Pipeline

CUPID Data-aug-Avg

CUPID predicts pairwise interactions between non-coding RNAs from their sequences.

Sources

Computational understanding of non-coding RNA pairwise interactions · Abstract (paragraph 1); Methods/Negative examples generation (paragraph 1)

1 evaluation · 1 result

How it worksEvaluated procedure (conceptual)

Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.

Sources

Computational understanding of non-coding RNA pairwise interactions · Methods/Model architecture/The classification unit (paragraph 1); Methods/Model architecture/The overall CUPID architecture (paragraph 1)

Overview

Model type

Study-specific predictive method; this record is the paper-specific evaluated configuration.

Sources

Biological inputs

Pairs of non-coding RNA sequences

Sources

Computational understanding of non-coding RNA pairwise interactions · Methods/Negative examples generation (paragraph 4); Methods/Dataset (paragraph 1)

Outputs

Predicted ncRNA–ncRNA interaction labels or scores

Sources

Computational understanding of non-coding RNA pairwise interactions · Methods/Dataset (paragraph 8); Methods/Dataset (paragraph 1)

Access

Official study implementation and usage documentation: https://github.com/AnacletoLAB/ncRNA-CUPID/blob/f663c10d2f6c33f8513614badbbc673e654a64d8/README.md. This pinned documentation revision is not automatically the evaluated weight revision.

Sources

AnacletoLAB/ncRNA-CUPID README.md · README.md; installation, model download and usage instructions

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

1 evaluation · 1 result. 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
Pipeline: CUPID Data-aug-Avg	Task: non-coding RNA pairwise interaction prediction Dataset: ncRNA interaction pairs	0.919 AUROC fraction · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CUPID Data-aug-Avg: non-coding RNA pairwise interaction prediction Data augmentation with average pooling for molecule-level ncRNA embeddings Aggregation: Not reported Computational understanding of non-coding RNA pairwise interactions · Table 1, CUPID > Data-aug-Avg row, AUROC column

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

Use this model

How it works, versions and access

How it works

How the evaluated method works

GenerRNA sequence embeddings feed a feed-forward interaction classifier. The Data-aug-Avg configuration uses the paper’s augmented training pairs and averaging variant.

Sources

What was evaluated

The linked evaluation record identifies CUPID Data-aug-Avg: non-coding RNA pairwise interaction prediction. Its dataset, split, adaptation and evidence origin remain attached to the reported results.

Sources

Computational understanding of non-coding RNA pairwise interactions · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b4-007

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

Uses sequence representations across several ncRNA interaction types without requiring explicit thermodynamic folding features.
Sources
Computational understanding of non-coding RNA pairwise interactions · Methods/Dataset (paragraph 8); Discussion (paragraph 1)

Limitations and conditions

RNA pairs exceeding the study’s length filter are excluded; this restricts the distribution on which the reported result is established.
Sources
Computational understanding of non-coding RNA pairwise interactions · Methods/Dataset (paragraph 5); Methods/Dataset (paragraph 4)

Profile review details

Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.

