Configuration

MINTIE (Silverstein et al. 2026)

Configuration of MINTIE: version v0.4.1; FASTQ against ten GTEx tissue-matched controls; splice_motif_mismatch = 3; FDR 5%; splice-related outliers only.

1 evaluation · 9 results

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Evaluations and 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

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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'

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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-config-mintie

areas: rna-transcriptomes
contexts: clinical_research
method types: conventional_pipeline
reported name: MINTIE
foundation model eligible: false
version: v0.4.1
parameters: FASTQ against ten GTEx tissue-matched controls; splice_motif_mismatch = 3; FDR 5%; splice-related outliers only
access reuse: Open-source tool; run by the authors on the NIH Biowulf cluster
source locator: Methods 'Case vs Control Splice Tools'; Table S9 row label
provenance note: MINTIE as run in the Silverstein et al. 2026 benchmark.

Related records

configuration of: MINTIE
system: MINTIE on the NIH neuromuscular diagnosed RNA-seq truth set (splicing)

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