Taxonomic Classification of Ants (Formicidae) from Images using Deep Learning

The well-documented, species-rich, and diverse group of ants (Formicidae) are important ecological bioindicators for species richness, ecosystem health, and biodiversity, but ant species identification is complex and requires specific knowledge. In the past few years, insect identification from images has seen increasing interest and success, with processing speed improving and costs lowering. Here we propose deep learning (in the form of a convolutional neural network (CNN)) to classify ants at species level using AntWeb images. We used an Inception-ResNet-V2-based CNN to classify ant images, and three shot types with 10,204 images for 97 species, in addition to a multi-view approach, for training and testing the CNN while also testing a worker-only set and an AntWeb protocol-deviant test set. Top 1 accuracy reached 62% - 81%, top 3 accuracy 80% - 92%, and genus accuracy 79% - 95% on species classification for different shot type approaches. The head shot type outperformed other shot type approaches. Genus accuracy was broadly similar to top 3 accuracy. Removing reproductives from the test data improved accuracy only slightly. Accuracy on AntWeb protocol-deviant data was very low. In addition, we make recommendations for future work concerning image threshold, distribution, and quality, multi-view approaches, metadata, and on protocols; potentially leading to higher accuracy with less computational effort.

[1]  Jiri Matas,et al.  Systematic evaluation of convolution neural network advances on the Imagenet , 2017, Comput. Vis. Image Underst..

[2]  Qiang Chen,et al.  Network In Network , 2013, ICLR.

[3]  R. Bouckaert,et al.  bModelTest: Bayesian phylogenetic site model averaging and model comparison , 2015, BMC Evolutionary Biology.

[4]  Kevin J. Gaston,et al.  Image analysis, neural networks, and the taxonomic impediment to biodiversity studies , 1997, Biodiversity & Conservation.

[5]  Kevin J. Gaston,et al.  Automating insect identification: exploring the limitations of a prototype system , 1999 .

[6]  Michael S. Lew,et al.  Deep learning for visual understanding: A review , 2016, Neurocomputing.

[7]  Jimmy Ba,et al.  Adam: A Method for Stochastic Optimization , 2014, ICLR.

[8]  I. Oliver,et al.  Invertebrate Morphospecies as Surrogates for Species: A Case Study , 1996 .

[9]  Nitish Srivastava,et al.  Dropout: a simple way to prevent neural networks from overfitting , 2014, J. Mach. Learn. Res..

[10]  Vicki A. Funk,et al.  Applications of deep convolutional neural networks to digitized natural history collections , 2017, Biodiversity data journal.

[11]  Patrick Mäder,et al.  Automated plant species identification—Trends and future directions , 2018, PLoS Comput. Biol..

[12]  Sebastian Ruder,et al.  An overview of gradient descent optimization algorithms , 2016, Vestnik komp'iuternykh i informatsionnykh tekhnologii.

[13]  Anthony D. Griffiths,et al.  Using ants as bioindicators in land management: simplifying assessment of ant community responses , 2002 .

[14]  A. Andersen Using Ants as bioindicators: Multiscale Issues in Ant Community Ecology , 1997 .

[15]  Rutger A. Vos,et al.  OrchID: a Generalized Framework for Taxonomic Classification of Images Using Evolved Artificial Neural Networks , 2016, bioRxiv.

[16]  David Coderre,et al.  Understanding data , 2020, An SPSS Guide for Tourism, Hospitality and Events Researchers.

[17]  M. Kaspari,et al.  A life history continuum in the males of a Neotropical ant assemblage: refuting the sperm vessel hypothesis , 2012, Naturwissenschaften.

[18]  J. Orivel,et al.  A new method based on taxonomic sufficiency to simplify studies on Neotropical ant assemblages , 2010 .

[19]  Martín Abadi,et al.  TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems , 2016, ArXiv.

[20]  Silvio Savarese,et al.  Robust single-view instance recognition , 2016, 2016 IEEE International Conference on Robotics and Automation (ICRA).

[21]  Henrik Skov Midtiby,et al.  Plant species classification using deep convolutional neural network , 2016 .

[22]  I. Oliver,et al.  Taxonomic sufficiency in ecological studies of terrestrial invertebrates , 1999 .

[23]  Mark A. O'Neill,et al.  Automated identification of live moths (Macrolepidoptera) using digital automated identification System (DAISY) , 2004 .

[24]  Geoffrey E. Hinton,et al.  Deep Learning , 2015, Nature.

[25]  Timothy Dozat,et al.  Incorporating Nesterov Momentum into Adam , 2016 .

[26]  R. Levy IDENTIFICATION GUIDE TO THE ANT GENERA OF THE WORLD , 1995 .

[27]  Changshui Zhang,et al.  DeepFish: Accurate underwater live fish recognition with a deep architecture , 2016, Neurocomputing.

