Showing papers on "Modularity (networks) published in 2005"
TL;DR: It is found that the most accurate methods tend to be more computationally expensive, and that both aspects need to be considered when choosing a method for practical purposes.
Abstract: We compare recent approaches to community structure identification in terms of sensitivity and computational cost. The recently proposed modularity measure is revisited and the performance of the methods as applied to ad hoc networks with known community structure, is compared. We find that the most accurate methods tend to be more computationally expensive, and that both aspects need to be considered when choosing a method for practical purposes. The work is intended as an introduction as well as a proposal for a standard benchmark test of community detection methods.
2,630 citations
TL;DR: The method outperforms the optimal modularity found by the existing algorithms in the literature and is feasible to be used for the accurate identification of community structure in large complex networks.
Abstract: We propose a method to find the community structure in complex networks based on an extremal optimization of the value of modularity The method outperforms the optimal modularity found by the existing algorithms in the literature giving a better understanding of the community structure We present the results of the algorithm for computer-simulated and real networks and compare them with other approaches The efficiency and accuracy of the method make it feasible to be used for the accurate identification of community structure in large complex networks
1,534 citations
TL;DR: In this article, the authors compare several approaches to community structure identification in terms of sensitivity and computational cost, and find that the most accurate methods tend to be more computationally expensive, and that both aspects need to be considered when choosing a method for practical purposes.
Abstract: We compare recent approaches to community structure identification in terms of sensitivity and computational cost. The recently proposed modularity measure is revisited and the performance of the methods as applied to ad hoc networks with known community structure, is compared. We find that the most accurate methods tend to be more computationally expensive, and that both aspects need to be considered when choosing a method for practical purposes. The work is intended as an introduction as well as a proposal for a standard benchmark test of community detection methods.
1,265 citations
Book•
09 Dec 2005TL;DR: Bayesian methods have become widespread in marketing literature as mentioned in this paper, and they have been used extensively in marketing problems, especially in situations in which there is limited information about a large number of units or where the information comes from different sources.
Abstract: Bayesian methods have become widespread in marketing literature. We review the essence of the Bayesian approach and explain why it is particularly useful for marketing problems. While the appeal of the Bayesian approach has long been noted by researchers, recent developments in computational methods and expanded availability of detailed marketplace data has fueled the growth in application of Bayesian methods in marketing. We emphasize the modularity and flexibility of modern Bayesian approaches. The usefulness of Bayesian methods in situations in which there is limited information about a large number of units or where the information comes from different sources is noted. We include an extensive discussion of open issues and directions for future research.
1,090 citations
TL;DR: Light is shed on the evolutionary forces that promote structural simplicity in biological networks and ways to improve the evolutionary design of engineered systems are offered.
Abstract: Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns termed network motifs. Little is known about the evolutionary origin of these properties. Current models of biological evolution typically produce networks that are highly nonmodular and lack understandable motifs. Here, we suggest a possible explanation for the origin of modularity and network motifs in biology. We use standard evolutionary algorithms to evolve networks. A key feature in this study is evolution under an environment (evolutionary goal) that changes in a modular fashion. That is, we repeatedly switch between several goals, each made of a different combination of subgoals. We find that such “modularly varying goals” lead to the spontaneous evolution of modular network structure and network motifs. The resulting networks rapidly evolve to satisfy each of the different goals. Such switching between related goals may represent biological evolution in a changing environment that requires different combinations of a set of basic biological functions. The present study may shed light on the evolutionary forces that promote structural simplicity in biological networks and offers ways to improve the evolutionary design of engineered systems.
873 citations
IBM1
TL;DR: A CELL processor is a multi-core chip consisting of a 64b power architecture processor, multiple streaming processors, a flexible IO interface, and a memory interface controller that is implemented in 90nm SOI technology.
