Yong-Yeol Ahn

Clustering is one of the most universal approaches for understanding complex data. A pivotal aspect of clustering analysis is quantitatively comparing clusterings; clustering comparison is the basis for many tasks such as clustering evaluation, consensus clustering, and tracking the temporal evolution of clusters. In particular, the extrinsic evaluation of clustering methods requires comparing the uncovered clusterings to planted clusterings or known metadata. Yet, as we demonstrate, existing clustering comparison measures have critical biases which undermine their usefulness, and no measure accommodates both overlapping and hierarchical clusterings. Here we unify the comparison of disjoint, overlapping, and hierarchically structured clusterings by proposing a new element-centric framework: elements are compared based on the relationships induced by the cluster structure, as opposed to the traditional cluster …

<h3 class="gsh_h3">Background</h3>Clinical and preclinical studies have shown that there are sex-based differences at the genetic, cellular, biochemical, and physiological levels. Despite this, numerous studies have shown poor levels of inclusion of female populations into medical research. These disparities in sex inclusion in research are further complicated by the absence of sufficient reporting and analysis by sex of study populations. Disparities in the inclusion of the sexes in medical research substantially reduce the utility of the results of such research for the entire population. The absence of sex-related reporting are problematical for the translation of research from the preclinical to clinical and applied health settings. Large-scale studies are needed to identify the extent of sex-related reporting and where disparities are more prevalent. In addition, while several studies have shown the dearth of female researchers in science, few …

A series of authored and edited monographs that utilize quantitative and computational methods to model, analyze and interpret large-scale social phenomena. Titles within the series contain methods and practices that test and develop theories of complex social processes through bottom-up modeling of social interactions. Of particular interest is the study of the coevolution of modern communication technology and social behavior and norms, in connection with emerging issues such as trust, risk, security and privacy in novel socio-technical environments.Computational Social Sciences is explicitly transdisciplinary: quantitative methods from fields such as dynamical systems, artificial intelligence, network theory, agent based modeling, and statistical mechanics are invoked and combined with state-of theart mining and analysis of large data sets to help us understand social agents, their interactions on and offline …

Human history has been marked by social instability and conflict, often driven by the irreconcilability of opposing sets of beliefs, ideologies, and religious dogmas. The dynamics of belief systems has been studied mainly from two distinct perspectives, namely how cognitive biases lead to individual belief rigidity and how social influence leads to social conformity. Here we propose a unifying framework that connects cognitive and social forces together in order to study the dynamics of societal belief evolution. Each individual is endowed with a network of interacting beliefs that evolves through interaction with other individuals in a social network. The adoption of beliefs is affected by both internal coherence and social conformity. Our framework may offer explanations for how social transitions can arise in otherwise homogeneous populations, how small numbers of zealots with highly coherent beliefs can overturn societal consensus, and how belief rigidity protects fringe groups and cults against invasion from mainstream beliefs, allowing them to persist and even thrive in larger societies. Our results suggest that strong consensus may be insufficient to guarantee social stability, that the cognitive coherence of belief-systems is vital in determining their ability to spread, and that coherent belief-systems may pose a serious problem for resolving social polarization, due to their ability to prevent consensus even under high levels of social exposure. We argue that the inclusion of cognitive factors into a social model could provide a more complete picture of collective human dynamics.

Increasingly detailed data on the network topology of neural circuits create a need for theoretical principles that explain how these networks shape neural communication. Here we use a model of cascade spreading to reveal architectural features of human brain networks that facilitate spreading. Using an anatomical brain network derived from high-resolution diffusion spectrum imaging (DSI), we investigate scenarios where perturbations initiated at seed nodes result in global cascades that interact either cooperatively or competitively. We find that hub regions and a backbone of pathways facilitate early spreading, while the shortest path structure of the connectome enables cooperative effects, accelerating the spread of cascades. Finally, competing cascades become integrated by converging on polysensory associative areas. These findings show that the organizational principles of brain networks shape global …

We investigate the impact of community structure on information diffusion with the linear threshold model. Our results demonstrate that modular structure may have counterintuitive effects on information diffusion when social reinforcement is present. We show that strong communities can facilitate global diffusion by enhancing local, intracommunity spreading. Using both analytic approaches and numerical simulations, we demonstrate the existence of an optimal network modularity, where global diffusion requires the minimal number of early adopters.

