GMM vs CNN paper by Bonhomme et al. (sub) all scripts and data

Abstract

Taxonomical identification of archaeological fruit and seed is of prime importance for any archaeobotanical studies. We compared the relative performance of deep learning and geometric morphometrics at identifying pairs of plant taxa. We used their seeds and fruit stones that are the most abundant recovered organs in archaeobotanical assemblages, and whose morphological identification, chiefly between wild and domesticated types, allow to document their domestication and biogeographical history. We used existing modern datasets of four plant taxa (date palm, barley, olive and grapevine) corresponding to photographs of two orthogonal views of their seeds that were analysed separately to offer a larger spectrum of shape diversity. On these eight datasets, we compared the performance of a deep learning approach, here convolutional neural networks (CNN), to that of a geometric morphometric approach, here outline analyses using elliptical Fourier transforms (EFT). Sample sizes were at minimum eight hundred seeds in each class, which is quite small when training deep learning models but of typical magnitude for archaeobotanical studies. Our objectives were twofold: i) to test whether deep learning can beat geometric morphometrics in taxonomic identification and if so, ii) to test which minimal sample size is required. We ran simulations on the full datasets and also on subsets, starting from 50 images in each binary class. For CNN networks, we deliberately used a candid approach relying on pre-parameterised VGG16 network. For EFT, we used a state-of-the art morphometrical pipeline. The main difference rests in the data used by each model: CNN used bare photographs where EFT used (x, y) outline coordinates. This “pre-distilled” geometrical description of seed outlines is often the most time-consuming part of morphometric studies. Results show that CNN beats EFT in most cases, even for very small datasets. We finally discuss the potential of CNN for archaeobotany, why outline analyses and morphometrics have not yet said their last word by providing quantitative descriptions, and how bioarchaeological studies could embrace both approaches, used in a complementary way, to better assess and understand the past history of species.</p