Task-Dependent Evolution of Modularity in Neural Networks1
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Modularity As a Concept Modern Ideas About Mental Modularity Typically Use Fodor (1983) As a Key Touchstone
COGNITIVE PROCESSING International Quarterly of Cognitive Science Mental modularity, metaphors, and the marriage of evolutionary and cognitive sciences GARY L. BRASE University of Missouri – Columbia Abstract - As evolutionary approaches in the behavioral sciences become increasingly prominent, issues arising from the proposition that the mind is a collection of modular adaptations (the multi-modular mind thesis) become even more pressing. One purpose of this paper is to help clarify some valid issues raised by this thesis and clarify why other issues are not as critical. An aspect of the cognitive sciences that appears to both promote and impair progress on this issue (in different ways) is the use of metaphors for understand- ing the mind. Utilizing different metaphors can yield different perspectives and advancement in our understanding of the nature of the human mind. A second purpose of this paper is to outline the kindred natures of cognitive science and evolutionary psychology, both of which cut across traditional academic divisions and engage in functional analyses of problems. Key words: Evolutionary Theory, Cognitive Science, Modularity, Metaphors Evolutionary approaches in the behavioral sciences have begun to influence a wide range of fields, from cognitive neuroscience (e.g., Gazzaniga, 1998), to clini- cal psychology (e.g., Baron-Cohen, 1997; McGuire and Troisi, 1998), to literary theory (e.g., Carroll, 1999). At the same time, however, there are ongoing debates about the details of what exactly an evolutionary approach – often called evolu- tionary psychology— entails (Holcomb, 2001). Some of these debates are based on confusions of terminology, implicit arguments, or misunderstandings – things that can in principle be resolved by clarifying current ideas. -
Networks in Nature: Dynamics, Evolution, and Modularity
Networks in Nature: Dynamics, Evolution, and Modularity Sumeet Agarwal Merton College University of Oxford A thesis submitted for the degree of Doctor of Philosophy Hilary 2012 2 To my entire social network; for no man is an island Acknowledgements Primary thanks go to my supervisors, Nick Jones, Charlotte Deane, and Mason Porter, whose ideas and guidance have of course played a major role in shaping this thesis. I would also like to acknowledge the very useful sug- gestions of my examiners, Mark Fricker and Jukka-Pekka Onnela, which have helped improve this work. I am very grateful to all the members of the three Oxford groups I have had the fortune to be associated with: Sys- tems and Signals, Protein Informatics, and the Systems Biology Doctoral Training Centre. Their companionship has served greatly to educate and motivate me during the course of my time in Oxford. In particular, Anna Lewis and Ben Fulcher, both working on closely related D.Phil. projects, have been invaluable throughout, and have assisted and inspired my work in many different ways. Gabriel Villar and Samuel Johnson have been col- laborators and co-authors who have helped me to develop some of the ideas and methods used here. There are several other people who have gener- ously provided data, code, or information that has been directly useful for my work: Waqar Ali, Binh-Minh Bui-Xuan, Pao-Yang Chen, Dan Fenn, Katherine Huang, Patrick Kemmeren, Max Little, Aur´elienMazurie, Aziz Mithani, Peter Mucha, George Nicholson, Eli Owens, Stephen Reid, Nico- las Simonis, Dave Smith, Ian Taylor, Amanda Traud, and Jeffrey Wrana. -
Modularity in Static and Dynamic Networks
Modularity in static and dynamic networks Sarah F. Muldoon University at Buffalo, SUNY OHBM – Brain Graphs Workshop June 25, 2017 Outline 1. Introduction: What is modularity? 2. Determining community structure (static networks) 3. Comparing community structure 4. Multilayer networks: Constructing multitask and temporal multilayer dynamic networks 5. Dynamic community structure 6. Useful references OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon Introduction: What is Modularity? OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon What is Modularity? Modularity (Community Structure) • A module (community) is a subset of vertices in a graph that have more connections to each other than to the rest of the network • Example social networks: groups of friends Modularity in the brain: • Structural networks: communities are groups of brain areas that are more highly connected to each other than the rest of the brain • Functional networks: communities are groups of brain areas with synchronous activity that is not synchronous with other brain activity OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon Findings: The Brain is Modular Structural networks: cortical thickness correlations sensorimotor/spatial strategic/executive mnemonic/emotion olfactocentric auditory/language visual processing Chen et al. (2008) Cereb Cortex OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon Findings: The Brain is Modular • Functional networks: resting state fMRI He et al. (2009) PLOS One OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon Findings: The -
