Papers

Pattern formations are apparent in natural systems ranging from clouds to animal markings, and from sand dunes to shells of microscopic marine organisms. Despite the astonishing range and variety of such structures, many have comparable features. In this article, Philip Ball reviews some of the common patterns found in nature. He explains how they are typically formed through simple, local interactions between many components of a system – a form of physical computation that gives rise to self-organisation and emergent structures and behaviours.

Pattern Formation in Nature: Physical Constraints and Self-Organising Characteristics
Philip Ball

Architectural Design
Special Issue: Material Computation: Higher Integration in Morphogenetic Design
Volume 82, Issue 2, pages 22–27, March/April 2012

http://dx.doi.org/10.1002/ad.1375

Animals behave adaptively in the environment with multiply competing goals. Understanding of the mechanisms underlying such goal-directed behavior remains a challenge for neuroscience as well for adaptive system research. To address this problem we developed an evolutionary model of adaptive behavior in the multigoal stochastic environment. Proposed neuroevolutionary algorithm is based on neuron's duplication as a basic mechanism of agent's recurrent neural network development. Results of simulation demonstrate that in the course of evolution agents acquire the ability to store the short-term memory and, therefore, use it in behavioral strategies with alternative actions. We found that evolution discovered two mechanisms for short-term memory. The first mechanism is integration of sensory signals and ongoing internal neural activity, resulting in emergence of cell groups specialized on alternative actions. And the second mechanism is slow neurodynamical processes that makes possible to code the previous behavioral choice.

Neuroevolution Results in Emergence of Short-Term Memory for Goal-Directed Behavior

Konstantin Lakhman, Mikhail Burtsev

http://arxiv.org/abs/1204.3221

It is very likely that life began with some RNA (or RNA-like) molecules, self-replicating by base-pairing and exhibiting enzyme-like functions that favored the self-replication. Different functional molecules may have emerged by favoring their own self-replication at different aspects. Then, a direct route towards complexity/efficiency may have been through the coexistence/cooperation of these molecules.

Ma W, Hu J (2012) Computer Simulation on the Cooperation of Functional Molecules during the Early Stages of Evolution. PLoS ONE 7(4): e35454. doi:10.1371/journal.pone.0035454

We consider a simplified model of a social network in which individuals have one of two opinions (called 0 and 1) and their opinions and the network connections coevolve. Edges are picked at random. If the two connected individuals hold different opinions then, with probability 1 - α, one imitates the opinion of the other; otherwise (i.e., with probability α), the link between them is broken and one of them makes a new connection to an individual chosen at random (i) from those with the same opinion or (ii) from the network as a whole. The evolution of the system stops when there are no longer any discordant edges connecting individuals with different opinions. Letting ρ be the fraction of voters holding the minority opinion after the evolution stops, we are interested in how ρ depends on α and the initial fraction u of voters with opinion 1. In case (i), there is a critical value αc which does not depend on u, with ρ ≈ u for α > αc and ρ ≈ 0 for α < αc. In case (ii), the transition point αc(u) depends on the initial density u. For α > αc(u), ρ ≈ u, but for α < αc(u), we have ρ(α,u) = ρ(α,1/2). Using simulations and approximate calculations, we explain why these two nearly identical models have such dramatically different phase transitions.

Graph fission in an evolving voter model
Richard Durrett et al.

PNAS March 6, 2012 vol. 109 no. 10 3682-3687

http://dx.doi.org/10.1073/pnas.1200709109

In marking Alan Turing's centenary, it's worth asking what was his most fundamental achievement and what he left for future science to take up when he took his own life in 1954. His success in World War II, as the chief scientific figure in the British cryptographic effort, with hands-on responsibility for the Atlantic naval conflict, had a great and immediate impact. But in its ever-growing influence since that time, the principle of the universal machine, which Turing published in 1937, beats even this.

Beyond Turing's Machines
Andrew Hodges

Science 13 April 2012: Vol. 336 no. 6078 pp. 163-164
http://dx.doi.org/10.1126/science.1218417

A discussion of computational biology has to start with a pioneer of the field, Alan Turing, especially in this centennial year of his birth. He introduced us to the digital computer and proposed that much biology could be described by mathematical equations—the number of spirals in a sunflower is a Fibonacci number and pattern formation in animal skins can be described by a reaction diffusion model. Turing lacked the data and the computing power to substantiate his models. Today, the availability of vast quantities of new data, together with striking advances in computing power, is promising to give us new insights into the mechanisms of life. This special section, together with related content in Science Signaling and Science Careers, highlights recent advances and outstanding challenges.

