132 research outputs found

    Investigating the Potential of UAV-Based Low-Cost Camera Imagery for Measuring Biophysical Variables in Maize

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    The potential for improved crop productivity is readily investigated in agronomic field experiments. Frequent measurements of biophysical crop variables are necessary to allow for confident statements on crop performance. Commonly, in-field measurements are tedious, labour-intensive, costly and spatially selective and therefore pose a challenge in field experiments. With the versatile, flexible employment of the platform and the high spatial and temporal resolution of the sensor data, Unmanned Aerial Vehicle (UAV)-based remote sensing offers the possibility to derive variables quickly, contactless and at low cost. This thesis examined if UAV-borne modified low-cost camera imagery allowed for remote estimation of the crop variables green leaf area index (gLAI) and radiation use efficiency (RUE) in a maize field trial under different management influences. For this, a field experiment was established at the university's research station Campus Klein-Altendorf southwest of Bonn in the years 2015 and 2016. In four treatments (two levels of nitrogen fertilisation and two levels of plant density) with five repetitions each, leaf growth of maize plants was supposed to occur differently. gLAI and biomass was measured destructively, UAV-based data was acquired in 14-day intervals over the entire experiment. Three studies were conducted and submitted for peer-review in international journals. In study I, three selected spectral vegetation indices (NDVI, GNDVI, 3BSI) were related to the gLAI measurements. Differing but definite relationships per treatment factor were found. gLAI estimation using the two-band indices (NDVI, GNDVI) yielded good results up to gLAI values of 3. The 3-bands approach (3BSI) did not provide improved accuracies. Comparing gLAI results to the spectral vegetation indices, it was determined that sole reliance on these was insufficient to draw the right conclusions on the impact of management factors on leaf area development in maize canopies. Study II evaluated parametric and non-parametric regression methods on their capability to estimate gLAI in maize, relying on UAV-based low-cost camera imagery with non-plants pixels (i.e. shaded and illuminated soil background) a) included in and b) excluded from the analysis. With regard to the parametric regression methods, all possible band combinations for a selected number of two- and three-band formulations as well as different fitting functions were tested. With regard to non-parametric methods, six regression algorithms (Random Forests Regression, Support Vector Regression, Relevance Vector Machines, Gaussian Process Regression, Kernel Regularized Least Squares, Extreme Learning Machine) were tested. It was found that all non-parametric methods performed better than the parametric methods, and that kernel-based algorithms outperformed the other tested algorithms. Excluding non-plant pixels from the analysis deteriorated models' performances. When using parametric regression methods, signal saturation occurred at gLAI values of about 3, and at values around 4 when employing non-parametric methods. Study III investigated if a) UAV-based low-cost camera imagery allowed estimating RUEs in different experimental plots where maize was cultivated in the growing season of 2016, b) those values were different from the ones previously reported in literature and c) there was a difference between RUEtotal and RUEgreen. Fractional cover and canopy reflectance was determined based on the RS imagery. Our study showed that RUEtotal ranges between 4.05 and 4.59, and RUEgreen between 4.11 and 4.65. These values were higher than those published in other research articles, but not outside the range of plausibility. The difference between RUEtotal and RUEgreen was minimal, possibly due to prolonged canopy greenness induced by the stay-green trait of the cultivar grown. In conclusion, UAV-based low-cost camera imagery allows for estimation of plant variables within a range of limitations

    Advanced Sensors for Real-Time Monitoring Applications

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    It is impossible to imagine the modern world without sensors, or without real-time information about almost everything—from local temperature to material composition and health parameters. We sense, measure, and process data and act accordingly all the time. In fact, real-time monitoring and information is key to a successful business, an assistant in life-saving decisions that healthcare professionals make, and a tool in research that could revolutionize the future. To ensure that sensors address the rapidly developing needs of various areas of our lives and activities, scientists, researchers, manufacturers, and end-users have established an efficient dialogue so that the newest technological achievements in all aspects of real-time sensing can be implemented for the benefit of the wider community. This book documents some of the results of such a dialogue and reports on advances in sensors and sensor systems for existing and emerging real-time monitoring applications

    3D Remote Sensing Applications in Forest Ecology: Composition, Structure and Function

