Understanding Health and Disease with Multidimensional Single-Cell Methods

Current efforts in the biomedical sciences and related interdisciplinary fields are focused on gaining a molecular understanding of health and disease, which is a problem of daunting complexity that spans many orders of magnitude in characteristic length scales, from small molecules that regulate cell function to cell ensembles that form tissues and organs working together as an organism. In order to uncover the molecular nature of the emergent properties of a cell, it is essential to measure multiple cell components simultaneously in the same cell. In turn, cell heterogeneity requires multiple cells to be measured in order to understand health and disease in the organism. This review summarizes current efforts towards a data-driven framework that leverages single-cell technologies to build robust signatures of healthy and diseased phenotypes. While some approaches focus on multicolor flow cytometry data and other methods are designed to analyze high-content image-based screens, we emphasize the so-called Supercell/SVM paradigm (recently developed by the authors of this review and collaborators) as a unified framework that captures mesoscopic-scale emergence to build reliable phenotypes. Beyond their specific contributions to basic and translational biomedical research, these efforts illustrate, from a larger perspective, the powerful synergy that might be achieved from bringing together methods and ideas from statistical physics, data mining, and mathematics to solve the most pressing problems currently facing the life sciences.Comment: 25 pages, 7 figures; revised version with minor changes. To appear in J. Phys.: Cond. Mat

Rough sets based on Galois connections

Rough set theory is an important tool to extract knowledge from relational databases. The original definitions of approximation operators are based on an indiscernibility relation, which is an equivalence one. Lately. different papers have motivated the possibility of considering arbitrary relations. Nevertheless, when those are taken into account, the original definitions given by Pawlak may lose fundamental properties. This paper proposes a possible solution to the arising problems by presenting an alternative definition of approximation operators based on the closure and interior operators obtained from an isotone Galois connection. We prove that the proposed definition satisfies interesting properties and that it also improves object classification tasks

Algorithmic Compositional Methods and their Role in Genesis: A Multi-Functional Real-Time Computer Music System

Algorithmic procedures have been applied in computer music systems to generate compositional products using conventional musical formalism, extensions of such musical formalism and extra-musical disciplines such as mathematical models. This research investigates the applicability of such algorithmic methodologies for real-time musical composition, culminating in Genesis, a multi-functional real-time computer music system written for Mac OS X in the SuperCollider object-oriented programming language, and contained in the accompanying DVD. Through an extensive graphical user interface, Genesis offers musicians the opportunity to explore the application of the sonic features of real-time sound-objects to designated generative processes via different models of interaction such as unsupervised musical composition by Genesis and networked control of external Genesis instances. As a result of the applied interactive, generative and analytical methods, Genesis forms a unique compositional process, with a compositional product that reflects the character of its interactions between the sonic features of real-time sound-objects and its selected algorithmic procedures. Within this thesis, the technologies involved in algorithmic methodologies used for compositional processes, and the concepts that define their constructs are described, with consequent detailing of their selection and application in Genesis, with audio examples of algorithmic compositional methods demonstrated on the accompanying DVD. To demonstrate the real-time compositional abilities of Genesis, free explorations with instrumentalists, along with studio recordings of the compositional processes available in Genesis are presented in audiovisual examples contained in the accompanying DVD. The evaluation of the Genesis system’s capability to form a real-time compositional process, thereby maintaining real-time interaction between the sonic features of real-time sound objects and its selected algorithmic compositional methods, focuses on existing evaluation techniques founded in HCI and the qualitative issues such evaluation methods present. In terms of the compositional products generated by Genesis, the challenges in quantifying and qualifying its compositional outputs are identified, demonstrating the intricacies of assessing generative methods of compositional processes, and their impact on a resulting compositional product. The thesis concludes by considering further advances and applications of Genesis, and inviting further dissemination of the Genesis system and promotion of research into evaluative methods of generative techniques, with the hope that this may provide additional insight into the relative success of products generated by real-time algorithmic compositional processes

