Deep learning applications for evaluating taxonomic and morphological diversity in ferns

Alex White

Mike Trizna, Sylvia Orli, Eric Schuettpelz, Paul Frandsen, Rebecca Dikow, Larry Dorr

Smithsonian Institution National Museum of Natural History – Dept. of Botany Data Science Lab Where are we at?

U.S. National Herb: 2 million specimens are digitized

Fern collection is completely digitized: 215,000 specimens with global representation 86 genera with >500 specimens

Past work focused on binary classification: Mercury staining and 2 genera of clubmoss

Build a more robust taxonomic classification model?

Will taxonomic classification inform us about ecological differences in shape?

Schuettpelz et al. 2017 Equisetopsida, Equisetales, Equisetaceae, Equisetum Marattiopsida, Marattiales, Marattiaceae, Angiopteris 1.0 Marattiopsida, Marattiales, Marattiaceae, Danaea Polypodiopsida, Cyatheales, Cyatheaceae, Alsophila Polypodiopsida, Cyatheales, Cyatheaceae, Cyathea Polypodiopsida, Cyatheales, Cyatheaceae, Sphaeropteris Polypodiopsida, Cyatheales, Dicksoniaceae, Dicksonia Polypodiopsida, Cyatheales, Dicksoniaceae, Lophosoria Polypodiopsida, Gleicheniales, Gleicheniaceae, Dicranopteris 0.8 Polypodiopsida, Gleicheniales, Gleicheniaceae, Sticherus Polypodiopsida, Hymenophyllales, Hymenophyllaceae, Abrodictyum Polypodiopsida, Hymenophyllales, Hymenophyllaceae, Crepidomanes Polypodiopsida, Hymenophyllales, Hymenophyllaceae, Didymoglossum Where are we at? Polypodiopsida, Hymenophyllales, Hymenophyllaceae, Hymenophyllum Polypodiopsida, Hymenophyllales, Hymenophyllaceae, Polyphlebium Polypodiopsida, Hymenophyllales, Hymenophyllaceae, Trichomanes 0.6 Polypodiopsida, Hymenophyllales, Hymenophyllaceae, Vandenboschia Polypodiopsida, Osmundales, Osmundaceae, Osmunda Polypodiopsida, Polypodiales, Aspleniaceae, Asplenium Polypodiopsida, Polypodiales, Athyriaceae, Athyrium Polypodiopsida, Polypodiales, Athyriaceae, Deparia Polypodiopsida, Polypodiales, Athyriaceae, Diplazium Polypodiopsida, Polypodiales, Blechnaceae, Blechnum 0.4 175,000 specimens in 86 genera (>500) Polypodiopsida, Polypodiales, Blechnaceae, Woodwardia Polypodiopsida, Polypodiales, Davalliaceae, Davallia Polypodiopsida, Polypodiales, Dennstaedtiaceae, Pteridium Polypodiopsida, Polypodiales, Dryopteridaceae, Arachniodes Some genera >15,000 specimens Polypodiopsida, Polypodiales, Dryopteridaceae, Ctenitis Polypodiopsida, Polypodiales, Dryopteridaceae, Dryopteris Polypodiopsida, Polypodiales, Dryopteridaceae, Elaphoglossum 0.2 Polypodiopsida, Polypodiales, Dryopteridaceae, Polybotrya Polypodiopsida, Polypodiales, Dryopteridaceae, Polystichum Polypodiopsida, Polypodiales, Lindsaeaceae, Lindsaea Polypodiopsida, Polypodiales, Nephrolepidaceae, Nephrolepis Polypodiopsida, Polypodiales, Polypodiaceae, Alansmia 97% accuracy for 86 genera Polypodiopsida, Polypodiales, Polypodiaceae, Campyloneurum Polypodiopsida, Polypodiales, Polypodiaceae, Cochlidium 0.0 Polypodiopsida, Polypodiales, Polypodiaceae, Drynaria Polypodiopsida, Polypodiales, Polypodiaceae, Goniophlebium Polypodiopsida, Polypodiales, Polypodiaceae, Lepisorus Polypodiopsida, Polypodiales, Polypodiaceae, Leptochilus Polypodiopsida, Polypodiales, Polypodiaceae, Melpomene Polypodiopsida, Polypodiales, Polypodiaceae, Microgramma Polypodiopsida, Polypodiales, Polypodiaceae, Microsorum The taxonomic classifier: Polypodiopsida, Polypodiales, Polypodiaceae, Moranopteris Polypodiopsida, Polypodiales, Polypodiaceae, Niphidium

