NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC. Scored with Zero-shot MCC on NABench deep mutational scanning assays. Aggregated by the NABench authors across NABench deep mutational scanning assays.
Overview
Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC. Scored with Zero-shot MCC on NABench deep mutational scanning assays. Aggregated by the NABench authors across NABench deep mutational scanning assays.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- AIDO.RNA on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- BiRNA-BERT on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- Crafts on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- Dnabert_6 on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- Dnabert on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- Enformer on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- Evo_1.5_8k_base on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- Evo_1_8k_base on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- Evo_1_8k on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- Evo2-7B-base on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- Evo2-7B on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- GENA-LM-large on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
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. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
mcc (correlation) · Higher values are better for this metric.
Every method NABench reports on Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC, scored with Zero-shot MCC on NABench deep mutational scanning assays.
Evaluation protocol · NABench deep mutational scanning assays (NABench split)
- RNA-FM · Configuration · Author-reported evaluation0.068
- RNAernie · Configuration · Author-reported evaluation0.044
- SPACE · Configuration · Author-reported evaluation0.051
- AIDO.RNA · Configuration · Author-reported evaluation0.049
- BiRNA-BERT · Configuration · Author-reported evaluation0.042
- Crafts · Configuration · Author-reported evaluation0.057
- Dnabert · Configuration · Author-reported evaluation0.045
- Dnabert_6 · Configuration · Author-reported evaluation0.035
- Enformer · Configuration · Author-reported evaluation0.053
- Evo2-7B · Configuration · Author-reported evaluation0.077
- Evo2-7B-base · Configuration · Author-reported evaluation0.079
- Evo_1.5_8k_base · Configuration · Author-reported evaluation0.085
- Evo_1_8k · Configuration · Author-reported evaluation0.078
- Evo_1_8k_base · Configuration · Author-reported evaluation0.078
- GENA-LM-large · Configuration · Author-reported evaluation0.045
- GENERator-3B · Configuration · Author-reported evaluation0.045
- GenerRNA · Configuration · Author-reported evaluation0.043
- GenSLM · Configuration · Author-reported evaluation0.040
- HyenaDNA · Configuration · Author-reported evaluation0.047
- LucaOne · Configuration · Author-reported evaluation0.057
- LucaVirus · Configuration · Author-reported evaluation0.049
- N.T.-v2-50m · Configuration · Author-reported evaluation0.044
- RESM · Configuration · Author-reported evaluation0.084
- RiNALMo_giga · Configuration · Author-reported evaluation0.050
- structRFM · Configuration · Author-reported evaluation0.065
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.
NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, column(Zero-shot MCC)Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| RNA-FM · Configuration | 0.068 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNA-FM), column(Zero-shot MCC) |
| RNAernie · Configuration | 0.044 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNAernie), column(Zero-shot MCC) |
| SPACE · Configuration | 0.051 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(SPACE), column(Zero-shot MCC) |
| AIDO.RNA · Configuration | 0.049 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(AIDO.RNA), column(Zero-shot MCC) |
| BiRNA-BERT · Configuration | 0.042 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(BiRNA-BERT), column(Zero-shot MCC) |
| Crafts · Configuration | 0.057 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Crafts), column(Zero-shot MCC) |
| Dnabert · Configuration | 0.045 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Dnabert), column(Zero-shot MCC) |
| Dnabert_6 · Configuration | 0.035 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Dnabert_6), column(Zero-shot MCC) |
| Enformer · Configuration | 0.053 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Enformer), column(Zero-shot MCC) |
| Evo2-7B · Configuration | 0.077 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo2-7B), column(Zero-shot MCC) |
| Evo2-7B-base · Configuration | 0.079 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo2-7B-base), column(Zero-shot MCC) |
| Evo_1.5_8k_base · Configuration | 0.085 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo_1.5_8k_base), column(Zero-shot MCC) |
| Evo_1_8k · Configuration | 0.078 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo_1_8k), column(Zero-shot MCC) |
| Evo_1_8k_base · Configuration | 0.078 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo_1_8k_base), column(Zero-shot MCC) |
| GENA-LM-large · Configuration | 0.045 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(GENA-LM-large), column(Zero-shot MCC) |
| GENERator-3B · Configuration | 0.045 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(GENERator-3B), column(Zero-shot MCC) |
| GenerRNA · Configuration | 0.043 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(GenerRNA), column(Zero-shot MCC) |
| GenSLM · Configuration | 0.040 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(GenSlm), column(Zero-shot MCC) |
| HyenaDNA · Configuration | 0.047 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(HyenaDNA), column(Zero-shot MCC) |
| LucaOne · Configuration | 0.057 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(LucaOne), column(Zero-shot MCC) |
| LucaVirus · Configuration | 0.049 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(LucaVirus), column(Zero-shot MCC) |
| N.T.-v2-50m · Configuration | 0.044 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(N.T.-v2-50m), column(Zero-shot MCC) |
| RESM · Configuration | 0.084 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RESM), column(Zero-shot MCC) |
| RiNALMo_giga · Configuration | 0.050 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RiNALMo_giga), column(Zero-shot MCC) |
| structRFM · Configuration | 0.065 correlation | Not reported | Author-reported evaluation · source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(structRFM), column(Zero-shot MCC) |
Scope and limitations
- Author-reported numbers, source checked but not independently reproduced.