Stable record: reported-model-2894d253c5e8a8

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. 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	Study-specific predictive method; this record is the paper-specific evaluated configuration. Sources Computational understanding of non-coding RNA pairwise interactions · Methods/Model architecture/The classification unit (paragraph 1); Methods/Model architecture/The overall CUPID architecture (paragraph 1)
Architecture / procedure	GenerRNA sequence embeddings feed a feed-forward interaction classifier. The Data-aug-Avg configuration uses the paper’s augmented training pairs and averaging variant. Sources Computational understanding of non-coding RNA pairwise interactions · Methods/Model architecture/The classification unit (paragraph 1); Methods/Model architecture/The overall CUPID architecture (paragraph 1)
Biological inputs	Pairs of non-coding RNA sequences Sources Computational understanding of non-coding RNA pairwise interactions · Methods/Negative examples generation (paragraph 4); Methods/Dataset (paragraph 1)
Outputs	Predicted ncRNA–ncRNA interaction labels or scores Sources Computational understanding of non-coding RNA pairwise interactions · Methods/Dataset (paragraph 8); Methods/Dataset (paragraph 1)
Parameters	An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sources Sources (2) Computational understanding of non-coding RNA pairwise interactions; AnacletoLAB/ncRNA-CUPID README.md · Methods/Dataset; Methods/Data augmentation; Methods/Negative examples generation; Methods/Model architecture/The overall CUPID architecture; Methods/Model architecture/Pooling techniques; Methods/Model architecture/The classification unit; Methods/Model architecture/Mini-batch balancing; Methods/Experimental evaluation/Data preparation and splitting; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision
Known versions / configuration	CUPID Data-aug-Avg is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sources Sources Computational understanding of non-coding RNA pairwise interactions · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label.
Training data / fitting	The study’s filtered ncRNA-interaction dataset; augmentation produces four training instances per original pair. Sources Computational understanding of non-coding RNA pairwise interactions · Methods/Dataset (paragraph 1); Methods/Dataset (paragraph 8)
Context limits	Input filtering is tied to GenerRNA token capacity; the paper describes approximately 4,096 nucleotides, with BPE compression affecting the correspondence. Sources Computational understanding of non-coding RNA pairwise interactions · Methods/Dataset (paragraph 4); Methods/Model architecture/The overall CUPID architecture (paragraph 2)
Access	Official study implementation and usage documentation: https://github.com/AnacletoLAB/ncRNA-CUPID/blob/f663c10d2f6c33f8513614badbbc673e654a64d8/README.md. This pinned documentation revision is not automatically the evaluated weight revision. Sources AnacletoLAB/ncRNA-CUPID README.md · README.md; installation, model download and usage instructions
Code licence	Apache 2.0 (study repository code at the cited revision; this does not establish every dependency or historical checkpoint licence). Sources AnacletoLAB/ncRNA-CUPID LICENSE.txt · LICENSE.txt; complete licence text
Weights licence	The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sources Sources AnacletoLAB/ncRNA-CUPID README.md · README.md; checkpoint/access documentation and licence scope

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.

