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Using Protein Interaction Networks to Understand Complex Diseases

Recent developments in biotechnology have enabled interrogation of the cell at various levels, leading to many types of "omic" data that provide valuable information on multiple genetic and environmental factors and their interactions. The featured Web extra is a video interview with Mehmet Koyutürk of Case Western Reserve about how biotechnology can track genetic markers to advance cancer research.

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Bees

Bees | Papers | Scoop.it

The world of bees is fascinating and varied. The common honeybee is the most well-known and well-studied species, but there are thousands of wild bee species that enliven our landscapes and help to pollinate crops and wildflowers. The widely reported threats to honeybees, which cause their colonies to collapse, also jeopardize the lives of these lesser-known and under-appreciated bee species.


http://www.nature.com/nature/outlook/bees/index.html 

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Phase transitions in Pareto optimal complex networks

The organization of interactions in complex systems can be described by networks connecting different units. These graphs are useful representations of the local and global complexity of the underlying systems. The origin of their topological structure can be diverse, resulting from different mechanisms including multiplicative processes and optimization. In spatial networks or in graphs where cost constraints are at work, as it occurs in a plethora of situations from power grids to the wiring of neurons in the brain, optimization plays an important part in shaping their organization. In this paper we study network designs resulting from a Pareto optimization process, where different simultaneous constraints are the targets of selection. We analyze three variations on a problem finding phase transitions of different kinds. Distinct phases are associated to different arrangements of the connections; but the need of drastic topological changes does not determine the presence, nor the nature of the phase transitions encountered. Instead, the functions under optimization do play a determinant role. This reinforces the view that phase transitions do not arise from intrinsic properties of a system alone, but from the interplay of that system with its external constraints.


Phase transitions in Pareto optimal complex networks
Luís F Seoane, Ricard Solé

http://arxiv.org/abs/1505.06937

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A U.S. Research Roadmap for Human Computation

The Web has made it possible to harness human cognition en masse to achieve new capabilities. Some of these successes are well known; for example Wikipedia has become the go-to place for basic information on all things; Duolingo engages millions of people in real-life translation of text, while simultaneously teaching them to speak foreign languages; and fold.it has enabled public-driven scientific discoveries by recasting complex biomedical challenges into popular online puzzle games. These and other early successes hint at the tremendous potential for future crowd-powered capabilities for the benefit of health, education, science, and society. In the process, a new field called Human Computation has emerged to better understand, replicate, and improve upon these successes through scientific research. Human Computation refers to the science that underlies online crowd-powered systems and was the topic of a recent visioning activity in which a representative cross-section of researchers, industry practitioners, visionaries, funding agency representatives, and policy makers came together to understand what makes crowd-powered systems successful. Teams of experts considered past, present, and future human computation systems to explore which kinds of crowd-powered systems have the greatest potential for societal impact and which kinds of research will best enable the efficient development of new crowd-powered systems to achieve this impact. This report summarize the products and findings of those activities as well as the unconventional process and activities employed by the workshop, which were informed by human computation research.


A U.S. Research Roadmap for Human Computation
Pietro Michelucci, Lea Shanley, Janis Dickinson, Haym Hirsh

http://arxiv.org/abs/1505.07096

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Predicting traffic volumes and estimating the effects of shocks in massive transportation systems

We propose a new approach to analyzing massive transportation systems that leverages traffic information about individual travelers. The goals of the analysis are to quantify the effects of shocks in the system, such as line and station closures, and to predict traffic volumes. We conduct an in-depth statistical analysis of the Transport for London railway traffic system. The proposed methodology is unique in the way that past disruptions are used to predict unseen scenarios, by relying on simple physical assumptions of passenger flow and a system-wide model for origin–destination movement. The method is scalable, more accurate than blackbox approaches, and generalizable to other complex transportation systems. It therefore offers important insights to inform policies on urban transportation.


Predicting traffic volumes and estimating the effects of shocks in massive transportation systems
Ricardo Silva, Soong Moon Kang, and Edoardo M. Airoldi

http://dx.doi.org/10.1073/pnas.1412908112
PNAS May 5, 2015 vol. 112 no. 18 5643-5648


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Artificial Life in Quantum Technologies

We develop a quantum information protocol that models the biological behaviors of individuals living in a natural selection scenario. The artificially engineered evolution of the quantum living units shows the fundamental features of life in a common environment, such as self-replication, mutation, interaction of individuals, and death. We propose how to mimic these bio-inspired features in a quantum-mechanical formalism, which allows for an experimental implementation achievable with current quantum platforms. This result paves the way for the realization of artificial life and embodied evolution with quantum technologies.


