Model

RNA-FM

RNA-FM learns contextual representations of RNA nucleotides for downstream RNA analyses.

Sources (2)

ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table

67 evaluations · 67 results · 1 evaluated configuration using this model

How it worksRNA-FM workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources (2)

ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table

Overview

Model type

Masked-token RNA transformer encoder

Inputs

RNA sequences tokenized at nucleotide resolution.

Outputs

Contextual token embeddings for a specified downstream RNA task.

Access

Official project documentation and implementation: https://github.com/ml4bio/RNA-FM

Sources (2)

ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table

limited source coverage · Automated source review, 2026-09-23. All specifications and missing details

Evaluations and results

67 evaluations · 67 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: RNA-FM	Task: BEACON APA: Alternative polyadenylation isoform prediction Dataset subset: APARENT (BEACON split)	70.32(0.97)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.97 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON APA: Alternative polyadenylation isoform prediction BEACON harness, fixed downstream head per task. Train/validation/test 145,463/33,170/49,755; dataset APARENT. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(APA)
Configuration: RNA-FM	Task: BEACON CMP: Contact map prediction Dataset subset: RNAcontact (BEACON split)	47.56(6.73)% precision_at_l percent · higher Uncertainty: type: standard_deviation; value: 6.73 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON CMP: Contact map prediction BEACON harness, fixed downstream head per task. Train/validation/test 188/23/80; dataset RNAcontact. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(CMP)
Configuration: RNA-FM	Task: BEACON CRI-Off: CRISPR off-target effect prediction Dataset subset: DeepCRISPR (BEACON split)	2.49(1.56)% spearman_corr percent · higher Uncertainty: type: standard_deviation; value: 1.56 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON CRI-Off: CRISPR off-target effect prediction BEACON harness, fixed downstream head per task. Train/validation/test 14,223/2,032/4,064; dataset DeepCRISPR. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(CRI-Off)
Configuration: RNA-FM	Task: BEACON CRI-On: CRISPR on-target efficiency prediction Dataset subset: DeepCRISPR (BEACON split)	31.62(1.16)% spearman_corr percent · higher Uncertainty: type: standard_deviation; value: 1.16 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON CRI-On: CRISPR on-target efficiency prediction BEACON harness, fixed downstream head per task. Train/validation/test 1,453/207/416; dataset DeepCRISPR. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(CRI-On)
Configuration: RNA-FM	Task: BEACON DMP: Distance map prediction Dataset subset: RNAcontact (BEACON split)	51.45(0.51)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.51 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON DMP: Distance map prediction BEACON harness, fixed downstream head per task. Train/validation/test 188/23/80; dataset RNAcontact. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(DMP)
Configuration: RNA-FM	Task: BEACON Modif: RNA modification site prediction Dataset subset: MultiRM (BEACON split)	94.98(0.042)% auc percent · higher Uncertainty: type: standard_deviation; value: 0.042 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON Modif: RNA modification site prediction BEACON harness, fixed downstream head per task. Train/validation/test 304,661/3,599/1,200; dataset MultiRM. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(Modif)
Configuration: RNA-FM	Task: BEACON MRL: Mean ribosome loading prediction Dataset subset: Optimus (BEACON split)	79.47(0.47)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.47 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON MRL: Mean ribosome loading prediction BEACON harness, fixed downstream head per task. Train/validation/test 76,319/7,600/7,600; dataset Optimus. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(MRL)
Configuration: RNA-FM	Task: BEACON ncRNA: Non-coding RNA family classification Dataset subset: Noorul's ncRNA set (BEACON split)	96.81(0.061)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.061 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON ncRNA: Non-coding RNA family classification BEACON harness, fixed downstream head per task. Train/validation/test 5,679/650/2,400; dataset Noorul's ncRNA set. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(ncRNA)
Configuration: RNA-FM	Task: BEACON PRS: Programmable RNA switch prediction Dataset subset: Angenent-Mari's switch set (BEACON split)	55.98(0.09)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.09 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON PRS: Programmable RNA switch prediction BEACON harness, fixed downstream head per task. Train/validation/test 73,227/9,153/9,154; dataset Angenent-Mari's switch set. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(PRS)
