Evaluation

MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing)

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 9 results. Different protocols are not a single leaderboard.

Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) · Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)

Sorted by Accuracy (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Accuracy (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	F1 (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	False negatives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	False positives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	MCC (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	Precision (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	Recall (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	True negatives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	True positives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))
MINTIE (Silverstein et al. 2026)Evaluation	0.25	0.4	15	9	-0.588	0.471	0.348	0	8

All 9 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: MINTIE (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.25 Accuracy (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell F3, row 'MINTIE', column 'Accuracy'
Configuration: MINTIE (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.4 F1 (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell I3, row 'MINTIE', column 'F1'
Configuration: MINTIE (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	15 False negatives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell C3, row 'MINTIE', column 'False Negatives'
Configuration: MINTIE (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	9 False positives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell E3, row 'MINTIE', column 'False Positives'
Configuration: MINTIE (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	-0.588 MCC (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell J3, row 'MINTIE', column 'MCC'
Configuration: MINTIE (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.471 Precision (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell G3, row 'MINTIE', column 'Precision'
Configuration: MINTIE (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.348 Recall (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell H3, row 'MINTIE', column 'Recall'
Configuration: MINTIE (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0 True negatives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell D3, row 'MINTIE', column 'True Negatives'
Configuration: MINTIE (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	8 True positives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell B3, row 'MINTIE', column 'True Positives'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools)

Configuration: MINTIE (Silverstein et al. 2026)
Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools)
Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-11
dataset version: NIH neuromuscular diagnosed RNA-seq truth set (dbGaP phs001272.v2.p1), as published
split: No split
population: 23 known splicing events (16 muscle, 7 fibroblast); 9 true-negative samples (6 muscle, 3 fibroblast)
inputs: Patient tissue RNA-seq aligned with STAR to GRCh38 (GTEx v10 pipeline); tool-specific controls as in parameters
adaptation: Not reported
metric implementation: Spreadsheet formulas over TP, FN, TN and FP (Table S9); MCC from the binary confusion matrix
aggregation: Sum over tissue sets
budget: Not reported
protocol id: rna-splicing-20261011-silverstein2026-protocol-splicing

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: No split
Adaptation: Not reported
Scoring implementation: Spreadsheet formulas over TP, FN, TN and FP (Table S9); MCC from the binary confusion matrix

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

36 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation Not reported Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation Not reported Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Sum over tissue sets Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Sum over tissue sets Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version NIH neuromuscular diagnosed RNA-seq truth set (dbGaP phs001272.v2.p1), as published Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version NIH neuromuscular diagnosed RNA-seq truth set (dbGaP phs001272.v2.p1), as published Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs Patient tissue RNA-seq aligned with STAR to GRCh38 (GTEx v10 pipeline); tool-specific controls as in parameters Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs Patient tissue RNA-seq aligned with STAR to GRCh38 (GTEx v10 pipeline); tool-specific controls as in parameters Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 3 ('MINTIE') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) · Original source · medRxiv preprint version 1, posted 2026-01-28; JATS source XML
Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Original source · medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML)

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261011-silverstein2026-eval-mintie

areas: rna-transcriptomes
contexts: clinical_research
origin: independent_paper
protocol: rna-splicing-20261011-silverstein2026-protocol-splicing
version: Primary source as retrieved 2026-10-11
comparison: dataset version: NIH neuromuscular diagnosed RNA-seq truth set (dbGaP phs001272.v2.p1), as published; split: No split; population: 23 known splicing events (16 muscle, 7 fibroblast); 9 true-negative samples (6 muscle, 3 fibroblast); inputs: Patient tissue RNA-seq aligned with STAR to GRCh38 (GTEx v10 pipeline); tool-specific controls as in parameters; adaptation: Not reported; metric implementation: Spreadsheet formulas over TP, FN, TN and FP (Table S9); MCC from the binary confusion matrix; aggregation: Sum over tissue sets; budget: Not reported; protocol id: rna-splicing-20261011-silverstein2026-protocol-splicing
source locator: Table S9 row 3 ('MINTIE')
missing metadata: comparison.adaptation: reason: inapplicable; note: No model training or tuning on the truth set; comparison.budget: reason: unreported

Related records

system: MINTIE (Silverstein et al. 2026)
assessment: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools)
data: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)
evaluation: MINTIE accuracy (Silverstein et al. Table S9)
evaluation: MINTIE f1-score (Silverstein et al. Table S9)
evaluation: MINTIE false-negative-count (Silverstein et al. Table S9)
evaluation: MINTIE false-positive-count (Silverstein et al. Table S9)
evaluation: MINTIE matthews-correlation-coefficient (Silverstein et al. Table S9)
evaluation: MINTIE precision (Silverstein et al. Table S9)
evaluation: MINTIE recall (Silverstein et al. Table S9)
evaluation: MINTIE true-negative-count (Silverstein et al. Table S9)
evaluation: MINTIE true-positive-count (Silverstein et al. Table S9)

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