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Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML · Peer-reviewed

DOI: 10.1093/bib/bbag098

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

Results

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

ValueMetricModel or configurationDatasetEvaluation
0.571±0.002 unitlessOne minus overlap ratio (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, 1 − OR, sampled-mean)
0.763±0.001 unitlessAUROC (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, AUC, sampled-mean)
0.705±0.001 unitlessF1 (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, F1, sampled-mean)
0.325±0.007 unitlessMCC (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, MCC, sampled-mean)
0.534±0.001 unitlessOne minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, 1 − OR, sampled-mean)
0.740±0.001 unitlessAUROC (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, AUC, sampled-mean)
0.696±0.001 unitlessF1 (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, F1, sampled-mean)
0.306±0.008 unitlessMCC (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K3) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, MCC, sampled-mean)
0.535±0.037 unitlessAUROC (PLL-D; mean over assays)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, mean)
0.517 unitlessAUROC (PLL-D; median over assays)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, median)
0.053±0.055 unitlessMCC (PLL-D; mean over assays)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, mean)
0.022 unitlessMCC (PLL-D; median over assays)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, median)
0.066±0.065 unitlessAbsolute spearman correlation (PLL-D; mean over assays)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, mean)
0.043 unitlessAbsolute spearman correlation (PLL-D; median over assays)3UTRBERT (K3) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K3) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, median)
0.291±0.003 unitlessOne minus overlap ratio (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, 1 − OR, sampled-mean)
0.621±0.001 unitlessAUROC (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, AUC, sampled-mean)
0.667±0.000 unitlessF1 (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, F1, sampled-mean)
0.025±0.003 unitlessMCC (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, MCC, sampled-mean)
0.307±0.005 unitlessOne minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, 1 − OR, sampled-mean)
0.623±0.002 unitlessAUROC (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, AUC, sampled-mean)
0.667±0.000 unitlessF1 (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, F1, sampled-mean)
0.015±0.003 unitlessMCC (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K3) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K3) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, MCC, sampled-mean)
0.022±0.027 unitlessF1 (attention; mean over structures)3UTRBERT (K3) (zero-shot, Wang et al. 2026)TS test set (70 PDB structures) (Wang et al. 2026)3UTRBERT (K3) zero-shot secondary structure on TS test set (70 PDB structures) (attention, F1 score, mean)
0.013 unitlessF1 (attention; median over structures)3UTRBERT (K3) (zero-shot, Wang et al. 2026)TS test set (70 PDB structures) (Wang et al. 2026)3UTRBERT (K3) zero-shot secondary structure on TS test set (70 PDB structures) (attention, F1 score, median)
0.004±0.030 unitlessMCC (attention; mean over structures)3UTRBERT (K3) (zero-shot, Wang et al. 2026)TS test set (70 PDB structures) (Wang et al. 2026)3UTRBERT (K3) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, mean)
-0.002 unitlessMCC (attention; median over structures)3UTRBERT (K3) (zero-shot, Wang et al. 2026)TS test set (70 PDB structures) (Wang et al. 2026)3UTRBERT (K3) zero-shot secondary structure on TS test set (70 PDB structures) (attention, MCC, median)
0.014±0.015 unitlessF1 (attention; mean over structures)3UTRBERT (K3) (zero-shot, Wang et al. 2026)TS-Hard test set (15 PDB structures) (Wang et al. 2026)3UTRBERT (K3) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, mean)
0.008 unitlessF1 (attention; median over structures)3UTRBERT (K3) (zero-shot, Wang et al. 2026)TS-Hard test set (15 PDB structures) (Wang et al. 2026)3UTRBERT (K3) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, F1 score, median)
0.000±0.014 unitlessMCC (attention; mean over structures)3UTRBERT (K3) (zero-shot, Wang et al. 2026)TS-Hard test set (15 PDB structures) (Wang et al. 2026)3UTRBERT (K3) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, MCC, mean)
-0.001 unitlessMCC (attention; median over structures)3UTRBERT (K3) (zero-shot, Wang et al. 2026)TS-Hard test set (15 PDB structures) (Wang et al. 2026)3UTRBERT (K3) zero-shot secondary structure on TS-Hard test set (15 PDB structures) (attention, MCC, median)
0.626±0.001 unitlessOne minus overlap ratio (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K4) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, 1 − OR, sampled-mean)
0.795±0.001 unitlessAUROC (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K4) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, AUC, sampled-mean)
0.722±0.001 unitlessF1 (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K4) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, F1, sampled-mean)
0.392±0.008 unitlessMCC (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K4) zero-shot family classification on RfamSample (561 Rfam families) (CLS embedding, MCC, sampled-mean)
0.486±0.000 unitlessOne minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K4) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, 1 − OR, sampled-mean)
0.691±0.001 unitlessAUROC (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K4) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, AUC, sampled-mean)
0.676±0.001 unitlessF1 (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K4) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, F1, sampled-mean)
0.176±0.009 unitlessMCC (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RfamSample (561 Rfam families) (Wang et al. 2026)3UTRBERT (K4) zero-shot family classification on RfamSample (561 Rfam families) (FFT embedding, MCC, sampled-mean)
0.550±0.037 unitlessAUROC (PLL-D; mean over assays)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K4) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, mean)
0.548 unitlessAUROC (PLL-D; median over assays)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K4) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, AUC, median)
0.076±0.059 unitlessMCC (PLL-D; mean over assays)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K4) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, mean)
0.075 unitlessMCC (PLL-D; median over assays)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K4) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, MCC, median)
0.100±0.077 unitlessAbsolute spearman correlation (PLL-D; mean over assays)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K4) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, mean)
0.093 unitlessAbsolute spearman correlation (PLL-D; median over assays)3UTRBERT (K4) (zero-shot, Wang et al. 2026)RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)3UTRBERT (K4) zero-shot fitness on RNAGym ncRNA DMS assays (31 assays) (PLL-D, SR, median)
0.326±0.003 unitlessOne minus overlap ratio (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, 1 − OR, sampled-mean)
0.640±0.001 unitlessAUROC (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, AUC, sampled-mean)
0.667±0.000 unitlessF1 (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, F1, sampled-mean)
0.003±0.003 unitlessMCC (CLS embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (CLS embedding, MCC, sampled-mean)
0.371±0.002 unitlessOne minus overlap ratio (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, 1 − OR, sampled-mean)
0.647±0.001 unitlessAUROC (FFT embedding; mean over random samplings of sequence pairs)3UTRBERT (K4) (zero-shot, Wang et al. 2026)ArchiveII-Nr (1273 RNAs) (Wang et al. 2026)3UTRBERT (K4) zero-shot RNA type classification on ArchiveII-Nr (1273 RNAs) (FFT embedding, AUC, sampled-mean)