Does It Compute?
Valda Vinson, Beverly A. Purnell, Laura M. Zahn, John Travis

Science 13 April 2012: Vol. 336 no. 6078 p. 171
http://dx.doi.org/10.1126/science.336.6078.171

The publication and open exchange of knowledge and material form the backbone of scientific progress and reproducibility and are obligatory for publicly funded research. Despite increasing reliance on computing in every domain of scientific endeavor, the computer source code critical to understanding and evaluating computer programs is commonly withheld, effectively rendering these programs “black boxes” in the research work flow. Exempting from basic publication and disclosure standards such a ubiquitous category of research tool carries substantial negative consequences.

Shining Light into Black Boxes
A. Morin et al.

Science 13 April 2012: Vol. 336 no. 6078 pp. 159-160
http://dx.doi.org/10.1126/science.1218263

With the increasing popularity of location-based services, we have accumulated a lot of location data on the Web. In this paper, we are interested in answering two popular location-related queries in our daily life: (1) if we want to do something such as sightseeing or dining in a large city like Beijing, where should we go? (2) If we want to visit a place such as the Birdʼs Nest in Beijing Olympic park, what can we do there? We develop a mobile recommendation system to answer these queries (...)

Towards mobile intelligence: Learning from GPS history data for collaborative recommendation
Vincent W. Zheng, Yu Zheng , Xing Xie, Qiang Yang

Artificial Intelligence
Volumes 184–185, June 2012, Pages 17–37

The advent of geographic online social networks such as Foursquare, where users voluntarily signal their current location, opens the door to powerful studies on human movement. In particular the fine granularity of the location data, with GPS accuracy down to 10 meters, and the worldwide scale of Foursquare adoption are unprecedented. In this paper we study urban mobility patterns of people in several metropolitan cities around the globe by analyzing a large set of Foursquare users. Surprisingly, while there are variations in human movement in different cities, our analysis shows that those are predominantly due to different distributions of places across different urban environments. Moreover, a universal law for human mobility is identified, which isolates as a key component the rank-distance, factoring in the number of places between origin and destination, rather than pure physical distance, as considered in some previous works. Building on our findings, we also show how a rank-based movement model accurately captures real human movements in different cities. Our results shed new light on the driving factors of urban human mobility, with potential applications for urban planning, location-based advertisement and even social studies.

A tale of many cities: universal patterns in human urban mobility

Anastasios Noulas, Salvatore Scellato, Renaud Lambiotte, Massimiliano Pontil, Cecilia Mascolo

http://arxiv.org/abs/1108.5355

Previous human foraging experiments have shown that human groups routinely undermatch environmental resources much like other animal species. In this experiment, we test whether humans also selectively rely on others as information sources when the environmental state is uncertain, and we also test whether overt signals of other foragers' success influences group matching behavior and group adaptation to a changing environment. The results show evidence of reliance on social information in specific conditions, but participants were primarily influenced by their individual assessments of food location rather than the success of other foragers.

Group Foraging in Dynamic Environments

Michael E. Roberts, Sam Cheesman, Patrick McMullen

http://arxiv.org/abs/1204.3673

The social media website last.fm provides a detailed snapshot of what its users in hundreds of cities listen to each week. After suitably normalizing this data, we use it to test three hypotheses related to the geographic flow of music. The first is that although many of the most popular artists are listened to around the world, music preferences are closely related to nationality, language, and geographic location. We find support for this hypothesis, with a couple of minor, yet interesting, exceptions. Our second hypothesis is that some cities are consistently early adopters of new music (and early to snub stale music). To test this hypothesis, we adapt a method previously used to detect the leadership networks present in flocks of birds. We find empirical support for the claim that a similar leadership network exists among cities, and this finding is the main contribution of the paper. Finally, we test the hypothesis that large cities tend to be ahead of smaller cities-we find only weak support for this hypothesis.