Configuration: RNA-FM	Task: BEACON SPL: Splice site prediction Dataset subset: SpliceAI (BEACON split)	34.84(0.87)% top_k_accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.87 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON SPL: Splice site prediction BEACON harness, fixed downstream head per task. Train/validation/test 144,628/18,078/16,505; dataset SpliceAI. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(SPL)
Configuration: RNA-FM	Task: BEACON SSI: Structure score imputation Dataset subset: StructureImpute (BEACON split)	42.36(0.24)% r2 percent · higher Uncertainty: type: standard_deviation; value: 0.24 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON SSI: Structure score imputation BEACON harness, fixed downstream head per task. Train/validation/test 14,049/1,756/3,095; dataset StructureImpute. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(SSI)
Configuration: RNA-FM	Task: BEACON SSP: Secondary structure prediction Dataset subset: bpRNA-1m (BEACON split)	68.50(0.54)% f1 percent · higher Uncertainty: type: standard_deviation; value: 0.54 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON SSP: Secondary structure prediction BEACON harness, fixed downstream head per task. Train/validation/test 10,814/1,300/1,305; dataset bpRNA-1m. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(SSP)
Configuration: RNA-FM	Task: BEACON VDP: Vaccine degradation prediction Dataset subset: OpenVaccine (BEACON split)	0.347(0.003) mcrmse error · lower Uncertainty: type: standard_deviation; value: 0.003 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on BEACON VDP: Vaccine degradation prediction BEACON harness, fixed downstream head per task. Train/validation/test 2,155/245/629; dataset OpenVaccine. Aggregation: Not reported BEACON: Benchmark for Comprehensive RNA Tasks and Language Models (arXiv:2406.10391v2) · Table3,p.8,row(RNA-FM),column(VDP)
Configuration: RNA-FM	Task: Mean ribosome load from MPRA Dataset: mRNABench MRL-MPRA	0.49 Pearson R unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source RNA-FM: Mean ribosome load from MPRA Linear probe; mean across ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, RNA-FM row, MRL MPRA column
Configuration: RNA-FM	Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split)	35% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench ECLIP: eCLIP binding site prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(eCLIP)
Configuration: RNA-FM	Task: mRNABench GO: Gene Ontology term prediction Dataset subset: mRNABench GO (mRNABench split)	32.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench GO: Gene Ontology term prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(GO)
Configuration: RNA-FM	Task: mRNABench HL: mRNA half life Dataset subset: mRNABench HL (mRNABench split)	0.47 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench HL: mRNA half life A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(HL)
Configuration: RNA-FM	Task: mRNABench MRL-HL-PAIR: Paired mean ribosome load and half life Dataset subset: mRNABench MRL-HL-Pair (mRNABench split)	0.49 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench MRL-HL-PAIR: Paired mean ribosome load and half life A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(MRL-HL-Pair)
Configuration: RNA-FM	Task: mRNABench MRL-MPRA: Mean ribosome load on an MPRA library Dataset subset: mRNABench MRL MPRA (mRNABench split)	0.49 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench MRL-MPRA: Mean ribosome load on an MPRA library A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(MRL MPRA)
Configuration: RNA-FM	Task: mRNABench MRL: Mean ribosome load Dataset subset: mRNABench MRL (mRNABench split)	0.29 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench MRL: Mean ribosome load A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(MRL)
Configuration: RNA-FM	Task: mRNABench MRNA-LOC-LR: mRNA localisation, long range Dataset subset: mRNABench mRNA Loc-LR (mRNABench split)	74.3% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench MRNA-LOC-LR: mRNA localisation, long range A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(mRNA Loc-LR)
Configuration: RNA-FM	Task: mRNABench MRNA-LOC-SR: mRNA localisation, short range Dataset subset: mRNABench mRNA Loc-SR (mRNABench split)	67% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench MRNA-LOC-SR: mRNA localisation, short range A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(mRNA Loc-SR)
Configuration: RNA-FM	Task: mRNABench PROT-LOC: Protein localisation Dataset subset: mRNABench Prot Loc (mRNABench split)	32.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench PROT-LOC: Protein localisation A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(Prot Loc)
Configuration: RNA-FM	Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split)	25.7% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNA-FM), column(VEP)
Configuration: RNA-FM	Task: NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation Dataset subset: NABench aptamer assays (NABench split)	0.115 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNA-FM on NABench CCV-CORR-APTAMER: Fitness prediction on aptamer assays, supervised, contiguous cross validation Scored supervised, contiguous cross validation across the NABench aptamer assays. Aggregation: Not reported NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction · Table 11, row(RNA-FM), column(aptamer)