Abstract: A CELL processor is a multi-core chip consisting of a 64b power architecture processor, multiple streaming processors, a flexible IO interface, and a memory interface controller This SoC is implemented in 90nm SOI technology The chip is designed with a high degree of modularity and reuse to maximize the custom circuit content and achieve a high-frequency clock-rate
611 citations
TL;DR: Three possible processing models are presented that vary in the way in which (and the extent to which) they instantiate the modularity claim and a modified concept of modularity is proposed for which an empirical program of research is more tractable.
Abstract: There is evidence, beginning with Cheng (1986), that mobile animals may use the geometry of surrounding areas to reorient following disorientation. Gallistel (1990) proposed that geometry is used to compute the major or minor axes of space and suggested that such information might form an encapsulated cognitive module. Research reviewed here, conducted on a wide variety of species since the initial discovery of the use of geometry and the formulation of the modularity claim, has supported some aspects of the approach, while casting doubt on others. Three possible processing models are presented that vary in the way in which (and the extent to which) they instantiate the modularity claim. The extant data do not permit us to discriminate among them. We propose a modified concept of modularity for which an empirical program of research is more tractable.
579 citations
TL;DR: In this paper, the concept of modularity is introduced as an approach to therapeutic protocol design and application, and a detailed example of a modular psychotherapy protocol is presented, which is defined in terms of four key properties: modularity, reusability of modules, ease of updating or reorganizing protocols and effectiveness.
Abstract: This paper introduces the concept of modularity as an approach to therapeutic protocol design and application. Modularity is defined in terms of four key properties, and a detailed example of a modular psychotherapy protocol is presented. By explicitly outlining clinical strategies and algorithms, modular design of psychotherapy protocols provides a promising framework for testing many of the assumptions underlying traditional therapy protocols. Modular design also offers numerous potential advantages in terms of design efficiency (reusability of modules, ease of updating or reorganizing protocols) and effectiveness (e.g., greater adaptability for applied contexts, increased therapist satisfaction). Finally, preliminary evidence for the efficacy of modular protocols is encouraging, and suggests that such design should preserve and could even enhance the efficacy of existing therapy protocols.
250 citations
TL;DR: In this paper, the authors conducted case studies of seven firms experiencing an environment of interfirm modularity and found that interdependencies continually emerged throughout the product development process, despite efforts to limit them.
206 citations
TL;DR: In this paper, the authors argue that there are cognitive limits to the extent of division of labour: what kinds of problems firms solve, and how they solve them, set limits to their ability to solve them.
Abstract: This paper builds upon current research into the organizational implications of ‘modularity’. Advocates of modularity argue that the ‘invisible hand’ of markets is reaching activities previously controlled through the visible hand of hierarchies. This paper argues that there are cognitive limits to the extent of division of labour: what kinds of problems firms solve, and how they solve them, set limits to the extent of division of labour, irrespective of the extent of the market. This paper analyses the cognitive limits to the division of labour, relying on an in-depth case study of engineering design activities. On this basis, it explains why coordinating increasingly specialized bodies of knowledge, and increasingly distributed learning processes, requires the presence of knowledge-integrating firms even in the presence of modular products. Such firms, relying on their wide in-house scientific and technological capabilities, have the ‘authority’ to identify, propose and implement solutions to complex pr...
199 citations
TL;DR: In the yeast Saccharomyces cerevisiae, protein interaction hubs situated in single modules are highly constrained, whereas those connecting different modules are more plastic, which could reflect a tendency for evolutionary innovations to occur by altering the proteins and interactions between rather than within modules.
Abstract: Modularity, which has been found in the functional and physical protein interaction networks of many organisms, has been postulated to affect both the mode and tempo of evolution. Here I show that in the yeast Saccharomyces cerevisiae, protein interaction hubs situated in single modules are highly constrained, whereas those connecting different modules are more plastic. This pattern of change could reflect a tendency for evolutionary innovations to occur by altering the proteins and interactions between rather than within modules, in a manner somewhat similar to the evolution of new proteins through the shuffling of conserved protein domains.