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    Dear Colleagues, The composition, structure and function of forest ecosystems are the key features characterizing their ecological properties, and can thus be crucially shaped and changed by various biotic and abiotic factors on multiple spatial scales. The magnitude and extent of these changes in recent decades calls for enhanced mitigation and adaption measures. Remote sensing data and methods are the main complementary sources of up-to-date synoptic and objective information of forest ecology. Due to the inherent 3D nature of forest ecosystems, the analysis of 3D sources of remote sensing data is considered to be most appropriate for recreating the forest’s compositional, structural and functional dynamics. In this Special Issue of Forests, we published a set of state-of-the-art scientific works including experimental studies, methodological developments and model validations, all dealing with the general topic of 3D remote sensing-assisted applications in forest ecology. We showed applications in forest ecology from a broad collection of method and sensor combinations, including fusion schemes. All in all, the studies and their focuses are as broad as a forest’s ecology or the field of remote sensing and, thus, reflect the very diverse usages and directions toward which future research and practice will be directed

    Machine Learning Approaches for Traffic Flow Forecasting

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    Intelligent Transport Systems (ITS) as a field has emerged quite rapidly in the recent years. A competitive solution coupled with big data gathered for ITS applications needs the latest AI to drive the ITS for the smart and effective public transport planning and management. Although there is a strong need for ITS applications like Advanced Route Planning (ARP) and Traffic Control Systems (TCS) to take the charge and require the minimum of possible human interventions. This thesis develops the models that can predict the traffic link flows on a junction level such as road traffic flows for a freeway or highway road for all traffic conditions. The research first reviews the state-of-the-art time series data prediction techniques with a deep focus in the field of transport Engineering along with the existing statistical and machine leaning methods and their applications for the freeway traffic flow prediction. This review setup a firm work focussed on the view point to look for the superiority in term of prediction performance of individual statistical or machine learning models over another. A detailed theoretical attention has been given, to learn the structure and working of individual chosen prediction models, in relation to the traffic flow data. In modelling the traffic flows from the real-world Highway England (HE) gathered dataset, a traffic flow objective function for highway road prediction models is proposed in a 3-stage framework including the topological breakdown of traffic network into virtual patches, further into nodes and to the basic links flow profiles behaviour estimations. The proposed objective function is tested with ten different prediction models including the statistical, shallow and deep learning constructed hybrid models for bi-directional links flow prediction methods. The effectiveness of the proposed objective function greatly enhances the accuracy of traffic flow prediction, regardless of the machine learning model used. The proposed prediction objective function base framework gives a new approach to model the traffic network to better understand the unknown traffic flow waves and the resulting congestions caused on a junction level. In addition, the results of applied Machine Learning models indicate that RNN variant LSTMs based models in conjunction with neural networks and Deep CNNs, when applied through the proposed objective function, outperforms other chosen machine learning methods for link flow predictions. The experimentation based practical findings reveal that to arrive at an efficient, robust, offline and accurate prediction model apart from feeding the ML mode with the correct representation of the network data, attention should be paid to the deep learning model structure, data pre-processing (i.e. normalisation) and the error matrices used for data behavioural learning. The proposed framework, in future can be utilised to address one of the main aims of the smart transport systems i.e. to reduce the error rates in network wide congestion predictions and the inflicted general traffic travel time delays in real-time

    Proceedings Of The 18th Annual Meeting Of The Asia Oceania Geosciences Society (Aogs 2021)

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    The 18th Annual Meeting of the Asia Oceania Geosciences Society (AOGS 2021) was held from 1st to 6th August 2021. This proceedings volume includes selected extended abstracts from a challenging array of presentations at this conference. The AOGS Annual Meeting is a leading venue for professional interaction among researchers and practitioners, covering diverse disciplines of geosciences

    Forestogram: Biclustering Visualization Framework with Applications in Public Transport and Bioinformatics