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Related configurations, pipelines and services

These configurations, services and pipelines use this model within their own configurations. Their results, where available, are not assigned to the underlying model.

rna-fm Pipeline · 8 results

Use this model

How it works, versions and access

Versions and evaluated configurations

RNA-FM · family
mRNA-FM · variant of
RNA-FM · family
RNA-FM · alias of
RNA-FM · family
RNA-FM · family
RNA-FM · family

How it works

RNA-FM converts an RNA sequence into one token per nucleotide. Twelve transformer encoder blocks use self-attention to produce a 640-dimensional representation at each position. During pretraining, the model learns to recover masked nucleotides from their surrounding sequence. The resulting representations can be supplied to a separately specified downstream model; they are not, by themselves, a structure or functional prediction.

Sources

RNA-FM original methods, arXiv v5 · arXiv:2204.00300v5, Methods: ncRNA data collection and preprocessing and RNA foundation model training details (p.22)

Versions and reproducibility

The nucleotide-based rna_fm_t12 and codon-based mrna_fm_t12 interfaces are distinct. The original RNA-FM paper sets a training input-length limit of 1,024 and describes a usable limit of 1,022 nucleotides. That limit should not be assigned to mRNA-FM without checking its separate configuration.

Sources (3)

ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py; RNA-FM original methods, arXiv v5 · Official README: Quick Start and RNA-FM/mRNA-FM examples; arXiv:2204.00300v5, Methods: training input length and SARS-CoV-2 genome embedding extraction (pp.22–23)

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

The repository exposes embedding extraction and examples for downstream RNA analyses.
Sources (2)
ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table

Limitations and conditions

Base-level RNA-FM and codon-level mRNA-FM are not interchangeable. The task head and tokenization must be specified in each evaluation.
Sources (2)
ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table

Profile review details

Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied.

