Literature DB >> 35773719

Species determination using AI machine-learning algorithms: Hebeloma as a case study.

Peter Bartlett1, Ursula Eberhardt2, Nicole Schütz3, Henry J Beker4,5,6.   

Abstract

The genus Hebeloma is renowned as difficult when it comes to species determination. Historically, many dichotomous keys have been published and used with varying success rate. Over the last 20 years the authors have built a database of Hebeloma collections containing not only metadata but also parametrized morphological descriptions, where for about a third of the cases micromorphological characters have been analysed and are included, as well as DNA sequences for almost every collection. The database now has about 9000 collections including nearly every type collection worldwide and represents over 120 different taxa. Almost every collection has been analysed and identified to species using a combination of the available molecular and morphological data in addition to locality and habitat information. Based on these data an Artificial Intelligence (AI) machine-learning species identifier has been developed that takes as input locality data and a small number of the morphological parameters. Using a random test set of more than 600 collections from the database, not utilized within the set of collections used to train the identifier, the species identifier was able to identify 77% correctly with its highest probabilistic match, 96% within its three most likely determinations and over 99% of collections within its five most likely determinations.
© 2022. The Author(s).

Entities:  

Keywords:  Agaricales; Ectomycorrhizal fungi; Identification keys; Neural networks; Taxonomy

Year:  2022        PMID: 35773719      PMCID: PMC9245212          DOI: 10.1186/s43008-022-00099-x

Source DB:  PubMed          Journal:  IMA Fungus        ISSN: 2210-6340            Impact factor:   8.044


  28 in total

Review 1.  Phylogenetic species recognition and species concepts in fungi.

Authors:  J W Taylor; D J Jacobson; S Kroken; T Kasuga; D M Geiser; D S Hibbett; M C Fisher
Journal:  Fungal Genet Biol       Date:  2000-10       Impact factor: 3.495

2.  The mind of the species problem.

Authors:  J Hey
Journal:  Trends Ecol Evol       Date:  2001-07-01       Impact factor: 17.712

3.  The evolution of non-reciprocal nuclear exchange in mushrooms as a consequence of genomic conflict.

Authors:  Duur K Aanen; Thomas W Kuyper; Alfons J M Debets; Rolf F Hoekstra
Journal:  Proc Biol Sci       Date:  2004-06-22       Impact factor: 5.349

Review 4.  Fungal species boundaries in the genomics era.

Authors:  Daniel R Matute; Victoria E Sepúlveda
Journal:  Fungal Genet Biol       Date:  2019-07-04       Impact factor: 3.495

5.  Deep learning-based quantification of arbuscular mycorrhizal fungi in plant roots.

Authors:  Edouard Evangelisti; Carl Turner; Alice McDowell; Liron Shenhav; Temur Yunusov; Aleksandr Gavrin; Emily K Servante; Clément Quan; Sebastian Schornack
Journal:  New Phytol       Date:  2021-09-16       Impact factor: 10.151

6.  Text Data Augmentation for Deep Learning.

Authors:  Connor Shorten; Taghi M Khoshgoftaar; Borko Furht
Journal:  J Big Data       Date:  2021-07-19

7.  Convolutional neural networks improve fungal classification.

Authors:  Duong Vu; Marizeth Groenewald; Gerard Verkley
Journal:  Sci Rep       Date:  2020-07-28       Impact factor: 4.379

8.  Deep learning approach to describe and classify fungi microscopic images.

Authors:  Bartosz Zieliński; Agnieszka Sroka-Oleksiak; Dawid Rymarczyk; Adam Piekarczyk; Monika Brzychczy-Włoch
Journal:  PLoS One       Date:  2020-06-30       Impact factor: 3.240

9.  Hebeloma in the Malay Peninsula: Masquerading within Psathyrella.

Authors:  Ursula Eberhardt; Nicole Schütz; Henry J Beker; Su See Lee; Egon Horak
Journal:  MycoKeys       Date:  2021-01-28       Impact factor: 2.984

10.  Molecular prospecting for cryptic species of the Hypholoma fasciculare complex: toward the effective and practical delimitation of cryptic macrofungal species.

Authors:  Hirotoshi Sato; Ryoma Ohta; Noriaki Murakami
Journal:  Sci Rep       Date:  2020-08-06       Impact factor: 4.379

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