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File-based localization of numerical perturbations in data analysis pipelines.

ABSTRACT:

Background

Data analysis pipelines are known to be affected by computational conditions, presumably owing to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise causes of such instabilities and the path along which they propagate in pipelines are unclear.

Method

We present Spot, a tool to identify which processes in a pipeline create numerical differences when executed in different computational conditions. Spot leverages system-call interception through ReproZip to reconstruct and compare provenance graphs without pipeline instrumentation.

Results

By applying Spot to the structural pre-processing pipelines of the Human Connectome Project, we found that linear and non-linear registration are the cause of most numerical instabilities in these pipelines, which confirms previous findings.

SUBMITTER: Salari A

PROVIDER: S-EPMC7710495 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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File-based localization of numerical perturbations in data analysis pipelines.

Salari Ali A Kiar Gregory G Lewis Lindsay L Evans Alan C AC Glatard Tristan T

GigaScience 20201201 12

<h4>Background</h4>Data analysis pipelines are known to be affected by computational conditions, presumably owing to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise causes of such instabilities and the path along which they propagate in pipelines are unclear.<h4>Method</h4>We present Spot, a tool to identify which processes in a pipeline create numerical differences when executed in different computat ...[more]

PMID: 33269388

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