Artificial Life in Quantum Technologies
U. Alvarez-Rodriguez, M. Sanz, L. Lamata, E. Solano

http://arxiv.org/abs/1505.03775

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Beyond Contact Tracing: Community-Based Early Detection for Ebola Response

Beyond Contact Tracing: Community-Based Early Detection for Ebola Response | Papers | Scoop.it

The 2014 Ebola outbreak in west Africa raised many questions about the control of infectious disease in an increasingly connected global society. Limited availability of contact information has made contact tracing difficult or impractical in combating the outbreak. We consider the development of multi-scale public health strategies and simulate policies for community-level response aimed at early screening of communities rather than individuals, as well as travel restrictions to prevent community cross-contamination. Our analysis shows community screening to be effective even at a relatively low level of compliance. In our simulations, 40% of individuals conforming to this policy is enough to stop the outbreak. Simulations with a 50% compliance rate are consistent with the case counts in Liberia during the period of rapid decline after mid September, 2014. We also find the travel restriction policies to be effective at reducing the risks associated with compliance substantially below the 40% level, shortening the outbreak and enabling efforts to be focused on affected areas. Our results suggest that the multi-scale approach could be applied to help end the outbreaks in Guinea and Sierra Leone, and the generality of our model can be used to further evolve public health strategy for defeating emerging epidemics.


D. Cooney, V. Wong, Y. Bar-Yam, Beyond contact tracing: Community-based early detection for Ebola response, ArXiv:1505.07020 [physics.soc-ph] (May 26, 2014); New England Complex Systems Institute Report 15-05-01

http://necsi.edu/research/social/pandemics/beyondcontact.html 

Complexity Digest's insight:

See Also: http://time.com/3892513/did-authorities-use-the-wrong-approach-to-stop-ebola/ 

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“Waiting for Carnot”: Information and complexity

The relationship between information and complexity is analyzed using a detailed literature analysis. Complexity is a multifaceted concept, with no single agreed definition. There are numerous approaches to defining and measuring complexity and organization, all involving the idea of information. Conceptions of complexity, order, organization, and “interesting order” are inextricably intertwined with those of information. Shannon's formalism captures information's unpredictable creative contributions to organized complexity; a full understanding of information's relation to structure and order is still lacking. Conceptual investigations of this topic should enrich the theoretical basis of the information science discipline, and create fruitful links with other disciplines that study the concepts of information and complexity.


“Waiting for Carnot”: Information and complexity
David Bawden and Lyn Robinson

Journal of the Association for Information Science and Technology
Early View

http://dx.doi.org/10.1002/asi.23535

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Topological effects of network structure on long-term social network dynamics in a wild mammal

Social structure influences ecological processes such as dispersal and invasion, and affects survival and reproductive success. Recent studies have used static snapshots of social networks, thus neglecting their temporal dynamics, and focused primarily on a limited number of variables that might be affecting social structure. Here, instead we modelled effects of multiple predictors of social network dynamics in the spotted hyena, using observational data collected during 20 years of continuous field research in Kenya. We tested the hypothesis that the current state of the social network affects its long-term dynamics. We employed stochastic agent-based models that allowed us to estimate the contribution of multiple factors to network changes. After controlling for environmental and individual effects, we found that network density and individual centrality affected network dynamics, but that social bond transitivity consistently had the strongest effects. Our results emphasise the significance of structural properties of networks in shaping social dynamics.


