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Learning interpretable RNA units to link RNA sequence, structure, and function
VQRNA Dataset and pretrained model weights 1. Overview This archive contains curated RNA datasets and model weights used in the VQ-RNA study, covering both structure-related and function-related downstream tasks. - Project name: `VQRNA_dataset` - Release
File Size793.1 MB
Data TypeDataset
Published2026
Licensecc-by-4.0
Total Views143
Total Downloads162
VQRNA Dataset and pretrained model weights
1. Overview
This archive contains curated RNA datasets and model weights used in the VQ-RNA study, covering both structure-related and function-related downstream tasks.
– Project name: `VQRNA_dataset`
– Release date: `2026-03-22`
– Scope: distance map prediction, secondary structure modeling, ncRNA classification, RNACentral RNA type classification, miRNA-mRNA interaction prediction, 5’UTR MRL regression, torsion angle prediction, motif analysis (MEME and VQ code-window FASTA)
– Root directory: this `README.md` is placed at the dataset root
2. Directory Layout
VQRNA_dataset/
├─ DistanceMap/
│ ├─ train.csv, val.csv, test.csv, RFAM19.csv
│ └─ distance_map/*.npy
├─ human_utr_mrl/
│ └─ GSM4084997_varying_length_25to100.csv
├─ nRC/
│ └─ *.csv
├─ Motif_Analysis/
│ ├─ fasta/
│ │ └─ code_*.fasta
│ │
│ └─ meme/*.meme
├─ RNACentral_type/
│ └─ *.fasta
├─ rr_inter/
│ └─ MirTarRAW.csv
├─ SS/
│ ├─ train_0.8_72025_1_17.pkl
│ ├─ TR0/TR0.pkl, TS0/TS0.pkl
│ ├─ ArchiveII/archiveII.pkl
│ ├─ bpRNAnew/bpRNAnew.pkl
│ ├─ rnastralign/train.pkl
│ ├─ RNA3DB_2D/bpseq/, pickle/, raw_pickle/
│ └─ casprna_2d/bpseq/, pkl/
├─ torsion_angle/
│ └─ data/fixed_final_output_TR,VL,TS1,TS2,TS3_seqs.csv
└─ weights/
├─ VQRNA_backbone_weights.pth
├─ VQRNA_distance_map.pth
├─ VQRNA_mrl.pth
├─ VQRNA_nrc.pth
├─ VQRNA_rr_inter.pth
├─ VQRNA_SS.pth
└─ VQRNA_torsion_angle.pth
3. Dataset Summary
3.1 DistanceMap
– Files:
– `DistanceMap/train.csv` (179 sequences)
– `DistanceMap/val.csv` (23 sequences)
– `DistanceMap/test.csv` (80 sequences)
– `DistanceMap/RFAM19.csv` (19 sequences)
– `DistanceMap/distance_map/*.npy` (distance matrices)
– CSV columns: `id,input`
– Typical usage: sequence-level input with paired 2D distance map regression target
3.2 Human UTR MRL
– File: `human_utr_mrl/GSM4084997_varying_length_25to100.csv` (106,530 rows)
– Key columns: `utr`, `set`, read-count-deri
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Files are hosted on the source repository. Click download to access the full dataset.
Fan, Xiaoya (2026). Learning interpretable RNA units to link RNA sequence, structure, and function. https://doi.org/10.5281/zenodo.19363040