TATA (probing)
system: BPNet (X-large) on NT benchmark Promoter TATA (probing)
system: BPNet (X-large) on NT benchmark Splice acceptor (probing)
system: BPNet (X-large) on NT benchmark Splice donor (probing)
system: BPNet (X-large) on NT benchmark Splice site all (probing)

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