Protocol

Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)

Human RNA 2OMe sites, five-fold cross-validation · ACC. 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.

Sources

2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC

7 evaluations · 49 metric rows

At a glance

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Datasets	Not extracted or verified for this record.
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Splits	Not extracted or verified for this record.
Allowed inputs	Not extracted or verified for this record.
Adaptation	Not extracted or verified for this record.
Metrics	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

How it works

Evaluation in this paper

41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.

Sources

Evaluation design

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

Tasks

human RNA 2-prime-O-methylation site prediction

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

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

Comparison and metric

Human RNA 2OMe sites, five-fold cross-validation · ACC

ACC (fraction) · Higher values are better for this metric.

41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.

Evaluation protocol · human RNA 2OMe sites

GloVe + MLP · Configuration · Author-reported evaluation0.795
GloVe + TextCNN + MLP · Configuration · Author-reported evaluation0.746
GloVe + Transformer + MLP · Configuration · Author-reported evaluation0.742
Word2vec + MLP · Configuration · Author-reported evaluation0.813
Word2vec + TextCNN + MLP · Configuration · Author-reported evaluation0.764
Word2Vec + Transformer + MLP · Configuration · Author-reported evaluation0.749
2OMe-LM · Configuration · Author-reported evaluation 0.846

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

Values, uncertainty and evidence

ACC: original source values
Tested entity	Printed value	Uncertainty	Evidence
GloVe + MLP · Configuration	0.795 fraction	Not reported	Author-reported evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 1. (btaf417-T1), row 2 GloVe + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC
GloVe + TextCNN + MLP · Configuration	0.746 fraction	Not reported	Author-reported evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC
GloVe + Transformer + MLP · Configuration	0.742 fraction	Not reported	Author-reported evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC
Word2vec + MLP · Configuration	0.813 fraction	Not reported	Author-reported evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC
Word2vec + TextCNN + MLP · Configuration	0.764 fraction	Not reported	Author-reported evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC
Word2Vec + Transformer + MLP · Configuration	0.749 fraction	Not reported	Author-reported evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC
2OMe-LM · Configuration	0.846 fraction	Not reported	Author-reported evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC

Scope and limitations

Do not pool cross-validation and independent-test scores. The 8:2 ratio is not converted into an exact test count. Training-data overlap for pre-existing predictors is not established by this table. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 7 evaluations · 49 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
2OMe-LM: human RNA 2-prime-O-methylation site prediction Configuration: 2OMe-LMProtocol: Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)Dataset: human RNA 2OMe sites 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set. Author-reported evaluation · Evaluation metadata: needs review
0.919 AUC Unit: fraction · Direction: higher	Uncertainty: not reported in legacy extract 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 1, 2OMe-LM row, AUC column Source checking is not independent reproduction.
0.929 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 1. (btaf417-T1), row 8 2OMe-LM, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR Source checking is not independent reproduction.
0.873 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 1. (btaf417-T1), row 8 2OMe-LM, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision Source checking is not independent reproduction.
0.846 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 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC Source checking is not independent reproduction.
0.811 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 1. (btaf417-T1), row 8 2OMe-LM, column 5: Human RNA 2OMe sites, five-fold cross-validation Recall Source checking is not independent reproduction.
0.695 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 1. (btaf417-T1), row 8 2OMe-LM, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC Source checking is not independent reproduction.
GloVe + TextCNN + MLP: Human RNA 2OMe sites, five-fold cross-validation Configuration: GloVe + TextCNN + MLPProtocol: Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)Dataset: human RNA 2OMe sites 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set. Author-reported evaluation · Evaluation metadata: needs review
0.502 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 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC Source checking is not independent reproduction.
0.805 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 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision Source checking is not independent reproduction.
0.842 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 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 6: Human RNA 2OMe sites, five-fold cross-validation AUC Source checking is not independent reproduction.
0.746 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 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC Source checking is not independent reproduction.
GloVe + Transformer + MLP: Human RNA 2OMe sites, five-fold cross-validation Configuration: GloVe + Transformer + MLPProtocol: Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)Dataset: human RNA 2OMe sites 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set. Author-reported evaluation · Evaluation metadata: needs review
0.832 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 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 6: Human RNA 2OMe sites, five-fold cross-validation AUC Source checking is not independent reproduction.
0.490 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 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC Source checking is not independent reproduction.
0.720 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 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score Source checking is not independent reproduction.
Word2vec + TextCNN + MLP: Human RNA 2OMe sites, five-fold cross-validation Configuration: Word2vec + TextCNN + MLPProtocol: Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)Dataset: human RNA 2OMe sites 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set. Author-reported evaluation · Evaluation metadata: needs review
0.852 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 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR Source checking is not independent reproduction.
0.764 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 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC Source checking is not independent reproduction.
0.772 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 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision Source checking is not independent reproduction.
0.761 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 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score Source checking is not independent reproduction.
GloVe + MLP: Human RNA 2OMe sites, five-fold cross-validation Configuration: GloVe + MLPProtocol: Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)Dataset: human RNA 2OMe sites 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set. Author-reported evaluation · Evaluation metadata: needs review
0.872 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 1. (btaf417-T1), row 2 GloVe + MLP, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR Source checking is not independent reproduction.
0.843 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 1. (btaf417-T1), row 2 GloVe + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision Source checking is not independent reproduction.
0.780 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 1. (btaf417-T1), row 2 GloVe + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score Source checking is not independent reproduction.
Word2Vec + Transformer + MLP: Human RNA 2OMe sites, five-fold cross-validation Configuration: Word2Vec + Transformer + MLPProtocol: Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)Dataset: human RNA 2OMe sites 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set. Author-reported evaluation · Evaluation metadata: needs review
0.749 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 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC Source checking is not independent reproduction.
0.741 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 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score Source checking is not independent reproduction.
0.833 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 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR Source checking is not independent reproduction.
Word2vec + MLP: Human RNA 2OMe sites, five-fold cross-validation Configuration: Word2vec + MLPProtocol: Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)Dataset: human RNA 2OMe sites 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set. Author-reported evaluation · Evaluation metadata: needs review
0.811 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 1. (btaf417-T1), row 5 Word2vec + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score Source checking is not independent reproduction.
0.819 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 1. (btaf417-T1), row 5 Word2vec + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision Source checking is not independent reproduction.

Papers and result coverage

Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.

Paper or primary resource	Version	Reference
2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model	journal full text in PMC	Read source DOI: 10.1093/bioinformatics/btaf417

What is still missing

exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.

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2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model 10.1093/bioinformatics/btaf417

Evidence locations

Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

No source-reviewed explanatory claims are recorded here yet.

Profile review details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Stable record: paper-protocol-1e891689a18fea3b65

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.

3 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
Evaluation in this paper 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set. Individual claims	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Introduction Human RNA 2OMe sites, five-fold cross-validation · ACC. 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set. Individual claims	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.summary` Source artifact SHA-256: `54fe4db6f35c03d0d4f3ef4da720eb26a832199372c56d0956609ff07af750ee` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: evaluates task reported-task-82fc7843f07324 Individual claims	2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model Original source ↗ Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC Version: journal full text in PMC Retrieved: 2026-09-16T10:33:38.332Z	source checked automated source review · 2026-09-17 Audit details Field: `links:evaluates_task:reported-task-82fc7843f07324` Claim: paper-claim-57f32b2ec51b3e840d 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

