“You Are Not My Type”: An Evaluation of Classification Methods for Automatic Phytolith Identification

Abstract Abstract Phytoliths can be an important source of information related to environmental and climatic change, as well as to ancient plant use by humans, particularly within the disciplines of paleoecology and archaeology. Currently, phytolith identification and categorization is performed manually by researchers, a time-consuming task liable to misclassifications. The automated classification of phytoliths would allow the standardization of identification processes, avoiding possible biases related to the classification capability of researchers. This paper presents a comparative analysis of six classification methods, using digitized microscopic images to examine the efficacy of different quantitative approaches for characterizing phytoliths. A comprehensive experiment performed on images of 429 phytoliths demonstrated that the automatic phytolith classification is a promising area of research that will help researchers to invest time more efficiently and improve their recognition accuracy rate.

[1]  F ROSENBLATT,et al.  The perceptron: a probabilistic model for information storage and organization in the brain. , 1958, Psychological review.

[2]  Peter E. Hart,et al.  Nearest neighbor pattern classification , 1967, IEEE Trans. Inf. Theory.

[3]  Mary Eubanks Dunn,et al.  Phytolith Analysis in Archaeology , 1983 .

[4]  Thomas C. Hart,et al.  Issues and directions in phytolith analysis , 2016 .

[5]  Manuel Ornelas,et al.  Automated classification of archaeological ceramic materials by means of texture measures , 2017, Journal of Archaeological Science: Reports.

[6]  Wei-Yin Loh,et al.  Classification and regression trees , 2011, WIREs Data Mining Knowl. Discov..

[7]  Susan Hockey,et al.  Electronic texts in the Humanities: A coming of age , 1994 .

[8]  Linda Scott Cummings,et al.  International Code for Phytolith Nomenclature (ICPN) 2.0. , 2019, Annals of botany.

[9]  David H. Wolpert,et al.  No free lunch theorems for optimization , 1997, IEEE Trans. Evol. Comput..

[10]  W. Kruskal,et al.  Use of Ranks in One-Criterion Variance Analysis , 1952 .

[11]  Marco Madella,et al.  Morphometric distinction between bilobate phytoliths from Panicum miliaceum and Setaria italica leaves , 2016, Archaeological and Anthropological Sciences.

[12]  Craig Alexander,et al.  Automated classification of petroglyphs , 2015, Digit. Appl. Archaeol. Cult. Heritage.

[13]  Carla Lancelotti,et al.  Directions in current and future phytolith research , 2016 .

[14]  Timothy J. Gallaher,et al.  3D shape analysis of grass silica short cell phytoliths (GSSCP): a new method for fossil classification and analysis of shape evolution. , 2020, The New phytologist.

[15]  Matthew J. Collins,et al.  Automated Classification of Starch Granules Using Supervised Pattern Recognition of Morphological Properties , 2010 .

[16]  Deborah M. Pearsall,et al.  Paleoethnobotany: A Handbook of Procedures , 1989 .

[17]  A. Caldera-Siu,et al.  Error rates and observer bias in dental microwear analysis using light microscopy , 2012 .

[18]  Luc Beaufort,et al.  Starch granules identification and automatic classification based on an extended set of morphometric and optical measurements , 2016 .

[19]  Sönke Szidat,et al.  Holocene land cover change in south-western Amazonia inferred from paleoflood archives , 2019, Global and Planetary Change.

[20]  Sayan Mukherjee,et al.  Feature Selection for SVMs , 2000, NIPS.

[21]  Caroline A.E. Strömberg,et al.  Methodological concerns for analysis of phytolith assemblages: Does count size matter? , 2009 .

[22]  Martin Tetard,et al.  Automated recognition by multiple convolutional neural networks of modern, fossil, intact and damaged pollen grains , 2020, Comput. Geosci..

[23]  Débora Zurro,et al.  One, two, three phytoliths: assessing the minimum phytolith sum for archaeological studies , 2018, Archaeological and Anthropological Sciences.

[24]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[25]  L. Bremond,et al.  Phytoliths of East African grasses: An assessment of their environmental and taxonomic significance based on floristic data , 2009 .

[26]  F. Wilcoxon Individual Comparisons by Ranking Methods , 1945 .

[27]  J. R. Flenley,et al.  Towards automation of palynology 2: the use of texture measures and neural network analysis for automated identification of optical images of pollen grains , 2004 .

