Result

AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings) of DNABERT-2 (zero-shot, GFMBench-API) on TraitGym Complex test set (GFMBench-API)

0.109 AUPRC (zero-shot; cosine similarity of reference and alternate sequence embeddings)

Methods

Tested configuration: DNABERT-2 (zero-shot, GFMBench-API)
Protocol: GFMBench-API TraitGym Complex, zs-embedding
Dataset: TraitGym Complex test set (GFMBench-API)
Procedure: GFMBench-API TraitGym Complex, zs-embedding
Evaluation: DNABERT-2 on GFMBench-API TraitGym Complex (zs-embedding)
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not reported by the source
Evidence: Independent external evaluation · source checkedGFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 3, task 'TraitGym Complex', row 'DNABERT-2', column 'Cos AUPRC'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Test split
Adaptation: zero-shot
Scoring implementation: GFMBench-API task metrics

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

1 evidence row 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
Reported result 0.1089 Individual claims	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ Table 3, task 'TraitGym Complex', row 'DNABERT-2', column 'Cos AUPRC' Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	source checked ["source-hash-verification","pdf-text-parse","independent-cell-check"] · 2026-10-11 independent paper Audit details Extraction: Parsed the pdftotext -layout text of the pinned PDF with tools/extract_gfmbench.py: model rows matched by name, task labels assigned to fixed blocks of model rows in printed order, block and row counts asserted. Table 3, task 'TraitGym Complex', row 'DNABERT-2', column 'Cos AUPRC' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md. Field: `attributes.printed_value` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Extraction artifact

How to read the evidence

Sources and history

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

1 source record and release history

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Original source · bioRxiv preprint version 2, posted 2026-08-11

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-gfmbench-result-dnabert-2-zero-shot-traitgym-complex-zs-embedding-cos-auprc

metric: auprc
metric direction: higher
unit: unitless
printed value: 0.1089
source locator: Table 3, task 'TraitGym Complex', row 'DNABERT-2', column 'Cos AUPRC'
review: method: source-hash-verification; pdf-text-parse; independent-cell-check; method note: Matched the archived PDF's SHA-256, re-parsed Tables 1-5 from pdftotext -layout with an independent block assignment confirmed from AUPRC prevalence; every printed and numeric value matches.; reviewer: claude; reviewer note: Claude review agent reviewer-gen-3, independent of the extractor lit-genomics; no human review claimed; date: 2026-10-11; artifact sha256: df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72; retrieval url: https://www.biorxiv.org/content/10.64898/2026.02.19.706811v2.full.pdf; note: Extraction: Parsed the pdftotext -layout text of the pinned PDF with tools/extract_gfmbench.py: model rows matched by name, task labels assigned to fixed blocks of model rows in printed order, block and row counts asserted. Table 3, task 'TraitGym Complex', row 'DNABERT-2', column 'Cos AUPRC' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md.
numeric value: 0.1089
metric qualifier: zero-shot; cosine similarity of reference and alternate sequence embeddings
missing metadata: uncertainty: reason: unreported

Related records

evaluation: DNABERT-2 on GFMBench-API TraitGym Complex (zs-embedding)

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