Pipeline

DNABERT-S

Frozen DNABERT-S mean-pooled last-hidden-state embeddings with task-specific logistic-regression or mini-batch k-means probe. Exact source checkpoint/evaluator revision is unreported.

16 evaluations · 16 metric rows

Overview

Frozen DNABERT-S mean-pooled last-hidden-state embeddings with task-specific logistic-regression or mini-batch k-means probe. Exact source checkpoint/evaluator revision is unreported.

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

Evaluations and results

16 evaluations · 16 metric rows. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
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 checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HMPD-disease: HMPD-disease genomic embedding evaluation Frozen 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: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HMPD-sex: HMPD-sex genomic embedding evaluation Dataset subset: HMPD-sex Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.367 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HMPD-sex: HMPD-sex genomic embedding evaluation Frozen 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-sex, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HMPD-single: HMPD-single genomic embedding evaluation Dataset subset: HMPD-single Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.293 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HMPD-single: HMPD-single genomic embedding evaluation Frozen 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-single, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HMPD-source: HMPD-source genomic embedding evaluation Dataset subset: HMPD-source Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.465 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HMPD-source: HMPD-source genomic embedding evaluation Frozen 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-source, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HMPR-p2p: HMPR-p2p genomic embedding evaluation Dataset subset: HMPR-p2p Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.580 v_measure dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HMPR-p2p: HMPR-p2p genomic embedding evaluation Frozen 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 HMPR-p2p, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HMPR-s2s-align: HMPR-s2s-align genomic embedding evaluation Dataset subset: HMPR-s2s-align Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.129 v_measure dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HMPR-s2s-align: HMPR-s2s-align genomic embedding evaluation Frozen 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 HMPR-s2s-align, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HMPR-s2s-small: HMPR-s2s-small genomic embedding evaluation Dataset subset: HMPR-s2s-small Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.421 v_measure dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HMPR-s2s-small: HMPR-s2s-small genomic embedding evaluation Frozen 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 HMPR-s2s-small, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HMPR-s2s-tiny: HMPR-s2s-tiny genomic embedding evaluation Dataset subset: HMPR-s2s-tiny Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.274 v_measure dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HMPR-s2s-tiny: HMPR-s2s-tiny genomic embedding evaluation Frozen 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 HMPR-s2s-tiny, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark Human-Virus-1: Human-Virus-1 genomic embedding evaluation Dataset subset: Human-Virus-1 Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.605 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark Human-Virus-1: Human-Virus-1 genomic embedding evaluation Frozen 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 Human-Virus-1, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark Human-Virus-2: Human-Virus-2 genomic embedding evaluation Dataset subset: Human-Virus-2 Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.510 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark Human-Virus-2: Human-Virus-2 genomic embedding evaluation Frozen 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 Human-Virus-2, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark Human-Virus-3: Human-Virus-3 genomic embedding evaluation Dataset subset: Human-Virus-3 Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.612 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark Human-Virus-3: Human-Virus-3 genomic embedding evaluation Frozen 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 Human-Virus-3, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark Human-Virus-4: Human-Virus-4 genomic embedding evaluation Dataset subset: Human-Virus-4 Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.551 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark Human-Virus-4: Human-Virus-4 genomic embedding evaluation Frozen 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 Human-Virus-4, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HVR-p2p: HVR-p2p genomic embedding evaluation Dataset subset: HVR-p2p Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.550 v_measure dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HVR-p2p: HVR-p2p genomic embedding evaluation Frozen 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 HVR-p2p, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HVR-s2s-align: HVR-s2s-align genomic embedding evaluation Dataset subset: HVR-s2s-align Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.241 v_measure dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HVR-s2s-align: HVR-s2s-align genomic embedding evaluation Frozen 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 HVR-s2s-align, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HVR-s2s-small: HVR-s2s-small genomic embedding evaluation Dataset subset: HVR-s2s-small Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.372 v_measure dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HVR-s2s-small: HVR-s2s-small genomic embedding evaluation Frozen 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 HVR-s2s-small, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1
Pipeline: DNABERT-S	Protocol: Gene-MTEB genomic embedding benchmark HVR-s2s-tiny: HVR-s2s-tiny genomic embedding evaluation Dataset subset: HVR-s2s-tiny Gene-MTEB data used in METAGENE-1 Table 3 (Gene-MTEB genomic embedding benchmark split)	0.753 v_measure dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · source checked Methods, coverage and source DNABERT-S on Gene-MTEB genomic embedding benchmark HVR-s2s-tiny: HVR-s2s-tiny genomic embedding evaluation Frozen 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 HVR-s2s-tiny, column DNABERT-S; Section 5.3 paragraphs S5.SS3.p2.1 and S5.SS3.p3.1

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