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Benchmark

Gene-MTEB

Genomic embedding evaluations covering sequence classification and clustering. Accuracy and V-measure remain separate metrics and each source task retains its own comparison.

80 evaluations · 80 metric rows

Overview

Genomic embedding evaluations covering sequence classification and clustering. Accuracy and V-measure remain separate metrics and each source task retains its own comparison.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation

accuracy (fraction) · Higher values are better.

Every method Gene-MTEB genomic embedding benchmark reports on HMPD-disease genomic embedding evaluation, scored with accuracy on HMPD-disease Gene-MTEB data used in METAGENE-1 Table 3.

Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation · HMPD-disease Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)

Evidence origin: Author-reported evaluation. Numerical source review does not establish independent reproduction.

METAGENE-1 v1: Gene-MTEB complete component tasks · Table 3 (S5.T3), row HMPD-disease, column DNABERT-2; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1

All 16 component tasks and five methods are included. Twenty-five printed aggregate cells are retained in a companion receipt, excluded from task-level result counts to avoid counting derived averages as extra experiments.

All comparison limitations (5)
  • All 16 component tasks and five methods are included. Twenty-five printed aggregate cells are retained in a companion receipt, excluded from task-level result counts to avoid counting derived averages as extra experiments.
  • Classification accuracy and clustering V-measure must not be combined into a universal performance metric.
  • Paper source does not pin exact evaluator/data revisions or per-task denominators. Current code metadata uses mutable dataset revision main; its development metadata is not asserted to be the evaluated paper version.
  • Paper calls embeddings zero-shot; this does not mean classification is label-free: logistic-regression probes use training labels.
  • No uncertainty intervals or repeats are printed.

Automated source review: 2026-09-23.

No unavailable values; missing scores remain labelled and are never plotted as zero.

Showing 5 of 5 matching rows.

Tested configuration
00.250.50.751
Reported score
  1. METAGENE-10.542
  2. NT-2.5b-Multi0.498
  3. NT-2.5b-1000g0.489
  4. DNABERT-S0.486
  5. DNABERT-20.480

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Protocols

These source-backed links do not make different protocols or scores interchangeable.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 32 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

Baseline status by linked protocol

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-23-2b89723c6dd9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run this benchmark

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Run this benchmark

The paper describes frozen embedding probes and references Gene-MTEB. Rewire has no maintained runner for this published evaluation. Original split hashes, checkpoint revisions and evaluator revision are not established.

A maintained rewire runner has not been verified for this benchmark. Check data access, weights, licences, dependencies and hardware in the linked official documentation; requirements have not been fully extracted.

METAGENE-1 v1: Gene-MTEB complete component tasks · Section 5.3
Strengths, limitations and unresolved questions

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.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-23-2b89723c6dd9
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Sources and history

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Release 2026-09-23-2b89723c6dd9 · Record review: source checked

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: discovery-benchmark-gene-mteb

areas
genomics
source locator
METAGENE-1 Section 5.3; Table 3
run documentation
record id: discovery-benchmark-gene-mteb; status: source_reviewed_not_executed; source ids: coverage-source-metagene-paper-v1; source locator: Section 5.3; summary: The paper describes frozen embedding probes and references Gene-MTEB. Rewire has no maintained runner for this published evaluation. Original split hashes, checkpoint revisions and evaluator revision are not established.
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