The emergent processes driving cultural history are a product of complex interactions among large numbers of individuals, determined by difficult-to-quantify historical conditions. To characterize these processes, we have reconstructed aggregate intellectual mobility over two millennia through the birth and death locations of more than 150,000 notable individuals. The tools of network and complexity theory were then used to identify characteristic statistical patterns and determine the cultural and historical relevance of deviations. The resulting network of locations provides a macroscopic perspective of cultural history, which helps us to retrace cultural narratives of Europe and North America using large-scale visualization and quantitative dynamical tools and to derive historical trends of cultural centers beyond the scope of specific events or narrow time intervals.

How does network structure affect diffusion? Recent studies suggest that the answer depends on the type of contagion. Complex contagions, unlike infectious diseases (simple contagions), are affected by social reinforcement and homophily. Hence, the spread within highly clustered communities is enhanced, while diffusion across communities is hampered. A common hypothesis is that memes and behaviors are complex contagions. We show that, while most memes indeed spread like complex contagions, a few viral memes spread across many communities, like diseases. We demonstrate that the future popularity of a meme can be predicted by quantifying its early spreading pattern in terms of community concentration. The more communities a meme permeates, the more viral it is. We present a practical method to translate data about community structure into predictive knowledge about what information will …

The cultural diversity of culinary practice, as illustrated by the variety of regional cuisines, raises the question of whether there are any general patterns that determine the ingredient combinations used in food today or principles that transcend individual tastes and recipes. We introduce a flavor network that captures the flavor compounds shared by culinary ingredients. Western cuisines show a tendency to use ingredient pairs that share many flavor compounds, supporting the so-called food pairing hypothesis. By contrast, East Asian cuisines tend to avoid compound sharing ingredients. Given the increasing availability of information on food preparation, our data-driven investigation opens new avenues towards a systematic understanding of culinary practice.

Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing about 6200 highly reliable interactions between about 2700 proteins. A global organization of plant biological processes emerges from community analyses of the resulting network, together with large numbers of novel hypothetical functional links between proteins and pathways. We observe a dynamic rewiring of interactions following gene duplication events, providing evidence for a model of evolution acting upon interactome networks. This and future plant interactome maps should facilitate systems approaches to better understand plant biology and improve crops.

Networks have become a key approach to understanding systems of interacting objects, unifying the study of diverse phenomena including biological organisms and human society 1, 2, 3. One crucial step when studying the structure and dynamics of networks is to identify communities 4, 5: groups of related nodes that correspond to functional subunits such as protein complexes 6, 7 or social spheres 8, 9, 10. Communities in networks often overlap 9, 10 such that nodes simultaneously belong to several groups. Meanwhile, many networks are known to possess hierarchical organization, where communities are recursively grouped into a hierarchical structure 11, 12, 13. However, the fact that many real networks have communities with pervasive overlap, where each and every node belongs to more than one group, has the consequence that a global hierarchy of nodes cannot capture the relationships between …

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Social networking services are a fast-growing business in the Internet. However, it is unknown if online relationships and their growth patterns are the same as in real-life social networks. In this paper, we compare the structures of three online social networking services: Cyworld, MySpace, and orkut, each with more than 10 million users, respectively. We have access to complete data of Cyworld's ilchon (friend) relationships and analyze its degree distribution, clustering property, degree correlation, and evolution over time. We also use Cyworld data to evaluate the validity of snowball sampling method, which we use to crawl and obtain partial network topologies of MySpace and orkut. Cyworld, the oldest of the three, demonstrates a changing scaling behavior over time in degree distribution. The latest Cyworld data's degree distribution exhibits a multi-scaling behavior, while those of MySpace and orkut have simple …

User Generated Content (UGC) is re-shaping the way people watch video and TV, with millions of video producers and consumers. In particular, UGC sites are creating new viewing patterns and social interactions, empowering users to be more creative, and developing new business opportunities. To better understand the impact of UGC systems, we have analyzed YouTube, the world's largest UGC VoD system. Based on a large amount of data collected, we provide an in-depth study of YouTube and other similar UGC systems. In particular, we study the popularity life-cycle of videos, the intrinsic statistical properties of requests and their relationship with video age, and the level of content aliasing or of illegal content in the system. We also provide insights on the potential for more efficient UGC VoD systems (eg utilizing P2P techniques or making better use of caching). Finally, we discuss the opportunities to …