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RNA & transcriptomes

RNA structure and transcript-level function. Explore models, applicable tests and evaluation requirements.

Models to test

These are candidates, not a ranked list. An applicable test may need a trained head, a scoring adapter, a specialist comparison, or access to a hosted service. No result is implied by appearing here.

  • Native prediction
  • Frozen embedding + trained head
  • Specialist / baseline
  • Adapter required
  • Conditional access

RNA-FM

ncRNAfoundation model

Public code and checkpoint instructions.

Official source ↗Paper-reported results →

Applicable tests

RNA secondary structure
native prediction

Repository provides a separately trained secondary-structure head; evaluate the complete released pipeline, not the embedding backbone alone.

RNA tertiary structure
adapter required

RNA-FM embeddings feed a separate 3D structure module such as RhoFold+.

RNA splice-site mapping
frozen embedding + trained head

Transcript embeddings need a splice-site classifier fitted on training genes.

mRNA-FM

codon-tokenisedfoundation model

Public checkpoint trained on coding sequences (CDS); input must be codon aligned. UTR-only sequences are outside its training modality.

Official source ↗Paper-reported results →

Applicable tests

Translation / RNA stability
frozen embedding + trained head

Applicable to coding-sequence translation/stability assays with codon-aligned inputs and a train-only head; not a direct match for UTR-only assays.

Test families

Each candidate test needs a defined dataset, split, metric and run protocol before it can become a benchmark.

RNA secondary structure

Candidate test

Compare predicted base pairs against held-out RNA structures.

Candidate models and comparators

RNA-FM
native prediction
RhoFold+
specialist / baseline

RNA tertiary structure

Candidate test

Compare predicted 3D folds against independently held-out structures.

Candidate models and comparators

RNA-FM
adapter required
RhoFold+
specialist / baseline

RNA splice-site mapping

Candidate test

Predict splice-site classes from transcript sequence, using a held-out gene split.

Candidate models and comparators

RNA-FM
frozen embedding + trained head
MIMIC
native prediction

Translation / RNA stability

Candidate test

Predict measured translation or stability effects; choose UTR or coding-sequence assays to match each model’s input modality.

Candidate models and comparators

mRNA-FM
frozen embedding + trained head
MIMIC
adapter required

Model sources and access descriptions checked 2026-09-16. Confirm licenses, terms and checkpoint revisions before any run.