Evaluation

NmRF: Human RNA 2OMe sites, independent test set

41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Held-out independent test set.

Evaluation procedure

41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Held-out independent test set.

Configuration: NmRF
Protocol: Human RNA 2OMe sites, independent test set (human RNA 2-prime-O-methylation site prediction)
Dataset: Human RNA 2OMe sites, independent test set

origin: Independent external evaluation
configuration: Public web server evaluated by 2OMe-LM authors
protocol id: paper-protocol-d933438afda70a21ef
dataset version: Not reported
split: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Held-out independent test set.
subset: Not reported
population: Not reported
aggregation: Not reported
inputs: Not reported
adaptation: Public web server evaluated by 2OMe-LM authors
budget: Not reported
metric implementation: Not reported

Metadata review: needs review. Unreported conditions prevent automatic comparisons.

Evaluation results

Release 2026-09-17-d277315f7d76 · 1 evaluation · 7 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
NmRF: Human RNA 2OMe sites, independent test set Configuration: NmRFProtocol: Human RNA 2OMe sites, independent test set (human RNA 2-prime-O-methylation site prediction)Dataset: Human RNA 2OMe sites, independent test set 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Held-out independent test set. Independent external evaluation · Evaluation metadata: needs review
0.624 F1-score Unit: fraction · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 2 NmRF, column 3: Human RNA 2OMe sites, independent test set F1-score Source checking is not independent reproduction.
0.586 AUC Unit: fraction · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 2 NmRF, column 6: Human RNA 2OMe sites, independent test set AUC Source checking is not independent reproduction.
0.508 Precision Unit: fraction · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 2 NmRF, column 4: Human RNA 2OMe sites, independent test set Precision Source checking is not independent reproduction.
0.512 ACC Unit: fraction · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC Source checking is not independent reproduction.
0.030 MCC Unit: unitless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 2 NmRF, column 8: Human RNA 2OMe sites, independent test set MCC Source checking is not independent reproduction.
0.614 AUPR Unit: fraction · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 2 NmRF, column 7: Human RNA 2OMe sites, independent test set AUPR Source checking is not independent reproduction.
0.810 Recall Unit: fraction · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 2 NmRF, column 5: Human RNA 2OMe sites, independent test set Recall Source checking is not independent reproduction.

Evidence table

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.

19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation Public web server evaluated by 2OMe-LM authors Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation No value recorded Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget No value recorded Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version No value recorded Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs No value recorded Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.metric_implementation No value recorded Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.population No value recorded Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.protocol_id paper-protocol-d933438afda70a21ef Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.split 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Held-out independent test set. Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.subset No value recorded Context-only references	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.subset` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Original source · journal full text in PMC

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Technical metadata and extraction receipts

Stable ID: paper-evaluation-08fc946fd84a041b19

areas: rna-transcriptomes
tasks: human RNA 2-prime-O-methylation site prediction
origin: independent_paper
protocol: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Held-out independent test set.
version: Public web server evaluated by 2OMe-LM authors
comparison: protocol id: paper-protocol-d933438afda70a21ef; dataset version: Not reported; split: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Held-out independent test set.; subset: Not reported; population: Not reported; aggregation: Not reported; inputs: Not reported; adaptation: Public web server evaluated by 2OMe-LM authors; budget: Not reported; metric implementation: Not reported
source locator: Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC
missing metadata: checkpoint revision: unextracted; budget: unreported; split manifest: unextracted

Related records

model: NmRF
benchmark: Human RNA 2OMe sites, independent test set (human RNA 2-prime-O-methylation site prediction)
dataset: Human RNA 2OMe sites, independent test set
evaluation: NmRF: F1-score on Human RNA 2OMe sites, independent test set
evaluation: NmRF: AUC on Human RNA 2OMe sites, independent test set
evaluation: NmRF: Precision on Human RNA 2OMe sites, independent test set
evaluation: NmRF: ACC on Human RNA 2OMe sites, independent test set
evaluation: NmRF: MCC on Human RNA 2OMe sites, independent test set
evaluation: NmRF: AUPR on Human RNA 2OMe sites, independent test set
evaluation: NmRF: Recall on Human RNA 2OMe sites, independent test set

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