Topological effects of network structure on long-term social network dynamics in a wild mammal
Amiyaal Ilany, Andrew S. Booms and Kay E. Holekamp

Ecology Letters
Early View

http://dx.doi.org/10.1111/ele.12447

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Why Our Genome and Technology Are Both Riddled With “Crawling Horrors”

Why Our Genome and Technology Are Both Riddled With “Crawling Horrors” | Papers | Scoop.it

When we build complex technologies, despite our best efforts and our desire for clean logic, they often end up being far messier than we intend. They often end up kluges: inelegant solutions that work just well enough. And a reason they end up being messy—despite being designed and engineered—is because fundamentally the way they grow and evolve is often more similar to biological systems than we realize.


http://nautil.us/blog/why-our-genome-and-technology-are-both-riddled-with-crawling-horrors

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Jeff Hawkins on Firing Up the Silicon Brain

Jeff Hawkins on Firing Up the Silicon Brain | Papers | Scoop.it

JEFF HAWKINS RECENTLY re-read his 2004 book On Intelligence, where the founder of Palm computing – the company that gave us the first handheld computer and later, first-generation smartphones – explains how the human brain learns. An electrical engineer by training, Hawkins had taken a deep interest in how the brain works and founded the Redwood Neuroscience Institute, a private, nonprofit research organization focused on understanding how the neocortex processes information, at UC Berkeley in 2002.
The big surprise? “There was very little I would change about that book,” Hawkins says. “There’s a lot I would add. There’s a ton of stuff where I know exactly how it works, that I didn’t know when I wrote it.”


http://www.wired.com/2015/05/jeff-hawkins-firing-silicon-brain


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Optimal Census by Quorum Sensing

Bacteria regulate gene expression in response to changes in cell density in a process called quorum sensing. To synchronize their gene-expression programs, these bacteria need to glean as much information as possible about their cell density. Our study is the first to physically model the flow of information in a quorum-sensing microbial community, wherein the internal regulator of the individuals response tracks the external cell density via an endogenously generated shared signal. Combining information theory and Lagrangian formalism, we find that quorum-sensing systems can improve their information capabilities by tuning circuit feedbacks. Our analysis suggests that achieving information benefit via feedback requires dedicated systems to control gene expression noise, such as sRNA-based regulation.


Optimal Census by Quorum Sensing
Thibaud Taillefumier, Ned S. Wingreen

PLoS Comput Biol 11(5): e1004238. http://dx.doi.org/10.1371/journal.pcbi.1004238 ;

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Pablo Vicente Munuera's curator insight, May 17, 4:15 AM

Quorum sensing is an interesting concept!

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On the Optimality and Predictability of Cultural Markets with Social Influence

Social influence is ubiquitous in cultural markets, from book recommendations in Amazon, to song popularities in iTunes and the ranking of newspaper articles in the online edition of the New York Times to mention only a few. Yet social influence is often presented in a bad light, often because it supposedly increases market unpredictability.
Here we study a model of trial-offer markets, in which participants try products and later decide whether to purchase. We consider a simple policy which ranks the products by quality when presenting them to market participants. We show that, in this setting, market efficiency always benefits from social influence. Moreover, we prove that the market converges almost surely to a monopoly for the product of highest quality, making the market both predictable and asymptotically optimal. Computational experiments confirm that the quality ranking policy identifies "blockbusters" in reasonable time, outperforms other policies, and is highly predictable. These results indicate that social influence does not necessarily increase market unpredicatibility. The outcome really depends on how social influence is used.


On the Optimality and Predictability of Cultural Markets with Social Influence
Pascal Van Hentenryck, Andres Abeliuk, Franco Berbeglia, Gerardo Berbeglia

http://arxiv.org/abs/1505.02469

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Duality between Temporal Networks and Signals: Extraction of the Temporal Network Structures

We develop a framework to track the structure of temporal networks with a signal processing approach. The method is based on the duality between networks and signals using a multidimensional scaling technique. This enables a study of the network structure using frequency patterns of the corresponding signals. An extension is proposed for temporal networks, thereby enabling a tracking of the network structure over time. A method to automatically extract the most significant frequency patterns and their activation coefficients over time is then introduced, using nonnegative matrix factorization of the temporal spectra. The framework, inspired by audio decomposition, allows transforming back these frequency patterns into networks, to highlight the evolution of the underlying structure of the network over time. The effectiveness of the method is first evidenced on a toy example, prior being used to study a temporal network of face-to-face contacts. The extraction of sub-networks highlights significant structures decomposed on time intervals.


