Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
Human RNA 2OMe sites, independent test set (human RNA 2-prime-O-methylation site prediction)
Human RNA 2OMe sites, independent test set · 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. Held-out independent test set.
Sources
2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · 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 ACCAt 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.
| 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. Held-out independent test set.
Sources
2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · 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 ACCEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
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.
Human RNA 2OMe sites, independent test set · 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. Held-out independent test set.
Evaluation protocol · Human RNA 2OMe sites, independent test set
- NmRF · Configuration · Independent external evaluation0.512
- BERT2OME · Configuration · Independent external evaluation0.795
- H2Opred · Configuration · Independent external evaluation0.819
- Meta-2OM · Configuration · Independent external evaluation0.780
- 2OMe-LM · Configuration · Author-reported evaluation 0.898
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.
2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · 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 ACCValues, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| NmRF · Configuration | 0.512 fraction | Not reported | Independent external evaluation · 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 |
| BERT2OME · Configuration | 0.795 fraction | Not reported | Independent external evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC |
| H2Opred · Configuration | 0.819 fraction | Not reported | Independent external evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC |
| Meta-2OM · Configuration | 0.780 fraction | Not reported | Independent external evaluation · source checked2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Table 2. (btaf417-T2), row 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC |
| 2OMe-LM · Configuration | 0.898 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 2. (btaf417-T2), row 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set 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 · 5 evaluations · 35 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| BERT2OME: Human RNA 2OMe sites, independent test set Configuration: BERT2OMEProtocol: 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 | ||
| 0.795 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 3 BERT2OME, column 2: Human RNA 2OMe sites, independent test set ACC Source checking is not independent reproduction. |
| 0.813 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 3 BERT2OME, column 4: Human RNA 2OMe sites, independent test set Precision Source checking is not independent reproduction. |
| 0.788 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 3 BERT2OME, column 3: Human RNA 2OMe sites, independent test set F1-score Source checking is not independent reproduction. |
| 0.878 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 3 BERT2OME, column 6: Human RNA 2OMe sites, independent test set AUC Source checking is not independent reproduction. |
| 2OMe-LM: Human RNA 2OMe sites, independent test set Configuration: 2OMe-LMProtocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
|
0.963
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 6 2OMe-LM, column 7: Human RNA 2OMe sites, independent test set AUPR Source checking is not independent reproduction. |
|
0.898
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 6 2OMe-LM, column 2: Human RNA 2OMe sites, independent test set ACC Source checking is not independent reproduction. |
|
0.952
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 6 2OMe-LM, column 6: Human RNA 2OMe sites, independent test set AUC Source checking is not independent reproduction. |
| 0.802 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 6 2OMe-LM, column 5: Human RNA 2OMe sites, independent test set Recall Source checking is not independent reproduction. |
|
0.887
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 6 2OMe-LM, column 3: Human RNA 2OMe sites, independent test set F1-score Source checking is not independent reproduction. |
|
0.993
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 6 2OMe-LM, column 4: Human RNA 2OMe sites, independent test set Precision Source checking is not independent reproduction. |
| H2Opred: Human RNA 2OMe sites, independent test set Configuration: H2OpredProtocol: 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 | ||
| 0.800 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 4 H2Opred, column 3: Human RNA 2OMe sites, independent test set F1-score Source checking is not independent reproduction. |
| 0.904 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 4 H2Opred, column 7: Human RNA 2OMe sites, independent test set AUPR Source checking is not independent reproduction. |
| 0.819 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 4 H2Opred, column 2: Human RNA 2OMe sites, independent test set ACC Source checking is not independent reproduction. |
| 0.890 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 4 H2Opred, column 4: Human RNA 2OMe sites, independent test set Precision Source checking is not independent reproduction. |
| 0.648 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 4 H2Opred, column 8: Human RNA 2OMe sites, independent test set MCC Source checking is not independent reproduction. |
| Meta-2OM: Human RNA 2OMe sites, independent test set Configuration: Meta-2OMProtocol: 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 | ||
| 0.881 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 5 Meta-2OM, column 7: Human RNA 2OMe sites, independent test set AUPR Source checking is not independent reproduction. |
| 0.891 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 5 Meta-2OM, column 4: Human RNA 2OMe sites, independent test set Precision Source checking is not independent reproduction. |
| 0.780 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 5 Meta-2OM, column 2: Human RNA 2OMe sites, independent test set ACC Source checking is not independent reproduction. |
| 0.639 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 5 Meta-2OM, column 5: Human RNA 2OMe sites, independent test set Recall Source checking is not independent reproduction. |
| 0.584 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 5 Meta-2OM, column 8: Human RNA 2OMe sites, independent test set MCC Source checking is not independent reproduction. |
| 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. |
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.
