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

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

Branching Boogaloo: Botanical Adventures in Multi-Mediated Morphologies

FormaLeaf is a software interface for exploring leaf morphology using parallel string rewriting grammars called L-systems. Scanned images of dicotyledonous angiosperm leaves removed from plants around Bard’s campus are displayed on the left and analyzed using the computer vision library OpenCV. Morphometrical information and terminological labels are reported in a side-panel. “Slider mode” allows the user to control the structural template and growth parameters of the generated L-system leaf displayed on the right. “Vision mode” shows the input and generated leaves as the computer ‘sees’ them. “Search mode” attempts to automatically produce a formally defined graphical representation of the input by evaluating the visual similarity of a generated pool of candidate leaves. The system seeks to derive a possible internal structural configuration for venation based purely off a visual analysis of external shape. The iterations of the generated L-system leaves when viewed in succession appear as a hypothetical development sequence. FormaLeaf was written in Processing

Approaches to the Use of Geometry in Architecture: A study of the works of Andrea Palladio, Frank Lloyd Wright, and Frank Gehry

Geometry deals with form, shape, and measurement and is a part of mathematics where visual thought is dominant. Both design and construction in architecture deal with visualization, and architects constantly employ geometry. Today, with the advent of computer software, architects can visualize forms that go beyond our everyday experience. Some architects claim that the complex forms of their works have correlations with non-Euclidean geometry, but the space we experience is still Euclidean. Given this context, I have explored possible correlations that might exist between mathematical concepts of geometry and the employment of geometry in architectural design from a historic perspective. The main focus will be to describe the two phenomena historically, and then investigate any connections that might emerge from the discussion. While discussing the way geometry has been approached in architecture, I have focused on the Renaissance, Modern, and Post-modern phases as they have a distinct style and expression. Andrea Palladio, Frank Lloyd Wright, and Frank Gehry's works will be case studies for the Renaissance, Modern, and Post-modern phases respectively. One of the important conclusions of this study is that architects use geometry in a more subconscious and intuitive manner while designing. Certain approaches to geometry can be determined by the way an architect deals with form and space. From the discussions of the works of Palladio, Wright, and Gehry, it can be concluded that from a two-dimensional simple approach to form and space in architecture, there has been a development of thinking about complex forms three dimensionally. Similarly, in mathematics, geometry has developed from a two-dimensional and abstract description of our surroundings to something that can capture the complex and specific nature of a phenomena. It is also shown that architects rarely come up with new concepts of geometry. Significant developments in geometry have always been in the domain of mathematics. Hence, most correlations between geometry in architecture and geometry in mathematics develop much later than the introduction of those concepts of geometry in mathematics. It is also found that the use of Euclidean geometry persists in architecture and that later concepts like non-Euclidean geometry cannot be used in an instrumental manner in architecture

Instructional strategies in explicating the discovery function of proof for lower secondary school students

In this paper, we report on the analysis of teaching episodes selected from our pedagogical and cognitive research on geometry teaching that illustrate how carefully-chosen instructional strategies can guide Grade 8 students to see and appreciate the discovery function of proof in geometr

Partners in Practice: Contemporary Irish Literature, World Literature and Digital Humanities

This dissertation examines the opportunities and implications afforded Irish literary studies by developments in the newly emergent disciplines of world literature and the digital humanities. Employing the world literature theories of Wai Chee Dimock, David Damrosch, Franco Moretti and Pascale Casanova in the critical analysis of works of contemporary Irish literature and Irish literary criticism produced in the period 1998-2010, it investigates how these theoretical approaches can generate new perspectives on Irish literature and argues that the real “problem” of world literature as it relates to Irish literary studies lies in establishing an interpretive method which enables considerations of the national within a global framework. This problem serves as the entry point to the engagement with the digital humanities presented throughout the dissertation. Situated within debates surrounding modes of “close” and “distant reading” (Moretti 2000) as they are played out in both the fields of world literature and digital literary studies, this work proposes an alternative digital humanities approach to the study of world literature to the modes of “distant reading” endorsed by literary critic, Franco Moretti and digital humanists such as Alan Liu (Liu 2012). Through a series of interdisciplinary case studies combining national and international, close and distant and old and new modes of literary scholarship, it argues that, rather than being opposed to a nationally-orientated form of literary criticism, the digital humanities have the tools and the methodologies necessary to bring Irish literary scholarship into a productive dialogue with perspectives from elsewhere and thus, to engender a form of Irish literary scholarship that transcends while not denying the significance of the nation state. By illustrating the manner in which the digital humanities can be employed to enhance and extend traditional approaches in Irish literary studies, this project demonstrates that Irish studies and the digital humanities can be “practicing partners” in a way that serves to advance work in both the fields of world literature and digital literary studies

