Genomic benchmarks: a collection of datasets for genomic sequence classification; PMC10150520

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Records in this release that cite this source. A record can cite several sources.

2 configurations
1 benchmark
18 tasks
9 dataset subsets
36 evaluations
36 results
18 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Model or configuration	Metric	Value	Dataset	Evaluation
Baseline CNN (PyTorch)	Accuracy	87.6 percent	demo_coding_vs_intergenomic_seqs (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-ACCURACY: demo_coding_vs_intergenomic_seqs, Accuracy
Baseline CNN (PyTorch)	F1 (binary, positive class)	86.8 percent	demo_coding_vs_intergenomic_seqs (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-F1: demo_coding_vs_intergenomic_seqs, F1 score
Baseline CNN (PyTorch)	Accuracy	93.0 percent	demo_human_or_worm (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks DEMO-HUMAN-OR-WORM-ACCURACY: demo_human_or_worm, Accuracy
Baseline CNN (PyTorch)	F1 (binary, positive class)	92.8 percent	demo_human_or_worm (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks DEMO-HUMAN-OR-WORM-F1: demo_human_or_worm, F1 score
Baseline CNN (PyTorch)	Accuracy	58.6 percent	drosophila_enhancers_stark (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-ACCURACY: drosophila_enhancers_stark, Accuracy
Baseline CNN (PyTorch)	F1 (binary, positive class)	44.5 percent	drosophila_enhancers_stark (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-F1: drosophila_enhancers_stark, F1 score
Baseline CNN (PyTorch)	Accuracy	69.0 percent	dummy_mouse_enhancers_ensembl (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-ACCURACY: dummy_mouse_enhancers_ensembl, Accuracy
Baseline CNN (PyTorch)	F1 (binary, positive class)	70.4 percent	dummy_mouse_enhancers_ensembl (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-F1: dummy_mouse_enhancers_ensembl, F1 score
Baseline CNN (PyTorch)	Accuracy	69.5 percent	human_enhancers_cohn (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-ENHANCERS-COHN-ACCURACY: human_enhancers_cohn, Accuracy
Baseline CNN (PyTorch)	F1 (binary, positive class)	67.1 percent	human_enhancers_cohn (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-ENHANCERS-COHN-F1: human_enhancers_cohn, F1 score
Baseline CNN (PyTorch)	Accuracy	68.9 percent	human_enhancers_ensembl (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-ACCURACY: human_enhancers_ensembl, Accuracy
Baseline CNN (PyTorch)	F1 (binary, positive class)	56.5 percent	human_enhancers_ensembl (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-F1: human_enhancers_ensembl, F1 score
Baseline CNN (PyTorch)	Accuracy	93.3 percent	human_ensembl_regulatory (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-ACCURACY: human_ensembl_regulatory, Accuracy
Baseline CNN (PyTorch)	Micro F1	93.3 percent	human_ensembl_regulatory (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-F1: human_ensembl_regulatory, F1 score
Baseline CNN (PyTorch)	Accuracy	84.6 percent	human_nontata_promoters (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-NONTATA-PROMOTERS-ACCURACY: human_nontata_promoters, Accuracy
Baseline CNN (PyTorch)	F1 (binary, positive class)	83.7 percent	human_nontata_promoters (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-NONTATA-PROMOTERS-F1: human_nontata_promoters, F1 score
Baseline CNN (PyTorch)	Accuracy	68.0 percent	human_ocr_ensembl (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-OCR-ENSEMBL-ACCURACY: human_ocr_ensembl, Accuracy
Baseline CNN (PyTorch)	F1 (binary, positive class)	66.1 percent	human_ocr_ensembl (Genomic Benchmarks split)	Baseline CNN (PyTorch) on Genomic Benchmarks HUMAN-OCR-ENSEMBL-F1: human_ocr_ensembl, F1 score
Baseline CNN (TensorFlow)	Accuracy	89.6 percent	demo_coding_vs_intergenomic_seqs (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-ACCURACY: demo_coding_vs_intergenomic_seqs, Accuracy
Baseline CNN (TensorFlow)	F1 (binary, positive class)	89.4 percent	demo_coding_vs_intergenomic_seqs (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-F1: demo_coding_vs_intergenomic_seqs, F1 score
Baseline CNN (TensorFlow)	Accuracy	94.2 percent	demo_human_or_worm (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks DEMO-HUMAN-OR-WORM-ACCURACY: demo_human_or_worm, Accuracy
Baseline CNN (TensorFlow)	F1 (binary, positive class)	93.2 percent	demo_human_or_worm (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks DEMO-HUMAN-OR-WORM-F1: demo_human_or_worm, F1 score
Baseline CNN (TensorFlow)	Accuracy	52.4 percent	drosophila_enhancers_stark (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-ACCURACY: drosophila_enhancers_stark, Accuracy
Baseline CNN (TensorFlow)	F1 (binary, positive class)	69.1 percent	drosophila_enhancers_stark (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-F1: drosophila_enhancers_stark, F1 score
Baseline CNN (TensorFlow)	Accuracy	50.0 percent	dummy_mouse_enhancers_ensembl (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-ACCURACY: dummy_mouse_enhancers_ensembl, Accuracy
Baseline CNN (TensorFlow)	F1 (binary, positive class)	66.9 percent	dummy_mouse_enhancers_ensembl (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-F1: dummy_mouse_enhancers_ensembl, F1 score
Baseline CNN (TensorFlow)	Accuracy	68.9 percent	human_enhancers_cohn (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-ENHANCERS-COHN-ACCURACY: human_enhancers_cohn, Accuracy
Baseline CNN (TensorFlow)	F1 (binary, positive class)	71.3 percent	human_enhancers_cohn (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-ENHANCERS-COHN-F1: human_enhancers_cohn, F1 score
Baseline CNN (TensorFlow)	Accuracy	81.1 percent	human_enhancers_ensembl (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-ACCURACY: human_enhancers_ensembl, Accuracy
Baseline CNN (TensorFlow)	F1 (binary, positive class)	74.6 percent	human_enhancers_ensembl (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-F1: human_enhancers_ensembl, F1 score
Baseline CNN (TensorFlow)	Accuracy	79.3 percent	human_ensembl_regulatory (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-ACCURACY: human_ensembl_regulatory, Accuracy
Baseline CNN (TensorFlow)	Micro F1	79.3 percent	human_ensembl_regulatory (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-F1: human_ensembl_regulatory, F1 score
Baseline CNN (TensorFlow)	Accuracy	86.5 percent	human_nontata_promoters (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-NONTATA-PROMOTERS-ACCURACY: human_nontata_promoters, Accuracy
Baseline CNN (TensorFlow)	F1 (binary, positive class)	84.4 percent	human_nontata_promoters (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-NONTATA-PROMOTERS-F1: human_nontata_promoters, F1 score
Baseline CNN (TensorFlow)	Accuracy	68.8 percent	human_ocr_ensembl (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-OCR-ENSEMBL-ACCURACY: human_ocr_ensembl, Accuracy
Baseline CNN (TensorFlow)	F1 (binary, positive class)	72.0 percent	human_ocr_ensembl (Genomic Benchmarks split)	Baseline CNN (TensorFlow) on Genomic Benchmarks HUMAN-OCR-ENSEMBL-F1: human_ocr_ensembl, F1 score