Models, benchmarks and other records

Benchmarks (1)

Protocols (36)

Datasets (5)

Evaluations (1,190)

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18 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
attributes.artifact_sha256
835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808
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Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

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Retrieved: 2026-10-11T21:27:04Z

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https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12963973/fullTextXML
Source metadata
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

Original source ↗

No field-specific location recorded

Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

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Doi
10.1093/bib/bbag098
Source metadata
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

Original source ↗

No field-specific location recorded

Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

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CC-BY-4.0
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Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

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Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
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Limitations
1 values
  • All benchmark numbers are in the supplementary Word file; the main text shows them as figures only.
Source metadata
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

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No field-specific location recorded

Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
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Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

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Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

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Publication status
peer_reviewed
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Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

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No field-specific location recorded

Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

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Retrieved at
2026-10-11T21:27:04Z
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Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

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Url
https://doi.org/10.1093/bib/bbag098
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Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

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Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
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Version
Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Source metadata
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning

Original source ↗

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Version: Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
Retrieved: 2026-10-11T21:27:04Z

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Stable ID: lit-rna-20261011-rnalm-zeroshot-source-wang2026

areas
rna-transcriptomes
contexts
research
url
https://doi.org/10.1093/bib/bbag098
artifact url
https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12963973/fullTextXML
version
Briefings in Bioinformatics 2026, bbag098 (issue date 2026-03-01); PMC12963973 full-text XML
retrieved at
2026-10-11T21:27:04Z
artifact sha256
835b64d52ae892cad113e798b2976c398dc9ed12178f675e0eabd2169f533808
doi
10.1093/bib/bbag098
publication status
peer_reviewed
licence
CC-BY-4.0
media type
application/xml
limitations
All benchmark numbers are in the supplementary Word file; the main text shows them as figures only.
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