Search and extraction details
complete tables extracted
Searches
- 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 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
Strengths and limitations
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-d933438afda70a21efEvidence 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
| 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. Held-out independent test set. Individual claims | 2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model 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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Introduction Human RNA 2OMe sites, independent test set · 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. Held-out independent test set. Individual claims | 2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model 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 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 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 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-49edd508eb9e7f56c9 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
1 source records and release history
- 2OMe-LM: predicting 2′-O-methylation sites in human RNA using a pre-trained RNA language model · Original source · journal full text in PMC
Technical metadata and extraction receipts
Stable ID: paper-protocol-d933438afda70a21ef
- 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. Held-out independent test set.
- comparison panels
- id: 2ome-lm-2025-btaf417-t2-accuracy; title: Human RNA 2OMe sites, independent test set · ACC; protocol id: paper-protocol-d933438afda70a21ef; dataset id: paper-dataset-64b51e2f952f2c1c09; metric: ACC; unit: fraction; direction: higher; result ids: paper-result-6cd0c965571a51b666; paper-result-0a3793081d7daa05a3; paper-result-90076f457aae558dd0; paper-result-6f26b2a32012628065; paper-result-172c48ff6795f50b97; source ids: 2ome-lm-2025; 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; 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. Held-out independent test 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-t2-F1; title: Human RNA 2OMe sites, independent test set · F1-score; protocol id: paper-protocol-d933438afda70a21ef; dataset id: paper-dataset-64b51e2f952f2c1c09; metric: F1-score; unit: fraction; direction: higher; result ids: paper-result-2901879d63427fece0; paper-result-703d9f2e0a92c08138; paper-result-1f1eb13ac1d3b0659c; paper-result-d219017e57658f8194; paper-result-a6ed9c1d07e0a8e3ac; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 3: Human RNA 2OMe sites, independent test set F1-score; Table 2. (btaf417-T2), row 3 BERT2OME, column 3: Human RNA 2OMe sites, independent test set F1-score; Table 2. (btaf417-T2), row 4 H2Opred, column 3: Human RNA 2OMe sites, independent test set F1-score; Table 2. (btaf417-T2), row 5 Meta-2OM, column 3: Human RNA 2OMe sites, independent test set F1-score; Table 2. (btaf417-T2), row 6 2OMe-LM, column 3: Human RNA 2OMe sites, independent test set 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. Held-out independent test 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-t2-precision; title: Human RNA 2OMe sites, independent test set · Precision; protocol id: paper-protocol-d933438afda70a21ef; dataset id: paper-dataset-64b51e2f952f2c1c09; metric: Precision; unit: fraction; direction: higher; result ids: paper-result-657a6c49b38ef8252b; paper-result-6489236abf51572541; paper-result-a070ec6c349b5e96ef; paper-result-2d7677257f873b4e29; paper-result-b90e8cd12cecf6951f; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 4: Human RNA 2OMe sites, independent test set Precision; Table 2. (btaf417-T2), row 3 BERT2OME, column 4: Human RNA 2OMe sites, independent test set Precision; Table 2. (btaf417-T2), row 4 H2Opred, column 4: Human RNA 2OMe sites, independent test set Precision; Table 2. (btaf417-T2), row 5 Meta-2OM, column 4: Human RNA 2OMe sites, independent test set Precision; Table 2. (btaf417-T2), row 6 2OMe-LM, column 4: Human RNA 2OMe sites, independent test set 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. Held-out independent test 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-t2-recall; title: Human RNA 2OMe sites, independent test set · Recall; protocol id: paper-protocol-d933438afda70a21ef; dataset id: paper-dataset-64b51e2f952f2c1c09; metric: Recall; unit: fraction; direction: higher; result ids: paper-result-eb25b223c10be4f330; paper-result-c8c5c199a2b0059317; paper-result-fab2a73ce6d700ff87; paper-result-7c85e27954addc7e14; paper-result-9980f6cb88d2219b02; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 