Configuration

NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)

NT-Multispecies-v2 (250M), parameter-efficient fine-tuning, a configuration of Nucleotide Transformer v2: parameter-efficient fine-tuning.

19 evaluations · 19 results

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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)
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark Splice donor, fine-tuning (PEFT), NT benchmark Splice donor	0.967 (± 0.004) (best in column)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark Splice site all, fine-tuning (PEFT), NT benchmark Splice site all	0.965 (± 0.003)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark Splice acceptor, fine-tuning (PEFT), NT benchmark Splice acceptor	0.95 (± 0.008)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark Promoter TATA, fine-tuning (PEFT), NT benchmark Promoter TATA	0.87 (± 0.019)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark Promoter non-TATA, fine-tuning (PEFT), NT benchmark Promoter non-TATA	0.785 (± 0.01)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark Promoter all, fine-tuning (PEFT), NT benchmark Promoter all	0.774 (± 0.013)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H4K20me1, fine-tuning (PEFT), NT benchmark H4K20me1	0.652 (± 0.006)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H3K4me3, fine-tuning (PEFT), NT benchmark H3K4me3	0.64 (± 0.009)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H3K36me3, fine-tuning (PEFT), NT benchmark H3K36me3	0.636 (± 0.012)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H3K27me3, fine-tuning (PEFT), NT benchmark H3K27me3	0.6 (± 0.009)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H3K4me2, fine-tuning (PEFT), NT benchmark H3K4me2	0.57 (± 0.009)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H3K9ac, fine-tuning (PEFT), NT benchmark H3K9ac	0.565 (± 0.021)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark Enhancer, fine-tuning (PEFT), NT benchmark Enhancer	0.525 (± 0.01)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H2AFZ, fine-tuning (PEFT), NT benchmark H2AFZ	0.513 (± 0.017)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H3K27ac, fine-tuning (PEFT), NT benchmark H3K27ac	0.497 (± 0.014)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark Enhancer types, fine-tuning (PEFT), NT benchmark Enhancer types	0.492 (± 0.01)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H3K4me1, fine-tuning (PEFT), NT benchmark H3K4me1	0.491 (± 0.006)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark H3K9me3, fine-tuning (PEFT), NT benchmark H3K9me3	0.467 (± 0.016)	Not reported
NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)Evaluation	NT benchmark normalised summed performance (Supplementary Table 9), NT benchmark, all 18 tasks	Not reported	0.769

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark Enhancer, fine-tuning (PEFT) Dataset: NT benchmark Enhancer	0.525 (± 0.01) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark Enhancer (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Enhancer'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark Enhancer types, fine-tuning (PEFT) Dataset: NT benchmark Enhancer types	0.492 (± 0.01) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark Enhancer types (fine-tuning) lit-genomics-20261011-ntbench-protocol-enhancer-types-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Enhancer types'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H2AFZ, fine-tuning (PEFT) Dataset: NT benchmark H2AFZ	0.513 (± 0.017) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.017 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H2AFZ (fine-tuning) lit-genomics-20261011-ntbench-protocol-h2afz-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H2AFZ'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H3K27ac, fine-tuning (PEFT) Dataset: NT benchmark H3K27ac	0.497 (± 0.014) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.014 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H3K27ac (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k27ac-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H3K27ac'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H3K27me3, fine-tuning (PEFT) Dataset: NT benchmark H3K27me3	0.6 (± 0.009) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H3K27me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k27me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H3K27me3'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H3K36me3, fine-tuning (PEFT) Dataset: NT benchmark H3K36me3	0.636 (± 0.012) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.012 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H3K36me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k36me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H3K36me3'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H3K4me1, fine-tuning (PEFT) Dataset: NT benchmark H3K4me1	0.491 (± 0.006) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H3K4me1 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me1-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H3K4me1'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H3K4me2, fine-tuning (PEFT) Dataset: NT benchmark H3K4me2	0.57 (± 0.009) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H3K4me2 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me2-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H3K4me2'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H3K4me3, fine-tuning (PEFT) Dataset: NT benchmark H3K4me3	0.64 (± 0.009) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H3K4me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k4me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H3K4me3'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H3K9ac, fine-tuning (PEFT) Dataset: NT benchmark H3K9ac	0.565 (± 0.021) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.021 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H3K9ac (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k9ac-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H3K9ac'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H3K9me3, fine-tuning (PEFT) Dataset: NT benchmark H3K9me3	0.467 (± 0.016) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.016 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H3K9me3 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h3k9me3-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H3K9me3'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark H4K20me1, fine-tuning (PEFT) Dataset: NT benchmark H4K20me1	0.652 (± 0.006) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark H4K20me1 (fine-tuning) lit-genomics-20261011-ntbench-protocol-h4k20me1-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'H4K20me1'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark Promoter all, fine-tuning (PEFT) Dataset: NT benchmark Promoter all	0.774 (± 0.013) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.013 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark Promoter all (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Promoter all'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark Promoter non-TATA, fine-tuning (PEFT) Dataset: NT benchmark Promoter non-TATA	0.785 (± 0.01) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark Promoter non-TATA (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-non-tata-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Promoter non-TATA'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark Promoter TATA, fine-tuning (PEFT) Dataset: NT benchmark Promoter TATA	0.87 (± 0.019) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.019 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark Promoter TATA (fine-tuning) lit-genomics-20261011-ntbench-protocol-promoter-tata-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Promoter TATA'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark Splice acceptor, fine-tuning (PEFT) Dataset: NT benchmark Splice acceptor	0.95 (± 0.008) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.008 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark Splice acceptor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-acceptor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Splice acceptor'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark Splice donor, fine-tuning (PEFT) Dataset: NT benchmark Splice donor	0.967 (± 0.004) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.004 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark Splice donor (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-donor-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Splice donor'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark Splice site all, fine-tuning (PEFT) Dataset: NT benchmark Splice site all	0.965 (± 0.003) MCC (median over 10 cross-validation folds) unitless · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) on NT benchmark Splice site all (fine-tuning) lit-genomics-20261011-ntbench-protocol-splice-site-all-fine-tuning Aggregation: Not reported Nucleotide Transformer: Supplementary Information (Supplementary Tables 1-12) · Supplementary Table 7, row 'NT-Multispecies-v2 (250M)', column 'Splice site all'
Configuration: NT-Multispecies-v2 (250M), parameter-efficient fine-tuning (NT benchmark)	Protocol: NT benchmark normalised summed performance (Supplementary Table 9) Dataset: NT benchmark, all 18 tasks	0.769 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	Author-reported evaluation · Source checked Methods, coverage and source NT-Multispecies-v2 (250M) (Finetuning) 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 'NT-Multispecies-v2 (250M)', approach 'Finetuning', column 'Average performance'

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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-nt-multispecies-v2-250m-parameter-efficient-fine-tuning

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: NT-Multispecies-v2 (250M)
foundation model eligible: true
parameters: parameter-efficient fine-tuning; hyperparameters in Supplementary Tables 1 and 8
access reuse: Public weights (Hugging Face InstaDeepAI collection)
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: NT-Multispecies-v2 (250M) as evaluated in the NT benchmark, parameter-efficient fine-tuning.

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