Creative management: theoretical foundations

У сучасному динамічному житті нові непередбачувані події, що відбуваються все більше і більше, повалюють, або приносять успіх і процвітання, або порушують життєвий шлях та діяльність багатьох людей, організацій, країн, регіонів. Наша неспроможність сприймати випадкові непрограмовані події обумовлена ​​тим, що результатом традиційної освіти є вміння логічно відображати та аналізувати інформацію. Для успішної роботи в умовах збільшення непередбачуваності та розбіжностей соціально-економічного розвитку необхідно, крім інфологічної парадигми сприйняття навколишнього світу, оволодіти парадигмою осягнення та творчої роботи. У цьому креативному менеджменті є способи та методи переключення тренінгів менеджерів, інженерів, підприємців на рівень конструктивного креативного мислення та активності шляхом поєднання логіки та евристичності. Монографія призначена для студентів та аспірантів, докторантів, керівників інструкторів та практиків менеджменту в економічній сфері, інженерних кадрів, усіх, хто хоче активно та цілеспрямовано працювати для процвітання своєї організації та творчого розвитку особистості. Це оригінальний ключ до розуміння сучасності та бачення майбутнього сучасної організації та соціально-економічного розвитку в цілому шляхом активізації гуманної творчої діяльності людини.В современной динамичной жизни происходят новые непредсказуемые события, все более свершающие, либо приносящие успех и процветание, либо нарушающие жизненный путь и деятельность многих людей, организаций, стран, регионов. Наша неготовность воспринимать случайные непрограммируемые события обусловлена ​​тем, что результатом традиционного образования является способность логически отражать и анализировать информацию. Для того, чтобы успешно работать в условиях повышения непредсказуемости и несоответствия социально-экономического развития, помимо парадигмы восприятия окружающего мира необходимо освоить парадигму понимания и творчества. В этом креативном менеджменте есть способы и способы переключения обучения менеджеров, инженеров, предпринимателей на уровень конструктивного творческого мышления и деятельности посредством сочетания логики и эвристики. Монография, предназначенная для студентов и аспирантов, докторантов, управленческих инструкторов и практиков менеджмента в экономической сфере, инженерных кадров, всех, кто хочет активно и целенаправленно работать ради процветания своей организации и творческого развития личности. Это оригинальный ключ к пониманию настоящего и видению будущего современной организации и социально-экономического развития в целом за счет активизации гуманной творческой деятельности человека.In a modern dynamic life new unpredictable events occurring more and more, overthrowing, either bringing success and prosperity or breaking a course of life and activity of many people, organizations, countries, regions. Our unreadiness to perceive random nonprogrammable events is caused by that the result of traditional education is ability to logically reflect and analyze the information. In order to work successfully under the conditions of increase of unpredictability and discrepancy of social and economic development, it is necessary besides infological paradigm of perception of the world around to master the paradigm of comprehension and creative work. In this creative management there are ways and methods of switching over of training of managers, engineers, entrepreneurs to level of constructive creative thinking and activity by way of combination of logic and heuristicity. The monograph meant for under- and postgraduate students, doctoral candidates, management instructors and practitioners of management in the economic sphere, engineering personnel, everybody who wants to work actively and purposefully for prosperity of one’s organization and personality creative development. This is an original key to understanding of the present and vision of the future of a modern organization and socioeconomic development on the whole through activation of humane creative activity of the person