- Zero-shot, few-shot and supervised cross validation figures come from different protocols and are not comparable to each other.
- The per-nucleotide-type figures and the overall figures describe the same runs at different resolutions, so they must not be combined.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-134cd1815de8 · 25 evaluations · 25 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AIDO.RNA on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: AIDO.RNATask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.049 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(AIDO.RNA), column(Zero-shot MCC) Source checking is not independent reproduction. |
| BiRNA-BERT on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: BiRNA-BERTTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.042 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(BiRNA-BERT), column(Zero-shot MCC) Source checking is not independent reproduction. |
| Crafts on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: CraftsTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.057 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Crafts), column(Zero-shot MCC) Source checking is not independent reproduction. |
| Dnabert_6 on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: Dnabert_6Task: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.035 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Dnabert_6), column(Zero-shot MCC) Source checking is not independent reproduction. |
| Dnabert on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: DnabertTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.045 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Dnabert), column(Zero-shot MCC) Source checking is not independent reproduction. |
| Enformer on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: EnformerTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.053 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Enformer), column(Zero-shot MCC) Source checking is not independent reproduction. |
| Evo_1.5_8k_base on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: Evo_1.5_8k_baseTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.085 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo_1.5_8k_base), column(Zero-shot MCC) Source checking is not independent reproduction. |
| Evo_1_8k_base on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: Evo_1_8k_baseTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.078 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo_1_8k_base), column(Zero-shot MCC) Source checking is not independent reproduction. |
| Evo_1_8k on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: Evo_1_8kTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.078 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo_1_8k), column(Zero-shot MCC) Source checking is not independent reproduction. |
| Evo2-7B-base on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: Evo2-7B-baseTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.079 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo2-7B-base), column(Zero-shot MCC) Source checking is not independent reproduction. |
| Evo2-7B on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: Evo2-7BTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.077 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(Evo2-7B), column(Zero-shot MCC) Source checking is not independent reproduction. |
| GENA-LM-large on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: GENA-LM-largeTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.045 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(GENA-LM-large), column(Zero-shot MCC) Source checking is not independent reproduction. |
| GENERator-3B on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: GENERator-3BTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.045 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(GENERator-3B), column(Zero-shot MCC) Source checking is not independent reproduction. |
| GenerRNA on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: GenerRNATask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.043 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(GenerRNA), column(Zero-shot MCC) Source checking is not independent reproduction. |
| GenSLM on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: GenSLMTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.040 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(GenSlm), column(Zero-shot MCC) Source checking is not independent reproduction. |
| HyenaDNA on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: HyenaDNATask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.047 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(HyenaDNA), column(Zero-shot MCC) Source checking is not independent reproduction. |
| LucaOne on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: LucaOneTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.057 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(LucaOne), column(Zero-shot MCC) Source checking is not independent reproduction. |