TL;DR: This work presents an analysis of communality structure in networks based on the application of simulated annealing techniques and uses as “cost function” the already introduced modularity Q (1), which isbased on the relative number of links within a commune against the number of Links that would correspond in case the links were distributed randomly.
Abstract: We present an analysis of communality structure in networks based on the application of simulated annealing techniques. In this case we use as “cost function” the already introduced modularity Q (1), which is based on the relative number of links within a commune against the number of links that would correspond in case the links were distributed randomly. We compare the results of our approach against other methodologies based on betweenness analysis and show that in all cases a better community structure can be attained.
25 Jul 2005
TL;DR: In this paper, the authors present a pointcut language that exploits information from different models of program semantics, such as the execution trace, the syntax tree, the heap, static type system, etc., and supports abstraction mechanisms analogous to functional abstraction.
Abstract: In aspect-oriented programming, pointcuts are used to describe crosscutting structure. Pointcuts that abstract over irrelevant implementation details are clearly desired to better support maintainability and modular reasoning.
We present an analysis which shows that current pointcut languages support localization of crosscutting concerns but are problematic with respect to information hiding. To cope with the problem, we present a pointcut language that exploits information from different models of program semantics, such as the execution trace, the syntax tree, the heap, static type system, etc., and supports abstraction mechanisms analogous to functional abstraction. We show how this raises the abstraction level and modularity of pointcuts and present first steps toward an efficient implementation by means of a static analysis technique.
Journal Article•
TL;DR: A pointcut language is presented that exploits information from different models of program semantics, such as the execution trace, the syntax tree, the heap, static type system, etc., and supports abstraction mechanisms analogous to functional abstraction.
Abstract: In aspect-oriented programming, pointcuts are used to describe crosscutting structure. Pointcuts that abstract over irrelevant implementation details are clearly desired to better support maintainability and modular reasoning. We present an analysis which shows that current pointcut languages support localization of crosscutting concerns but are problematic with respect to information hiding. To cope with the problem, we present a pointcut language that exploits information from different models of program semantics, such as the execution trace, the syntax tree, the heap, static type system, etc., and supports ion mechanisms analogous to functional abstraction. We show how this raises the abstraction level and modularity of pointcuts and present first steps toward an efficient implementation by means of a static analysis technique.
TL;DR: Optimization of and on the clusterization of two biological networks shows that the localized modularity identifies more cohesive clusters, yielding a complementary view of higher granularity.
Abstract: Many complex networks have an underlying modular structure, i.e., structural subunits (communities or clusters) characterized by highly interconnected nodes. The modularity $Q$ has been introduced as a measure to assess the quality of clusterizations. $Q$ has a global view, while in many real-world networks clusters are linked mainly locally among each other (local cluster connectivity). Here we introduce a measure of localized modularity $LQ$, which reflects local cluster structure. Optimization of $Q$ and $LQ$ on the clusterization of two biological networks shows that the localized modularity identifies more cohesive clusters, yielding a complementary view of higher granularity.
TL;DR: The definition of the modularity has been refined, making it more appropriate for networks such as these where multiple edges and self-connections are not included, and communities that are comparable to those expected from landscape analyses are found.
Abstract: Potential energy landscapes can be represented as a network of minima linked by transition states. The community structure of such networks has been obtained for a series of small Lennard-Jones (LJ) clusters. This community structure is compared to the concept of funnels in the potential energy landscape. Two existing algorithms have been used to find community structure, one involving removing edges with high betweenness, the other involving optimization of the modularity. The definition of the modularity has been refined, making it more appropriate for networks such as these where multiple edges and self-connections are not included. The optimization algorithm has also been improved, using Monte Carlo methods with simulated annealing and basin hopping, both often used successfully in other optimization problems. In addition to the small clusters, two examples with known heterogeneous landscapes, the 13-atom cluster (LJ13) with one labeled atom and the 38-atom cluster (LJ38) , were studied with this approach. The network methods found communities that are comparable to those expected from landscape analyses. This is particularly interesting since the network model does not take any barrier heights or energies of minima into account. For comparison, the network associated with a two-dimensional hexagonal lattice is also studied and is found to have high modularity, thus raising some questions about the interpretation of the community structure associated with such partitions.
