n_proteins int64 | mask_mode string | Q5 float64 | per_class dict | SOV dict | topology_accuracy float64 | sp_tm_confusion dict | bootstrap dict |
|---|---|---|---|---|---|---|---|
9,999 | split | 0.917483 | {
"i": {
"precision": 0.8911648384108761,
"recall": 0.980002025212898,
"f1": 0.9334745750572272,
"support": 1994852
},
"o": {
"precision": 0.9581757123986336,
"recall": 0.8664895988959304,
"f1": 0.9100291254170542,
"support": 1536135
},
"H": {
"precision": 0.919460176760887... | {
"i": 0.9745243080666607,
"o": 0.8160562328827037,
"H": 0.881367466778817,
"B": 0.7297525624175409,
"S": 0.9783007094501648,
"all": 0.9005172645268766
} | 0.740974 | {
"goldSP_predTM": 279,
"goldTM_predSP": 973
} | {
"n_boot": 1000,
"alpha": 0.05,
"Q5": {
"mean": 0.9176560440658355,
"lo": 0.9121205207443579,
"hi": 0.9230444816255653
},
"topology_accuracy": {
"mean": 0.7411314131413141,
"lo": 0.7323732373237324,
"hi": 0.7494774477447745
},
"recall": {
"i": {
"mean": 0.980108119250946... |
ralle TM topology dataset (v6.1)
Harmonized per-residue transmembrane topology dataset used to train and evaluate ralle, a single-sequence per-residue TM topology predictor (frozen ESMC embeddings + CNN + light-attention + grammar-CRF head).
This revision supersedes all earlier revisions (see git history / "Files and versions"). Current build: v6.1 — rebuilt 2026-08-25; see
audit_rebuild_v6.jsonfor the integrity audit.
Contents
| file | contents |
|---|---|
records_clean_v6.jsonl |
one JSON per protein: id, sequence, labels (per-residue), tier (evidence 1–3), source, meta |
splits_v6.json |
`id -> "train" |
clusters.tsv.gz |
MMseqs2 cluster assignment used for the leak repair |
audit_rebuild_v6.json |
automated integrity audit (schema, duplicates, leakage fixpoint) |
build_summary_rebuild.json |
build funnel + repair counts |
anchorify_report.json |
benchmark-anchor recovery report |
Label scheme
Per-residue, same length as sequence: H TM alpha-helix, B TM beta-strand,
S signal peptide, i inside/cytoplasmic, o outside; . = unannotated
(ignore index). DeepTMHMM conventions: globular proteins without a signal peptide
are all-i; residues after a signal-peptide run are o.
Numbers (v6.1)
| records (final) | 193,886 |
| train / val / test | 91,806 / 7,662 / 94,418 |
| all-vs-all pairs >=30% id / >=50% cov | 6,184,249 |
| records moved by leak repair | 15,132 |
| residual train<->eval pairs at fixpoint | 0 |
Per-source records: uniprot 92,449, uniprot_globular 51,101, pdb_globular 19,866, htp 13,304, pdbtm 8,065, topdb 5,529, deeptmhmm 3,571, uniprot_beta 1
Provenance & decontamination
Sources (evidence-tiered): PDBTM (structure-verified) > TOPDB v3.3 (experimental
topology) > UniProtKB/Swiss-Prot reviewed annotations; human TM proteome consensus
(CCTOP); PDB SEQRES globular chains and reviewed signal-peptide proteins as
negative/signal sets; DeepTMHMM legacy set reserved for evaluation. Complete
all-vs-all MMseqs2 decontamination with union-find component repair — zero
train<->eval similar pairs at fixpoint. Full details: docs/SETUP.md,
docs/REBUILD_DESIGN.md, and docs/references.md in the GitHub repo.
License & citation
CC-BY-4.0. If you use this dataset, cite the ralle repo and the underlying source
databases (PDBTM, TOPDB, UniProtKB/Swiss-Prot, CCTOP, DeepTMHMM) — see
docs/references.md for the ranked reference list.
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