The Geographic Flow of Music

Conrad Lee, Pádraig Cunningham

http://arxiv.org/abs/1204.2677

We consider voter dynamics on a directed adaptive network with fixed out-degree distribution. A transition between an active phase and a fragmented phase is observed. This transition is similar to the undirected case if the networks are sufficiently dense and have a narrow out-degree distribution. However, if a significant number of nodes with low out degree is present, then fragmentation can occur even far below the estimated critical point due to the formation of self-stabilizing structures that nucleate fragmentation. This process may be relevant for fragmentation in current political opinion formation processes.

Early fragmentation in the adaptive voter model on directed networks. Gerd Zschaler, Gesa A. Böhme, Michael Seißinger, Cristián Huepe, and Thilo Gross. Phys. Rev. E 85, 046107 (2012)

Understanding how interdependence among systems affects cascading behaviors is increasingly important across many fields of science and engineering. Inspired by cascades of load shedding in coupled electric grids and other infrastructure, we study the Bak–Tang–Wiesenfeld sandpile model on modular random graphs and on graphs based on actual, interdependent power grids. Starting from two isolated networks, adding some connectivity between them is beneficial, for it suppresses the largest cascades in each system. Too much interconnectivity, however, becomes detrimental for two reasons. First, interconnections open pathways for neighboring networks to inflict large cascades. Second, as in real infrastructure, new interconnections increase capacity and total possible load, which fuels even larger cascades. Using a multitype branching process and simulations we show these effects and estimate the optimal level of interconnectivity that balances their trade-offs. Such equilibria could allow, for example, power grid owners to minimize the largest cascades in their grid. We also show that asymmetric capacity among interdependent networks affects the optimal connectivity that each prefers and may lead to an arms race for greater capacity. Our multitype branching process framework provides building blocks for better prediction of cascading processes on modular random graphs and on multitype networks in general.

Suppressing cascades of load in interdependent networks
Charles D. Brummitt, Raissa M. D’Souza, and E. A. Leicht

http://dx.doi.org/10.1073/pnas.1110586109

The concept of contagion has steadily expanded from its original grounding in epidemic disease to describe a vast array of processes that spread across networks, notably social phenomena such as fads, political opinions, the adoption of new technologies, and financial decisions. (...) We find that the probability of contagion is tightly controlled by the number of connected components in an individual's contact neighborhood, rather than by the actual size of the neighborhood. Surprisingly, once this “structural diversity” is controlled for, the size of the contact neighborhood is in fact generally a negative predictor of contagion. More broadly, our analysis shows how data at the size and resolution of the Facebook network make possible the identification of subtle structural signals that go undetected at smaller scales yet hold pivotal predictive roles for the outcomes of social processes.

Structural diversity in social contagion
Johan Ugander, Lars Backstrom, Cameron Marlow, and Jon Kleinberg

PNAS

http://www.pnas.org/content/early/2012/03/27/1116502109.abstract

Hold up both hands and spread your fingers apart. Now put your palms together and fold your two middle fingers down till the knuckles on both fingers touch each other. While holding this position, one after the other, open and close each pair of opposing fingers by an inch or so. Notice anything? Of course you did. But could a computer without a body and without human experiences ever answer that question or a million others like it? And even if recent revolutionary advances in collecting, storing, retrieving, and analyzing data lead to such a computer, would this machine qualify as “intelligent”?

Dusting Off the Turing Test
Robert M. French

Science 13 April 2012: Vol. 336 no. 6078 pp. 164-165
http://dx.doi.org/10.1126/science.1218350

Networks that govern communication, growth, herd behavior, and other key processes in nature and society are becoming increasingly amenable to modeling, forecast, and control.

Networks in motion
Adilson E. Motter and Réka Albert
Physics Today / Volume 65 / Issue 4, April 2012, page 43
http://dx.doi.org/10.1063/PT.3.1518

Late nights in the lab, early morning commutes from the suburbs, Angry Birds videogame marathons into the wee hours—the demands and distractions of modern life are stealing our sleep and perhaps robbing us of our health. According to the longest sleep-limitation study to date, published this week in Science Translational Medicine, many people are on sleep and work schedules that prime them for diabetes and obesity.

Sleep Study Suggests Triggers for Diabetes and Obesity
Mitch Leslie

Science 13 April 2012: Vol. 336 no. 6078 p. 143
http://www.sciencemag.org/content/336/6078/143.summary ;