Configuration

CNN (DNALONGBENCH, TISP)

CNN: CNN trained for TISP.

Overview

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Evaluations and results

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

Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) · Dataset: DNALONGBENCH Transcription initiation signal prediction test set

Sorted by Pearson (average over TISP 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	Pearson (average over TISP conditions as printed)	Pearson (EC (ENCODE CAGE))	Pearson (ER (ENCODE RAMPAGE))	Pearson (FC (FANTOM CAGE))	Pearson (GC (GRO-cap))	Pearson (PC (PRO-cap))
CNN (DNALONGBENCH, TISP)Evaluation	0.042	0.038	0.043	0.029	0.037	0.066

All 6 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: CNN (DNALONGBENCH, TISP)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.042 Pearson (average over TISP conditions as printed) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'CNN', column 'Avg'
Configuration: CNN (DNALONGBENCH, TISP)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.038 Pearson (EC (ENCODE CAGE)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'CNN', column 'EC'
Configuration: CNN (DNALONGBENCH, TISP)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.043 Pearson (ER (ENCODE RAMPAGE)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'CNN', column 'ER'
Configuration: CNN (DNALONGBENCH, TISP)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.029 Pearson (FC (FANTOM CAGE)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'CNN', column 'FC'
Configuration: CNN (DNALONGBENCH, TISP)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.037 Pearson (GC (GRO-cap)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'CNN', column 'GC'
Configuration: CNN (DNALONGBENCH, TISP)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.066 Pearson (PC (PRO-cap)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'CNN', column 'PC'

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

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Evidence

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Evidence table

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Claims, original sources and review scope · 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-cnn-tisp

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: CNN
foundation model eligible: false
parameters: CNN trained for TISP
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: CNN as evaluated in DNALONGBENCH.

Related records

configuration of: DNALONGBENCH CNN baseline
system: CNN on DNALONGBENCH TISP

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