Geometric algorithms for cavity detection on protein surfaces

Macromolecular structures such as proteins heavily empower cellular processes or functions. These biological functions result from interactions between proteins and peptides, catalytic substrates, nucleotides or even human-made chemicals. Thus, several interactions can be distinguished: protein-ligand, protein-protein, protein-DNA, and so on. Furthermore, those interactions only happen under chemical- and shapecomplementarity conditions, and usually take place in regions known as binding sites. Typically, a protein consists of four structural levels. The primary structure of a protein is made up of its amino acid sequences (or chains). Its secondary structure essentially comprises -helices and -sheets, which are sub-sequences (or sub-domains) of amino acids of the primary structure. Its tertiary structure results from the composition of sub-domains into domains, which represent the geometric shape of the protein. Finally, the quaternary structure of a protein results from the aggregate of two or more tertiary structures, usually known as a protein complex. This thesis fits in the scope of structure-based drug design and protein docking. Specifically, one addresses the fundamental problem of detecting and identifying protein cavities, which are often seen as tentative binding sites for ligands in protein-ligand interactions. In general, cavity prediction algorithms split into three main categories: energy-based, geometry-based, and evolution-based. Evolutionary methods build upon evolutionary sequence conservation estimates; that is, these methods allow us to detect functional sites through the computation of the evolutionary conservation of the positions of amino acids in proteins. Energy-based methods build upon the computation of interaction energies between protein and ligand atoms. In turn, geometry-based algorithms build upon the analysis of the geometric shape of the protein (i.e., its tertiary structure) to identify cavities. This thesis focuses on geometric methods. We introduce here three new geometric-based algorithms for protein cavity detection. The main contribution of this thesis lies in the use of computer graphics techniques in the analysis and recognition of cavities in proteins, much in the spirit of molecular graphics and modeling. As seen further ahead, these techniques include field-of-view (FoV), voxel ray casting, back-face culling, shape diameter functions, Morse theory, and critical points. The leading idea is to come up with protein shape segmentation, much like we commonly do in mesh segmentation in computer graphics. In practice, protein cavity algorithms are nothing more than segmentation algorithms designed for proteins.Estruturas macromoleculares tais como as proteínas potencializam processos ou funções celulares. Estas funções resultam das interações entre proteínas e peptídeos, substratos catalíticos, nucleótideos, ou até mesmo substâncias químicas produzidas pelo homem. Assim, há vários tipos de interacções: proteína-ligante, proteína-proteína, proteína-DNA e assim por diante. Além disso, estas interações geralmente ocorrem em regiões conhecidas como locais de ligação (binding sites, do inglês) e só acontecem sob condições de complementaridade química e de forma. É também importante referir que uma proteína pode ser estruturada em quatro níveis. A estrutura primária que consiste em sequências de aminoácidos (ou cadeias), a estrutura secundária que compreende essencialmente por hélices e folhas , que são subsequências (ou subdomínios) dos aminoácidos da estrutura primária, a estrutura terciária que resulta da composição de subdomínios em domínios, que por sua vez representa a forma geométrica da proteína, e por fim a estrutura quaternária que é o resultado da agregação de duas ou mais estruturas terciárias. Este último nível estrutural é frequentemente conhecido por um complexo proteico. Esta tese enquadra-se no âmbito da conceção de fármacos baseados em estrutura e no acoplamento de proteínas. Mais especificamente, aborda-se o problema fundamental da deteção e identificação de cavidades que são frequentemente vistos como possíveis locais de ligação (putative binding sites, do inglês) para os seus ligantes (ligands, do inglês). De forma geral, os algoritmos de identificação de cavidades dividem-se em três categorias principais: baseados em energia, geometria ou evolução. Os métodos evolutivos baseiam-se em estimativas de conservação das sequências evolucionárias. Isto é, estes métodos permitem detectar locais funcionais através do cálculo da conservação evolutiva das posições dos aminoácidos das proteínas. Em relação aos métodos baseados em energia estes baseiam-se no cálculo das energias de interação entre átomos da proteína e do ligante. Por fim, os algoritmos geométricos baseiam-se na análise da forma geométrica da proteína para identificar cavidades. Esta tese foca-se nos métodos geométricos. Apresentamos nesta tese três novos algoritmos geométricos para detecção de cavidades em proteínas. A principal contribuição desta tese está no uso de técnicas de computação gráfica na análise e reconhecimento de cavidades em proteínas, muito no espírito da modelação e visualização molecular. Como pode ser visto mais à frente, estas técnicas incluem o field-of-view (FoV), voxel ray casting, back-face culling, funções de diâmetro de forma, a teoria de Morse, e os pontos críticos. A ideia principal é segmentar a proteína, à semelhança do que acontece na segmentação de malhas em computação gráfica. Na prática, os algoritmos de detecção de cavidades não são nada mais que algoritmos de segmentação de proteínas