Stable record: discovery-model-rna-fm

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-23. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Masked-token RNA transformer encoder Sources (2) ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table
Architecture	12-layer masked-token transformer encoder with hidden width 640 and 20 attention heads; nucleotide tokens produce contextual representations. Sources RNA-FM original methods, arXiv v5 · arXiv:2204.00300v5, Methods: ncRNA data collection and preprocessing and RNA foundation model training details (p.22)
Inputs	RNA sequences tokenized at nucleotide resolution. Sources (2) ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table
Outputs	Contextual token embeddings for a specified downstream RNA task. Sources (2) ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table
Parameters	99M, as printed in the official Foundation Models table. Sources (2) ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table
Known versions	rna_fm_t12 and mrna_fm_t12 are separate pretrained interfaces. Sources (2) ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table
Training data	23.7 million non-coding RNA sequences collected from RNAcentral. The authors replace T with U and remove identical sequences using CD-HIT-EST at 100% identity, naming the resulting corpus RNAcentral100. Sources RNA-FM original methods, arXiv v5 · arXiv:2204.00300v5, Methods: ncRNA data collection and preprocessing and RNA foundation model training details (p.22)
Training cutoff	The original Methods describe RNAcentral100 preprocessing but do not establish a dated RNAcentral release. RNAcentral100 is a processed-corpus label, not a release number. · Not reported in inspected sources Sources RNA-FM original methods, arXiv v5 · arXiv2204.00300v5, Methods: Large-scale pre-training dataset, p22
Context limits	The original paper sets a training input-length limit of 1,024 and describes a usable input limit of 1,022 nucleotides. These are the original RNA-FM settings, not a validated limit for later codon-based mRNA-FM checkpoints. Sources RNA-FM original methods, arXiv v5 · arXiv:2204.00300v5, Methods: RNA foundation model training details (pp.22–23) and RNA-FM application input-limit statement (p.23)
Weights licence	The official model-comparison table labels RNA-FM MIT, while the README footer explicitly refers to source code. Separate checkpoint-distribution terms remain unverified; the linked weight repository could not be retrieved during this review. · Not reported in inspected sources Sources (3) ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: LICENSE; rnafm loader: primary artifact · README: Related RNA Language Models, RNA-FM row; License footer; LICENSE. Linked https://huggingface.co/ml4bio/RNA-FM returned HTTP401 during the review.
Access	Official project documentation and implementation: https://github.com/ml4bio/RNA-FM Sources (2) ml4bio/RNA-FM: README.md; ml4bio/RNA-FM: fm/pretrained.py · README.md: Quick Start, embedding examples and RNA foundation model comparison table
Code licence	MIT Sources ml4bio/RNA-FM: LICENSE · LICENSE: licence text
Checkpoint identification	The official rna_fm_t12 loader downloads RNA-FM_pretrained.pth from the authors’ server. The inspected loader does not pin a checkpoint revision or publish a digest; a code commit alone cannot identify the bytes used by a published evaluation. · Not reported in inspected sources Sources rnafm loader: primary artifact · load_fm_model_and_alphabet_hub: rna_fm_t12 branch, lines155–162

Applicable tests and references

Applicability is distinct from a completed evaluation.

BEACON · Proposed association

Evidence

Source checking verifies the cited claim or transcription. It does not establish 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.

