Deep generalizable prediction of RNA secondary structure via base pair motif energy

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• 12 configurations
• 2 tasks
• 4 protocols
• 4 datasets
• 40 evaluations
• 160 results
• 12 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Claims

Statements this source supports, each with where in the source it was checked.

• ArchiveII (RNA secondary structure): links:evaluates_task:catalog-task-rna-secondary-structure: Evaluates task RNA secondary structure (Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII INF)
• ArchiveII (RNA secondary structure): links:evaluates_task:reported-task-dc82fcbfb44935: Evaluates task RNA secondary structure (Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 6: ArchiveII INF; Table 1 (Tab1), row 4 SPOT-RNA, column 6: ArchiveII INF; Table 1 (Tab1), row 5 MXfold2, column 6: ArchiveII INF; Table 1 (Tab1), row 6 ContextFold, column 6: ArchiveII INF; Table 1 (Tab1), row 7 CONTRAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 8 EternaFold, column 6: ArchiveII INF; Table 1 (Tab1), row 9 LinearFold, column 6: ArchiveII INF; Table 1 (Tab1), row 10 RNAfold, column 6: ArchiveII INF; Table 1 (Tab1), row 11 SimFold, column 6: ArchiveII INF; Table 1 (Tab1), row 12 RNAstructure, column 6: ArchiveII INF)
• BPfold · F1 · PDB RNA set: attributes.metric_direction: Metric direction higher (Table 2 (Tab2), row 3 BPfold, column 7: PDB F1)
• bpRNA-TS0 (RNA secondary structure): links:evaluates_task:catalog-task-rna-secondary-structure: Evaluates task RNA secondary structure (Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF)
• bpRNA-TS0 (RNA secondary structure): links:evaluates_task:reported-task-dc82fcbfb44935: Evaluates task RNA secondary structure (Sequence-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold), and non-ML methods (LinearFold, RNAfold, SimFold, and RNAstructure) on bpRNA-TS0 ( n  = 1305 RNAs) and ArchiveII ( n  = 3966 RNAs) datasets; Table 1 (Tab1), row 3 BPfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 4 SPOT-RNA, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 5 MXfold2, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 6 ContextFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 7 CONTRAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 8 EternaFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 9 LinearFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 10 RNAfold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 11 SimFold, column 2: bpRNA-TS0 INF; Table 1 (Tab1), row 12 RNAstructure, column 2: bpRNA-TS0 INF)
• PDB (RNA secondary structure): links:evaluates_task:catalog-task-rna-secondary-structure: Evaluates task RNA secondary structure (Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n  = 10,791 RNAs) and PDB ( n  = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB INF)
• PDB (RNA secondary structure): links:evaluates_task:reported-task-dc82fcbfb44935: Evaluates task RNA secondary structure (Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n  = 10,791 RNAs) and PDB ( n  = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 6: PDB INF; Table 2 (Tab2), row 4 SPOT-RNA, column 6: PDB INF; Table 2 (Tab2), row 5 MXfold2, column 6: PDB INF; Table 2 (Tab2), row 6 ContextFold, column 6: PDB INF; Table 2 (Tab2), row 7 CONTRAfold, column 6: PDB INF; Table 2 (Tab2), row 8 EternaFold, column 6: PDB INF; Table 2 (Tab2), row 9 LinearFold, column 6: PDB INF; Table 2 (Tab2), row 10 RNAfold, column 6: PDB INF; Table 2 (Tab2), row 11 SimFold, column 6: PDB INF; Table 2 (Tab2), row 12 RNAstructure, column 6: PDB INF)
• Reported F1 for BPfold: Printed value 0.814 (Table 2, BPfold row, PDB F1 column)
• Reported F1 for RNAfold: Printed value 0.747 (Table 2, RNAfold row, PDB F1 column)
• Rfam12.3–14.10 (RNA secondary structure): links:evaluates_task:catalog-task-rna-secondary-structure: Evaluates task RNA secondary structure (Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n  = 10,791 RNAs) and PDB ( n  = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF)
• Rfam12.3–14.10 (RNA secondary structure): links:evaluates_task:reported-task-dc82fcbfb44935: Evaluates task RNA secondary structure (Family-wise evaluation of three DL methods (BPfold, SPOT-RNA, and MXfold2), three shallow learning methods (ContextFold, CONTRAfold, and EternaFold) and non-learning methods (LinearFold, RNAfold, SimFold, and RNAstructure) on Rfam12.3–14.10 ( n  = 10,791 RNAs) and PDB ( n  = 116 RNAs) datasets; Table 2 (Tab2), row 3 BPfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 4 SPOT-RNA, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 5 MXfold2, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 6 ContextFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 7 CONTRAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 8 EternaFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 9 LinearFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 10 RNAfold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 11 SimFold, column 2: Rfam12.3–14.10 INF; Table 2 (Tab2), row 12 RNAstructure, column 2: Rfam12.3–14.10 INF)
• RNAfold · F1 · PDB RNA set: attributes.metric_direction: Metric direction higher (Table 2 (Tab2), row 10 RNAfold, column 7: PDB F1)

Models, benchmarks and other records

Evidence

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