14 Mar 2005
TL;DR: It is shown that dependency pairs can instead be used as a general concept to integrate arbitrary techniques for termination analysis and the benefits of different techniques can be combined and their modularity and power are increased significantly.
Abstract: The dependency pair approach is one of the most powerful techniques for automated termination proofs of term rewrite systems. Up to now, it was regarded as one of several possible methods to prove termination. In this paper, we show that dependency pairs can instead be used as a general concept to integrate arbitrary techniques for termination analysis. In this way, the benefits of different techniques can be combined and their modularity and power are increased significantly. We[2] refer to this new concept as the “dependency pair framework” to distinguish it from the old “dependency pair approach”. Moreover, this framework facilitates the development of new methods for termination analysis. To demonstrate this, we present several new techniques within the dependency pair framework which simplify termination problems considerably. We implemented the dependency pair framework in our termination prover AProVE and evaluated it on large collections of examples.
TL;DR: This paper argued that the enthusiasm for modularity has gone too far and pointed out that instead of exploring challenges and difficulties that management is facing in implementing modularity, there is a tendency in the "modularity" literature to generalize empirical observations that are context-specific and to confound them with prescription as well as prediction.
Abstract: Research on “modularity” has made an important contribution to the study of technical change and economic institutions. It demonstrates that progress in the division of labor in design (technical modularity) has created new opportunities for the organization of firms beyond vertical integration, by fostering vertical specialization in both manufacturing and innovation. However, a small, but growing revisionist literature contends that the enthusiasm for modularity has gone too far. Instead of exploring challenges and difficulties that management is facing in implementing modularity, there is a tendency in the “modularity” literature to generalize empirical observations that are context‐specific and to confound them with prescription as well as prediction. This paper sides with the revisionist literature in cautioning against claims of pervasive modularity. The objective is not to propose an alternative theory. More modestly, I am aiming to move the debate away from polemics to a scholarly discourse that a...
TL;DR: The results indicate that proteins, regardless of their structural class, show small-world network property, which provides indications of modularity in protein networks.
Abstract: Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show small-world network property. Various network parameters offer insight into the structural organisation of proteins and provide indications of modularity in protein networks.
TL;DR: Using computer simulation, it is demonstrated that a higher-than-expected modularity can arise during network growth through a simple model of gene duplication, without natural selection for modularity.
Abstract: Many complex networks such as computer and social networks exhibit modular structures, where links between nodes are much denser within modules than between modules. It is widely believed that cellular networks are also modular, reflecting the relative independence and coherence of different functional units in a cell. While many authors have claimed that observations from the yeast protein–protein interaction (PPI) network support the above hypothesis, the observed structural modularity may be an artifact because the current PPI data include interactions inferred from protein complexes through approaches that create modules (e.g., assigning pairwise interactions among all proteins in a complex). Here we analyze the yeast PPI network including protein complexes (PIC network) and excluding complexes (PEC network). We find that both PIC and PEC networks show a significantly greater structural modularity than that of randomly rewired networks. Nonetheless, there is little evidence that the structural modules correspond to functional units, particularly in the PEC network. More disturbingly, there is no evolutionary conservation among yeast, fly, and nematode modules at either the whole-module or protein-pair level. Neither is there a correlation between the evolutionary or phylogenetic conservation of a protein and the extent of its participation in various modules. Using computer simulation, we demonstrate that a higher-than-expected modularity can arise during network growth through a simple model of gene duplication, without natural selection for modularity. Taken together, our results suggest the intriguing possibility that the structural modules in the PPI network originated as an evolutionary byproduct without biological significance.