Duality between Temporal Networks and Signals: Extraction of the Temporal Network Structures
Ronan Hamon, Pierre Borgnat, Patrick Flandrin, Céline Robardet

http://arxiv.org/abs/1505.03044

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Relating land use and human intra-city mobility

Understanding human mobility patterns -- how people move in their everyday lives -- is an interdisciplinary research field. It is a question with roots back to the 19th century that has been dramatically revitalized with the recent increase in data availability. Models of human mobility often take the population distribution as a starting point. Another, sometimes more accurate, data source is land-use maps. In this paper, we discuss how the intra-city movement patterns, and consequently population distribution, can be predicted from such data sources. As a link between, land use and mobility, we show that the purposes of people's trips are strongly correlated with the land use of the trip's origin and destination. We calibrate, validate and discuss our model using survey data.


Relating land use and human intra-city mobility
Minjin Lee, Petter Holme

http://arxiv.org/abs/1505.07372

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Defining and identifying Sleeping Beauties in science

A Sleeping Beauty (SB) in science refers to a paper whose importance is not recognized for several years after publication. Its citation history exhibits a long hibernation period followed by a sudden spike of popularity. Previous studies suggest a relative scarcity of SBs. The reliability of this conclusion is, however, heavily dependent on identification methods based on arbitrary threshold parameters for sleeping time and number of citations, applied to small or monodisciplinary bibliographic datasets. Here we present a systematic, large-scale, and multidisciplinary analysis of the SB phenomenon in science. We introduce a parameter-free measure that quantifies the extent to which a specific paper can be considered an SB. We apply our method to 22 million scientific papers published in all disciplines of natural and social sciences over a time span longer than a century. Our results reveal that the SB phenomenon is not exceptional. There is a continuous spectrum of delayed recognition where both the hibernation period and the awakening intensity are taken into account. Although many cases of SBs can be identified by looking at monodisciplinary bibliographic data, the SB phenomenon becomes much more apparent with the analysis of multidisciplinary datasets, where we can observe many examples of papers achieving delayed yet exceptional importance in disciplines different from those where they were originally published. Our analysis emphasizes a complex feature of citation dynamics that so far has received little attention, and also provides empirical evidence against the use of short-term citation metrics in the quantification of scientific impact.


Defining and identifying Sleeping Beauties in science
Qing Ke, Emilio Ferrara, Filippo Radicchi, Alessandro Flammini

http://arxiv.org/abs/1505.06454

Complexity Digest's insight:

See Also: http://qke.github.io/projects/beauty/beauty.html 

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High resolution population estimates from telecommunications data

Spatial variations in the distribution and composition of populations inform urban development, health-risk analyses, disaster relief, and more. Despite the broad relevance and importance of such data, acquiring local census estimates in a timely and accurate manner is challenging because population counts can change rapidly, are often politically charged, and suffer from logistical and administrative challenges. These limitations necessitate the development of alternative or complementary approaches to population mapping. In this paper we develop an explicit connection between telecommunications data and the underlying population distribution of Milan, Italy. We go on to test the scale invariance of this connection and use telecommunications data in conjunction with high-resolution census data to create easily updated and potentially real time population estimates in time and space.


High resolution population estimates from telecommunications data
Rex W Douglass, David A Meyer, Megha Ram, David Rideout and Dongjin Song

EPJ Data Science 2015, 4:4  http://dx.doi.org/10.1140/epjds/s13688-015-0040-6 ;

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From Micro to Macro: Uncovering and Predicting Information Cascading Process with Behavioral Dynamics

Cascades are ubiquitous in various network environments. How to predict these cascades is highly nontrivial in several vital applications, such as viral marketing, epidemic prevention and traffic management. Most previous works mainly focus on predicting the final cascade sizes. As cascades are typical dynamic processes, it is always interesting and important to predict the cascade size at any time, or predict the time when a cascade will reach a certain size (e.g. an threshold for outbreak). In this paper, we unify all these tasks into a fundamental problem: cascading process prediction. That is, given the early stage of a cascade, how to predict its cumulative cascade size of any later time? For such a challenging problem, how to understand the micro mechanism that drives and generates the macro phenomenons (i.e. cascading proceese) is essential. Here we introduce behavioral dynamics as the micro mechanism to describe the dynamic process of a node's neighbors get infected by a cascade after this node get infected (i.e. one-hop subcascades). Through data-driven analysis, we find out the common principles and patterns lying in behavioral dynamics and propose a novel Networked Weibull Regression model for behavioral dynamics modeling. After that we propose a novel method for predicting cascading processes by effectively aggregating behavioral dynamics, and propose a scalable solution to approximate the cascading process with a theoretical guarantee. We extensively evaluate the proposed method on a large scale social network dataset. The results demonstrate that the proposed method can significantly outperform other state-of-the-art baselines in multiple tasks including cascade size prediction, outbreak time prediction and cascading process prediction.


