From 668112d266393c3b16185b7907dd9fefe1b34dbb Mon Sep 17 00:00:00 2001 From: David Neumann Date: Thu, 30 Apr 2026 11:09:57 +0200 Subject: [PATCH 1/2] Updated the Citation Updated the BibTeX citation in the read me and the `CITATION.cff` file. I also took the liberty to change the repository in the CFF file to ViRelAy, because I believe this is a better entrypoint for people trying to get to know the three software packages. Previously, the repository URL was set to CoRelAy, which is fine, but on the ViRelAy repository you would get directed to ViRelAy's documentation, which shows how to integrate Zennit, CoRelAy and ViRelAy, which makes for a better starting point for beginners. Please feel free to revert that change. --- CITATION.cff | 93 ++++++++++++++++++++++++++++++++++------------------ README.md | 17 ++++++---- 2 files changed, 72 insertions(+), 38 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 2100c0e..d250e7d 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,8 +1,7 @@ - cff-version: 1.2.0 title: >- - Software for Dataset-wide XAI: From Local Explanations to - Global Insights with Zennit, CoRelAy, and ViRelAy + Software for dataset-wide XAI: From local explanations to + global insights with Zennit, CoRelAy, and ViRelAy message: >- If you use this software, please cite it using the metadata from this file. @@ -11,49 +10,76 @@ authors: - given-names: Christopher J. family-names: Anders orcid: 'https://orcid.org/0000-0003-3295-8486' + affiliation: RIKEN Center for Advanced Intelligence Project - given-names: David family-names: Neumann orcid: 'https://orcid.org/0000-0003-1907-8329' + affiliation: >- + Fraunhofer Institute for Telecommunications, + Heinrich-Hertz-Institut, HHI - given-names: Wojciech family-names: Samek orcid: 'https://orcid.org/0000-0002-6283-3265' + affiliation: >- + Fraunhofer Institute for Telecommunications, + Heinrich-Hertz-Institut, HHI - given-names: Klaus-Robert family-names: Müller orcid: 'https://orcid.org/0000-0002-3861-7685' + affiliation: Technische Universität Berlin - given-names: Sebastian family-names: Lapuschkin orcid: 'https://orcid.org/0000-0002-0762-7258' + affiliation: >- + Fraunhofer Institute for Telecommunications, + Heinrich-Hertz-Institut, HHI identifiers: - type: doi - value: 10.48550/arXiv.2106.13200 - description: arXiv Preprint + value: 10.1371/journal.pone.0336683 + description: DOI - type: url - value: 'https://arxiv.org/abs/2106.13200' - description: arXiv Preprint -repository-code: 'https://github.com/virelay/corelay.git' -url: 'https://corelay.readthedocs.io/en/latest/' + value: >- + https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0336683 + description: PLOS One +repository-code: 'https://github.com/virelay/virelay.git' +url: 'https://virelay.readthedocs.io/en/latest/' abstract: >- - Deep Neural Networks (DNNs) are known to be strong - predictors, but their prediction strategies can rarely be - understood. With recent advances in Explainable Artificial - Intelligence (XAI), approaches are available to explore - the reasoning behind those complex models' predictions. - Among post-hoc attribution methods, Layer-wise Relevance - Propagation (LRP) shows high performance. For deeper - quantitative analysis, manual approaches exist, but - without the right tools they are unnecessarily labor - intensive. In this software paper, we introduce three - software packages targeted at scientists to explore model - reasoning using attribution approaches and beyond: (1) - Zennit - a highly customizable and intuitive attribution - framework implementing LRP and related approaches in - PyTorch, (2) CoRelAy - a framework to easily and quickly - construct quantitative analysis pipelines for dataset-wide - analyses of explanations, and (3) ViRelAy - a - web-application to interactively explore data, - attributions, and analysis results. With this, we provide - a standardized implementation solution for XAI, to - contribute towards more reproducibility in our field. + The predictive capabilities of Deep Neural Networks (DNNs) + are well-established, yet the underlying mechanisms + driving these predictions often remain opaque. The advent + of Explainable Artificial Intelligence (XAI) has + introduced novel methodologies to explore the reasoning + behind complex model predictions of complex models. Among + post-hoc attribution methods, Layer-wise Relevance + Propagation (LRP) has demonstrated notable adaptability + and performance for explaining individual predictions – + provided the method is used to its full potential. For + deeper dataset-wide and quantitative analyses, however, + the manual inspection of individual attribution maps + remains unnecessarily labor-intensive and time consuming. + While several approaches for dataset-wide XAI-analyses + have been