[28]  Marcel Salathé,et al.  Using Deep Learning for Image-Based Plant Disease Detection , 2016, Front. Plant Sci..

[29]  André Carlos Ponce de Leon Ferreira de Carvalho,et al.  Deep learning for biological image classification , 2017, Expert Syst. Appl..

[30]  Qingbin Zhan,et al.  A tool for developing an automatic insect identification system based on wing outlines , 2015, Scientific Reports.

[31]  Kevin J. Gaston,et al.  Automating the identification of insects: a new solution to an old problem , 1997 .

[32]  Paolo Remagnino,et al.  Deep-plant: Plant identification with convolutional neural networks , 2015, 2015 IEEE International Conference on Image Processing (ICIP).

[33]  Martin Drauschke,et al.  Identification of Africanized honey bees through wing morphometrics: two fast and efficient procedures , 2008, Apidologie.

[34]  J. Biesmeijer,et al.  Discrimination of haploid and diploid males of Bombus terrestris (Hymenoptera; Apidae) based on wing shape , 2015, Apidologie.

[35]  Ben C. Stöver,et al.  LeafNet: A computer vision system for automatic plant species identification , 2017, Ecol. Informatics.

[36]  Yu Sun,et al.  Deep Learning for Plant Identification in Natural Environment , 2017, Comput. Intell. Neurosci..

[37]  Geoffrey E. Hinton,et al.  ImageNet classification with deep convolutional neural networks , 2012, Commun. ACM.

[38]  Yoshua Bengio,et al.  How transferable are features in deep neural networks? , 2014, NIPS.

[39]  Gaines E. Miles,et al.  MACHINE VISION AND IMAGE PROCESSING FOR PLANT IDENTIFICATION. , 1986 .

[40]  Paolo Remagnino,et al.  Plant Identification System based on a Convolutional Neural Network for the LifeClef 2016 Plant Classification Task , 2016, CLEF.

[41]  Andrew Zisserman,et al.  Return of the Devil in the Details: Delving Deep into Convolutional Nets , 2014, BMVC.

[42]  Li Fei-Fei,et al.  ImageNet: A large-scale hierarchical image database , 2009, CVPR.

[43]  Liqiang Ji,et al.  The identification of butterfly families using content-based image retrieval , 2012 .

[44]  Jiangning Wang,et al.  A new automatic identification system of insect images at the order level , 2012, Knowl. Based Syst..

[45]  Chenglu Wen,et al.  Image-based orchard insect automated identification and classification method , 2012 .

[46]  Jeremy A. Miller,et al.  A quantitative assessment of the vegetation types on the island of St. Eustatius, Dutch Caribbean , 2016 .

[47]  Mark D. McDonnell,et al.  Understanding Data Augmentation for Classification: When to Warp? , 2016, 2016 International Conference on Digital Image Computing: Techniques and Applications (DICTA).

[48]  Seung-Ho Kang,et al.  Identification of butterfly species with a single neural network system , 2012 .

[49]  Shiliang Sun,et al.  Multi-view learning overview: Recent progress and new challenges , 2017, Inf. Fusion.

[50]  M. O'Neill,et al.  Automated species identification: why not? , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[51]  P. Bonnet,et al.  Going deeper in the automated identification of Herbarium specimens , 2017, BMC Evolutionary Biology.

[52]  M. Edwards,et al.  The potential for computer-aided identification in biodiversity research. , 1995, Trends in ecology & evolution.

[53]  Gary Marcus,et al.  Deep Learning: A Critical Appraisal , 2018, ArXiv.

[54]  S. Ferrier,et al.  Biogeographical concordance and efficiency of taxon indicators for establishing conservation priority in a tropical rainforest biota , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[55]  Pascal Vincent,et al.  Representation Learning: A Review and New Perspectives , 2012, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[56]  C. Grey,et al.  Mouse PRDM9 DNA-Binding Specificity Determines Sites of Histone H3 Lysine 4 Trimethylation for Initiation of Meiotic Recombination , 2011, PLoS biology.

[57]  I. Guarniero How Many Species Are There on Earth and in the Ocean? (PLOS Biology) , 2014 .

[58]  Silvio Savarese,et al.  Deep Learning for Single-View Instance Recognition , 2015, ArXiv.

[59]  P. S. Ward Phylogeny, classification, and species-level taxonomy of ants (Hymenoptera: Formicidae)* , 2007 .

[60]  Yoshua Bengio,et al.  Deep Sparse Rectifier Neural Networks , 2011, AISTATS.

[61]  D. Ellis Taxonomic sufficiency in pollution assessment , 1985 .

[62]  B. Bolton Book Review Identification Guide to the Ant Genera of the World , 1994 .