human RNA 2-prime-O-methylation site prediction

Stable ID: reported-task-82fc7843f07324

areas

rna-transcriptomes

tasks

human RNA 2-prime-O-methylation site prediction

entity level

task

version

Not reported

task

human RNA 2-prime-O-methylation site prediction

scope note

Paper-specific evaluation task; protocol completeness requires further extraction.

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; 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: evidence-expansion-2ome-lm-2025-54fe4db6; inspected locators: Table 1.; XML table btaf417-T1; Table 2.; XML table btaf417-T2; 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.

historical missing metadata

protocol version: not_reported_in_legacy_extract

metadata review scope

historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.

legacy kinds

benchmark

entity classification

review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: 2ome-lm-2025; source locator: Methods §§2.1, 2.4; Results §§3.1–3.2; cached text lines 11–14, 35–36, 43–48; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.

• dataset: human RNA 2OMe sites
• evaluates task: Human RNA 2OMe sites, five-fold cross-validation (human RNA 2-prime-O-methylation site prediction)
• evaluates task: Human RNA 2OMe sites, independent test set (human RNA 2-prime-O-methylation site prediction)