TL;DR: In this paper, the option value of modularity has a sizeable effect on the optimal dynamic strategy of the producer, in particular in terms of the optimal timing of the decision to invest in the first module.
TL;DR: The network information bottleneck (NIB) algorithm is applied to a number of real world networks, including the "social" network of co-authors at the 2004 APS March Meeting.
Abstract: Exploiting recent developments in information theory, we propose, illustrate, and validate a principled information-theoretic algorithm for module discovery and the resulting measure of network modularity. This measure is an order parameter (a dimensionless number between 0 and 1). Comparison is made with other approaches to module discovery and to quantifying network modularity (using Monte Carlo generated Erd\"os-like modular networks). Finally, the network information bottleneck (NIB) algorithm is applied to a number of real world networks, including the ``social'' network of coauthors at the 2004 APS March Meeting.
14 Mar 2005
TL;DR: An analysis of modularity in aspect oriented design using the theory of modular design developed by Baldwin and Clark using the three major elements of that theory, namely: Design Structure Matrix, an analysis and modeling tool; Modular Operators, units of variations for design evolution; and Net Options Value (NOV), a quantitative approach to evaluate design.
Abstract: We present an analysis of modularity in aspect oriented design using the theory of modular design developed by Baldwin and Clark [10]. We use the three major elements of that theory, namely: i) Design Structure Matrix (DSM), an analysis and modeling tool; ii) Modular Operators, units of variations for design evolution; and iii) Net Options Value (NOV), a quantitative approach to evaluate design. We study the design evolution of a Web Services application where we observe the effects of applying aspect oriented modularization.Based on our analysis we get to the following three main conclusions. First, on the structural part, it is possible to apply the DSM to aspect oriented modularizations in a straightforward manner, i.e. without modifications to DSMs basic model. This shows that aspects can, in fact, be treated as modules of design. Second, the evolution of a design into including aspect modules uses the modular operators proposed by Baldwin and Clark, with a variant of the Inversion operator. This variant captures taking redundant, scattered information hidden in modules and moving it down or keeping it at the same level in the design hierarchy. Third, when calculating and comparing NOVs of the different designs of our application, we obtained higher NOV for the design with aspects than for the design without aspects. This shows that, under this theory of modularity, certain aspect oriented modularizations can add value to the design.
TL;DR: A study of the manner in which the transition to modularity takes place in the aircraft and automobile industries and its main conclusion is that while it may be possible to posit a convergence between these two industries, the paths followed are still quite clearly opposed.
Abstract: Initial studies of modular manufacturing processes have shown that this dominant design required a fundamentally novel organisational structure of the industries. The underlying hypothesis of technological determinism merits a deeper exploration. The first part of the present paper aims at presenting the logic of this argument while making a distinction between the technological and organisational aspects of modularity. Based on this we then attempt a study of the manner in which the transition to modularity takes place in the aircraft and automobile industries. Our main conclusion is that while it may be possible to posit a convergence between these two industries, the paths followed are still quite clearly opposed.
01 Jan 2005
TL;DR: It is shown that technical constraints, such as light weighting, tight packaging and low power consumption, can drive designers towards more integral architectures.
Abstract: Modularity has become a pervasive theme in product development. Modular architecture, defined as having a one-to-one mapping from functional elements to the physical components of the product, or as “uncoupled design”, has many benefits from cost savings due to commonality to independent design of modules. However, a fully modular design may not always be achievable in designing engineering systems. In this paper, we show that technical constraints, such as light weighting, tight packaging and low power consumption, can drive designers towards more integral architectures. We quantify the degree of modularity by calculating three different modularity measures for two product pairs that represent business and technical constraint driven versions of the same product type. One of these metrics uses a singular value decomposition of the binary design structure matrix (DSM) as a measure of modularity.
