Evidence claim

Nucleotide Transformer + NN (middle): description

Description of Nucleotide Transformer + NN (middle)

Classifies gene fusion breakpoints from 10 kbp DNA windows using frozen Nucleotide Transformer embeddings, concatenating the middle embedding at the breakpoint of each sequence and training a small neural-network classifier on it.

Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value.

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.

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7 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
Claimed field description Context-only references	Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Original source ↗ Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `0f4d9de77f1e39cfd2164a20653d86370767da684dc22d17e09f589761abeb5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Identity as reported in this paper. Unspecified versions are not assumed equivalent to other papers. Context-only references	Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Original source ↗ Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `0f4d9de77f1e39cfd2164a20653d86370767da684dc22d17e09f589761abeb5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods Context-only references	Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Original source ↗ Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `0f4d9de77f1e39cfd2164a20653d86370767da684dc22d17e09f589761abeb5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value Classifies gene fusion breakpoints from 10 kbp DNA windows using frozen Nucleotide Transformer embeddings, concatenating the middle embedding at the breakpoint of each sequence and training a small neural-network classifier on it. Context-only references	Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Original source ↗ Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `0f4d9de77f1e39cfd2164a20653d86370767da684dc22d17e09f589761abeb5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value. Context-only references	Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Original source ↗ Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `0f4d9de77f1e39cfd2164a20653d86370767da684dc22d17e09f589761abeb5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: subject reported-model-1a67087ac262c5 Context-only references	Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Original source ↗ Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `links:subject:reported-model-1a67087ac262c5` Source artifact SHA-256: `0f4d9de77f1e39cfd2164a20653d86370767da684dc22d17e09f589761abeb5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name Nucleotide Transformer + NN (middle): description Context-only references	Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences Original source ↗ Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `0f4d9de77f1e39cfd2164a20653d86370767da684dc22d17e09f589761abeb5f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

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

1 source record and release history

Benchmarking genomic foundation models for binary classification of gene fusion breakpoints from DNA sequences · Original source · journal full text in PMC

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Technical metadata and extraction receipts

Stable ID: metadata-correction-42c7e7cd323f352f2190

areas: dna-genomes
field: description
previous value: Identity as reported in this paper. Unspecified versions are not assumed equivalent to other papers.
value: Classifies gene fusion breakpoints from 10 kbp DNA windows using frozen Nucleotide Transformer embeddings, concatenating the middle embedding at the breakpoint of each sequence and training a small neural-network classifier on it.
source locator: Reviewed profile (2026-09-16): summary at Discussion (paragraph 2); Results/Classification performance (paragraph 2); architecture fact at Methods/Evaluation metrics (paragraph 2); Methods (paragraph 1); description text also read at Methods/Embedding extraction; Abstract/Methods
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Extractor: Claude integrator agent for issue #88. Reviewer: a separate Claude review agent, independent of the extractor; no human review claimed.; date: 2026-10-11; method note: Compared the store diff with origin/main, read each new description against its cited source passage and checked the licence of each new source record.; note: Approved. Checked all 11 scTab and MPRabc method descriptions against PMC11298532 and PMC13232518, and Lazypipe-nt, scaLR, CATHe2, DiffDock-NMDN, PC-mer and Hi-Enhancer against their papers; all match. The other pipeline descriptions are consistent with their pinned papers.; receipt: data/omics/qa-descriptions-20261011-c/review.json

Related records

subject: Nucleotide Transformer + NN (middle)

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