Functional cartography of complex metabolic networks

High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major scientific challenge. Here, we propose a methodology that enables us to extract and display information contained in complex networks. Specifically, we demonstrate that one can (i) find functional modules in complex networks, and (ii) classify nodes into universal roles according to their pattern of intra- and inter-module connections. The method thus yields a ``cartographic representation'' of complex networks. Metabolic networks are among the most challenging biological networks and, arguably, the ones with more potential for immediate applicability. We use our method to analyze the metabolic networks of twelve organisms from three different super-kingdoms. We find that, typically, 80% of the nodes are only connected to other nodes within their respective modules, and that nodes with different roles are affected by different evolutionary constraints and pressures. Remarkably, we find that low-degree metabolites that connect different modules are more conserved than hubs whose links are mostly within a single module.Comment: 17 pages, 4 figures. Go to http://amaral.northwestern.edu for the PDF file of the reprin

Statistical Laws Governing Fluctuations in Word Use from Word Birth to Word Death

We analyze the dynamic properties of 10^7 words recorded in English, Spanish and Hebrew over the period 1800--2008 in order to gain insight into the coevolution of language and culture. We report language independent patterns useful as benchmarks for theoretical models of language evolution. A significantly decreasing (increasing) trend in the birth (death) rate of words indicates a recent shift in the selection laws governing word use. For new words, we observe a peak in the growth-rate fluctuations around 40 years after introduction, consistent with the typical entry time into standard dictionaries and the human generational timescale. Pronounced changes in the dynamics of language during periods of war shows that word correlations, occurring across time and between words, are largely influenced by coevolutionary social, technological, and political factors. We quantify cultural memory by analyzing the long-term correlations in the use of individual words using detrended fluctuation analysis.Comment: Version 1: 31 pages, 17 figures, 3 tables. Version 2 is streamlined, eliminates substantial material and incorporates referee comments: 19 pages, 14 figures, 3 table

Knowledge is at the Edge! How to Search in Distributed Machine Learning Models

With the advent of the Internet of Things and Industry 4.0 an enormous amount of data is produced at the edge of the network. Due to a lack of computing power, this data is currently send to the cloud where centralized machine learning models are trained to derive higher level knowledge. With the recent development of specialized machine learning hardware for mobile devices, a new era of distributed learning is about to begin that raises a new research question: How can we search in distributed machine learning models? Machine learning at the edge of the network has many benefits, such as low-latency inference and increased privacy. Such distributed machine learning models can also learn personalized for a human user, a specific context, or application scenario. As training data stays on the devices, control over possibly sensitive data is preserved as it is not shared with a third party. This new form of distributed learning leads to the partitioning of knowledge between many devices which makes access difficult. In this paper we tackle the problem of finding specific knowledge by forwarding a search request (query) to a device that can answer it best. To that end, we use a entropy based quality metric that takes the context of a query and the learning quality of a device into account. We show that our forwarding strategy can achieve over 95% accuracy in a urban mobility scenario where we use data from 30 000 people commuting in the city of Trento, Italy.Comment: Published in CoopIS 201

Tissue multifractality and Born approximation in analysis of light scattering: a novel approach for precancers detection

Multifractal, a special class of complex self-affine processes, are under recent intensive investigations because of their fundamental nature and potential applications in diverse physical systems. Here, we report on a novel light scattering-based inverse method for extraction/quantification of multifractality in the spatial distribution of refractive index of biological tissues. The method is based on Fourier domain pre-processing via the Born approximation, followed by the Multifractal Detrended Fluctuation Analysis. The approach is experimentally validated in synthetic multifractal scattering phantoms, and tested on biopsy tissue slices. The derived multifractal properties appear sensitive in detecting cervical precancerous alterations through an increase of multifractality with pathology progression, demonstrating the potential of the developed methodology for novel precancer biomarker identification and tissue diagnostic tool. The novel ability to delineate the multifractal optical properties from light scattering signals may also prove useful for characterizing a wide variety of complex scattering media of non-biological origin