| LucaVirus on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: LucaVirusTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.049 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(LucaVirus), column(Zero-shot MCC) Source checking is not independent reproduction. |
| N.T.-v2-50m on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: N.T.-v2-50mTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.044 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(N.T.-v2-50m), column(Zero-shot MCC) Source checking is not independent reproduction. |
| RESM on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: RESMTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.084 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RESM), column(Zero-shot MCC) Source checking is not independent reproduction. |
| RiNALMo_giga on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: RiNALMo_gigaTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.050 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RiNALMo_giga), column(Zero-shot MCC) Source checking is not independent reproduction. |
| RNA-FM on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: RNA-FMTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.068 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNA-FM), column(Zero-shot MCC) Source checking is not independent reproduction. |
| RNAernie on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: RNAernieTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.044 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(RNAernie), column(Zero-shot MCC) Source checking is not independent reproduction. |
| SPACE on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: SPACETask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.051 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(SPACE), column(Zero-shot MCC) Source checking is not independent reproduction. |
| structRFM on NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC Configuration: structRFMTask: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCCDataset subset: NABench deep mutational scanning assays (NABench split) Aggregated by the NABench authors across NABench deep mutational scanning assays. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.065 mcc Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedNABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 6, row(structRFM), column(Zero-shot MCC) Source checking is not independent reproduction. |
Evidence 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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-nabench Individual claims | NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction Table 6, column(Zero-shot MCC) Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: nabench-association-dms-zs-mcc Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Technical metadata and extraction receipts
Stable ID: nabench-task-dms-zs-mcc
- areas
- rna-transcriptomes
- tasks
- Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC
- metric
- Zero-shot MCC
- metric direction
- higher
- dataset
- NABench deep mutational scanning assays
- protocol
- Aggregated by the NABench authors across NABench deep mutational scanning assays.
- source locator
- Table 6, column(Zero-shot MCC)
- comparison panels
- id: nabench-panel-dms-zs-mcc; title: NABench DMS-ZS-MCC: Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC; protocol id: nabench-task-dms-zs-mcc; dataset id: nabench-dataset-nabench-deep-mutational-scanning-assays; metric: mcc; unit: correlation; direction: higher; result ids: nabench-result-rna-fm-dms-zs-mcc-mcc; nabench-result-rnaernie-dms-zs-mcc-mcc; nabench-result-space-dms-zs-mcc-mcc; nabench-result-aido-rna-dms-zs-mcc-mcc; nabench-result-birna-bert-dms-zs-mcc-mcc; nabench-result-crafts-dms-zs-mcc-mcc; nabench-result-dnabert-dms-zs-mcc-mcc; nabench-result-dnabert-6-dms-zs-mcc-mcc; nabench-result-enformer-dms-zs-mcc-mcc; nabench-result-evo2-7b-dms-zs-mcc-mcc; nabench-result-evo2-7b-base-dms-zs-mcc-mcc; nabench-result-evo-1-5-8k-base-dms-zs-mcc-mcc; nabench-result-evo-1-8k-dms-zs-mcc-mcc; nabench-result-evo-1-8k-base-dms-zs-mcc-mcc; nabench-result-gena-lm-large-dms-zs-mcc-mcc; nabench-result-generator-3b-dms-zs-mcc-mcc; nabench-result-generrna-dms-zs-mcc-mcc; nabench-result-genslm-dms-zs-mcc-mcc; nabench-result-hyenadna-dms-zs-mcc-mcc; nabench-result-lucaone-dms-zs-mcc-mcc; nabench-result-lucavirus-dms-zs-mcc-mcc; nabench-result-n-t-v2-50m-dms-zs-mcc-mcc; nabench-result-resm-dms-zs-mcc-mcc; nabench-result-rinalmo-giga-dms-zs-mcc-mcc; nabench-result-structrfm-dms-zs-mcc-mcc; source ids: evidence-expansion-nabench-fefd48d5; source locator: Table 6, column(Zero-shot MCC); context: Every method NABench reports on Overall fitness prediction on NABench deep mutational scanning assays, Zero-shot MCC, scored with Zero-shot MCC on NABench deep mutational scanning assays.; caveats: Author-reported numbers, source checked but not independently reproduced.; Zero-shot, few-shot and supervised cross validation figures come from different protocols and are not comparable to each other.; The per-nucleotide-type figures and the overall figures describe the same runs at different resolutions, so they must not be combined.; review: method: automated_source_review; date: 2026-09-18
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