37 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	ml4bio/RNA-FM: fm/pretrained.py Original source ↗ README.md: Quick Start, embedding examples and RNA foundation model comparison table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T19:46:19.769679+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `ab7271f8dbb876dbc5e2010e2d88b086088aada096f04149436d315a4f256aac` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	ml4bio/RNA-FM: README.md Original source ↗ README.md: Quick Start, embedding examples and RNA foundation model comparison table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T19:46:19.769679+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `f9f1c1d62adc471661ca98b30c0250e9f3ce0cff7433830f149f5f48ea41c3da` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps RNA sequence Nucleotide tokenizer 12-layer transformer encoder Contextual nucleotide representations Individual claims	ml4bio/RNA-FM: fm/pretrained.py Original source ↗ README.md: Quick Start, embedding examples and RNA foundation model comparison table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T19:46:19.769679+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `ab7271f8dbb876dbc5e2010e2d88b086088aada096f04149436d315a4f256aac` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps RNA sequence Nucleotide tokenizer 12-layer transformer encoder Contextual nucleotide representations Individual claims	ml4bio/RNA-FM: README.md Original source ↗ README.md: Quick Start, embedding examples and RNA foundation model comparison table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T19:46:19.769679+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `f9f1c1d62adc471661ca98b30c0250e9f3ce0cff7433830f149f5f48ea41c3da` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title RNA-FM workflow Individual claims	ml4bio/RNA-FM: fm/pretrained.py Original source ↗ README.md: Quick Start, embedding examples and RNA foundation model comparison table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T19:46:19.769679+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `ab7271f8dbb876dbc5e2010e2d88b086088aada096f04149436d315a4f256aac` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title RNA-FM workflow Individual claims	ml4bio/RNA-FM: README.md Original source ↗ README.md: Quick Start, embedding examples and RNA foundation model comparison table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T19:46:19.769679+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `f9f1c1d62adc471661ca98b30c0250e9f3ce0cff7433830f149f5f48ea41c3da` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Masked-token RNA transformer encoder Individual claims	ml4bio/RNA-FM: fm/pretrained.py Original source ↗ README.md: Quick Start, embedding examples and RNA foundation model comparison table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T19:46:19.769679+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `ab7271f8dbb876dbc5e2010e2d88b086088aada096f04149436d315a4f256aac` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Masked-token RNA transformer encoder Individual claims	ml4bio/RNA-FM: README.md Original source ↗ README.md: Quick Start, embedding examples and RNA foundation model comparison table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T19:46:19.769679+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `f9f1c1d62adc471661ca98b30c0250e9f3ce0cff7433830f149f5f48ea41c3da` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture 12-layer masked-token transformer encoder with hidden width 640 and 20 attention heads; nucleotide tokens produce contextual representations. Individual claims	RNA-FM original methods, arXiv v5 Original source ↗ arXiv:2204.00300v5, Methods: ncRNA data collection and preprocessing and RNA foundation model training details (p.22) Version: 2204.00300v5 Retrieved: 2026-09-16T21:10:17.419803+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `b3945c283c5ca6e8a346cfeb3e8d6609dac6e4a3874fd38dc2436c35eeb6074a` Hash scope: Hash scope not separately documented; inspect source record Format: original_pdf Inspected artifact
Access Official project documentation and implementation: https://github.com/ml4bio/RNA-FM Individual claims	ml4bio/RNA-FM: fm/pretrained.py Original source ↗ README.md: Quick Start, embedding examples and RNA foundation model comparison table Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 348951516e0963d22bbb33b3c9fc18c89081d38e Retrieved: 2026-09-16T19:46:19.769679+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Checkpoint identification, Training cutoff, Weights licence. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `ab7271f8dbb876dbc5e2010e2d88b086088aada096f04149436d315a4f256aac` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Release 2026-09-29-06401fd5b220 · Record review: discovered

6 source records and release history

ml4bio/RNA-FM official source · Original source · 348951516e0963d22bbb33b3c9fc18c89081d38e
RNA-FM original methods, arXiv v5 · Original source · 2204.00300v5
ml4bio/RNA-FM: README.md · Original source · 348951516e0963d22bbb33b3c9fc18c89081d38e
ml4bio/RNA-FM: fm/pretrained.py · Original source · 348951516e0963d22bbb33b3c9fc18c89081d38e
ml4bio/RNA-FM: LICENSE · Original source · 348951516e0963d22bbb33b3c9fc18c89081d38e
rnafm loader: primary artifact · Original source · 348951516e0963d22bbb33b3c9fc18c89081d38e

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Technical metadata and extraction receipts

Stable ID: discovery-model-rna-fm

areas: rna
access: official_source_linked
benchmark applicability: candidate; not evidence of a reported evaluation
candidate benchmark ids: discovery-benchmark-beacon
entity level: family
reported name: RNA-FM
version: Not reported
historical missing metadata: checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
entity classification: review date: 2026-09-17; rationale: The cited profile describes a named learned biological predictor or representation model/family. Preserve this identity separately from task-specific fitting, individual checkpoints, pipelines and hosted access.; source ids: evidence-final-model-rna-fm-paper; evidence-official-fd8e332abdf04a75195b; evidence-official-e17e3864c464d981afc7; source locator: arXiv:2204.00300v5, Methods: ncRNA data collection and preprocessing and RNA foundation model training details (p.22) | README.md: Quick Start, embedding examples and RNA foundation model comparison table; ambiguities: None recorded

Related records

applicable to: BEACON
family: RNA-FM
variant of: mRNA-FM
family: RNA-FM
alias of: RNA-FM
family: RNA-FM
uses model: rna-fm
family: RNA-FM
family: RNA-FM

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