Automatic pollen recognition using convolutional neural networks: The case of the main pollens present in Spanish citrus and rosemary honey

[EN] The automation of honey pollen visual sorting overcomes the limitations of the conventional procedure helping the specialist in this time-consuming task. In this work, a novel and comprehensive Ground Truth of almost 19,000 images (from optical microscopy) of the 16 most abundant types of grains/pollen particles present in citrus and rosemary honey from Spain was constructed. This task was assisted by a HoneyApp (also developed herein) for the labelling and annotation process. Subsequently, the effectiveness of different pre-existing automatic pollen recognizers based on convolutional neural networks (CNN) (VGG16, VGG19, InceptionV3, Xception, ResNet50, DenseNet201, MobileNetV2 and EfficientNetV2M) was tested together with a new network proposed in this paper (PolleNetV1). The extreme complexity of those pre-existing CNN and extensive use of millions of parameters makes this new proposal especially promising. Although with a slightly lower accuracy (average 96%) in determining the relative frequencies of different types of pollen grains/particles, it has considerable advantages such as simplicity and ability to be included in the future functionality to automate pollen recognition in honey. This is the first step to finally achieving an objective tool that allows the correct labelling of any types of pollen in honey, thus contributing to its transparency in the market.This work is part of Spanish project PID2019-106800RB-I00 (2019) with financial support from the Ministerio de Ciencia e Innovacion (MCIN), Agencia Estatal de Investigacion MCIN/AEI/10.13039/501100011033/. It has been also part of the project AGROALNEXT/2022/043, funded by the Next Generation European Union and the Plan de Recuperacion, Transformacion y Resiliencia of the Spanish Government, with the support of Generalitat Valenciana. The authors would like to thank the CRUE-Universitat Politecnica deValencia for providing the funds for open access publication.Valiente González, JM.; Juan-Borras, MDS.; López García, F.; Escriche Roberto, MI. (2023). Automatic pollen recognition using convolutional neural networks: The case of the main pollens present in Spanish citrus and rosemary honey. Journal of Food Composition and Analysis. 123:1-10. https://doi.org/10.1016/j.jfca.2023.10560511012

Addressing subjectivity in the classification of palaeoenvironmental remains with supervised deep learning convolutional neural networks

Archaeological object identifications have been traditionally undertaken through a comparative methodology where each artefact is identified through a subjective, interpretative act by a professional. Regarding palaeoenvironmental remains, this comparative methodology is given boundaries by using reference materials and codified sets of rules, but subjectivity is nevertheless present. The problem with this traditional archaeological methodology is that higher level of subjectivity in the identification of artefacts leads to inaccuracies, which then increases the potential for Type I and Type II errors in the testing of hypotheses. Reducing the subjectivity of archaeological identifications would improve the statistical power of archaeological analyses, which would subsequently lead to more impactful research. In this thesis, it is shown that the level of subjectivity in palaeoenvironmental research can be reduced by applying deep learning convolutional neural networks within an image recognition framework. The primary aim of the presented research is therefore to further the on-going paradigm shift in archaeology towards model-based object identifications, particularly within the realm of palaeoenvironmental remains. Although this thesis focuses on the identification of pollen grains and animal bones, with the latter being restricted to the astragalus of sheep and goats, there are wider implications for archaeology as these methods can easily be extended beyond pollen and animal remains. The previously published POLEN23E dataset is used as the pilot study of applying deep learning in pollen grain classification. In contrast, an image dataset of modern bones was compiled for the classification of sheep and goat astragali due to a complete lack of available bone image datasets and a double blind study with inexperienced and experienced zooarchaeologists was performed to have a benchmark to which image recognition models can be compared. In both classification tasks, the presented models outperform all previous formal modelling methods and only the best human analysts match the performance of the deep learning model in the sheep and goat astragalus separation task. Throughout the thesis, there is a specific focus on increasing trust in the models through the visualization of the models’ decision making and avenues of improvements to Grad-CAM are explored. This thesis makes an explicit case for the phasing out of the comparative methods in favour of a formal modelling framework within archaeology, especially in palaeoenvironmental object identification

Pollen as the link between floral phenotype and fitness

Pollen plays a key role in plant reproductive biology. Despite the long history of research on pollen and pollination, recent advances in pollen‐tracking methods and statistical approaches to linking plant phenotype, pollination performance, and reproductive fitness yield a steady flow of exciting new insights. In this introduction to the Special Issue “Pollen as the Link Between Phenotype and Fitness,” we start by describing a general conceptual model linking functional classes of floral phenotypic traits to pollinationrelated performance metrics and reproductive fitness. We use this model as a framework for synthesizing the relevant literature, highlighting the studies included in the Special Issue, and identifying gaps in our understanding and opportunities for further development of the field. The papers that follow in this Special Issue provide new insights into the relationships between pollen production, presentation, flower morphology, and pollination performance (e.g., pollen deposition onto stigmas), the role of pollinators in pollen transfer, and the consequences of heterospecific pollen deposition. Several of the studies demonstrate exciting experimental and analytical approaches that should pave the way for continued work addressing the intriguing role of pollen in linking plant phenotypes to reproductive fitness.Swedish Research Council 2021-04777Spanish Government PID2021-127264NB-I00Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ) 308107/2021-7Austrian Science Fund (FWF) T-118

A method for the molecular classification of pollen for forensic purposes

Forensic palynology and the identification of pollen grains using DNA barcoding is an underutilised field in criminal investigations. Successful identification of pollen grains is used to establish links between an offender or body and location-­‐related crimes. The use of palynology in criminal investigations has been limited due to slow speed of identification, limited expert specialization and poor taxonomic resolution. To fill the gap, DNA barcoding overcomes these limitations by offering taxonomic resolution down to species in a faster, more accessible way. Despite this, there are technical applications that need to be addressed before DNA barcoding can be implemented as a laboratory standard for forensic palynology. This study aims to address these gaps, and highlight the need to make DNA barcoding more accessible in the future of forensic palynology