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B. M ü ller, G ü nter P. Wagner, and Werner Callebaut, editors The Evolution of Cognition , edited by Cecilia Heyes and Ludwig Huber, 2000 Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology , edited by Gerd B. M ü ller and Stuart A. Newman, 2003 Environment, Development, and Evolution: Toward a Synthesis , edited by Brian K. Hall, Roy D. Pearson, and Gerd B. M ü ller, 2004 Evolution of Communication Systems: A Comparative Approach , edited by D. Kimbrough Oller and Ulrike Griebel, 2004 Modularity: Understanding the Development and Evolution of Natural Complex Systems , edited by Werner Callebaut and Diego Rasskin-Gutman, 2005 Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution , by Richard A. Watson, 2006 Biological Emergences: Evolution by Natural Experiment , by Robert G. B. Reid, 2007 Modeling Biology: Structure, Behaviors, Evolution , edited by Manfred D. Laubichler and Gerd B. M ü ller, 2007 Evolution of Communicative Flexibility: Complexity, Creativity, and Adaptability in Human and Animal Communication , edited by Kimbrough D. Oller and Ulrike Griebel, 2008 Functions in Biological and Artifi cial Worlds: Comparative Philosophical Perspectives , edited by Ulrich Krohs and Peter Kroes, 2009 Cognitive Biology: Evolutionary and Developmental Perspectives on Mind, Brain, and Behavior , edited by Luca Tommasi, Mary A. Peterson, and Lynn Nadel, 2009 Innovation in Cultural Systems: Contributions from Evolutionary Anthropology , edited by Michael J. O ’ Brien and Stephen J. Shennan, 2010 The Major Transitions in Evolution Revisited , edited by Brett Calcott and Kim Sterelny, 2011 Transformations of Lamarckism: From Subtle Fluids to Molecular Biology , edited by Snait B. -
Multidimensional Network Analysis
Universita` degli Studi di Pisa Dipartimento di Informatica Dottorato di Ricerca in Informatica Ph.D. Thesis Multidimensional Network Analysis Michele Coscia Supervisor Supervisor Fosca Giannotti Dino Pedreschi May 9, 2012 Abstract This thesis is focused on the study of multidimensional networks. A multidimensional network is a network in which among the nodes there may be multiple different qualitative and quantitative relations. Traditionally, complex network analysis has focused on networks with only one kind of relation. Even with this constraint, monodimensional networks posed many analytic challenges, being representations of ubiquitous complex systems in nature. However, it is a matter of common experience that the constraint of considering only one single relation at a time limits the set of real world phenomena that can be represented with complex networks. When multiple different relations act at the same time, traditional complex network analysis cannot provide suitable an- alytic tools. To provide the suitable tools for this scenario is exactly the aim of this thesis: the creation and study of a Multidimensional Network Analysis, to extend the toolbox of complex network analysis and grasp the complexity of real world phenomena. The urgency and need for a multidimensional network analysis is here presented, along with an empirical proof of the ubiquity of this multifaceted reality in different complex networks, and some related works that in the last two years were proposed in this novel setting, yet to be systematically defined. Then, we tackle the foundations of the multidimensional setting at different levels, both by looking at the basic exten- sions of the known model and by developing novel algorithms and frameworks for well-understood and useful problems, such as community discovery (our main case study), temporal analysis, link prediction and more. -
The Impact of Component Modularity on Design Evolution: Evidence from the Software Industry
08-038 The Impact of Component Modularity on Design Evolution: Evidence from the Software Industry Alan MacCormack John Rusnak Carliss Baldwin Copyright © 2007 by Alan MacCormack, John Rusnak, and Carliss Baldwin. Working papers are in draft form. This working paper is distributed for purposes of comment and discussion only. It may not be reproduced without permission of the copyright holder. Copies of working papers are available from the author. Abstract Much academic work asserts a relationship between the design of a complex system and the manner in which this system evolves over time. In particular, designs which are modular in nature are argued to be more “evolvable,” in that these designs facilitate making future adaptations, the nature of which do not have to be specified in advance. In essence, modularity creates “option value” with respect to new and improved designs, which is particularly important when a system must meet uncertain future demands. Despite the conceptual appeal of this research, empirical work exploring the relationship between modularity and evolution has had limited success. Three major challenges persist: first, it is difficult to measure modularity in a robust and repeatable fashion; second, modularity is a property of individual components, not systems as a whole, hence we must examine these dynamics at the microstructure level; and third, evolution is a temporal phenomenon, in that the conditions at time t affect the nature of the design at time t+1, hence exploring this phenomenon requires longitudinal data. In this paper, we tackle these challenges by analyzing the evolution of a successful commercial software product over its entire lifetime, comprising six major “releases.” In particular, we develop measures of modularity at the component level, and use these to predict patterns of evolution between successive versions of the design. -
A Network Approach to Define Modularity of Components In