TL;DR: It is shown that the spectral density of hierarchical networks follows a very different pattern, which can be used as a fingerprint of modularity, related to the homeostatic response of the network.
Abstract: The eigenvalues and eigenvectors of the connectivity matrix of complex networks contain information about its topology and its collective behavior. In particular, the spectral density $\ensuremath{\rho}(\ensuremath{\lambda})$ of this matrix reveals important network characteristics: random networks follow Wigner's semicircular law whereas scale-free networks exhibit a triangular distribution. In this paper we show that the spectral density of hierarchical networks follows a very different pattern, which can be used as a fingerprint of modularity. Of particular importance is the value $\ensuremath{\rho}(0)$, related to the homeostatic response of the network: it is maximum for random and scale-free networks but very small for hierarchical modular networks. It is also large for an actual biological protein-protein interaction network, demonstrating that the current leading model for such networks is not adequate.
TL;DR: It is shown that duplicated complexes retain the same overall function, but have different binding specificities and regulation, revealing that duplication of these modules is associated with functional specialization.
Abstract: A functional module can be defined as a spatially or chemically isolated set of functionally associated components that accomplishes a discrete biological process. Modularity is a key attribute of cellular systems, but the mechanisms that underlie the evolution of functional modules are largely unknown. Duplication of modules has been shown to be an efficient mechanism for the generation of functional innovation in the field of artificial intelligence, but has not been studied in biological networks. Therefore, we ask whether module duplication occurs in cellular networks. We developed a generic framework for the analysis of module duplication, and use it in a large-scale analysis of Saccharomyces cerevisiae protein complexes. Protein complexes are well defined, experimentally derived, functional modules. We observe that at least 6%-20% of the protein complexes have strong similarity to other complexes; thus a considerable fraction has evolved by duplication. Our results indicate that many complexes evolved by step-wise partial duplications. We show that duplicated complexes retain the same overall function, but have different binding specificities and regulation, revealing that duplication of these modules is associated with functional specialization.
Posted Content•
TL;DR: In this article, the authors make a distinction between the technological and organisational aspects of modularity, and attempt to study the manner in which the transition to modularity takes place in the aircraft and automobile industries.
Abstract: Initial studies of modular manufacturing processes have shown that this dominant design required a fundamentally novel organisational structure of the industries. The underlying hypothesis of technological determinism merits a deeper exploration. The first part of the present paper aims at presenting the logic of this argument while making a distinction between the technological and organisational aspects of modularity. Based on this we then attempt a study of the manner in which the transition to modularity takes place in the aircraft and automobile industries. Our main conclusion is that while it may be possible to posit a convergence between these two industries, the paths followed are still quite clearly opposed. (This abstract was borrowed from another version of this item.)
01 Jan 2005
TL;DR: A new way to simplify the construction of precise broad-coverage grammars, employing typologicallymotivated, customizable extensions to a language-independent core grammar, and each ‘module’ represents a salient dimension of cross-linguistic variation.
Abstract: We present a new way to simplify the construction of precise broad-coverage grammars, employing typologicallymotivated, customizable extensions to a language-independent core grammar. Each ‘module’ represents a salient dimension of cross-linguistic variation, and presents the grammar developer with simple choices that result in automatically generated language-specific software. We illustrate the approach for several phenomena and explore the interdependence of the modules.
28 Jul 2005
TL;DR: This method combines spectral properties of some matrices encoding the network topology, with well known hierarchical clustering techniques, and the use of the modularity parameter to quantify the goodness of any possible community subdivision.
Abstract: We review and improve a recently introduced method for the detection of communities in complex networks. This method combines spectral properties of some matrices encoding the network topology, with well known hierarchical clustering techniques, and the use of the modularity parameter to quantify the goodness of any possible community subdivision. This provides one of the best available methods for the detection of community structures in complex systems.