Self-similarity of complex networks

Complex networks have been studied extensively due to their relevance to many real systems as diverse as the World-Wide-Web (WWW), the Internet, energy landscapes, biological and social networks \cite{ab-review,mendes,vespignani,newman,amaral}. A large number of real networks are called ``scale-free'' because they show a power-law distribution of the number of links per node \cite{ab-review,barabasi1999,faloutsos}. However, it is widely believed that complex networks are not {\it length-scale} invariant or self-similar. This conclusion originates from the ``small-world'' property of these networks, which implies that the number of nodes increases exponentially with the ``diameter'' of the network \cite{erdos,bollobas,milgram,watts}, rather than the power-law relation expected for a self-similar structure. Nevertheless, here we present a novel approach to the analysis of such networks, revealing that their structure is indeed self-similar. This result is achieved by the application of a renormalization procedure which coarse-grains the system into boxes containing nodes within a given "size". Concurrently, we identify a power-law relation between the number of boxes needed to cover the network and the size of the box defining a finite self-similar exponent. These fundamental properties, which are shown for the WWW, social, cellular and protein-protein interaction networks, help to understand the emergence of the scale-free property in complex networks. They suggest a common self-organization dynamics of diverse networks at different scales into a critical state and in turn bring together previously unrelated fields: the statistical physics of complex networks with renormalization group, fractals and critical phenomena.Comment: 28 pages, 12 figures, more informations at http://www.jamlab.or

Languages cool as they expand: Allometric scaling and the decreasing need for new words

We analyze the occurrence frequencies of over 15 million words recorded in millions of books published during the past two centuries in seven different languages. For all languages and chronological subsets of the data we confirm that two scaling regimes characterize the word frequency distributions, with only the more common words obeying the classic Zipf law. Using corpora of unprecedented size, we test the allometric scaling relation between the corpus size and the vocabulary size of growing languages to demonstrate a decreasing marginal need for new words, a feature that is likely related to the underlying correlations between words. We calculate the annual growth fluctuations of word use which has a decreasing trend as the corpus size increases, indicating a slowdown in linguistic evolution following language expansion. This ‘‘cooling pattern’’ forms the basis of a third statistical regularity, which unlike the Zipf and the Heaps law, is dynamical in nature

Evolution of Cooperation and Coordination in a Dynamically Networked Society

Situations of conflict giving rise to social dilemmas are widespread in society and game theory is one major way in which they can be investigated. Starting from the observation that individuals in society interact through networks of acquaintances, we model the co-evolution of the agents' strategies and of the social network itself using two prototypical games, the Prisoner's Dilemma and the Stag Hunt. Allowing agents to dismiss ties and establish new ones, we find that cooperation and coordination can be achieved through the self-organization of the social network, a result that is non-trivial, especially in the Prisoner's Dilemma case. The evolution and stability of cooperation implies the condensation of agents exploiting particular game strategies into strong and stable clusters which are more densely connected, even in the more difficult case of the Prisoner's Dilemma.Comment: 18 pages, 14 figures. to appea

Multifractality in Human Heartbeat Dynamics

Recent evidence suggests that physiological signals under healthy conditions may have a fractal temporal structure. We investigate the possibility that time series generated by certain physiological control systems may be members of a special class of complex processes, termed multifractal, which require a large number of exponents to characterize their scaling properties. We report on evidence for multifractality in a biological dynamical system --- the healthy human heartbeat. Further, we show that the multifractal character and nonlinear properties of the healthy heart rate are encoded in the Fourier phases. We uncover a loss of multifractality for a life-threatening condition, congestive heart failure.Comment: 19 pages, latex2e using rotate and epsf, with 5 ps figures; to appear in Nature, 3 June, 199

Detecting rich-club ordering in complex networks

Uncovering the hidden regularities and organizational principles of networks arising in physical systems ranging from the molecular level to the scale of large communication infrastructures is the key issue for the understanding of their fabric and dynamical properties [1-5]. The ``rich-club'' phenomenon refers to the tendency of nodes with high centrality, the dominant elements of the system, to form tightly interconnected communities and it is one of the crucial properties accounting for the formation of dominant communities in both computer and social sciences [4-8]. Here we provide the analytical expression and the correct null models which allow for a quantitative discussion of the rich-club phenomenon. The presented analysis enables the measurement of the rich-club ordering and its relation with the function and dynamics of networks in examples drawn from the biological, social and technological domains.Comment: 1 table, 3 figure

Structural efficiency of percolation landscapes in flow networks

Complex networks characterized by global transport processes rely on the presence of directed paths from input to output nodes and edges, which organize in characteristic linked components. The analysis of such network-spanning structures in the framework of percolation theory, and in particular the key role of edge interfaces bridging the communication between core and periphery, allow us to shed light on the structural properties of real and theoretical flow networks, and to define criteria and quantities to characterize their efficiency at the interplay between structure and functionality. In particular, it is possible to assess that an optimal flow network should look like a "hairy ball", so to minimize bottleneck effects and the sensitivity to failures. Moreover, the thorough analysis of two real networks, the Internet customer-provider set of relationships at the autonomous system level and the nervous system of the worm Caenorhabditis elegans --that have been shaped by very different dynamics and in very different time-scales--, reveals that whereas biological evolution has selected a structure close to the optimal layout, market competition does not necessarily tend toward the most customer efficient architecture.Comment: 8 pages, 5 figure