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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-protocol-1e891689a18fea3b65

areas: rna-transcriptomes
tasks: human RNA 2-prime-O-methylation site prediction
entity level: protocol
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. Average of five validation folds of the training set.
comparison panels: id: 2ome-lm-2025-btaf417-t1-accuracy; title: Human RNA 2OMe sites, five-fold cross-validation · ACC; protocol id: paper-protocol-1e891689a18fea3b65; dataset id: reported-dataset-bd3d8e7d6cd196; metric: ACC; unit: fraction; direction: higher; result ids: paper-result-d7aa3ed3ecdcfb7659; paper-result-7eeb7cd00870d4b822; paper-result-975e1e3b3cef0095d6; paper-result-bd40af36b346c6babe; paper-result-212ef20ae0523df179; paper-result-40dcbc4ba963adc002; paper-result-4bf3c3f0eec618c5cf; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; context: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.; caveats: Do not pool cross-validation and independent-test scores. The 8:2 ratio is not converted into an exact test count. Training-data overlap for pre-existing predictors is not established by this table. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: 2ome-lm-2025-btaf417-t1-F1; title: Human RNA 2OMe sites, five-fold cross-validation · F1-score; protocol id: paper-protocol-1e891689a18fea3b65; dataset id: reported-dataset-bd3d8e7d6cd196; metric: F1-score; unit: fraction; direction: higher; result ids: paper-result-7fa777341a7b054db1; paper-result-db5c42675cc3446cac; paper-result-3b51683bec36f2abaa; paper-result-5a1e3c197818f5eef1; paper-result-3b60f80651245fd9b6; paper-result-5a0302f7287f4744fe; paper-result-98d984a2c66d9da9cc; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score; Table 1. (btaf417-T1), row 8 2OMe-LM, column 3: Human RNA 2OMe sites, five-fold cross-validation F1-score; context: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.; caveats: Do not pool cross-validation and independent-test scores. The 8:2 ratio is not converted into an exact test count. Training-data overlap for pre-existing predictors is not established by this table. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: 2ome-lm-2025-btaf417-t1-precision; title: Human RNA 2OMe sites, five-fold cross-validation · Precision; protocol id: paper-protocol-1e891689a18fea3b65; dataset id: reported-dataset-bd3d8e7d6cd196; metric: Precision; unit: fraction; direction: higher; result ids: paper-result-3eeedfbb867730e5ae; paper-result-1acfee83326c80f579; paper-result-edd616527eedbbdd6e; paper-result-5b8226a4362a18dc2f; paper-result-3265bdf784a6414dad; paper-result-e4f14db506e688bbf3; paper-result-2fdf47de24865482a1; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision; Table 1. (btaf417-T1), row 8 2OMe-LM, column 4: Human RNA 2OMe sites, five-fold cross-validation Precision; context: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.; caveats: Do not pool cross-validation and independent-test scores. The 8:2 ratio is not converted into an exact test count. Training-data overlap for pre-existing predictors is not established by this table. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: 2ome-lm-2025-btaf417-t1-recall; title: Human RNA 2OMe sites, five-fold cross-validation · Recall; protocol id: paper-protocol-1e891689a18fea3b65; dataset id: reported-dataset-bd3d8e7d6cd196; metric: Recall; unit: fraction; direction: higher; result ids: paper-result-a63abaf273d6997c8f; paper-result-c3fa62647b4acefdab; paper-result-ff7373a626f7495c54; paper-result-dbd9c2c21ebea1c98f; paper-result-e56df473e582088515; paper-result-dca07f72da08e9b1aa; paper-result-671f931ffacbf39ee5; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 5: Human RNA 2OMe sites, five-fold cross-validation Recall; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 5: Human RNA 2OMe sites, five-fold cross-validation Recall; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 5: Human RNA 2OMe sites, five-fold cross-validation Recall; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 5: Human RNA 2OMe sites, five-fold cross-validation Recall; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 5: Human RNA 2OMe sites, five-fold cross-validation Recall; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 5: Human RNA 2OMe sites, five-fold cross-validation Recall; Table 1. (btaf417-T1), row 8 2OMe-LM, column 5: Human RNA 2OMe sites, five-fold cross-validation Recall; context: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.; caveats: Do not pool cross-validation and independent-test scores. The 8:2 ratio is not converted into an exact test count. Training-data overlap for pre-existing predictors is not established by this table. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: 2ome-lm-2025-btaf417-t1-AUROC; title: Human RNA 2OMe sites, five-fold cross-validation · AUC; protocol id: paper-protocol-1e891689a18fea3b65; dataset id: reported-dataset-bd3d8e7d6cd196; metric: AUC; unit: fraction; direction: higher; result ids: paper-result-d2c72c9538f864b13d; paper-result-5046ce3e5b1283c839; paper-result-138834d6ec841f6c4d; paper-result-928adade90586a2477; paper-result-b3a1db1d2e30c1ab66; paper-result-9ce02fe7f446cb3868; b2-2ome-lm-2025; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 6: Human RNA 2OMe sites, five-fold cross-validation AUC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 6: Human RNA 2OMe sites, five-fold cross-validation AUC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 6: Human RNA 2OMe sites, five-fold cross-validation AUC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 6: Human RNA 2OMe sites, five-fold cross-validation AUC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 6: Human RNA 2OMe sites, five-fold cross-validation AUC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 6: Human RNA 2OMe sites, five-fold cross-validation AUC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 6: Human RNA 2OMe sites, five-fold cross-validation AUC; context: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.; caveats: Do not pool cross-validation and independent-test scores. The 8:2 ratio is not converted into an exact test count. Training-data overlap for pre-existing predictors is not established by this table. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: 2ome-lm-2025-btaf417-t1-AUPRC; title: Human RNA 2OMe sites, five-fold cross-validation · AUPR; protocol id: paper-protocol-1e891689a18fea3b65; dataset id: reported-dataset-bd3d8e7d6cd196; metric: AUPR; unit: fraction; direction: higher; result ids: paper-result-256879a6ad6287f562; paper-result-cca7eb69b40055db2f; paper-result-a14ee136864e50bd74; paper-result-da3bae3411f4589cf5; paper-result-17e76530dee5b1fe4f; paper-result-84c2a332b94869bbbe; paper-result-18ce292cd466151112; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR; Table 1. (btaf417-T1), row 8 2OMe-LM, column 7: Human RNA 2OMe sites, five-fold cross-validation AUPR; context: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.; caveats: Do not pool cross-validation and independent-test scores. The 8:2 ratio is not converted into an exact test count. Training-data overlap for pre-existing predictors is not established by this table. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17; id: 2ome-lm-2025-btaf417-t1-MCC; title: Human RNA 2OMe sites, five-fold cross-validation · MCC; protocol id: paper-protocol-1e891689a18fea3b65; dataset id: reported-dataset-bd3d8e7d6cd196; metric: MCC; unit: unitless; direction: higher; result ids: paper-result-9f3d430c64f27de03d; paper-result-038d30f130b6a4c64b; paper-result-2ca6b64f9aa1a9748e; paper-result-e408a58902cb9dc5bf; paper-result-93ccc046cae95aea0c; paper-result-fe6771186123a657fd; paper-result-71c551bcf9091644da; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 8: Human RNA 2OMe sites, five-fold cross-validation MCC; context: 41-nt centred RNA windows; balanced 8,037 positive and 8,037 negative samples after 80% identity filtering, then 8:2 train/test division. Average of five validation folds of the training set.; caveats: Do not pool cross-validation and independent-test scores. The 8:2 ratio is not converted into an exact test count. Training-data overlap for pre-existing predictors is not established by this table. Origins are labelled per method; appearance in one table does not constitute independent replication of every model.; review: method: automated_source_review; date: 2026-09-17
benchmark research: review date: 2026-09-17; status: complete_tables_extracted; primary sources: 2ome-lm-2025; inspected locators: Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; searched queries: 2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model 10.1093/bioinformatics/btaf417; gaps: exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM and deep learning baseline models using 5-fold CV. a; Table 1. (btaf417-T1), row 2 GloVe + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 3 GloVe + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 4 GloVe + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 5 Word2vec + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 6 Word2vec + TextCNN + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 7 Word2Vec + Transformer + MLP, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; Table 1. (btaf417-T1), row 8 2OMe-LM, column 2: Human RNA 2OMe sites, five-fold cross-validation ACC; ambiguities: None recorded

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