From Micro to Macro: Uncovering and Predicting Information Cascading Process with Behavioral Dynamics
Linyun Yu, Peng Cui, Fei Wang, Chaoming Song, Shiqiang Yang

http://arxiv.org/abs/1505.07193

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An Image is Worth More than a Thousand Favorites: Surfacing the Hidden Beauty of Flickr Pictures

The dynamics of attention in social media tend to obey power laws. Attention concentrates on a relatively small number of popular items and neglecting the vast majority of content produced by the crowd. Although popularity can be an indication of the perceived value of an item within its community, previous research has hinted to the fact that popularity is distinct from intrinsic quality. As a result, content with low visibility but high quality lurks in the tail of the popularity distribution. This phenomenon can be particularly evident in the case of photo-sharing communities, where valuable photographers who are not highly engaged in online social interactions contribute with high-quality pictures that remain unseen. We propose to use a computer vision method to surface beautiful pictures from the immense pool of near-zero-popularity items, and we test it on a large dataset of creative-commons photos on Flickr. By gathering a large crowdsourced ground truth of aesthetics scores for Flickr images, we show that our method retrieves photos whose median perceived beauty score is equal to the most popular ones, and whose average is lower by only 1.5%.


An Image is Worth More than a Thousand Favorites: Surfacing the Hidden Beauty of Flickr Pictures
Rossano Schifanella, Miriam Redi, Luca Aiello

http://arxiv.org/abs/1505.07096 

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Computational aesthetics

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Complexity in Industrial Ecology: Models, Analysis, and Actions

This special issue brings together articles that illustrate the recent advances of studying complex adaptive systems in industrial ecology (IE). The authors explore the emergent behavior of sociotechnical systems, including product systems, industrial symbiosis (IS) networks, cities, resource consumption, and co-authorship networks, and offer application of complex systems models and analyses. The articles demonstrate the links, relevance, and implications of many (often emerging) fields of study to IE, including network analysis, participatory modeling, nonequilibrium thermodynamics, and agent-based modeling. Together, these articles show that IE itself is a complex adaptive system, where knowledge, frameworks, methods, and tools evolve with and by their applications and use in small and large case studies—multidisciplinary knowledge ecology.


Complexity in Industrial Ecology: Models, Analysis, and Actions
Gerard P.J. Dijkema, Ming Xu, Sybil Derrible and Reid Lifset

Journal of Industrial Ecology
Special Issue: Advances in Complex Adaptive Systems and Industrial Ecology
Volume 19, Issue 2, pages 189–194, April 2015

http://dx.doi.org/10.1111/jiec.12280

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You Asked: Are My Devices Messing With My Brain?

You Asked: Are My Devices Messing With My Brain? | Papers | Scoop.it
Yes—and you're probably suffering from phantom text syndrome, too.

First it was radio. Then it was television. Now doomsayers are offering scary predictions about the consequences of smartphones and all the other digital devices to which we’ve all grown so attached. So why should you pay any attention to the warnings this time?

Apart from portability, the big difference between something like a traditional TV and your tablet is the social component, says Dr. David Strayer, a professor of cognition and neural science at the University of Utah. “Through Twitter or Facebook or email, someone in your social network is contacting you in some way all the time,” Strayer says.

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Regularity underlies erratic population abundances in marine ecosystems

The abundance of a species' population in an ecosystem is rarely stationary, often exhibiting large fluctuations over time. Using historical data on marine species, we show that the year-to-year fluctuations of population growth rate obey a well-defined double-exponential (Laplace) distribution. This striking regularity allows us to devise a stochastic model despite seemingly irregular variations in population abundances. The model identifies the effect of reduced growth at low population density as a key factor missed in current approaches of population variability analysis and without which extinction risks are severely underestimated. The model also allows us to separate the effect of demographic stochasticity and show that single-species growth rates are dominantly determined by stochasticity common to all species. This dominance—and the implications it has for interspecies correlations, including co-extinctions—emphasizes the need for ecosystem-level management approaches to reduce the extinction risk of the individual species themselves.