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    RÉSUMÉ : Dans de nombreux problèmes d’analyse de données, les données sont exprimées dans une matrice avec les sujets en ligne et les attributs en colonne. Les méthodes de segmentations traditionnelles visent à regrouper les sujets (lignes), selon des critères de similitude entre ces sujets. Le but est de constituer des groupes de sujets (lignes) qui partagent un certain degré de ressemblance. Les groupes obtenus permettent de garantir que les sujets partagent des similitudes dans leurs attributs (colonnes), il n’y a cependant aucune garantie sur ce qui se passe au niveau des attributs (les colonnes). Dans certaines applications, un regroupement simultané des lignes et des colonnes appelé biclustering de la matrice de données peut être souhaité. Pour cela, nous concevons et développons un nouveau cadre appelé Forestogram, qui permet le calcul de ce regroupement simultané des lignes et des colonnes (biclusters)dans un mode hiérarchique. Le regroupement simultané des lignes et des colonnes de manière hiérarchique peut aider les praticiens à mieux comprendre comment les groupes évoluent avec des propriétés théoriques intéressantes. Forestogram, le nouvel outil de calcul et de visualisation proposé, pourrait être considéré comme une extension 3D du dendrogramme, avec une fusion orthogonale étendue. Chaque bicluster est constitué d’un groupe de lignes (ou de sujets) qui déplie un schéma fortement corrélé avec le groupe de colonnes (ou attributs) correspondantes. Cependant, au lieu d’effectuer un clustering bidirectionnel indépendamment de chaque côté, nous proposons un algorithme de biclustering hiérarchique qui prend les lignes et les colonnes en même temps pour déterminer les biclusters. De plus, nous développons un critère d’information basé sur un modèle qui fournit un nombre estimé de biclusters à travers un ensemble de configurations hiérarchiques au sein du forestogramme sous des hypothèses légères. Nous étudions le cadre suggéré dans deux perspectives appliquées différentes, l’une dans le domaine du transport en commun, l’autre dans le domaine de la bioinformatique. En premier lieu, nous étudions le comportement des usagers dans le transport en commun à partir de deux informations distinctes, les données temporelles et les coordonnées spatiales recueillies à partir des données de transaction de la carte à puce des usagers. Dans de nombreuses villes, les sociétés de transport en commun du monde entier utilisent un système de carte à puce pour gérer la perception des tarifs. L’analyse de cette information fournit un aperçu complet de l’influence de l’utilisateur dans le réseau de transport en commun interactif. À cet égard, l’analyse des données temporelles, décrivant l’heure d’entrée dans le réseau de transport en commun est considérée comme la composante la plus importante des données recueillies à partir des cartes à puce. Les techniques classiques de segmentation, basées sur la distance, ne sont pas appropriées pour analyser les données temporelles. Une nouvelle projection intuitive est suggérée pour conserver le modèle de données horodatées. Ceci est introduit dans la méthode suggérée pour découvrir le modèle temporel comportemental des utilisateurs. Cette projection conserve la distance temporelle entre toute paire arbitraire de données horodatées avec une visualisation significative. Par conséquent, cette information est introduite dans un algorithme de classification hiérarchique en tant que méthode de segmentation de données pour découvrir le modèle des utilisateurs. Ensuite, l’heure d’utilisation est prise en compte comme une variable latente pour rendre la métrique euclidienne appropriée dans l’extraction du motif spatial à travers notre forestogramme. Comme deuxième application, le forestogramme est testé sur un ensemble de données multiomiques combinées à partir de différentes mesures biologiques pour étudier comment l’état de santé des patientes et les modalités biologiques correspondantes évoluent hiérarchiquement au cours du terme de la grossesse, dans chaque bicluster. Le maintien de la grossesse repose sur un équilibre finement équilibré entre la tolérance à l’allogreffe foetale et la protection mécanismes contre les agents pathogènes envahissants. Malgré l’impact bien établi du développement pendant les premiers mois de la grossesse sur les résultats à long terme, les interactions entre les divers mécanismes biologiques qui régissent la progression de la grossesse n’ont pas été étudiées en détail. Démontrer la chronologie de ces adaptations à la grossesse à terme fournit le cadre pour de futures études examinant les déviations impliquées dans les pathologies liées à la grossesse, y compris la naissance prématurée et la prééclampsie. Nous effectuons une analyse multi-physique de 51 échantillons de 17 femmes enceintes, livrant à terme. Les ensembles de données comprennent des mesures de l’immunome, du transcriptome, du microbiome, du protéome et du métabolome d’échantillons obtenus simultanément chez les mêmes patients. La modélisation prédictive multivariée utilisant l’algorithme Elastic Net est utilisée pour mesurer la capacité de chaque ensemble de données à prédire l’âge gestationnel. En utilisant la généralisation empilée, ces ensembles de données sont combinés en un seul modèle. Ce modèle augmente non seulement significativement le pouvoir prédictif en combinant tous les ensembles de données, mais révèle également de nouvelles interactions entre différentes modalités biologiques. En outre, notre forestogramme suggéré est une autre ligne directrice avec l’âge gestationnel au moment de l’échantillonnage qui fournit un modèle non supervisé pour montrer combien d’informations supervisées sont nécessaires pour chaque trimestre pour caractériser les changements induits par la grossesse dans Microbiome, Transcriptome, Génome, Exposome et Immunome réponses efficacement.