GUANinE v1.1 reveals complementarity of supervised and genomic language models; Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML

What this source contributed

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

8 models
8 methods
55 configurations
1 benchmark
8 protocols
8 datasets
225 evaluations
225 results
3 evidence claims

Results

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

Value	Metric	Model or configuration	Dataset	Evaluation
27.46 unitless	Spearman (GUANinE v1.1 test set)	⋆ T5 (fine-tuned, GUANinE v1.1)	GUANinE ccre-propensity test set	⋆ T5 on GUANinE ccre-propensity
52.56 unitless	Spearman (GUANinE v1.1 test set)	⋆ T5 (fine-tuned, GUANinE v1.1)	GUANinE cons30 test set	⋆ T5 on GUANinE cons30
44.05 unitless	Spearman (GUANinE v1.1 test set)	⋆ T5 (fine-tuned, GUANinE v1.1)	GUANinE cons100 test set	⋆ T5 on GUANinE cons100
33.05 unitless	Spearman (GUANinE v1.1 test set)	⋆ T5 (fine-tuned, GUANinE v1.1)	GUANinE dnase-propensity test set	⋆ T5 on GUANinE dnase-propensity
84.67 unitless	Spearman (GUANinE v1.1 test set)	⋆ T5 (fine-tuned, GUANinE v1.1)	GUANinE gpra-c test set	⋆ T5 on GUANinE gpra-c
88.59 unitless	Spearman (GUANinE v1.1 test set)	⋆ T5 (fine-tuned, GUANinE v1.1)	GUANinE gpra-d test set	⋆ T5 on GUANinE gpra-d
23.36 unitless	Spearman (GUANinE v1.1 test set)	5-mer kNN (fine-tuned, GUANinE v1.1)	GUANinE ccre-propensity test set	5-mer kNN on GUANinE ccre-propensity
52.58 unitless	Spearman (GUANinE v1.1 test set)	5-mer kNN (fine-tuned, GUANinE v1.1)	GUANinE cons30 test set	5-mer kNN on GUANinE cons30
44.54 unitless	Spearman (GUANinE v1.1 test set)	5-mer kNN (fine-tuned, GUANinE v1.1)	GUANinE cons100 test set	5-mer kNN on GUANinE cons100
31.99 unitless	Spearman (GUANinE v1.1 test set)	5-mer kNN (fine-tuned, GUANinE v1.1)	GUANinE dnase-propensity test set	5-mer kNN on GUANinE dnase-propensity
58.56 unitless	Spearman (GUANinE v1.1 test set)	5-mer kNN (fine-tuned, GUANinE v1.1)	GUANinE gpra-c test set	5-mer kNN on GUANinE gpra-c
62.11 unitless	Spearman (GUANinE v1.1 test set)	5-mer kNN (fine-tuned, GUANinE v1.1)	GUANinE gpra-d test set	5-mer kNN on GUANinE gpra-d
26.37 unitless	Spearman (GUANinE v1.1 test set)	5-mer LinSVR (fine-tuned, GUANinE v1.1)	GUANinE ccre-propensity test set	5-mer LinSVR on GUANinE ccre-propensity
49.35 unitless	Spearman (GUANinE v1.1 test set)	5-mer LinSVR (fine-tuned, GUANinE v1.1)	GUANinE cons30 test set	5-mer LinSVR on GUANinE cons30
45.05 unitless	Spearman (GUANinE v1.1 test set)	5-mer LinSVR (fine-tuned, GUANinE v1.1)	GUANinE cons100 test set	5-mer LinSVR on GUANinE cons100
36.30 unitless	Spearman (GUANinE v1.1 test set)	5-mer LinSVR (fine-tuned, GUANinE v1.1)	GUANinE dnase-propensity test set	5-mer LinSVR on GUANinE dnase-propensity
69.43 unitless	Spearman (GUANinE v1.1 test set)	5-mer LinSVR (fine-tuned, GUANinE v1.1)	GUANinE gpra-c test set	5-mer LinSVR on GUANinE gpra-c
73.65 unitless	Spearman (GUANinE v1.1 test set)	5-mer LinSVR (fine-tuned, GUANinE v1.1)	GUANinE gpra-d test set	5-mer LinSVR on GUANinE gpra-d
35.38 unitless	Spearman (GUANinE v1.1 test set)	AIDO.DNA_300m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE ccre-propensity test set	AIDO.DNA_300m on GUANinE ccre-propensity
60.99 unitless	Spearman (GUANinE v1.1 test set)	AIDO.DNA_300m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cons30 test set	AIDO.DNA_300m on GUANinE cons30
51.50 unitless	Spearman (GUANinE v1.1 test set)	AIDO.DNA_300m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cons100 test set	AIDO.DNA_300m on GUANinE cons100
42.66 unitless	Spearman (GUANinE v1.1 test set)	AIDO.DNA_300m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE dnase-propensity test set	AIDO.DNA_300m on GUANinE dnase-propensity
73.52 unitless	Spearman (GUANinE v1.1 test set)	AIDO.DNA_300m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE gpra-c test set	AIDO.DNA_300m on GUANinE gpra-c
77.25 unitless	Spearman (GUANinE v1.1 test set)	AIDO.DNA_300m (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE gpra-d test set	AIDO.DNA_300m on GUANinE gpra-d
93.17 unitless	Spearman (GUANinE v1.1 test set)	AlphaGenome-K562 (evaluation mode not printed (Table 4 has no Eval. column), GUANinE v1.1)	GUANinE clinvar-snv test set	AlphaGenome-K562 on GUANinE clinvar-snv