A Network Approach to Define Modularity of Components Manuel E. Sosa1 Technology and Operations Management Area, in Complex Products INSEAD, 77305 Fontainebleau, France Modularity has been defined at the product and system levels. However, little effort has e-mail: [email protected] gone into defining and quantifying modularity at the component level. We consider com- plex products as a network of components that share technical interfaces (or connections) Steven D. Eppinger in order to function as a whole and define component modularity based on the lack of Sloan School of Management, connectivity among them. Building upon previous work in graph theory and social net- Massachusetts Institute of Technology, work analysis, we define three measures of component modularity based on the notion of Cambridge, Massachusetts 02139 centrality. Our measures consider how components share direct interfaces with adjacent components, how design interfaces may propagate to nonadjacent components in the Craig M. Rowles product, and how components may act as bridges among other components through their Pratt & Whitney Aircraft, interfaces. We calculate and interpret all three measures of component modularity by East Hartford, Connecticut 06108 studying the product architecture of a large commercial aircraft engine. We illustrate the use of these measures to test the impact of modularity on component redesign. Our results show that the relationship between component modularity and component redesign de- pends on the type of interfaces connecting product components. We also discuss direc- tions for future work. ͓DOI: 10.1115/1.2771182͔ 1 Introduction The need to measure modularity has been highlighted implicitly by Saleh ͓12͔ in his recent invitation “to contribute to the growing Previous research on product architecture has defined modular- field of flexibility in system design” ͑p. -
Analyzing Social Media Network for Students in Presidential Election 2019 with Nodexl
ANALYZING SOCIAL MEDIA NETWORK FOR STUDENTS IN PRESIDENTIAL ELECTION 2019 WITH NODEXL Irwan Dwi Arianto Doctoral Candidate of Communication Sciences, Airlangga University Corresponding Authors: [email protected] Abstract. Twitter is widely used in digital political campaigns. Twitter as a social media that is useful for building networks and even connecting political participants with the community. Indonesia will get a demographic bonus starting next year until 2030. The number of productive ages that will become a demographic bonus if not recognized correctly can be a problem. The election organizer must seize this opportunity for the benefit of voter participation. This study aims to describe the network structure of students in the 2019 presidential election. The first debate was held on January 17, 2019 as a starting point for data retrieval on Twitter social media. This study uses data sources derived from Twitter talks from 17 January 2019 to 20 August 2019 with keywords “#pilpres2019 OR #mahasiswa since: 2019-01-17”. The data obtained were analyzed by the communication network analysis method using NodeXL software. Our Analysis found that Top Influencer is @jokowi, as well as Top, Mentioned also @jokowi while Top Tweeters @okezonenews and Top Replied-To @hasmi_bakhtiar. Jokowi is incumbent running for re-election with Ma’ruf Amin (Senior Muslim Cleric) as his running mate against Prabowo Subianto (a former general) and Sandiaga Uno as his running mate (former vice governor). This shows that the more concentrated in the millennial generation in this case students are presidential candidates @jokowi. @okezonenews, the official twitter account of okezone.com (MNC Media Group). -
Modularity in Animal Development and Evolution: Elements of a Conceptual Framework for Evodevo
JOURNAL OF EXPERIMENTAL ZOOLOGY (MOL DEV EVOL) 285:307–325 (1999) Modularity in Animal Development and Evolution: Elements of a Conceptual Framework for EvoDevo GEORGE VON DASSOW*AND ED MUNRO Department of Zoology, University of Washington, Seattle, Washington 98195-1800 ABSTRACT For at least a century biologists have been talking, mostly in a black-box sense, about developmental mechanisms. Only recently have biologists succeeded broadly in fishing out the contents of these black boxes. Unfortunately the view from inside the black box is almost as obscure as that from without, and developmental biologists increasingly confront the need to synthesize known facts about developmental phenomena into mechanistic descriptions of com- plex systems. To evolutionary biologists, the emerging understanding of developmental mecha- nisms is an opportunity to understand the origins of variation not just in the selective milieu but also in the variability of the developmental process, the substrate for morphological change. Ultimately, evolutionary developmental biology (EvoDevo) expects to articulate how the diversity of organic form results from adaptive variation in development. This ambition demands a shift in the way biologists describe causality, and the central problem of EvoDevo is to understand how the architecture of development confers evolvability. We argue in this essay that it makes little sense to think of this question in terms of individual gene function or isolated morphometrics, but rather in terms of higher-order modules such as gene networks and homologous characters. We outline the conceptual challenges raised by this shift in perspective, then present a selection of case studies we believe to be paradigmatic for how biologists think about modularity in devel- opment and evolution. -
The Emergence of Modularity in Biological Systems
