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Tan 2019
Tan 2019
mtulig@nybg.org sjb344@cornell.edu
Abstract
1
needed to automatically identify species using herbarium
specimens alone and under conditions that more accurately
reflect the distribution of specimen images available for
species present in herbaria.
There are approximately 3,000 herbaria world-wide with
an estimated 380 million specimens. The New York Botan-
ical Garden (NYBG) has more than 7.8 million herbarium
specimens, and over 3 million of these have been imaged.
Each specimen is accompanied by an approximate standard Figure 2. Different specimens of the same species, varying by
set of metadata, including the name of the plant, a descrip- specimen age.
tion of the location where it was collected, name of the col-
lector, the accession number of the collector, and the date of
collection.
2
Figure 5. Final challenge leaderboard.
3
cluding DEB-1343612 and DEB-0818399 to F.A.M. and works by iterative matrix square root normalization. CoRR,
DBI-0749751, DBI-9987500, DBI-0543335 DBI-1053290 abs/1712.01034, 2017.
to B.T as well as funding from the Google, Mellon, and [13] David J. Mabberley. Mabberley’s Plant-book: A Portable
Sloan Foundations to NYBG. Dictionary of Plants, their Classification and Uses. Cam-
We would also like to thank: Srikanth Belwadi, R.V. bridge University Press, 4 edition, 2017.
Guha and Kiran Panesar from dataCommons.org for help [14] Olga Russakovsky, Jia Deng, Hao Su, Jonathan Krause, San-
with preparing the dataset; Christine Kaeser-Chen and jeev Satheesh, Sean Ma, Zhiheng Huang, Andrej Karpathy,
Hartwig Adam from Google Research; Maggie Demkin Aditya Khosla, Michael S. Bernstein, Alexander C. Berg,
from Kaggle; the Herbarium Challenge 2019 competitors, and Fei-Fei Li. Imagenet large scale visual recognition chal-
and the FGVC2019 workshop organizers. lenge. CoRR, abs/1409.0575, 2014.
[15] Eric Schuettpelz, Paul B. Frandsen, Rebecca B. Dikow, Abel
References Brown, Sylvia Orli, Melinda Peters, Adam Metallo, Vicki
Funk, and Laurence J. Dorr. Applications of deep convo-
[1] Summary of United Nations report from the Intergovernmen- lutional neural networks to digitized natural history collec-
tal Science-Policy Platform on Biodiversity and Ecosystem tions. Biodiversity Data Journal, 5:e21139, 11 2017.
Services (IPBES). May 2019. [16] Christian Szegedy, Sergey Ioffe, and Vincent Vanhoucke.
[2] Daniel P. Bebber, Mark A. Carine, John R. I. Wood, Alexan- Inception-v4, Inception-ResNet and the Impact of Residual
dra H. Wortley, David J. Harris, Ghillean T. Prance, Ger- Connections on Learning. CoRR, abs/1602.07261, 2016.
rit Davidse, Jay Paige, Terry D. Pennington, Norman K. B. [17] Jakob Unger, Dorit Merhof, and Susanne Renner. Computer
Robson, and Robert W. Scotland. Herbaria are a major vision applied to herbarium specimens of german trees: Test-
frontier for species discovery. Proceedings of the National ing the future utility of the millions of herbarium specimen
Academy of Sciences, 107(51):22169–22171, 2010. images for automated identification. BMC Evolutionary Bi-
[3] Alessandro Bissacco, Mark Cummins, Yuval Netzer, and ology, 16, 12 2016.
Hartmut Neven. PhotoOCR: Reading text in uncontrolled [18] Jana Wäldchen and Patrick Mäder. Plant Species Identifi-
conditions. In Proceedings of the IEEE International Con- cation Using Computer Vision Techniques: A Systematic
ference on Computer Vision, pages 785–792, 2013. Literature Review. Archives of Computational Methods in
[4] Jose Carranza-Rojas, Herve Goeau, Pierre Bonnet, Erick Engineering, 25(2):507–543, Apr 2018.
Mata-Montero, and Alexis Joly. Going deeper in the auto- [19] D Wijesingha and Faiz Marikar. Automatic Detection Sys-
mated identification of Herbarium specimens. BMC Evolu- tem for the Identification of Plants Using Herbarium Speci-
tionary Biology, 17(1):181, Aug 2017. men Images. Tropical Agricultural Research, 23, 09 2012.
[5] J. Y. Clark, D. P. A. Corney, and H. L. Tang. Automated plant [20] Peter Wilf, Shengping Zhang, Sharat Chikkerur, Stefan A.
identification using artificial neural networks. In 2012 IEEE Little, Scott L. Wing, and Thomas Serre. Computer vision
Symposium on Computational Intelligence in Bioinformatics cracks the leaf code. Proceedings of the National Academy
and Computational Biology (CIBCB), pages 343–348, May of Sciences, 113(12):3305–3310, 2016.
2012. [21] Saining Xie, Ross B. Girshick, Piotr Dollár, Zhuowen Tu,
[6] James S. Cope, David Corney, Jonathan Y. Clark, Paolo Re- and Kaiming He. Aggregated residual transformations for
magnino, and Paul Wilkin. Plant species identification using deep neural networks. CoRR, abs/1611.05431, 2016.
digital morphometrics: A review. Expert Systems with Ap- [22] Sohaib Younis, Claus Weiland, Robert Hoehndorf, Stefan
plications, 39(8):7562 – 7573, 2012. Dressler, Thomas Hickler, Bernhard Seeger, and Marco
[7] Yin Cui, Menglin Jia, Tsung-Yi Lin, Yang Song, and Serge J. Schmidt. Taxon and trait recognition from digitized herbar-
Belongie. Class-balanced loss based on effective number of ium specimens using deep convolutional neural networks.
samples. CoRR, abs/1901.05555, 2019. Botany Letters, 03 2018.
[8] Jifeng Dai, Haozhi Qi, Yuwen Xiong, Yi Li, Guodong [23] Zhun Zhong, Liang Zheng, Guoliang Kang, Shaozi Li, and
Zhang, Han Hu, and Yichen Wei. Deformable convolutional Yi Yang. Random erasing data augmentation. CoRR,
networks. CoRR, abs/1703.06211, 2017. abs/1708.04896, 2017.
[9] Grant Van Horn, Oisin Mac Aodha, Yang Song, Alexan-
der Shepard, Hartwig Adam, Pietro Perona, and Serge J.
Belongie. The iNaturalist Challenge 2017 Dataset. CoRR,
abs/1707.06642, 2017.
[10] Jie Hu, Li Shen, and Gang Sun. Squeeze-and-excitation net-
works. CoRR, abs/1709.01507, 2017.
[11] Soon Jye Kho, Sugumaran Manickam, Sorayya Malek, Mo-
geeb Mosleh, and Sarinder Kaur Dhillon. Automated plant
identification using artificial neural network and support vec-
tor machine. Frontiers in Life Science, 10(1):98–107, 2017.
[12] Peihua Li, Jiangtao Xie, Qilong Wang, and Zilin Gao.
Towards faster training of global covariance pooling net-