NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction

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Records in this release that cite this source. A record can cite several sources.

• 27 configurations
• 1 benchmark
• 43 tasks
• 8 dataset subsets
• 1,101 evaluations
• 1,101 results
• 52 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.

• Evo2-7B-base: family Evo 2: Family Evo 2 (NABench model inventory explicit Evo2-7B / Evo2-7B-base; LAMBDA Table 1 explicit EVO2 7B; official Evo2 7B checkpoint list | Existing reviewed locator: Table 7, row(Evo2-7B-base))
• Evo2-7B-base: family Evo 2: Family Evo 2 (Primary paper model-inventory and results tables: mRNABench Table 2; NABench model inventory; LAMBDA Table 1 (EVO2 7B); source-labelled configuration Evo2-7B-base | Existing reviewed locator: Table 7, row(Evo2-7B-base))
• Evo2-7B: family Evo 2: Family Evo 2 (NABench model inventory explicit Evo2-7B / Evo2-7B-base; LAMBDA Table 1 explicit EVO2 7B; official Evo2 7B checkpoint list | Existing reviewed locator: Table 7, row(Evo2-7B))
• Evo2-7B: family Evo 2: Family Evo 2 (Primary paper model-inventory and results tables: mRNABench Table 2; NABench model inventory; LAMBDA Table 1 (EVO2 7B); source-labelled configuration Evo2-7B | Existing reviewed locator: Table 7, row(Evo2-7B))
• N.T.-500m: family Nucleotide Transformer: Family Nucleotide Transformer (mRNABench Table 2/Appendix model inventory; GenomeOcean Table 2; respective model methods; NABench model inventory; GENEB Table 8; source-labelled configuration N.T.-500m | Existing reviewed locator: Table 7, row(N.T.-500m))
• N.T.-v2-50m: family Nucleotide Transformer: Family Nucleotide Transformer (mRNABench Table 2/Appendix model inventory; GenomeOcean Table 2; respective model methods; NABench model inventory; GENEB Table 8; source-labelled configuration N.T.-v2-50m | Existing reviewed locator: Table 7, row(N.T.-v2-50m))
• N.T.-v2-50m: family Nucleotide Transformer v2: Family Nucleotide Transformer v2 (GENEB Table 8 NT-v2-50M-MS; NABench model inventory N.T.v2 50M; official v2-50m-multi-species model card | Existing reviewed locator: Table 7, row(N.T.-v2-50m))
• N.T.-v2-500m: family Nucleotide Transformer: Family Nucleotide Transformer (mRNABench Table 2/Appendix model inventory; GenomeOcean Table 2; respective model methods; NABench model inventory; GENEB Table 8; source-labelled configuration N.T.-v2-500m | Existing reviewed locator: Table 7, row(N.T.-v2-500m))
• NABench CCV-CORR-APTAMER: part of discovery-benchmark-nabench: Part of NABench (Table 11, column(aptamer))
• NABench CCV-CORR-ENHANCER: part of discovery-benchmark-nabench: Part of NABench (Table 11, column(enhancer))
• NABench CCV-CORR-MRNA: part of discovery-benchmark-nabench: Part of NABench (Table 11, column(mRNA))
• NABench CCV-CORR-PROMOTER: part of discovery-benchmark-nabench: Part of NABench (Table 11, column(promoter))
• NABench CCV-CORR-RIBOZYME: part of discovery-benchmark-nabench: Part of NABench (Table 11, column(ribozyme))
• NABench CCV-CORR-TRNA: part of discovery-benchmark-nabench: Part of NABench (Table 11, column(tRNA))
• NABench DMS-CCV: part of discovery-benchmark-nabench: Part of NABench (Table 6, column(Contiguous cross validation Spearman ρ))
• NABench DMS-FS: part of discovery-benchmark-nabench: Part of NABench (Table 6, column(Few-shot Spearman ρ))
• NABench DMS-RCV: part of discovery-benchmark-nabench: Part of NABench (Table 6, column(Random cross validation Spearman ρ))
• NABench DMS-ZS-AUC: part of discovery-benchmark-nabench: Part of NABench (Table 6, column(Zero-shot AUC))
• NABench DMS-ZS-CORR: part of discovery-benchmark-nabench: Part of NABench (Table 6, column(Zero-shot Spearman ρ))
• NABench DMS-ZS-MCC: part of discovery-benchmark-nabench: Part of NABench (Table 6, column(Zero-shot MCC))
• NABench DMS-ZS-NDCG: part of discovery-benchmark-nabench: Part of NABench (Table 6, column(Zero-shot NDCG))
• NABench FS-CORR-APTAMER: part of discovery-benchmark-nabench: Part of NABench (Table 9, column(aptamer))
• NABench FS-CORR-ENHANCER: part of discovery-benchmark-nabench: Part of NABench (Table 9, column(enhancer))
• NABench FS-CORR-MRNA: part of discovery-benchmark-nabench: Part of NABench (Table 9, column(mRNA))
• NABench FS-CORR-PROMOTER: part of discovery-benchmark-nabench: Part of NABench (Table 9, column(promoter))

Models, benchmarks and other records

Evidence

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