Author

Auguste Gardette

Sorbonne UniversitéORCID 0009-0009-7635-8344Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:metagenomics· 3 Research Focus:benchmarking· 2 Organism:fungi (other)· 2 Approach:statistical model· 2 Approach:benchmark study· 1 Research Focus:database / resource· 1 Approach:deep learning· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Aaron O’BrieniD· 2 shared César MaríniD· 1 shared Edi PriftiiD· 1 shared Eugeni BeldaiD· 1 shared Jean‐Daniel ZuckeriD· 1 shared Pilar ParadaiD· 1 shared

Activity by Year

2026-2026 · peak 3/yr

Co-Author Collaboration Network

6 top collaborators · 6 mutual co-author links

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2 shared papersBioinformatics

Aaron O’BrienORCID

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3 papers

Recent·Most cited

A learned fungal ITS embedding does not outperform correctly configured alignment in open-world evaluation

Aaron O’Brien, Auguste Gardette

The paper evaluates learned fungal ITS embeddings against correctly configured alignment and finds alignment performs better in open-world settings due to evaluation choices.

bioRxiv · Sep 25, 2026 · PreprintBioinformatics

Classical baselines outperform released deep-learning ITS classifiers, which collapse on ITS2 where predictions follow the flanking regions

Aaron O’Brien, Auguste Gardette, César Marín, Pilar Parada

MycoAI ITS classifiers trail alignment, SINTAX and HiTaC on full-length ITS and drop to 28.3% and 18.5% seen-genus family accuracy on ITS2, as predictions track flanking regions.

bioRxiv · Sep 10, 2026 · PreprintBioinformatics✦ In-depth digest

CurateMake: an auditable workflow for multi-source ITS reference database harmonisation and phylogenetic validation

Auguste Gardette, Eugeni Belda, Edi Prifti, Jean‐Daniel Zucker

CurateMake is a workflow for harmonizing and validating ITS reference databases, improving taxonomic coherence and error correction through nomenclatural standardization and phylogenetic validation.

bioRxiv · Jul 16, 2026 · PreprintBioinformatics