On the design of advanced filters for biological networks using graph theoretic properties

Network modeling of biological systems is a powerful tool for analysis of high-throughput datasets by computational systems biologists. Integration of networks to form a heterogeneous model requires that each network be as noise-free as possible while still containing relevant biological information. In earlier work, we have shown that the graph theoretic properties of gene correlation networks can be used to highlight and maintain important structures such as high degree nodes, clusters, and critical links between sparse network branches while reducing noise. In this paper, we propose the design of advanced network filters using structurally related graph theoretic properties. While spanning trees and chordal subgraphs provide filters with special advantages, we hypothesize that a hybrid subgraph sampling method will allow for the design of a more effective filter preserving key properties in biological networks. That the proposed approach allows us to optimize a number of parameters associated with the filtering process which in turn improves upon the identification of essential genes in mouse aging networks

Proceedings of the ECCS 2005 satellite workshop: embracing complexity in design - Paris 17 November 2005

Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr). Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr)

The MVGC multivariate Granger causality toolbox: a new approach to Granger-causal inference

Background: Wiener-Granger causality (“G-causality”) is a statistical notion of causality applicable to time series data, whereby cause precedes, and helps predict, effect. It is defined in both time and frequency domains, and allows for the conditioning out of common causal influences. Originally developed in the context of econometric theory, it has since achieved broad application in the neurosciences and beyond. Prediction in the G-causality formalism is based on VAR (Vector AutoRegressive) modelling. New Method: The MVGC Matlab c Toolbox approach to G-causal inference is based on multiple equivalent representations of a VAR model by (i) regression parameters, (ii) the autocovariance sequence and (iii) the cross-power spectral density of the underlying process. It features a variety of algorithms for moving between these representations, enabling selection of the most suitable algorithms with regard to computational efficiency and numerical accuracy. Results: In this paper we explain the theoretical basis, computational strategy and application to empirical G-causal inference of the MVGC Toolbox. We also show via numerical simulations the advantages of our Toolbox over previous methods in terms of computational accuracy and statistical inference. Comparison with Existing Method(s): The standard method of computing G-causality involves estimation of parameters for both a full and a nested (reduced) VAR model. The MVGC approach, by contrast, avoids explicit estimation of the reduced model, thus eliminating a source of estimation error and improving statistical power, and in addition facilitates fast and accurate estimation of the computationally awkward case of conditional G-causality in the frequency domain. Conclusions: The MVGC Toolbox implements a flexible, powerful and efficient approach to G-causal inference. Keywords: Granger causality, vector autoregressive modelling, time series analysi

A Decentralized Mobile Computing Network for Multi-Robot Systems Operations

Collective animal behaviors are paradigmatic examples of fully decentralized operations involving complex collective computations such as collective turns in flocks of birds or collective harvesting by ants. These systems offer a unique source of inspiration for the development of fault-tolerant and self-healing multi-robot systems capable of operating in dynamic environments. Specifically, swarm robotics emerged and is significantly growing on these premises. However, to date, most swarm robotics systems reported in the literature involve basic computational tasks---averages and other algebraic operations. In this paper, we introduce a novel Collective computing framework based on the swarming paradigm, which exhibits the key innate features of swarms: robustness, scalability and flexibility. Unlike Edge computing, the proposed Collective computing framework is truly decentralized and does not require user intervention or additional servers to sustain its operations. This Collective computing framework is applied to the complex task of collective mapping, in which multiple robots aim at cooperatively map a large area. Our results confirm the effectiveness of the cooperative strategy, its robustness to the loss of multiple units, as well as its scalability. Furthermore, the topology of the interconnecting network is found to greatly influence the performance of the collective action.Comment: Accepted for Publication in Proc. 9th IEEE Annual Ubiquitous Computing, Electronics & Mobile Communication Conferenc

Evaluation of statistical correlation and validation methods for construction of gene co-expression networks

High-throughput technologies such as microarrays have led to the rapid accumulation of large scale genomic data providing opportunities to systematically infer gene function and co-expression networks. Typical steps of co-expression network analysis using microarray data consist of estimation of pair-wise gene co-expression using some similarity measure, construction of co-expression networks, identification of clusters of co-expressed genes and post-cluster analyses such as cluster validation. This dissertation is primarily concerned with development and evaluation of approaches for the first and the last steps – estimation of gene co-expression matrices and validation of network clusters. Since clustering methods are not a focus, only a paraclique clustering algorithm will be used in this evaluation. First, a novel Bayesian approach is presented for combining the Pearson correlation with prior biological information from Gene Ontology, yielding a biologically relevant estimate of gene co-expression. The addition of biological information by the Bayesian approach reduced noise in the paraclique gene clusters as indicated by high silhouette and increased homogeneity of clusters in terms of molecular function. Standard similarity measures including correlation coefficients from Pearson, Spearman, Kendall’s Tau, Shrinkage, Partial, and Mutual information, and Euclidean and Manhattan distance measures were evaluated. Based on quality metrics such as cluster homogeneity and stability with respect to ontological categories, clusters resulting from partial correlation and mutual information were more biologically relevant than those from any other correlation measures. Second, statistical quality of clusters was evaluated using approaches based on permutation tests and Mantel correlation to identify significant and informative clusters that capture most of the covariance in the dataset. Third, the utility of statistical contrasts was studied for classification of temporal patterns of gene expression. Specifically, polynomial and Helmert contrast analyses were shown to provide a means of labeling the co-expressed gene sets because they showed similar temporal profiles

Surface networks

© Copyright CASA, UCL. The desire to understand and exploit the structure of continuous surfaces is common to researchers in a range of disciplines. Few examples of the varied surfaces forming an integral part of modern subjects include terrain, population density, surface atmospheric pressure, physico-chemical surfaces, computer graphics, and metrological surfaces. The focus of the work here is a group of data structures called Surface Networks, which abstract 2-dimensional surfaces by storing only the most important (also called fundamental, critical or surface-specific) points and lines in the surfaces. Surface networks are intelligent and “natural ” data structures because they store a surface as a framework of “surface ” elements unlike the DEM or TIN data structures. This report presents an overview of the previous works and the ideas being developed by the authors of this report. The research on surface networks has fou

The State-of-the-Art of Set Visualization

Sets comprise a generic data model that has been used in a variety of data analysis problems. Such problems involve analysing and visualizing set relations between multiple sets defined over the same collection of elements. However, visualizing sets is a non-trivial problem due to the large number of possible relations between them. We provide a systematic overview of state-of-the-art techniques for visualizing different kinds of set relations. We classify these techniques into six main categories according to the visual representations they use and the tasks they support. We compare the categories to provide guidance for choosing an appropriate technique for a given problem. Finally, we identify challenges in this area that need further research and propose possible directions to address these challenges. Further resources on set visualization are available at http://www.setviz.net