----------ABSTRACT : In many statistical modeling problems data are expressed in a matrix with subjects in row and attributes in column. In this regard, simultaneous grouping of rows and columns known as biclustering of the data matrix is desired. We design and develop a new framework called Forestogram, with the aim of fast computational and hierarchical illustration of biclusters. Often in practical data analysis, we deal with a two-dimensional object known as the data matrix, where observations are expressed as samples (or subjects) in rows, and attributes (or features) in columns. Thus, simultaneous grouping of rows and columns in a hierarchical manner helps practitioners better understanding how clusters evolve. Forestogram, a novel computational and visualization tool, could be thought of as a 3D expansion of dendrogram, with extended orthogonal merge. Each bicluster consists of group of rows (or samples) that unfolds a highly-correlated schema with their corresponding group of columns (or attributes). However, instead of performing two-way clustering independently on each side, we propose a hierarchical biclustering algorithm which takes rows and columns at the same time to determine the biclusters. Furthermore, we develop a model-based information criterion which provides an estimated number of biclusters through a set of hierarchical configurations within the forestogram under mild assumptions. We study the suggested framework in two different applied perspectives, one in public transit domain, another one in bioinformatics field. First, we investigate the users’ behavior in public transit based on two distinct information, temporal data and spatial coordinates gathered from smart card. In many cities, worldwide public transit companies use smart card system to manage fare collection. Analysis of this information provides a comprehensive insight of user’s influence in the interactive public transit network. In this regard, analysis of temporal data, describing the time of entering to the public transit network is considered as the most substantial component of the data gathered from the smart cards. Classical distance-based techniques are not always suitable to analyze this time series data. A novel projection with intuitive visual map from higher dimension into a three-dimensional clock-like space is suggested to reveal the underlying temporal pattern of public transit users. This projection retains the temporal distance between any arbitrary pair of time-stamped data with meaningful visualization. Consequently, this information is fed into a hierarchical clustering algorithm as a method of data segmentation to discover the pattern of users. Then, the time of the usage is taken as a latent variable into account to make the Euclidean metric appropriate for extracting the spatial pattern through our forestogram. As a second application, forestogram is tested on a multiomics dataset combined from different biological measurements to study how patients and corresponding biological modalities evolve hierarchically in each bicluster over the term of pregnancy. The maintenance of pregnancy relies on a finely-tuned balance between tolerance to the fetal allograft and protective mechanisms against invading pathogens. Despite the well-established impact of development during the early months of pregnancy on long-term outcomes, the interactions between various biological mechanisms that govern the progression of pregnancy have not been studied in details. Demonstrating the chronology of these adaptations to term pregnancy provides the framework for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia. We perform a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets include measurements from the immunome, transcriptome, microbiome, proteome, and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net algorithm is used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets are combined into a single model. This model not only significantly increases the predictive power by combining all datasets, but also reveals novel interactions between different biological modalities. Furthermore, our suggested forestogram is another guideline along with the gestational age at time of sampling that provides an unsupervised model to show how much supervised information is necessary for each trimester to characterize the pregnancy-induced changes in Microbiome, Transcriptome, Genome, Exposome, and Immunome responses effectively

