HMPD-disease Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)
Dataset subset reported in METAGENE-1 v1: Gene-MTEB complete component tasks. Exact split manifest remains unextracted; source-table identity is retained.
Evaluation results
5 evaluations · 5 metric rows. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: DNABERT-2 | Protocol: Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation Dataset subset: HMPD-disease Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split) | 0.480 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceFrozen model last-hidden-state embeddings, mean pooled. Logistic regression for eight classification tasks and mini-batch k-means for eight clustering tasks. Source paper Section 5.3. Current official gene-mteb implementation corroborates task identities but its commit is not proven identical to the paper evaluator. Exact dataset release, split hash, scored counts and evaluator commit are unreported in the paper. Do not substitute current mutable HF main for the original split. Aggregation: Not reported 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 |
| Pipeline: DNABERT-S | Protocol: Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation Dataset subset: HMPD-disease Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split) | 0.486 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceFrozen model last-hidden-state embeddings, mean pooled. Logistic regression for eight classification tasks and mini-batch k-means for eight clustering tasks. Source paper Section 5.3. Current official gene-mteb implementation corroborates task identities but its commit is not proven identical to the paper evaluator. Exact dataset release, split hash, scored counts and evaluator commit are unreported in the paper. Do not substitute current mutable HF main for the original split. Aggregation: Not reported METAGENE-1 v1: Gene-MTEB complete component tasks · Table 3 (S5.T3), row HMPD-disease, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1 |
| Pipeline: METAGENE-1 | Protocol: Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation Dataset subset: HMPD-disease Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split) | 0.542 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceFrozen model last-hidden-state embeddings, mean pooled. Logistic regression for eight classification tasks and mini-batch k-means for eight clustering tasks. Source paper Section 5.3. Current official gene-mteb implementation corroborates task identities but its commit is not proven identical to the paper evaluator. Exact dataset release, split hash, scored counts and evaluator commit are unreported in the paper. Do not substitute current mutable HF main for the original split. Aggregation: Not reported METAGENE-1 v1: Gene-MTEB complete component tasks · Table 3 (S5.T3), row HMPD-disease, column METAGENE-1; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1 |
| Pipeline: NT-2.5b-1000g | Protocol: Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation Dataset subset: HMPD-disease Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split) | 0.489 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceFrozen model last-hidden-state embeddings, mean pooled. Logistic regression for eight classification tasks and mini-batch k-means for eight clustering tasks. Source paper Section 5.3. Current official gene-mteb implementation corroborates task identities but its commit is not proven identical to the paper evaluator. Exact dataset release, split hash, scored counts and evaluator commit are unreported in the paper. Do not substitute current mutable HF main for the original split. Aggregation: Not reported METAGENE-1 v1: Gene-MTEB complete component tasks · Table 3 (S5.T3), row HMPD-disease, column NT-2.5b-1000g; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1 |
| Pipeline: NT-2.5b-Multi | Protocol: Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation Dataset subset: HMPD-disease Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split) | 0.498 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceFrozen model last-hidden-state embeddings, mean pooled. Logistic regression for eight classification tasks and mini-batch k-means for eight clustering tasks. Source paper Section 5.3. Current official gene-mteb implementation corroborates task identities but its commit is not proven identical to the paper evaluator. Exact dataset release, split hash, scored counts and evaluator commit are unreported in the paper. Do not substitute current mutable HF main for the original split. Aggregation: Not reported METAGENE-1 v1: Gene-MTEB complete component tasks · Table 3 (S5.T3), row HMPD-disease, column NT-2.5b-Multi; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1 |
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Subset and evaluation context
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| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description Dataset subset reported in METAGENE-1 v1: Gene-MTEB complete component tasks. Exact split manifest remains unextracted; source-table identity is retained. Context-only references | METAGENE-1 v1: Gene-MTEB complete component tasks No field-specific location recorded Version: arXiv:2501.02045v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| name HMPD-disease Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split) Context-only references | METAGENE-1 v1: Gene-MTEB complete component tasks No field-specific location recorded Version: arXiv:2501.02045v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
1 source records and release history
- METAGENE-1 v1: Gene-MTEB complete component tasks · Original source · arXiv:2501.02045v1
Technical metadata and extraction receipts
Stable ID: metagene-gene-mteb-dataset-hmpd-disease-gene-mteb-data-used-in-metagene-1-table-3
- areas
- dna-genomes
- missing metadata
- version: unreported; url: unextracted
Related records
- dataset: DNABERT-2 on Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation
- dataset: DNABERT-S on Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation
- dataset: METAGENE-1 on Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation
- dataset: NT-2.5b-1000g on Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation
- dataset: NT-2.5b-Multi on Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation