Overlap-free Drawing of Generalized Pythagoras Trees for Hierarchy Visualization

Generalized Pythagoras trees were developed for visualizing hierarchical data, producing organic, fractal-like representations. However, the drawback of the original layout algorithm is visual overlap of tree branches. To avoid such overlap, we introduce an adapted drawing algorithm using ellipses instead of circles to recursively place tree nodes representing the subhierarchies. Our technique is demonstrated by resolving overlap in diverse real-world and generated datasets, while comparing the results to the original approach

Lifemap: Exploring the Entire Tree of Life

International audienceThe Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a satisfying manner. By combining methods used in modern cartography, such as OpenStreetMap, with a new way of representing tree-like structures, I created Lifemap, a tool allowing the exploration of a complete representation of the ToL (between 800,000 and 2.2 million species depending on the data source) in a zoomable interface. A server version of Lifemap also allows users to visualize their own trees. This should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of our current knowledge of the evolutionary relationships linking all organisms

User Interfaces and Difference Visualizations for Alternatives

Designers often create multiple iterations to evaluate alternatives. Todays computer-based tools do not support such easy exploration of a design space, despite the fact that such support has been advocated. This dissertation is centered on this. I begin by investigating the effectiveness of various forms of difference visualizations and support for merging changes within a system targeted at diagrams with node and edge attributes. I evaluated the benefits of the introduced difference visualization techniques in two user studies. I found that the basic side-by-side juxtaposition visualization was not effective and also not well received. For comparing diagrams with matching node positions, participants preferred the side-by-side option with a difference layer. For diagrams with non-matching positions animation was beneficial, but the combination with a difference layer was preferred. Thus, the difference layer technique was useful and a good complement to animation. I continue by investigating if explicit support for design alternatives better supports exploration and creativity in a generative design system. To investigate the new techniques to better support exploration, I built a new system that supports parallel exploration of alternative designs and generation of new structural combinations. I investigate the usefulness of my prototype in two user studies and interviews. The results and feedback suggest and confirm that supporting design alternatives explicitly enables designers to work more creatively. Generative models are often represented as DAGs (directed acyclic graphs) in a dataflow programming environment. Existing approaches to compare such DAGs do not generalize to multiple alternatives. Informed by and building on the first part of my dissertation, I introduce a novel user interface that enables visual differencing and editing alternative graphsspecifically more than two alternatives simultaneously, something that has not been presented before. I also explore multi-monitor support to demonstrate that the difference visualization technique scales well to up to 18 alternatives. The novel jamming space feature makes organizing alternatives on a 23 monitor system easier. To investigate the usability of the new difference visualization method I conducted an exploratory interview with three expert designers. The received comments confirmed that it meets their design goals

Predictive lithological mapping through machine learning methods: a case study in the Cinzento Lineament, Carajás Province, Brazil

The Cinzento Lineament (Carajás Mineral Province) represents a complex deformational system with great associated mineral potential, mainly for IOCG deposits. However, the tropical vegetation of the Amazon rainforest considerably limits the number of outcrops available for systematic geological mapping. Therefore, the use of remote data such as airborne geophysics and remote sensing is essential to provide a reliable geological map. The airborne magnetometric data to define lithological units and its boundaries is a challenge, especially in regions with low magnetic latitude and/or remanent magnetization. In this work, we proposed an approach using Magnetization Vector Inversion (MVI) to map the distribution of the magnetic susceptibility, in order to replace techniques such as pole reduction and total gradient. We applied the Random Forest algorithm (supervised Machine Learning algorithm) to recognize patterns in remote data and improve the current mapped lithological units. With 1400 training samples (2.5% of the total samples), we produced two Predictive lithological maps: a first with remote data only and a second with remote data and spatial coordinates. We evaluate the advantages and disadvantages of each Predictive map, and we conclude that both maps need to be analyzed together for the refinement of the current geological map. These predictive maps represent a powerful tool to combine remote data to improve current geological maps, or even generate the first-pass geological map for regions with scarce geological knowledge

Automated Analysis of Retinal and Choroidal OCT and OCTA Images in AMD

La dégénérescence maculaire liée à l'âge (DMLA) est une maladie oculaire progressive qui se manifeste principalement au niveau de la rétine externe et de la choroïde. Le projet de recherche vise à déterminer si des mesures obtenues à partir d'images de tomographie par cohérence optique (OCT) et d'angiographie OCT (OCTA) peuvent être utilisées afin de fournir de nouvelles informations sur des biomarqueurs de la DMLA, ainsi qu’une méthode de détection précoce de la maladie. À cette fin, un appareil permettant l’OCT et l’OCTA a été utilisé pour imager des sujets DMLA précoces et intermédiaires, et des sujets témoins. À la configuration sélectionnée de l’appareil OCT, chaque acquisition d'un œil fournit un volume de données qui est constitué de 300 images transversales appelées B-scan. Au total, des acquisitions de 10 yeux de sujets atteints de DMLA précoce et intermédiaire (3000 images B-scan) et un cas de DMLA néovasculaire, 12 yeux de sujets âgés de plus de 50 ans (3600 images B-scan) et 11 yeux de sujets âgés de moins de 50 ans (3300 images B-scan) ont été obtenues. Cinq méthodes d'extraction de caractéristiques ont été reproduites ou développées afin de déterminer si des différences significatives au niveau de l’œil pouvaient être observées entre les sujets atteints de DMLA précoce et intermédiaire et les sujets témoins d’âge similaire. Grâce à des tests non paramétriques, il a été établi que deux méthodes connues d'extraction de biomarqueurs de la DMLA (analyse d’absence de signal de débit sanguin au niveau de la choriocapillaire et une méthode de segmentation des drusen) produisent des mesures qui montrent des différences significatives entre les groupes, et qui sont représentées de façon uniforme à travers le plan frontal de l’œil. Il a ensuite été souhaité de tirer parti des mesures et de générer un modèle de classification de la DMLA interprétable basé sur l'apprentissage automatique au niveau des B-scans. Des spectres de fréquence résultant de la transformé de Fourier rapide de séries spatiales dérivées de mesures considérées comme représentatives des deux biomarqueurs ont été obtenues, et utilisées comme caractéristiques pour former un classifieur de type forêt aléatoire et un classifieur de type forêt profonde. L'analyse en composantes principales (PCA) a été utilisée pour réduire la dimensionnalité de l’espace des caractéristiques, et la performance des modèles et l'importance des prédicteurs ont été évaluées. Une nouvelle méthode a été conçue qui permet une reconstruction 3D automatisée et une évaluation quantitative de la structure des signaux OCTA et ainsi des vaisseaux rétiniens. Des mesures représentatives des drusen et de la choriocapillaire ont été utilisées pour créer des modèles interprétables pour la classification de la DMLA précoce et intermédiaire. Alors que la prévalence mondiale de la DMLA augmente et que les appareils OCT deviennent plus disponibles, un plus grand nombre de personnes hautement qualifiées est nécessaire pour interpréter les informations médicales et fournir les soins cliniques appropriés. L'analyse et le classement du niveau de sévérité de la DMLA par des experts par le biais d'images OCT sont coûteux et prennent du temps. Les modèles proposés pourraient servir à automatiser la détection de la DMLA, même lorsqu'elle est asymptomatique, et signaler à un ophtalmologue la nécessité de surveiller et de traiter la condition avant la survenue de pertes graves de la vision. Les modèles sont transparents et sont en mesure de fournir une classification à partir d’une seule image transversale. Par conséquent, l'outil diagnostic automatisé pourrait également être utilisé dans des situations où seules des données médicales partielles sont disponibles ou lorsque l'accès aux ressources de soins de santé est limité.----------ABSTRACT Age-related macular degeneration (AMD) is a progressive eye disease which manifests primarily at the outer retina and choroid. The research project aimed to determine whether measures obtained from optical coherence tomography (OCT) and OCT angiography (OCTA) images could be used to provide novel AMD biomarker insight and an early disease detection method. To that end, an OCT and OCTA enabled device was used to image AMD subjects and controls. At the selected device scan size, each scan of one eye gathered using an OCT device provides a volume of data which is constructed of 300 cross-sectional images termed B-scans. In total, scans of 10 eyes from subjects with early and intermediate AMD (3,000 B-scan images) and a case of neovascular AMD, 12 eyes from subjects over the age of 50 years old (3,600 B-scan images), and 11 eyes from subjects under the age of 50 years old (3,300 B-scan images) were obtained. Five feature extraction methods were either reproduced or developed in order to determine if significant differences could be observed between the early and intermediate AMD subjects and control subjects at the eye level. Through non-parametric testing it was established that two AMD biomarker extraction methods (choriocapillaris flow voids analysis and a drusen segmentation method) produced measures which showed significant differences between groups, and which were also uniformly represented across the frontal plane of the eye. It was then desired to leverage the measures and generate a B-scan level, interpretable machine learning-based AMD classification model. Frequency spectrums resulting from the fast Fourier transforms of spatial series derived from measures believed to be representative of the two biomarkers were obtained and used as features to train a random forest and a deep forest classifier. Principal component analysis was used to reduce dimensionality of the feature space, and model performance and predictor importance were assessed. A new method was devised which allows automated 3D reconstruction and quantitative evaluation of retinal flow signal patterns and incidentally of retinal microvasculature. Measures representative of drusen and choriocapillaris were leveraged to create interpretable models for the classification of early and intermediate AMD. As the worldwide prevalence of AMD increases and OCT devices are becoming more available, a greater number of highly trained personnel is needed to interpret medical information and provide the appropriate clinical care. Expert analysis and grading of AMD through OCT images are expensive and time consuming. The models proposed could serve to automate AMD detection, even when it is asymptomatic, and signal to an ophthalmologist the need to monitor and treat the condition before the occurrence of severe visual loss. The models are transparent and provide classification from single cross-sectional images. Therefore, the automated diagnosis tool could also be used in situations where only partial medical data are available, or where there is limited access to health care resources

Healing music and its literary representation in the early modern period

This interdisciplinary thesis explores how music is used in the art of healing in two distinct ways in the early modern period: namely, through the use of performed music accompanying the healing process itself, and as ‘speculative music’, the latter providing a philosophical model for understanding the interplay of music with body, mind and soul. Redefining an existing enquiry in a specific way, my research seeks to enhance an understanding of the construction of a therapeutic modality that revitalizes the ancient belief in the healing powers of music, manifest since antiquity through the classical legends of Orpheus and Pythagoras. The Pythagorean hypothesis – that earthly music reflected the celestial harmony of the spheres – was believed to govern the internal music of the human body, giving credence to the notion of the harmonious balancing of the four bodily humours. Tracing the tradition of healing music from antiquity, I argue that Marsilio Ficino’s paradigmatic magico-musical philosophy refashions the Pythagorean and Neoplatonic explanations of music’s curative potentiality, offering a new interpretat ion of music’s effective power to heal the rift between body and soul. I examine how this Ficinian interpretation is discernible in the work of Robert Fludd, Michael Maier, William Shakespeare, Robert Burton and Thomas Campion. I analyse their observations of the body’s physical and emotional response to music’s healing power. Drawing on early modern models that appropriate the rhetoric of the music of the spheres, I argue that a cultural moment is established in which the motifs and tropes of Neoplatonic love and the healing power of music culminate in allegories of philosophical contemplation and spiritual fulfilment in the Jacobean court masques. In conclusion, my thesis’s examination of music as a healing modality provides a historical framework to support the contemporary use of music as a recognized therapeutic intervention