BioBench Atlas
Nucleic-acid results
Tasks/T14

D2 · Structure & conformation

RNA secondary-structure base-pair prediction

Predict base pairs or dot-bracket secondary structure.

T14RNAstructured prediction

Task definition

Input granularity
sequence
Biological target
canonical base pairs
Output representation
pairing matrix/dot-bracket
ML formulation
structured prediction
Counting notes
NR

Benchmark coverage

5 benchmarks cover this task

B09Numeric results available

BEACON

Thirteen native tasks; some reuse OpenVaccine, Optimus and CRISPR datasets.

13 benchmark-wide protocols · 221 benchmark-wide rows (not a task subtotal)
B10Numeric results available

RNA-Scope

Board is public; DeepASmRNA and DeeReCT-PolyA/PAS are exposed as distinct tracks; verify exact release and frozen splits before comparative claims.

79 benchmark-wide protocols · 2,093 benchmark-wide rows (not a task subtotal)
B11Numeric results available

RNAGym

Three core tasks plus a task-family view of the ribozyme-assay subset; the subset track is separated from the aggregate DMS-effect track.

2 benchmark-wide protocols · 7 benchmark-wide rows (not a task subtotal)
B33No public numeric result

OmniGenBench

Meta-suite packaging RGB, BEACON, GUE, Genomic Benchmarks and PGB; native_task_count=5 suites, not the sum of their downstream tasks.

0 benchmark-wide protocols · 0 benchmark-wide rows (not a task subtotal)
B34Numeric results available

ERNIE-RNA downstream evaluation study

One-time model study spanning 15 named data packages; PrismNet is additionally stratified into 17 HeLa RBP assays.

12 benchmark-wide protocols · 231 benchmark-wide rows (not a task subtotal)

Evaluation protocols

40 protocol units

ProtocolTrackSplit / subsetComparability
PROT-B09-SSP-OFFICIAL-TRAIN-VALIDATION-TEST-SPLIT-SSP-2C3CC744SSP
B09-TR01		official train/validation/test split
SSP		same_table_comparable
external_data_policy;inference_budget
PROT-B09-SSI-OFFICIAL-TRAIN-VALIDATION-TEST-SPLIT-SSI-187B601ESSI
B09-TR01		official train/validation/test split
SSI		same_table_comparable
external_data_policy;inference_budget
PROT-B10-BPRNA-INTRA-FAMILY-PRECISION-49A347D1bpRNA
B10-TR04		intra-family
Precision		official_board_comparable
external_data_policy;inference_budget
PROT-B10-BPRNA-INTRA-FAMILY-RECALL-9A874F35bpRNA
B10-TR04		intra-family
Recall		official_board_comparable
external_data_policy;inference_budget
PROT-B10-BPRNA-INTRA-FAMILY-F1-EDFA8580bpRNA
B10-TR04		intra-family
F1		official_board_comparable
external_data_policy;inference_budget
PROT-B10-BPRNA-INTER-FAMILY-PRECISION-C19C4F65bpRNA
B10-TR04		inter-family
Precision		official_board_comparable
external_data_policy;inference_budget
PROT-B10-BPRNA-INTER-FAMILY-RECALL-59F4E9D1bpRNA
B10-TR04		inter-family
Recall		official_board_comparable
external_data_policy;inference_budget
PROT-B10-BPRNA-INTER-FAMILY-F1-49442E70bpRNA
B10-TR04		inter-family
F1		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-A-INTRA-FAMILY-PRECISION-C310A81CSet A
B10-TR04		intra-family
Precision		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-A-INTRA-FAMILY-RECALL-FE3E988FSet A
B10-TR04		intra-family
Recall		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-A-INTRA-FAMILY-F1-F1F4E6A7Set A
B10-TR04		intra-family
F1		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-A-INTER-FAMILY-PRECISION-A8315656Set A
B10-TR04		inter-family
Precision		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-A-INTER-FAMILY-RECALL-03BC96AFSet A
B10-TR04		inter-family
Recall		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-A-INTER-FAMILY-F1-3BFF992CSet A
B10-TR04		inter-family
F1		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-B-INTRA-FAMILY-PRECISION-A588C966Set B
B10-TR04		intra-family
Precision		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-B-INTRA-FAMILY-RECALL-C3B400CESet B
B10-TR04		intra-family
Recall		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-B-INTRA-FAMILY-F1-561486A7Set B
B10-TR04		intra-family
F1		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-B-INTER-FAMILY-PRECISION-02B088C1Set B
B10-TR04		inter-family
Precision		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-B-INTER-FAMILY-RECALL-2E5C779ESet B
B10-TR04		inter-family
Recall		official_board_comparable
external_data_policy;inference_budget
PROT-B10-SET-B-INTER-FAMILY-F1-6C603852Set B
B10-TR04		inter-family
F1		official_board_comparable
external_data_policy;inference_budget
PROT-B34-BPRNA-1M-80-TEST-SET-OFFICIAL-TEST--7C329CF2-8DADB680bpRNA-1m (80) test set
B34-TR01		official test set
Precision (binary)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-BPRNA-1M-80-TEST-SET-OFFICIAL-TEST--4D546F87-9DD1358EbpRNA-1m (80) test set
B34-TR01		official test set
Recall (binary)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-BPRNA-1M-80-TEST-SET-OFFICIAL-TEST--FD202093-2C6AE2DFbpRNA-1m (80) test set
B34-TR01		official test set
F1-Score (binary)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-BPRNA-1M-80-TEST-SET-OFFICIAL-TEST--498F365C-A219241CbpRNA-1m (80) test set
B34-TR01		official test set
Precision (macro-avg)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-BPRNA-1M-80-TEST-SET-OFFICIAL-TEST--15AA5D6C-F536B1B7bpRNA-1m (80) test set
B34-TR01		official test set
Recall (macro-avg)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-BPRNA-1M-80-TEST-SET-OFFICIAL-TEST--F7423224-26AC5174bpRNA-1m (80) test set
B34-TR01		official test set
F1-Score (macro-avg)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-BPRNA-NEW-OFFICIAL-TEST-SET-PRECISION-BINARY-8F9A5827bpRNA-new
B34-TR01		official test set
Precision (binary)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-BPRNA-NEW-OFFICIAL-TEST-SET-RECALL-BINARY-AB4958C9bpRNA-new
B34-TR01		official test set
Recall (binary)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-BPRNA-NEW-OFFICIAL-TEST-SET-F1-SCORE-BINARY-ED989D1CbpRNA-new
B34-TR01		official test set
F1-Score (binary)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-RNA3DB-2D-OFFICIAL-TEST-SET-PRECISION-BINARY-82CCCB31RNA3DB-2D
B34-TR01		official test set
Precision (binary)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-RNA3DB-2D-OFFICIAL-TEST-SET-RECALL-BINARY-BD144389RNA3DB-2D
B34-TR01		official test set
Recall (binary)		same_table_comparable
external_data_policy;inference_budget
PROT-B34-RNA3DB-2D-OFFICIAL-TEST-SET-F1-SCORE-BINARY-A979C535RNA3DB-2D
B34-TR01		official test set
F1-Score (binary)		same_table_comparable
external_data_policy;inference_budget
PROT-B38-ETERNABENCH-PACKAGE-EVALUATION-VIRA-F0CBD0BF-A25B18C8EternaBench package evaluation
NR		Viral genomic RNA
package Z-score		same_table_comparable
external_data_policy;inference_budget
PROT-B38-ETERNABENCH-PACKAGE-EVALUATION-SARS-5682CF9A-E8AF0C08EternaBench package evaluation
NR		SARS-CoV-2 genomic RNA
package Z-score		same_table_comparable
external_data_policy;inference_budget
PROT-B38-ETERNABENCH-PACKAGE-EVALUATION-MRNA-6E24C10C-2E3403F6EternaBench package evaluation
NR		mRNA
package Z-score		same_table_comparable
external_data_policy;inference_budget
PROT-B38-ETERNABENCH-PACKAGE-EVALUATION-SYNT-EFF3F19F-D7BBB321EternaBench package evaluation
NR		Synthetic RNA
package Z-score		same_table_comparable
external_data_policy;inference_budget
PROT-B38-ETERNABENCH-PACKAGE-EVALUATION-AVER-4BA1A84E-25FC6980EternaBench package evaluation
NR		average across all 31 datasets
package Z-score		same_table_comparable
external_data_policy;inference_budget
PROT-B38-ETERNABENCH-PACKAGE-EVALUATION-CHEM-A16AAD0F-8612873FEternaBench package evaluation
NR		ChemMapping Z-score mean(std)
package Z-score		same_table_comparable
external_data_policy;inference_budget
PROT-B38-ETERNABENCH-PACKAGE-EVALUATION-RIBO-4FFDE52B-AAC482F3EternaBench package evaluation
NR		Riboswitch Z-score mean(std)
package Z-score		same_table_comparable
external_data_policy;inference_budget
PROT-B38-ETERNABENCH-PACKAGE-EVALUATION-COMB-8ABFDD22-947039D3EternaBench package evaluation
NR		combined chemical-mapping and riboswitch datasets
package Z-score		same_table_comparable
external_data_policy;inference_budget