Carl T. Bergstrom

Bio: Carl T. Bergstrom is an academic researcher from University of Washington. The author has contributed to research in topics: Population & Eigenfactor. The author has an hindex of 58, co-authored 146 publications receiving 16229 citations. Previous affiliations of Carl T. Bergstrom include Santa Fe Institute & Stanford University.

Maps of random walks on complex networks reveal community structure

Abstract: To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network—including physics, chemistry, molecular biology, and medicine—information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.

An information-theoretic framework for resolving community structure in complex networks

Abstract: To understand the structure of a large-scale biological, social, or technological network, it can be helpful to decompose the network into smaller subunits or modules. In this article, we develop an information-theoretic foundation for the concept of modularity in networks. We identify the modules of which the network is composed by finding an optimal compression of its topology, capitalizing on regularities in its structure. We explain the advantages of this approach and illustrate them by partitioning a number of real-world and model networks.

The map equation

Abstract: Many real-world networks are so large that we must simplify their structure before we can extract useful information about the systems they represent. As the tools for doing these simplifications proliferate within the network literature, researchers would benefit from some guidelines about which of the so-called community detection algorithms are most appropriate for the structures they are studying and the questions they are asking. Here we show that different methods highlight different aspects of a network's structure and that the the sort of information that we seek to extract about the system must guide us in our decision. For example, many community detection algorithms, including the popular modularity maximization approach, infer module assignments from an underlying model of the network formation process. However, we are not always as interested in how a system's network structure was formed, as we are in how a network's extant structure influences the system's behavior. To see how structure influences current behavior, we will recognize that links in a network induce movement across the network and result in system-wide interdependence. In doing so, we explicitly acknowledge that most networks carry flow. To highlight and simplify the network structure with respect to this flow, we use the map equation. We present an intuitive derivation of this flow-based and information-theoretic method and provide an interactive on-line application that anyone can use to explore the mechanics of the map equation. The differences between the map equation and the modularity maximization approach are not merely conceptual. Because the map equation attends to patterns of flow on the network and the modularity maximization approach does not, the two methods can yield dramatically different results for some network structures. To illustrate this and build our understanding of each method, we partition several sample networks. We also describe an algorithm and provide source code to efficiently decompose large weighted and directed networks based on the map equation.

Science of science

Abstract: BACKGROUND The increasing availability of digital data on scholarly inputs and outputs—from research funding, productivity, and collaboration to paper citations and scientist mobility—offers unprecedented opportunities to explore the structure and evolution of science. The science of science (SciSci) offers a quantitative understanding of the interactions among scientific agents across diverse geographic and temporal scales: It provides insights into the conditions underlying creativity and the genesis of scientific discovery, with the ultimate goal of developing tools and policies that have the potential to accelerate science. In the past decade, SciSci has benefited from an influx of natural, computational, and social scientists who together have developed big data–based capabilities for empirical analysis and generative modeling that capture the unfolding of science, its institutions, and its workforce. The value proposition of SciSci is that with a deeper understanding of the factors that drive successful science, we can more effectively address environmental, societal, and technological problems. ADVANCES Science can be described as a complex, self-organizing, and evolving network of scholars, projects, papers, and ideas. This representation has unveiled patterns characterizing the emergence of new scientific fields through the study of collaboration networks and the path of impactful discoveries through the study of citation networks. Microscopic models have traced the dynamics of citation accumulation, allowing us to predict the future impact of individual papers. SciSci has revealed choices and trade-offs that scientists face as they advance both their own careers and the scientific horizon. For example, measurements indicate that scholars are risk-averse, preferring to study topics related to their current expertise, which constrains the potential of future discoveries. Those willing to break this pattern engage in riskier careers but become more likely to make major breakthroughs. Overall, the highest-impact science is grounded in conventional combinations of prior work but features unusual combinations. Last, as the locus of research is shifting into teams, SciSci is increasingly focused on the impact of team research, finding that small teams tend to disrupt science and technology with new ideas drawing on older and less prevalent ones. In contrast, large teams tend to develop recent, popular ideas, obtaining high, but often short-lived, impact. OUTLOOK SciSci offers a deep quantitative understanding of the relational structure between scientists, institutions, and ideas because it facilitates the identification of fundamental mechanisms responsible for scientific discovery. These interdisciplinary data-driven efforts complement contributions from related fields such as scientometrics and the economics and sociology of science. Although SciSci seeks long-standing universal laws and mechanisms that apply across various fields of science, a fundamental challenge going forward is accounting for undeniable differences in culture, habits, and preferences between different fields and countries. This variation makes some cross-domain insights difficult to appreciate and associated science policies difficult to implement. The differences among the questions, data, and skills specific to each discipline suggest that further insights can be gained from domain-specific SciSci studies, which model and identify opportunities adapted to the needs of individual research fields.

Mapping change in large networks

Abstract: Change is a fundamental ingredient of interaction patterns in biology, technology, the economy, and science itself: Interactions within and between organisms change; transportation patterns by air, land, and sea all change; the global financial flow changes; and the frontiers of scientific research change. Networks and clustering methods have become important tools to comprehend instances of these large-scale structures, but without methods to distinguish between real trends and noisy data, these approaches are not useful for studying how networks change. Only if we can assign significance to the partitioning of single networks can we distinguish meaningful structural changes from random fluctuations. Here we show that bootstrap resampling accompanied by significance clustering provides a solution to this problem. To connect changing structures with the changing function of networks, we highlight and summarize the significant structural changes with alluvial diagrams and realize de Solla Price's vision of mapping change in science: studying the citation pattern between about 7000 scientific journals over the past decade, we find that neuroscience has transformed from an interdisciplinary specialty to a mature and stand-alone discipline.

The Theory of Island Biogeography

Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

Community detection in graphs

Abstract: The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.