[28]  Song Ge,et al.  Machine learning algorithms improve the power of phytolith analysis: A case study of the tribe Oryzeae (Poaceae) , 2017 .

[29]  Lynda Hardman,et al.  Impact Analysis of OCR Quality on Research Tasks in Digital Archives , 2015, TPDL.

[30]  Rob Q. Cuthrell,et al.  A conceptual framework for a computer-assisted, morphometric-based phytolith analysis and classification system , 2016 .

[31]  A.W.G. Duller,et al.  A new approach to automated pollen analysis , 2000 .

[32]  Matthew C. Mihlbachler,et al.  Magnification and resolution in dental microwear analysis using light microscopy , 2012 .

[33]  Jürgen Böhner,et al.  How old is the human footprint in the world's largest alpine ecosystem? A review of multiproxy records from the Tibetan Plateau from the ecologists' viewpoint , 2014 .

[34]  Jammi L. Ladwig,et al.  Morphometric analysis of phytoliths: recommendations towards standardization from the International Committee for Phytolith Morphometrics , 2016 .

[35]  L. Peperzak,et al.  An objective procedure to remove observer-bias from phytoplankton time-series , 2010 .

[36]  Jon Atli Benediktsson,et al.  Deep Learning for Hyperspectral Image Classification: An Overview , 2019, IEEE Transactions on Geoscience and Remote Sensing.

[37]  Dolores R. Piperno,et al.  Amazonia and the Anthropocene: What was the spatial extent and intensity of human landscape modification in the Amazon Basin at the end of prehistory? , 2015 .

[38]  Charlene Murphy,et al.  Advances in Morphometrics in Archaeobotany , 2019, Environmental Archaeology.

[39]  Sanja Fidler,et al.  3D Object Proposals Using Stereo Imagery for Accurate Object Class Detection , 2016, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[40]  J. L. Hodges,et al.  Discriminatory Analysis - Nonparametric Discrimination: Consistency Properties , 1989 .

[41]  Christoph T. Weidemann,et al.  Recognition of micro‐scale deformation structures in glacial sediments – pattern perception, observer bias and the influence of experience , 2013 .

[42]  Dylan S. Davis Object‐based image analysis: a review of developments and future directions of automated feature detection in landscape archaeology , 2018, Archaeological Prospection.

[43]  Santiago T. Pérez,et al.  Pollen Classification Based on Geometrical, Descriptors and Colour Features Using Decorrelation Stretching Method , 2011, EANN/AIAI.

[44]  Isabelle Guyon,et al.  An Introduction to Variable and Feature Selection , 2003, J. Mach. Learn. Res..

[45]  J. R. Flenley,et al.  Towards automation of palynology 1: analysis of pollen shape and ornamentation using simple geometric measures, derived from scanning electron microscope images , 2004 .

[46]  Bernhard E. Boser,et al.  A training algorithm for optimal margin classifiers , 1992, COLT '92.

[47]  David Bamman,et al.  eScience and the humanities , 2007, International Journal on Digital Libraries.

[48]  José Iriarte,et al.  Integrated palaeoecology and archaeology – a powerful approach for understanding pre-Columbian Amazonia , 2014 .

[49]  Javier Ruiz-Pérez,et al.  Sonication improves the efficiency, efficacy and safety of phytolith extraction , 2016 .

[50]  Xiaogang Wang,et al.  Hybrid Deep Learning for Face Verification , 2013, 2013 IEEE International Conference on Computer Vision.

[51]  J. Friedman Greedy function approximation: A gradient boosting machine. , 2001 .

[52]  Marco Madella,et al.  A Simple Method of Extraction of Opal Phytoliths from Sediments Using a Non-Toxic Heavy Liquid , 1998 .

[53]  Arvid Lundervold,et al.  An overview of deep learning in medical imaging focusing on MRI , 2018, Zeitschrift fur medizinische Physik.

[54]  A Alexandre,et al.  International code for phytolith nomenclature 1.0. , 2005, Annals of botany.

[55]  Dolores R. Piperno,et al.  Phytolith analysis : an archaeological and geological perspective , 1990 .

[56]  Patti J. Wright,et al.  Methodological Issues in Paleoethnobotany: A consideration of Issues, Methods, and Cases , 2010 .

[57]  John C. Russ,et al.  Darwin and Design in Phytolith Systematics: Morphometric Methods for Mitigating Redundancy , 1992 .

[58]  Charles R. Giardina,et al.  Elliptic Fourier features of a closed contour , 1982, Comput. Graph. Image Process..