The Emergence of Modularity in Biological Systems Zhenyu Wang Dec. 2007 Abstract: Modularity is a ubiquitous phenomenon in various biological systems, both in genotype and in phenotype. Biological modules, which consist of components relatively independent in functions as well as in morphologies, have facilitated daily performance of biological systems and their long time evolution in history. How did modularity emerge? A mechanism with horizontal gene transfer and a biological version of spin-glass model is addressed here. When the spontaneous symmetry is broken in an evolving environment, here comes modularity. Further improvement is also discussed at the end. 1 Introduction Modularity is an important concept with broad applications in computer science, especially in programming. A module, usually composed of various components, is a relatively independent entity in its operation with respect to other entities in the whole system. For a programmer, the employment of a module will increase the efficiency of coding, decrease the potential of errors, enhance the stability of the operation and facilitate the further improvement of the program. Coincidently, the nature thinks the same in its programming life: various biological systems are also in a modular fashion! Let us take the model organism fruit fly Drosophila melanogaster as an example to sip the ubiquitous modularity in biological systems. In view of morphology, Drosophila is a typical modular insect, whose adult is composed of an anterior head, followed by three thoracic segments, and eight abdominal segments at posterior[1](Fig. 1). Such a kind of segmentation is induced by a cascade of transcription factors in the embryo. First, maternal effect genes which are expressed in the mother’s ovary cells distribute cytoplasmic determinants unevenly in fertilized eggs, which thus determines anterior-posterior and dorsal-ventral axis. -
Ensemble-Based Community Detection in Multilayer Networks
ENSEMBLE-BASED COMMUNITY DETECTION IN MULTILAYER NETWORKS Andrea Tagarelli, Alessia Amelio, Francesco Gullo The 2017 European Conference on Machine Learning & Principles and Practice of Knowledge Discovery in DataBases Experimental evaluation Datasets • Our experimental evaluation was mainly conducted on seven real-world multilayer network datasets Experimental evaluation Datasets • We also resorted to a synthetic multilayer network generator, mLFR Benchmark, mainly for our evaluation of efficiency of the M-EMCD method • We used mLFR to create a multilayer network with 1 million of nodes, setting other available parameters as follows: • 10 layers, • average degree 30, • maximum degree 100, • mixing at 20% , • layer mixing 2. Experimental evaluation Competing methods • flattening methods • apply a community detection method on the flattened graph of the input multilayer network • it is a weighted multigraph having V as set of nodes, the set of edges, and edge weights that express the number of layers on which two nodes are connected • Nerstrand algorithm1 1 D. LaSalle and G. Karypis, "Multi-threaded modularity based graph clustering using the multilevel paradigm", J. Parallel Distrib. Comput., 76:66–80, 2015. Experimental evaluation Competing methods • aggregation methods • detect a community structure separately for each network layer, after that an aggregation mechanism is used to obtain the final community structure • Principal Modularity Maximization (PMM)2 • frequent pAttern mining-BAsed Community discoverer in mUltidimensional networkS (ABACUS)3 2 L. Tang, X. Wang, and H. Liu, “Uncovering groups via heterogeneous interaction analysis,” in Proc. ICDM, 2009, pp. 503–512. 3 M. Berlingerio, F. Pinelli, and F. Calabrese, "ABACUS: frequent pattern mining-based community discovery in multidimensional networks", Data Min. -
On Community Structure in Complex Networks: Challenges and Opportunities
On community structure in complex networks: challenges and opportunities Hocine Cherifi · Gergely Palla · Boleslaw K. Szymanski · Xiaoyan Lu Received: November 5, 2019 Abstract Community structure is one of the most relevant features encoun- tered in numerous real-world applications of networked systems. Despite the tremendous effort of a large interdisciplinary community of scientists working on this subject over the past few decades to characterize, model, and analyze communities, more investigations are needed in order to better understand the impact of community structure and its dynamics on networked systems. Here, we first focus on generative models of communities in complex networks and their role in developing strong foundation for community detection algorithms. We discuss modularity and the use of modularity maximization as the basis for community detection. Then, we follow with an overview of the Stochastic Block Model and its different variants as well as inference of community structures from such models. Next, we focus on time evolving networks, where existing nodes and links can disappear, and in parallel new nodes and links may be introduced. The extraction of communities under such circumstances poses an interesting and non-trivial problem that has gained considerable interest over Hocine Cherifi LIB EA 7534 University of Burgundy, Esplanade Erasme, Dijon, France E-mail: hocine.cherifi@u-bourgogne.fr Gergely Palla MTA-ELTE Statistical and Biological Physics Research Group P´azm´any P. stny. 1/A, Budapest, H-1117, Hungary E-mail: [email protected] Boleslaw K. Szymanski Department of Computer Science & Network Science and Technology Center Rensselaer Polytechnic Institute 110 8th Street, Troy, NY 12180, USA E-mail: [email protected] Xiaoyan Lu Department of Computer Science & Network Science and Technology Center Rensselaer Polytechnic Institute 110 8th Street, Troy, NY 12180, USA E-mail: [email protected] arXiv:1908.04901v3 [physics.soc-ph] 6 Nov 2019 2 Cherifi, Palla, Szymanski, Lu the last decade.