New Computational Methods for Automated Large-Scale Archaeological Site Detection

Aquesta tesi doctoral presenta una sèrie d'enfocaments, fluxos de treball i models innovadors en el camp de l'arqueologia computacional per a la detecció automatitzada a gran escala de jaciments arqueològics. S'introdueixen nous conceptes, enfocaments i estratègies, com ara lidar multitemporal, aprenentatge automàtic híbrid, refinament, curriculum learning i blob analysis; així com diferents mètodes d'augment de dades aplicats per primera vegada en el camp de l'arqueologia. S'utilitzen múltiples fonts, com ara imatges de satèl·lits multiespectrals, fotografies RGB de plataformes VANT, mapes històrics i diverses combinacions de sensors, dades i fonts. Els mètodes creats durant el desenvolupament d'aquest doctorat s'han avaluat en projectes en curs: Urbanització a Hispània i la Gàl·lia Mediterrània en el primer mil·lenni aC, detecció de monticles funeraris utilitzant algorismes d'aprenentatge automàtic al nord-oest de la Península Ibèrica, prospecció arqueològica intel·ligent basada en drons (DIASur), i cartografiat del patrimoni arqueològic al sud d'Àsia (MAHSA), per a la qual s'han dissenyat fluxos de treball adaptats als reptes específics del projecte. Aquests nous mètodes han aconseguit proporcionar solucions als problemes comuns d'estudis arqueològics presents en estudis similars, com la baixa precisió en detecció i les poques dades d'entrenament. Els mètodes validats i presentats com a part de la tesi doctoral s'han publicat en accés obert amb el codi disponible perquè puguin implementar-se en altres estudis arqueològics.Esta tesis doctoral presenta una serie de enfoques, flujos de trabajo y modelos innovadores en el campo de la arqueología computacional para la detección automatizada a gran escala de yacimientos arqueológicos. Se introducen nuevos conceptos, enfoques y estrategias, como lidar multitemporal, aprendizaje automático híbrido, refinamiento, curriculum learning y blob analysis; así como diferentes métodos de aumento de datos aplicados por primera vez en el campo de la arqueología. Se utilizan múltiples fuentes, como lidar, imágenes satelitales multiespectrales, fotografías RGB de plataformas VANT, mapas históricos y varias combinaciones de sensores, datos y fuentes. Los métodos creados durante el desarrollo de este doctorado han sido evaluados en proyectos en curso: Urbanización en Iberia y la Galia Mediterránea en el Primer Milenio a. C., Detección de túmulos mediante algoritmos de aprendizaje automático en el Noroeste de la Península Ibérica, Prospección Arqueológica Inteligente basada en Drones (DIASur), y cartografiado del Patrimonio del Sur de Asia (MAHSA), para los que se han diseñado flujos de trabajo adaptados a los retos específicos del proyecto. Estos nuevos métodos han logrado proporcionar soluciones a problemas comunes de la prospección arqueológica presentes en estudios similares, como la baja precisión en detección y los pocos datos de entrenamiento. Los métodos validados y presentados como parte de la tesis doctoral se han publicado en acceso abierto con su código disponible para que puedan implementarse en otros estudios arqueológicos.This doctoral thesis presents a series of innovative approaches, workflows and models in the field of computational archaeology for the automated large-scale detection of archaeological sites. New concepts, approaches and strategies are introduced such as multitemporal lidar, hybrid machine learning, refinement, curriculum learning and blob analysis; as well as different data augmentation methods applied for the first time in the field of archaeology. Multiple sources are used, such as lidar, multispectral satellite imagery, RGB photographs from UAV platform, historical maps, and several combinations of sensors, data, and sources. The methods created during the development of this PhD have been evaluated in ongoing projects: Urbanization in Iberia and Mediterranean Gaul in the First Millennium BC, Detection of burial mounds using machine learning algorithms in the Northwest of the Iberian Peninsula, Drone-based Intelligent Archaeological Survey (DIASur), and Mapping Archaeological Heritage in South Asia (MAHSA), for which workflows adapted to the project’ s specific challenges have been designed. These new methods have managed to provide solutions to common archaeological survey problems, presented in similar large-scale site detection studies, such as the low precision in previous detection studies and how to handle problems with few training data. The validated approaches for site detection presented as part of the PhD have been published as open access papers with freely available code so can be implemented in other archaeological studies

On Improving Generalization of CNN-Based Image Classification with Delineation Maps Using the CORF Push-Pull Inhibition Operator

Deployed image classification pipelines are typically dependent on the images captured in real-world environments. This means that images might be affected by different sources of perturbations (e.g. sensor noise in low-light environments). The main challenge arises by the fact that image quality directly impacts the reliability and consistency of classification tasks. This challenge has, hence, attracted wide interest within the computer vision communities. We propose a transformation step that attempts to enhance the generalization ability of CNN models in the presence of unseen noise in the test set. Concretely, the delineation maps of given images are determined using the CORF push-pull inhibition operator. Such an operation transforms an input image into a space that is more robust to noise before being processed by a CNN. We evaluated our approach on the Fashion MNIST data set with an AlexNet model. It turned out that the proposed CORF-augmented pipeline achieved comparable results on noise-free images to those of a conventional AlexNet classification model without CORF delineation maps, but it consistently achieved significantly superior performance on test images perturbed with different levels of Gaussian and uniform noise