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Akita (DNALONGBENCH)

Configuration of Akita: Expert model for CMP: Akita contact-map model.

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Evaluations and results

1 evaluation · 6 results. Different protocols are not a single leaderboard.

Protocol: DNALONGBENCH Contact map prediction (Table 4) · Dataset: DNALONGBENCH Contact map prediction test set

Sorted by Stratum adjusted correlation coefficient (average over CMP conditions as printed) (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	Stratum adjusted correlation coefficient (average over CMP conditions as printed)	Stratum adjusted correlation coefficient (GM12878)	Stratum adjusted correlation coefficient (H1hESC)	Stratum adjusted correlation coefficient (HCT116)	Stratum adjusted correlation coefficient (HFF)	Stratum adjusted correlation coefficient (IMR90)
Akita (DNALONGBENCH)Evaluation	0.23	0.227	0.247	0.21	0.258	0.21

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.23 Stratum adjusted correlation coefficient (average over CMP conditions as printed) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Expert Model on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'Avg'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.227 Stratum adjusted correlation coefficient (GM12878) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Expert Model on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'GM12878'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.247 Stratum adjusted correlation coefficient (H1hESC) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Expert Model on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'H1hESC'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.21 Stratum adjusted correlation coefficient (HCT116) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Expert Model on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'HCT116'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.258 Stratum adjusted correlation coefficient (HFF) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Expert Model on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'HFF'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.21 Stratum adjusted correlation coefficient (IMR90) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Expert Model on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'IMR90'

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

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Sources and history

Release 2026-10-23-5347695500ed · Record review: source checked

1 source record and release history

DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Original source · Nature Communications 16, published 2025-11-18; PMC12627797 full-text XML

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-dnalongbench-config-akita

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: Expert Model (Akita)
foundation model eligible: false
parameters: Expert model for CMP: Akita contact-map model
access reuse: Not stated in the main text
source locator: Methods 'Expert model', 'CNN' and 'DNA Foundation Model'
missing metadata: version: reason: unreported; note: Checkpoint or release not printed beyond the model name
provenance note: Akita as evaluated in DNALONGBENCH.

Related records

configuration of: Akita
system: Expert Model on DNALONGBENCH CMP

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