5: Human RNA 2OMe sites, independent test set Recall; Table 2. (btaf417-T2), row 3 BERT2OME, column 5: Human RNA 2OMe sites, independent test set Recall; Table 2. (btaf417-T2), row 4 H2Opred, column 5: Human RNA 2OMe sites, independent test set Recall; Table 2. (btaf417-T2), row 5 Meta-2OM, column 5: Human RNA 2OMe sites, independent test set Recall; Table 2. (btaf417-T2), row 6 2OMe-LM, column 5: Human RNA 2OMe sites, independent test set 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. Held-out independent test 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-t2-AUROC; title: Human RNA 2OMe sites, independent test set · AUC; protocol id: paper-protocol-d933438afda70a21ef; dataset id: paper-dataset-64b51e2f952f2c1c09; metric: AUC; unit: fraction; direction: higher; result ids: paper-result-48c539e46e8e0de49c; paper-result-c5e158015fb2c59552; paper-result-da8a9134bd3530143b; paper-result-ce07a0b8b72a4068f5; paper-result-76e7297a1974a4704a; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 6: Human RNA 2OMe sites, independent test set AUC; Table 2. (btaf417-T2), row 3 BERT2OME, column 6: Human RNA 2OMe sites, independent test set AUC; Table 2. (btaf417-T2), row 4 H2Opred, column 6: Human RNA 2OMe sites, independent test set AUC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 6: Human RNA 2OMe sites, independent test set AUC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 6: Human RNA 2OMe sites, independent test set 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. Held-out independent test 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-t2-AUPRC; title: Human RNA 2OMe sites, independent test set · AUPR; protocol id: paper-protocol-d933438afda70a21ef; dataset id: paper-dataset-64b51e2f952f2c1c09; metric: AUPR; unit: fraction; direction: higher; result ids: paper-result-cf762cdb6f3083c1e5; paper-result-ea74464791a87509df; paper-result-79788c7d80922dad49; paper-result-209a40abae677db031; paper-result-13e1c3729d85f66b41; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 7: Human RNA 2OMe sites, independent test set AUPR; Table 2. (btaf417-T2), row 3 BERT2OME, column 7: Human RNA 2OMe sites, independent test set AUPR; Table 2. (btaf417-T2), row 4 H2Opred, column 7: Human RNA 2OMe sites, independent test set AUPR; Table 2. (btaf417-T2), row 5 Meta-2OM, column 7: Human RNA 2OMe sites, independent test set AUPR; Table 2. (btaf417-T2), row 6 2OMe-LM, column 7: Human RNA 2OMe sites, independent test set 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. Held-out independent test 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-t2-MCC; title: Human RNA 2OMe sites, independent test set · MCC; protocol id: paper-protocol-d933438afda70a21ef; dataset id: paper-dataset-64b51e2f952f2c1c09; metric: MCC; unit: unitless; direction: higher; result ids: paper-result-acad7ffaf81174cddb; paper-result-d947e45a8a87762a5f; paper-result-abe41dfecafe879c49; paper-result-85be9319f746a0dd77; paper-result-e68cc241f300063bca; source ids: 2ome-lm-2025; source locator: Performance comparison of 2OMe-LM with existing predictors on the independent test set. a; Table 2. (btaf417-T2), row 2 NmRF, column 8: Human RNA 2OMe sites, independent test set MCC; Table 2. (btaf417-T2), row 3 BERT2OME, column 8: Human RNA 2OMe sites, independent test set MCC; Table 2. (btaf417-T2), row 4 H2Opred, column 8: Human RNA 2OMe sites, independent test set MCC; Table 2. (btaf417-T2), row 5 Meta-2OM, column 8: Human RNA 2OMe sites, independent test set MCC; Table 2. (btaf417-T2), row 6 2OMe-LM, column 8: Human RNA 2OMe sites, independent test set 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. Held-out independent test 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 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; 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 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; ambiguities: None recorded
Related records
- evaluates task: human RNA 2-prime-O-methylation site prediction
- subject: Human RNA 2OMe sites, independent test set (human RNA 2-prime-O-methylation site prediction): links:evaluates_task:reported-task-82fc7843f07324
- benchmark: NmRF: Human RNA 2OMe sites, independent test set
- benchmark: Meta-2OM: Human RNA 2OMe sites, independent test set
- benchmark: 2OMe-LM: Human RNA 2OMe sites, independent test set
- benchmark: H2Opred: Human RNA 2OMe sites, independent test set
- benchmark: BERT2OME: Human RNA 2OMe sites, independent test set