Santa Fe Institute

About: Santa Fe Institute is a nonprofit organization based out in Santa Fe, New Mexico, United States. It is known for research contribution in the topics: Population & Context (language use). The organization has 558 authors who have published 4558 publications receiving 396015 citations. The organization is also known as: SFI.

Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality

Abstract: Using computer databases of scientific papers in physics, biomedical research, and computer science, we have constructed networks of collaboration between scientists in each of these disciplines. In these networks two scientists are considered connected if they have coauthored one or more papers together. Here we study a variety of nonlocal statistics for these networks, such as typical distances between scientists through the network, and measures of centrality such as closeness and betweenness. We further argue that simple networks such as these cannot capture variation in the strength of collaborative ties and propose a measure of collaboration strength based on the number of papers coauthored by pairs of scientists, and the number of other scientists with whom they coauthored those papers.

Network Robustness and Fragility: Percolation on Random Graphs

Abstract: Recent work on the Internet, social networks, and the power grid has addressed the resilience of these networks to either random or targeted deletion of network nodes or links. Such deletions include, for example, the failure of Internet routers or power transmission lines. Percolation models on random graphs provide a simple representation of this process but have typically been limited to graphs with Poisson degree distribution at their vertices. Such graphs are quite unlike real-world networks, which often possess power-law or other highly skewed degree distributions. In this paper we study percolation on graphs with completely general degree distribution, giving exact solutions for a variety of cases, including site percolation, bond percolation, and models in which occupation probabilities depend on vertex degree. We discuss the application of our theory to the understanding of network resilience.

Growth, innovation, scaling, and the pace of life in cities

Abstract: ‡§ ¶ Humanity has just crossed a major landmark in its history with the majority of people now living in cities. Cities have long been known to be society’s predominant engine of innovation and wealth creation, yet they are also its main source of crime, pollution, and disease. The inexorable trend toward urbanization worldwide presents an urgent challenge for developing a predictive, quantitative theory of urban organization and sustainable development. Here we present empirical evidence indicating that the processes relating urbanization to economic development and knowledge creation are very general, being shared by all cities belonging to the same urban system and sustained across different nations and times. Many diverse properties of cities from patent production and personal income to electrical cable length are shown to be power law functions of population size with scaling exponents, , that fall into distinct universality classes. Quantities reflecting wealth creation and innovation have 1.2 >1 (increasing returns), whereas those accounting for infrastructure display 0.8 <1 (economies of scale). We predict that the pace of social life in the city increases with population size, in quantitative agreement with data, and we discuss how cities are similar to, and differ from, biological organisms, for which <1. Finally, we explore possible consequences of these scaling relations by deriving growth equations, which quantify the dramatic difference between growth fueled by innovation versus that driven by economies of scale. This difference suggests that, as population grows, major innovation cycles must be generated at a continually accelerating rate to sustain growth and avoid stagnation or collapse. population sustainability urban studies increasing returns economics of scale

Hierarchical structure and the prediction of missing links in networks

Abstract: Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, in which vertices divide into groups that further subdivide into groups of groups, and so forth over multiple scales. In many cases the groups are found to correspond to known functional units, such as ecological niches in food webs, modules in biochemical networks (protein interaction networks, metabolic networks or genetic regulatory networks) or communities in social networks. Here we present a general technique for inferring hierarchical structure from network data and show that the existence of hierarchy can simultaneously explain and quantitatively reproduce many commonly observed topological properties of networks, such as right-skewed degree distributions, high clustering coefficients and short path lengths. We further show that knowledge of hierarchical structure can be used to predict missing connections in partly known networks with high accuracy, and for more general network structures than competing techniques. Taken together, our results suggest that hierarchy is a central organizing principle of complex networks, capable of offering insight into many network phenomena.

Fast folding and comparison of RNA secondary structures

Abstract: Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities. An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment. All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.