20.99 unitless	Spearman (GUANinE v1.1 test set)	Borzoi (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cadd-snv test set	Borzoi on GUANinE cadd-snv
57.69 unitless	Spearman (GUANinE v1.1 test set)	Borzoi (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE ccre-propensity test set	Borzoi on GUANinE ccre-propensity
71.55 unitless	Spearman (GUANinE v1.1 test set)	Borzoi (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cons30 test set	Borzoi on GUANinE cons30
59.69 unitless	Spearman (GUANinE v1.1 test set)	Borzoi (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cons100 test set	Borzoi on GUANinE cons100
70.69 unitless	Spearman (GUANinE v1.1 test set)	Borzoi (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE dnase-propensity test set	Borzoi on GUANinE dnase-propensity
71.53 unitless	Spearman (GUANinE v1.1 test set)	Borzoi (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE gpra-c test set	Borzoi on GUANinE gpra-c
75.18 unitless	Spearman (GUANinE v1.1 test set)	Borzoi (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE gpra-d test set	Borzoi on GUANinE gpra-d
19.66 unitless	Spearman (GUANinE v1.1 test set)	CADD v1.7 (Position) (zero-shot, GUANinE v1.1)	GUANinE cadd-snv test set	CADD v1.7 (Position) on GUANinE cadd-snv
83.68 unitless	Spearman (GUANinE v1.1 test set)	CADD v1.7 (Position) (evaluation mode not printed (Table 4 has no Eval. column), GUANinE v1.1)	GUANinE clinvar-snv test set	CADD v1.7 (Position) on GUANinE clinvar-snv
18.15 unitless	Spearman (GUANinE v1.1 test set)	CADD v1.7 (zero-shot, GUANinE v1.1)	GUANinE cadd-snv test set	CADD v1.7 on GUANinE cadd-snv
84.64 unitless	Spearman (GUANinE v1.1 test set)	CADD v1.7 (evaluation mode not printed (Table 4 has no Eval. column), GUANinE v1.1)	GUANinE clinvar-snv test set	CADD v1.7 on GUANinE clinvar-snv
41.32 unitless	Spearman (GUANinE v1.1 test set)	Caduceus-PS (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE ccre-propensity test set	Caduceus-PS on GUANinE ccre-propensity
74.37 unitless	Spearman (GUANinE v1.1 test set)	Caduceus-PS (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cons30 test set	Caduceus-PS on GUANinE cons30
62.38 unitless	Spearman (GUANinE v1.1 test set)	Caduceus-PS (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cons100 test set	Caduceus-PS on GUANinE cons100
42.97 unitless	Spearman (GUANinE v1.1 test set)	Caduceus-PS (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE dnase-propensity test set	Caduceus-PS on GUANinE dnase-propensity
72.44 unitless	Spearman (GUANinE v1.1 test set)	Caduceus-PS (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE gpra-c test set	Caduceus-PS on GUANinE gpra-c
76.03 unitless	Spearman (GUANinE v1.1 test set)	Caduceus-PS (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE gpra-d test set	Caduceus-PS on GUANinE gpra-d
17.29 unitless	Spearman (GUANinE v1.1 test set)	ChromBPNet-ATAC-F0 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cadd-snv test set	ChromBPNet-ATAC-F0 on GUANinE cadd-snv
40.42 unitless	Spearman (GUANinE v1.1 test set)	ChromBPNet-ATAC-F0 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE ccre-propensity test set	ChromBPNet-ATAC-F0 on GUANinE ccre-propensity
47.78 unitless	Spearman (GUANinE v1.1 test set)	ChromBPNet-ATAC-F0 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cons30 test set	ChromBPNet-ATAC-F0 on GUANinE cons30
41.49 unitless	Spearman (GUANinE v1.1 test set)	ChromBPNet-ATAC-F0 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cons100 test set	ChromBPNet-ATAC-F0 on GUANinE cons100
41.49 unitless	Spearman (GUANinE v1.1 test set)	ChromBPNet-ATAC-F0 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE dnase-propensity test set	ChromBPNet-ATAC-F0 on GUANinE dnase-propensity
71.09 unitless	Spearman (GUANinE v1.1 test set)	ChromBPNet-ATAC-F0 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE gpra-c test set	ChromBPNet-ATAC-F0 on GUANinE gpra-c
74.93 unitless	Spearman (GUANinE v1.1 test set)	ChromBPNet-ATAC-F0 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE gpra-d test set	ChromBPNet-ATAC-F0 on GUANinE gpra-d
16.76 unitless	Spearman (GUANinE v1.1 test set)	ChromBPNet-ATAC-F3 (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE cadd-snv test set	ChromBPNet-ATAC-F3 on GUANinE cadd-snv