    Machine learning for biological network inference

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    Artificial Neural Networks in Agriculture

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    Modern agriculture needs to have high production efficiency combined with a high quality of obtained products. This applies to both crop and livestock production. To meet these requirements, advanced methods of data analysis are more and more frequently used, including those derived from artificial intelligence methods. Artificial neural networks (ANNs) are one of the most popular tools of this kind. They are widely used in solving various classification and prediction tasks, for some time also in the broadly defined field of agriculture. They can form part of precision farming and decision support systems. Artificial neural networks can replace the classical methods of modelling many issues, and are one of the main alternatives to classical mathematical models. The spectrum of applications of artificial neural networks is very wide. For a long time now, researchers from all over the world have been using these tools to support agricultural production, making it more efficient and providing the highest-quality products possible

    Maintaining privacy during continuous motion sensing

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    Mobile devices contain sensors which allow continuous recording of a user's motion allowing the development of activity, fitness and health applications. With varied applications, the motion sensors present new privacy problems which require protection. This dissertation builds on previous work with activity and fitness machine learning techniques demonstrating the ability to predict medical values from motion data using smartphones. We conduct two clinical trials collecting a data set of eighty-eight patients and forty-five hours of monitoring to analyze the privacy implications of releasing motion data. We extract a comprehensive set of statistical features from all available smartphone sensors and evaluate feature selection techniques and machine learning models. We find we can predict user identity, phone identity, speed, FEV1/FVC, and activity from the motion signal. Designing a privacy protection mechanism for motion data requires a precise understanding of how the signal predicts the sensitive information. We develop algorithms to conduct private feature selection which identifies features useful for prediction. We find that simply blocking all private features significantly reduces the usefulness of the signal for other predictions. We develop a sensitivity estimation framework to calibrate the noise for each private feature requiring an order of magnitude less noise than differential privacy sensitivity. We find adding noise to private features calibrated using the sensitivity estimate is effective at reducing the prediction of five tested target predictions. Our methods hide both user and phone identification while allowing other prediction but cannot hide activity, FEV1/FVC and speed without significantly lowering the accuracy of other predictions. Our methods are still effective when the attacker has prior knowledge of the noise distribution. The methods presented in this dissertation demonstrate the need for privacy in motion data and provide a framework for protecting sensitive user information in motion readings

    Mining Explicit and Implicit Relationships in Data Using Symbolic Regression

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    Identification of implicit and explicit relations within observed data is a generic problem commonly encountered in several domains including science, engineering, finance, and more. It forms the core component of data analytics, a process of discovering useful information from data sets that are potentially huge and otherwise incomprehensible. In industries, such information is often instrumental for profitable decision making, whereas in science and engineering it is used to build empirical models, propose new or verify existing theories and explain natural phenomena. In recent times, digital and internet based technologies have proliferated, making it viable to generate and collect large amount of data at low cost. This inturn has resulted in an ever growing need for methods to analyse and draw interpretations from such data quickly and reliably. With this overarching goal, this thesis attempts to make contributions towards developing accurate and efficient methods for discovering such relations through evolutionary search, a method commonly referred to as Symbolic Regression (SR). A data set of input variables x and a corresponding observed response y is given. The aim is to find an explicit function y = f (x) or an implicit function f (x, y) = 0, which represents the data set. While seemingly simple, the problem is challenging for several reasons. Some of the conventional regression methods try to “guess” a functional form such as linear/quadratic/polynomial, and attempt to do a curve-fitting of the data to the equation, which may limit the possibility of discovering more complex relations, if they exist. On the other hand, there are meta-modelling techniques such as response surface method, Kriging, etc., that model the given data accurately, but provide a “black-box” predictor instead of an expression. Such approximations convey little or no insights about how the variables and responses are dependent on each other, or their relative contribution to the output. SR attempts to alleviate the above two extremes by providing a structure which evolves mathematical expressions instead of assuming them. Thus, it is flexible enough to represent the data, but at the same time provides useful insights instead of a black-box predictor. SR can be categorized as part of Explainable Artificial Intelligence and can contribute to Trustworthy Artificial Intelligence. The works proposed in this thesis aims to integrate the concept of “semantics” deeper into Genetic Programming (GP) and Evolutionary Feature Synthesis, which are the two algorithms usually employed for conducting SR. The semantics will be integrated into well-known components of the algorithms such as compactness, diversity, recombination, constant optimization, etc. The main contribution of this thesis is the proposal of two novel operators to generate expressions based on Linear Programming and Mixed Integer Programming with the aim of controlling the length of the discovered expressions without compromising on the accuracy. In the experiments, these operators are proven to be able to discover expressions with better accuracy and interpretability on many explicit and implicit benchmarks. Moreover, some applications of SR on real-world data sets are shown to demonstrate the practicality of the proposed approaches. Besides, in related to practical problems, how GP can be applied to effectively solve the Resource Constrained Scheduling Problems is also presented
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