Regularity underlies erratic population abundances in marine ecosystems
Jie Sun, Sean P. Cornelius, John Janssen, Kimberly A. Gray, Adilson E. Motter
J. R. Soc. Interface 2015 12 20150235; http://dx.doi.org/10.1098/rsif.2015.0235


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On the tail risk of violent conflict and its underestimation

We examine all possible statistical pictures of violent conflicts over common era history with a focus on dealing with incompleteness and unreliability of data. We apply methods from extreme value theory on log-transformed data to remove compact support, then, owing to the boundedness of maximum casualties, retransform the data and derive expected means. We find the estimated mean likely to be at least three times larger than the sample mean, meaning severe underestimation of the severity of conflicts from naive observation. We check for robustness by sampling between high and low estimates and jackknifing the data. We study inter-arrival times between tail events and find (first-order) memorylessless of events. The statistical pictures obtained are at variance with the claims about "long peace".


On the tail risk of violent conflict and its underestimation
Pasquale Cirillo, Nassim Nicholas Taleb

http://arxiv.org/abs/1505.04722

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Understanding Brains: Details, Intuition, and Big Data

Understanding Brains: Details, Intuition, and Big Data | Papers | Scoop.it

Understanding how the brain works requires a delicate balance between the appreciation of the importance of a multitude of biological details and the ability to see beyond those details to general principles. As technological innovations vastly increase the amount of data we collect, the importance of intuition into how to analyze and treat these data may, paradoxically, become more important.


Marder E (2015) Understanding Brains: Details, Intuition, and Big Data. PLoS Biol 13(5): e1002147. http://dx.doi.org/10.1371/journal.pbio.1002147 

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The Intrafirm Complexity of Systemically Important Financial Institutions

In November, 2011, the Financial Stability Board, in collaboration with the International Monetary Fund, published a list of 29 "systemically important financial institutions" (SIFIs). This designation reflects a concern that the failure of any one of them could have dramatic negative consequences for the global economy and is based on "their size, complexity, and systemic interconnectedness". While the characteristics of "size" and "systemic interconnectedness" have been the subject of a good deal of quantitative analysis, less attention has been paid to measures of a firm's "complexity." In this paper we take on the challenges of measuring the complexity of a financial institution and to that end explore the use of the structure of an individual firm's control hierarchy as a proxy for institutional complexity. The control hierarchy is a network representation of the institution and its subsidiaries. We show that this mathematical representation (and various associated metrics) provides a consistent way to compare the complexity of firms with often very disparate business models and as such may provide the foundation for determining a SIFI designation. By quantifying the level of complexity of a firm, our approach also may prove useful should firms need to reduce their level of complexity either in response to business or regulatory needs. Using a data set containing the control hierarchies of many of the designated SIFIs, we find that in the past two years, these firms have decreased their level of complexity, perhaps in response to regulatory requirements.


The Intrafirm Complexity of Systemically Important Financial Institutions
Robin L. Lumsdaine, Daniel N. Rockmore, Nicholas Foti, Gregory Leibon, J. Doyne Farmer

http://arxiv.org/abs/1505.02305

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Ecological collapse and the emergence of traveling waves at the onset of shear turbulence

The transition to turbulence exhibits remarkable spatio-temporal behavior that continues to defy detailed understanding. Near the onset to turbulence in pipes, transient turbulent regions decay either directly or, at higher Reynolds numbers through splitting, with characteristic time-scales that exhibit a super-exponential dependence on Reynolds number. Here we report numerical simulations of transitional pipe flow, showing that a zonal flow emerges at large scales, activated by anisotropic turbulent fluctuations; in turn, the zonal flow suppresses the small-scale turbulence leading to stochastic predator-prey dynamics. We show that this "ecological" model of transitional turbulence reproduces the super-exponential lifetime statistics and phenomenology of pipe flow experiments. Our work demonstrates that a fluid on the edge of turbulence is mathematically analogous to an ecosystem on the edge of extinction, and provides an unbroken link between the equations of fluid dynamics and the directed percolation universality class.


Ecological collapse and the emergence of traveling waves at the onset of shear turbulence
Hong-Yan Shih, Tsung-Lin Hsieh, Nigel Goldenfeld

http://arxiv.org/abs/1505.02807

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