Claims

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

GPN-MSA (evaluation mode not printed (Table 4 has no Eval. column), GUANinE v1.1): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)
GPN-MSA (Position) (zero-shot, GUANinE v1.1): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA (Position)); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)
GPN-MSA (zero-shot, GUANinE v1.1): configuration of GPN-MSA: Configuration of GPN-MSA (Configuration name as printed in its source (GPN-MSA); GPN-MSA identity from gfm-guides-20261014-gpnmsa-source-biorxiv-v2 (Abstract) and gfm-guides-20261014-gpnmsa-source-gpn-msa-doc)

Models, benchmarks and other records

Models (8)

Methods (8)

Configurations (55)

Benchmarks (1)

GUANinE v1.1

Protocols (8)

Datasets (8)

Evidence

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Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

23 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
attributes.artifact_sha256 f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79 Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13501288/fullTextXML Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Doi 10.1093/bioinformatics/btag427 Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Licence CC-BY-4.0 Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.licence` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 2 values The XML does not carry the blue colouring that Table 2 uses to mark previously reported performances, so which Table 2 cells repeat earlier GUANinE results cannot be told from this artifact. The supplementary PDF (btag427_supplementary_data.pdf) is a scanned print with no text layer and was not read. Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Media type application/xml Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.media_type` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Publication status peer_reviewed Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.publication_status` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Retrieved at 2026-10-11T00:40:24Z Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Review: date 2026-10-11 Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.review.date` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Review: method note Artifact re-retrieved or unpacked and SHA-256 matched. Source metadata	GUANinE v1.1 reveals complementarity of supervised and genomic language models Original source ↗ No field-specific location recorded Version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML Retrieved: 2026-10-11T00:40:24Z	catalogued No individual claim review recorded Audit details Field: `attributes.review.method_note` Source artifact SHA-256: `f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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

Primary source retrieved and hashed for the 2026-10-11 genomics literature pass.

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-guanine-source-robson2026

areas: dna-genomes
contexts: research
url: https://doi.org/10.1093/bioinformatics/btag427
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13501288/fullTextXML
version: Bioinformatics 2026, btag427 (issue date 2026-08-01); PMC13501288 full-text XML
retrieved at: 2026-10-11T00:40:24Z
artifact sha256: f6cc4294a1519fb5579eebb29ffd919afad0198a3bf8b751635d73b17b33ef79
doi: 10.1093/bioinformatics/btag427
publication status: peer_reviewed
licence: CC-BY-4.0
media type: application/xml
limitations: The XML does not carry the blue colouring that Table 2 uses to mark previously reported performances, so which Table 2 cells repeat earlier GUANinE results cannot be told from this artifact.; The supplementary PDF (btag427_supplementary_data.pdf) is a scanned print with no text layer and was not read.
review: method: source-hash-verification; method note: Artifact re-retrieved or unpacked and SHA-256 matched.; reviewer: claude; reviewer note: Claude review agent reviewer-gen-3, independent of the extractor lit-genomics; no human review claimed; date: 2026-10-11

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