20 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 input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims	Computational understanding of non-coding RNA pairwise interactions Original source ↗ Methods/Model architecture/The classification unit (paragraph 1); Methods/Model architecture/The overall CUPID architecture (paragraph 1) Version: PMC archival version PMC12957212.1 Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `0e6719410b390ee9c4858bb9321042851100fb74df3aa109bf2af2b8aaff7ac1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps Pairs of non-coding RNA sequences CUPID Data-aug-Avg Predicted ncRNA–ncRNA interaction labels or scores Individual claims	Computational understanding of non-coding RNA pairwise interactions Original source ↗ Methods/Model architecture/The classification unit (paragraph 1); Methods/Model architecture/The overall CUPID architecture (paragraph 1) Version: PMC archival version PMC12957212.1 Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `0e6719410b390ee9c4858bb9321042851100fb74df3aa109bf2af2b8aaff7ac1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Evaluated procedure (conceptual) Individual claims	Computational understanding of non-coding RNA pairwise interactions Original source ↗ Methods/Model architecture/The classification unit (paragraph 1); Methods/Model architecture/The overall CUPID architecture (paragraph 1) Version: PMC archival version PMC12957212.1 Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `0e6719410b390ee9c4858bb9321042851100fb74df3aa109bf2af2b8aaff7ac1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Model type Study-specific predictive method; this record is the paper-specific evaluated configuration. Individual claims	Computational understanding of non-coding RNA pairwise interactions Original source ↗ Methods/Model architecture/The classification unit (paragraph 1); Methods/Model architecture/The overall CUPID architecture (paragraph 1) Version: PMC archival version PMC12957212.1 Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `0e6719410b390ee9c4858bb9321042851100fb74df3aa109bf2af2b8aaff7ac1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Architecture / procedure GenerRNA sequence embeddings feed a feed-forward interaction classifier. The Data-aug-Avg configuration uses the paper’s augmented training pairs and averaging variant. Individual claims	Computational understanding of non-coding RNA pairwise interactions Original source ↗ Methods/Model architecture/The classification unit (paragraph 1); Methods/Model architecture/The overall CUPID architecture (paragraph 1) Version: PMC archival version PMC12957212.1 Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `0e6719410b390ee9c4858bb9321042851100fb74df3aa109bf2af2b8aaff7ac1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Weights licence The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims	AnacletoLAB/ncRNA-CUPID README.md Original source ↗ README.md; checkpoint/access documentation and licence scope Version: f663c10d2f6c33f8513614badbbc673e654a64d8 Retrieved: 2026-09-16T19:54:13.686121+00:00	unreported automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `17e3dbece27b0cd7b6031ecc817f941ad351c95ee0416e0bd8e4020ecaed7f5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Biological inputs Pairs of non-coding RNA sequences Individual claims	Computational understanding of non-coding RNA pairwise interactions Original source ↗ Methods/Negative examples generation (paragraph 4); Methods/Dataset (paragraph 1) Version: PMC archival version PMC12957212.1 Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `0e6719410b390ee9c4858bb9321042851100fb74df3aa109bf2af2b8aaff7ac1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Outputs Predicted ncRNA–ncRNA interaction labels or scores Individual claims	Computational understanding of non-coding RNA pairwise interactions Original source ↗ Methods/Dataset (paragraph 8); Methods/Dataset (paragraph 1) Version: PMC archival version PMC12957212.1 Retrieved: 2026-09-16T10:41:06Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `0e6719410b390ee9c4858bb9321042851100fb74df3aa109bf2af2b8aaff7ac1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims	Computational understanding of non-coding RNA pairwise interactions Original source ↗ Methods/Dataset; Methods/Data augmentation; Methods/Negative examples generation; Methods/Model architecture/The overall CUPID architecture; Methods/Model architecture/Pooling techniques; Methods/Model architecture/The classification unit; Methods/Model architecture/Mini-batch balancing; Methods/Experimental evaluation/Data preparation and splitting; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC archival version PMC12957212.1 Retrieved: 2026-09-16T10:41:06Z	unreported automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `0e6719410b390ee9c4858bb9321042851100fb74df3aa109bf2af2b8aaff7ac1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims	AnacletoLAB/ncRNA-CUPID README.md Original source ↗ Methods/Dataset; Methods/Data augmentation; Methods/Negative examples generation; Methods/Model architecture/The overall CUPID architecture; Methods/Model architecture/Pooling techniques; Methods/Model architecture/The classification unit; Methods/Model architecture/Mini-batch balancing; Methods/Experimental evaluation/Data preparation and splitting; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: f663c10d2f6c33f8513614badbbc673e654a64d8 Retrieved: 2026-09-16T19:54:13.686121+00:00	unreported automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `17e3dbece27b0cd7b6031ecc817f941ad351c95ee0416e0bd8e4020ecaed7f5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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

3 source records and release history

Computational understanding of non-coding RNA pairwise interactions · Original source · PMC archival version PMC12957212.1
AnacletoLAB/ncRNA-CUPID README.md · Original source · f663c10d2f6c33f8513614badbbc673e654a64d8
AnacletoLAB/ncRNA-CUPID LICENSE.txt · Original source · f663c10d2f6c33f8513614badbbc673e654a64d8

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Technical metadata and extraction receipts

Stable ID: reported-model-2894d253c5e8a8

areas: rna-transcriptomes
entity level: method
version: Not reported
reported name: CUPID Data-aug-Avg
historical missing metadata: version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
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.
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This record identifies a composed analysis workflow with separately identifiable upstream models, representations or tools and a downstream prediction/scoring procedure. Results belong to that complete composition rather than to an upstream model alone.; source ids: cupid-rna-interactions-2026; source locator: Methods/Model architecture/The classification unit (paragraph 1); Methods/Model architecture/The overall CUPID architecture (paragraph 1) | Abstract (paragraph 1); Methods/Negative examples generation (paragraph 1); ambiguities: This is the paper-specific pipeline identity; unspecified component checkpoints or implementation versions are not inferred from its name.

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model: CUPID Data-aug-Avg: non-coding RNA pairwise interaction prediction

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