Conference Program

Document provides a list of the sessions, speakers, workshops, and committees of the 32nd Summer Conference on Topology and Its Applications

The logic of systems of granular partitions

The theory of granular partitions is designed to capture in a formal framework important aspects of the selective character of common-sense views of reality. It comprehends not merely the ways in which we can view reality by conceiving its objects as gathered together not merely into sets, but also into wholes of various kinds, partitioned into parts at various levels of granularity. We here represent granular partitions as triples consisting of a rooted tree structure as first component, a domain satisfying the axioms of Extensional Mereology as second component, and a mapping (called ’projection’) of the first into the second as a third component. We define ordering relations among granular partitions the resulting structures are called partition frames. We then introduce an axiomatic theory which sentences are interpreted in partition frame

Robust approach to object recognition through fuzzy clustering and hough transform based methods

Object detection from two dimensional intensity images as well as three dimensional range images is considered. The emphasis is on the robust detection of shapes such as cylinders, spheres, cones, and planar surfaces, typically found in mechanical and manufacturing engineering applications. Based on the analyses of different HT methods, a novel method, called the Fast Randomized Hough Transform (FRHT) is proposed. The key idea of FRHT is to divide the original image into multiple regions and apply random sampling method to map data points in the image space into the parameter space or feature space, then obtain the parameters of true clusters. This results in the following characteristics, which are highly desirable in any method: high computation speed, low memory requirement, high result resolution and infinite parameter space. This project also considers use of fuzzy clustering techniques, such as Fuzzy C Quadric Shells (FCQS) clustering algorithm but combines the concept of noise prototype to form the Noise FCQS clustering algorithm that is robust against noise. Then a novel integrated clustering algorithm combining the advantages of FRHT and NFCQS methods is proposed. It is shown to be a robust clustering algorithm having the distinct advantages such as: the number of clusters need not be known in advance, the results are initialization independent, the detection accuracy is greatly improved, and the computation speed is very fast. Recent concepts from robust statistics, such as least trimmed squares estimation (LTS), minimum volume ellipsoid estimator (MVE) and the generalized MVE are also utilized to form a new robust algorithm called the generalized LTS for Quadric Surfaces (GLTS-QS) algorithm is developed. The experimental results indicate that the clustering method combining the FRHT and the GLTS-QS can improve clustering performance. Moreover, a new cluster validity method for circular clusters is proposed by considering the distribution of the points on the circular edge. Different methods for the computation of distance of a point from a cluster boundary, a common issue in all the range image clustering algorithms, are also discussed. The performance of all these algorithms is tested using various real and synthetic range and intensity images. The application of the robust clustering methods to the experimental granular flow research is also included