Actual Genus Polypodiopsida, Polypodiales, Polypodiaceae, Pecluma Polypodiopsida, Polypodiales, Polypodiaceae, Phlebodium • CNN with res-net 101 backbone Polypodiopsida, Polypodiales, Polypodiaceae, Pleopeltis Polypodiopsida, Polypodiales, Polypodiaceae, Polypodium Polypodiopsida, Polypodiales, Polypodiaceae, Pyrrosia Polypodiopsida, Polypodiales, Polypodiaceae, Selliguea • Built in PyTorch Polypodiopsida, Polypodiales, Polypodiaceae, Serpocaulon Polypodiopsida, Polypodiales, Pteridaceae, Acrostichum Polypodiopsida, Polypodiales, Pteridaceae, Adiantum Polypodiopsida, Polypodiales, Pteridaceae, Antrophyum • 256 x 256 images Polypodiopsida, Polypodiales, Pteridaceae, Cheilanthes Polypodiopsida, Polypodiales, Pteridaceae, Doryopteris Polypodiopsida, Polypodiales, Pteridaceae, Gaga Polypodiopsida, Polypodiales, Pteridaceae, Haplopteris • Trained using the 1cycle policy (Smith, 2018) in fastai Polypodiopsida, Polypodiales, Pteridaceae, Jamesonia Polypodiopsida, Polypodiales, Pteridaceae, Myriopteris Polypodiopsida, Polypodiales, Pteridaceae, Notholaena Polypodiopsida, Polypodiales, Pteridaceae, Pellaea • Transforms = flipping, rotating, zooming, lighting Polypodiopsida, Polypodiales, Pteridaceae, Pityrogramma Polypodiopsida, Polypodiales, Pteridaceae, Polytaenium Polypodiopsida, Polypodiales, Pteridaceae, Pteris Polypodiopsida, Polypodiales, Pteridaceae, Vittaria Polypodiopsida, Polypodiales, Tectariaceae, Tectaria Polypodiopsida, Polypodiales, Thelypteridaceae, Amauropelta Polypodiopsida, Polypodiales, Thelypteridaceae, Christella Polypodiopsida, Polypodiales, Thelypteridaceae, Cyclosorus Polypodiopsida, Polypodiales, Thelypteridaceae, Goniopteris Polypodiopsida, Polypodiales, Thelypteridaceae, Parathelypteris Polypodiopsida, Polypodiales, Thelypteridaceae, Phegopteris Polypodiopsida, Polypodiales, Thelypteridaceae, Sphaerostephanos Polypodiopsida, Polypodiales, Thelypteridaceae, Steiropteris Polypodiopsida, Polypodiales, Thelypteridaceae, Thelypteris Polypodiopsida, Polypodiales, Woodsiaceae, Woodsia Polypodiopsida, Salviniales, Marsileaceae, Marsilea Polypodiopsida, Schizaeales, Anemiaceae, Anemia Polypodiopsida, Schizaeales, Lygodiaceae, Lygodium Polypodiopsida, Schizaeales, Schizaeaceae, Schizaea Psilotopsida, Ophioglossales, Ophioglossaceae, Botrychium Psilotopsida, Ophioglossales, Ophioglossaceae, Ophioglossum Psilotopsida, Psilotales, Psilotaceae, Psilotum

Gaga Pteris Danaea Deparia Ctenitis Pellaea Vittaria Anemia Cyathea Davallia Lindsaea Drynaria Pecluma Pyrrosia Tectaria WoodsiaMarsilea Schizaea Psilotum Alsophila Dicksonia Sticherus Osmunda AthyriumDiplazium Pteridium Alansmia Lepisorus Pleopeltis Selliguea Adiantum Christella Lygodium Equisetum Lophosoria Asplenium Blechnum DryopterisPolybotrya Niphidium Jamesonia Cyclosorus Angiopteris PolystichumNephrolepis Cochlidium LeptochilusMelpomeneMicrosorum PhlebodiumPolypodium CheilanthesDoryopterisHaplopterisMyriopterisNotholaena GoniopterisPhegopterisSteiropterisThelypteris Botrychium Abrodictyum Trichomanes Woodwardia Arachniodes Moranopteris SerpocaulonAcrostichumAntrophyum Polytaenium Amauropelta Sphaeropteris Dicranopteris Polyphlebium Microgramma Pityrogramma Ophioglossum Crepidomanes Vandenboschia Elaphoglossum Goniophlebium Parathelypteris DidymoglossumHymenophyllum Campyloneurum Sphaerostephanos Predicted Genus Where are we going?

Given the model accuracy, can the features of the model tell us something about morphological similarity?

Take the embedding vectors from our classifier and use UMAP for dimensionality reduction

Can this 2D space be thought of as a morpho-space?

Problems: coloration, other materials on the sheet

Appalaraju 2017