Claims

Statements this source supports, each with where in the source it was checked.

Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-ACCURACY: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(demo_coding_vs_intergenomic_seqs))
Genomic Benchmarks DEMO-CODING-VS-INTERGENOMIC-SEQS-F1: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(demo_coding_vs_intergenomic_seqs))
Genomic Benchmarks DEMO-HUMAN-OR-WORM-ACCURACY: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(demo_human_or_worm))
Genomic Benchmarks DEMO-HUMAN-OR-WORM-F1: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(demo_human_or_worm))
Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-ACCURACY: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(drosophila_enhancers_stark))
Genomic Benchmarks DROSOPHILA-ENHANCERS-STARK-F1: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(drosophila_enhancers_stark))
Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-ACCURACY: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(dummy_mouse_enhancers_ensembl))
Genomic Benchmarks DUMMY-MOUSE-ENHANCERS-ENSEMBL-F1: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(dummy_mouse_enhancers_ensembl))
Genomic Benchmarks HUMAN-ENHANCERS-COHN-ACCURACY: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_enhancers_cohn))
Genomic Benchmarks HUMAN-ENHANCERS-COHN-F1: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_enhancers_cohn))
Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-ACCURACY: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_enhancers_ensembl))
Genomic Benchmarks HUMAN-ENHANCERS-ENSEMBL-F1: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_enhancers_ensembl))
Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-ACCURACY: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_ensembl_regulatory))
Genomic Benchmarks HUMAN-ENSEMBL-REGULATORY-F1: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_ensembl_regulatory))
Genomic Benchmarks HUMAN-NONTATA-PROMOTERS-ACCURACY: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_nontata_promoters))
Genomic Benchmarks HUMAN-NONTATA-PROMOTERS-F1: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_nontata_promoters))
Genomic Benchmarks HUMAN-OCR-ENSEMBL-ACCURACY: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_ocr_ensembl))
Genomic Benchmarks HUMAN-OCR-ENSEMBL-F1: part of discovery-benchmark-genomic-benchmarks: Part of Genomic Benchmarks (Table 2, row(human_ocr_ensembl))

Models, benchmarks and other records

Configurations (2)

Benchmarks (1)

Genomic Benchmarks

Tasks (18)

Dataset subsets (9)

Evaluations (36)

Evidence

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Evidence table

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16 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Artifact SHA-256 bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0 Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Doi 10.1186/s12863-023-01123-8 Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Hash scope Exact retrieved primary paper artifact bytes. Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.hash_scope` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Retrieved at 2026-09-16T21:07:13.681402+00:00 Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review method 1 values automated-source-review Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.method` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review: scope Source identification and table transcription; no independent experimental reproduction. Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.scope` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Version PMC10150520 Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Primary reference; inspect retrieval status and review scope. Source metadata	Genomic benchmarks: a collection of datasets for genomic sequence classification Original source ↗ No field-specific location recorded Version: PMC10150520 Retrieved: 2026-09-16T21:07:13.681402+00:00	catalogued No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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Stable ID: expansion-p3-genomic-benchmarks

url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML
doi: 10.1186/s12863-023-01123-8
version: PMC10150520
retrieved at: 2026-09-16T21:07:13.681402+00:00
artifact sha256: bda6fe51e3363a5d2fc8d265ca536897d3e83eb76458fc95066c21933e3bd0c0
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10150520/fullTextXML
hash scope: Exact retrieved primary paper artifact bytes.
review: scope: Source identification and table transcription; no independent experimental reproduction.; method: automated-source-review

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