Sistemas granulares evolutivos

Orientador: Fernando Antonio Campos GomideTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de ComputaçãoResumo: Recentemente tem-se observado um crescente interesse em abordagens de modelagem computacional para lidar com fluxos de dados do mundo real. Métodos e algoritmos têm sido propostos para obtenção de conhecimento a partir de conjuntos de dados muito grandes e, a princípio, sem valor aparente. Este trabalho apresenta uma plataforma computacional para modelagem granular evolutiva de fluxos de dados incertos. Sistemas granulares evolutivos abrangem uma variedade de abordagens para modelagem on-line inspiradas na forma com que os humanos lidam com a complexidade. Esses sistemas exploram o fluxo de informação em ambiente dinâmico e extrai disso modelos que podem ser linguisticamente entendidos. Particularmente, a granulação da informação é uma técnica natural para dispensar atenção a detalhes desnecessários e enfatizar transparência, interpretabilidade e escalabilidade de sistemas de informação. Dados incertos (granulares) surgem a partir de percepções ou descrições imprecisas do valor de uma variável. De maneira geral, vários fatores podem afetar a escolha da representação dos dados tal que o objeto representativo reflita o significado do conceito que ele está sendo usado para representar. Neste trabalho são considerados dados numéricos, intervalares e fuzzy; e modelos intervalares, fuzzy e neuro-fuzzy. A aprendizagem de sistemas granulares é baseada em algoritmos incrementais que constroem a estrutura do modelo sem conhecimento anterior sobre o processo e adapta os parâmetros do modelo sempre que necessário. Este paradigma de aprendizagem é particularmente importante uma vez que ele evita a reconstrução e o retreinamento do modelo quando o ambiente muda. Exemplos de aplicação em classificação, aproximação de função, predição de séries temporais e controle usando dados sintéticos e reais ilustram a utilidade das abordagens de modelagem granular propostas. O comportamento de fluxos de dados não-estacionários com mudanças graduais e abruptas de regime é também analisado dentro do paradigma de computação granular evolutiva. Realçamos o papel da computação intervalar, fuzzy e neuro-fuzzy em processar dados incertos e prover soluções aproximadas de alta qualidade e sumário de regras de conjuntos de dados de entrada e saída. As abordagens e o paradigma introduzidos constituem uma extensão natural de sistemas inteligentes evolutivos para processamento de dados numéricos a sistemas granulares evolutivos para processamento de dados granularesAbstract: In recent years there has been increasing interest in computational modeling approaches to deal with real-world data streams. Methods and algorithms have been proposed to uncover meaningful knowledge from very large (often unbounded) data sets in principle with no apparent value. This thesis introduces a framework for evolving granular modeling of uncertain data streams. Evolving granular systems comprise an array of online modeling approaches inspired by the way in which humans deal with complexity. These systems explore the information flow in dynamic environments and derive from it models that can be linguistically understood. Particularly, information granulation is a natural technique to dispense unnecessary details and emphasize transparency, interpretability and scalability of information systems. Uncertain (granular) data arise from imprecise perception or description of the value of a variable. Broadly stated, various factors can affect one's choice of data representation such that the representing object conveys the meaning of the concept it is being used to represent. Of particular concern to this work are numerical, interval, and fuzzy types of granular data; and interval, fuzzy, and neurofuzzy modeling frameworks. Learning in evolving granular systems is based on incremental algorithms that build model structure from scratch on a per-sample basis and adapt model parameters whenever necessary. This learning paradigm is meaningful once it avoids redesigning and retraining models all along if the system changes. Application examples in classification, function approximation, time-series prediction and control using real and synthetic data illustrate the usefulness of the granular approaches and framework proposed. The behavior of nonstationary data streams with gradual and abrupt regime shifts is also analyzed in the realm of evolving granular computing. We shed light upon the role of interval, fuzzy, and neurofuzzy computing in processing uncertain data and providing high-quality approximate solutions and rule summary of input-output data sets. The approaches and framework introduced constitute a natural extension of evolving intelligent systems over numeric data streams to evolving granular systems over granular data streamsDoutoradoAutomaçãoDoutor em Engenharia Elétric

SMC 2009: 6th Sound and Music Computing Conference | 23 - 25 | July Casa da Música | Porto

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Computational Geometric and Algebraic Topology

Computational topology is a young, emerging field of mathematics that seeks out practical algorithmic methods for solving complex and fundamental problems in geometry and topology. It draws on a wide variety of techniques from across pure mathematics (including topology, differential geometry, combinatorics, algebra, and discrete geometry), as well as applied mathematics and theoretical computer science. In turn, solutions to these problems have a wide-ranging impact: already they have enabled significant progress in the core area of geometric topology, introduced new methods in applied mathematics, and yielded new insights into the role that topology has to play in fundamental problems surrounding computational complexity. At least three significant branches have emerged in computational topology: algorithmic 3-manifold and knot theory, persistent homology and surfaces and graph embeddings. These branches have emerged largely independently. However, it is clear that they have much to offer each other. The goal of this workshop was to be the first significant step to bring these three areas together, to share ideas in depth, and to pool our expertise in approaching some of the major open problems in the field