proposed, unified and accessible implementations + of such tools are still lacking. Furthermore, there is a + notable absence of dedicated visualization and analysis + software to support stakeholders in interpreting both + local and global XAI results effectively. This gap + underscores the need for comprehensive software tools that + facilitate both granular and holistic understanding of + model behavior, as well as easing the adaptability of XAI + in applications and the sciences. To address these + challenges, we present three software packages designed to + facilitate the exploration of model reasoning using + attribution approaches and beyond: (1) Zennit – a highly + customizable and intuitive attribution framework + implementing LRP and related methods in PyTorch, (2) + CoRelAy – a framework to easily and quickly construct + quantitative analysis pipelines for dataset-wide analyses + of explanations, and (3) ViRelAy – an interactive + web-application for exploring data, attributions, and + analysis results. By providing a standardized + implementation for XAI, we aim to promote reproducibility + in our field and empower scientists and practitioners to + uncover the intricacies of complex model behavior. keywords: - Explainable Artificial Intelligence - XAI @@ -64,4 +90,9 @@ keywords: - Zennit - CoRelAy - ViRelAy -license: GPL-3.0-or-later AND LGPL-3.0-or-later +license: + - GPL-3.0-or-later + - LGPL-3.0-or-later +commit: 8c9b9286ab4bf8ec59eafdceda6bb009c72e4b76 +version: 1.0.0 +date-released: '2025-08-06' diff --git a/README.md b/README.md index e327796..0474382 100644 --- a/README.md +++ b/README.md @@ -29,16 +29,19 @@ For more information about CoRelAy, getting started guides, in-depth tutorials, If you find CoRelAy useful for your research, why not cite our related [paper](https://arxiv.org/abs/2106.13200): ```bibtex -@article{anders2021software, - author = {Anders, Christopher J. and +@article{bibliography:software-for-dataset-wide-xai, + author = {Anders, {Christopher J.} and Neumann, David and Samek, Wojciech and - Müller, Klaus-Robert and + Müller, {Klaus-Robert} and Lapuschkin, Sebastian}, - title = {Software for Dataset-wide XAI: From Local Explanations to Global Insights with {Zennit}, {CoRelAy}, and {ViRelAy}}, - year = {2021}, - volume = {abs/2106.13200}, - journal = {CoRR} + title = {Software for {dataset-wide} {XAI}: From local explanations to global insights with Zennit, {CoRelAy}, and {ViRelAy}}, + year = {2026}, + month = jan, + journal = {{PLOS} One}, + volume = {21}, + number = {1}, + pages = {1--38} } ``` From df94f0f05bfb150c9ecd5b83fe265404d77a6e8a Mon Sep 17 00:00:00 2001 From: David Neumann Date: Thu, 30 Apr 2026 11:48:07 +0200 Subject: [PATCH 2/2] Fixed MyPy & Spelling Errors The distance metrics supported by `scipy.spatial.distance.pdist` seem to have changed since the last time MyPy was run, which led a MyPy type error. I have updated the literal that was used to specify the distance metric to match the current version of `scipy.spatial.distance.pdist`. Additionally, there were some words in the new citation that were not recognized by CSpell and are now added to the dictionary. --- src/corelay/processor/distance.py | 4 ---- tests/linters/cspell/.cspell.json | 5 +++++ 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/corelay/processor/distance.py b/src/corelay/processor/distance.py index cdaff9b..6d1ff82 100644 --- a/src/corelay/processor/distance.py +++ b/src/corelay/processor/distance.py @@ -56,12 +56,10 @@ class SciPyPDist(Distance): * "pnorm" * "jaccard", "jacc", "ja", "j" * "jensenshannon", "js" - * "kulczynski1" * "mahalanobis", "mahal", "mah" * "rogerstanimoto" * "russellrao" * "seuclidean", "se", "s" - * "sokalmichener" * "sokalsneath" * "sqeuclidean", "sqe", "sqeuclid" * "yule" @@ -124,7 +122,6 @@ def function(self, data: typing.Any) -> typing.Any: 'j', 'jensenshannon', 'js', - 'kulczynski1', 'mahalanobis', 'mahal', 'mah', @@ -133,7 +130,6 @@ def function(self, data: typing.Any) -> typing.Any: 'seuclidean', 'se', 's', - 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'sqe', diff --git a/tests/linters/cspell/.cspell.json b/tests/linters/cspell/.cspell.json index 5811756..08d76de 100644 --- a/tests/linters/cspell/.cspell.json +++ b/tests/linters/cspell/.cspell.json @@ -148,6 +148,7 @@ "ifmat", "imgmath", "incollection", + "Institut", "intersphinx", "issn", "issuetitle", @@ -191,6 +192,7 @@ "pdist", "pearsonr", "Pickler", + "PLOS", "Plugboards", "pnorm", "posargs", @@ -203,6 +205,7 @@ "rcfile", "reftypes", "regionref", + "RIKEN", "rodolphebarbanneau", "rogerstanimoto", "russellrao", @@ -224,6 +227,7 @@ "SSIM", "synset", "tamasfe", + "Technische", "testpaths", "texlive", "toarray", @@ -234,6 +238,7 @@ "ufunc", "Ulrike", "umap", + "Universität", "urldate", "varnames", "vimrc",