Luís A. Nunes Amaral

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 we can find functional modules in complex networks, and 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 most potential for immediate applicability. We use our method to analyse the metabolic networks of twelve organisms from three different superkingdoms. 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 metabolites that participate in only a few reactions but that connect different modules are more conserved than hubs whose links are mostly within a single module.

The web of human sexual contacts.

Promiscuous individuals are the vulnerable nodes to target in safe-sex campaigns.

Multifractality in Human Heartbeat Dynamics.

There is evidence that physiological signals under healthy conditions may have a fractal temporal structure. Here 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 onevidence for multifractality in a biological dynamical system, the healthy human heartbeat, and 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.

The worldwide air transportation network: Anomalous centrality, community structure, and cities' global roles

We analyze the global structure of the worldwide air transportation network, a critical infrastructure with an enormous impact on local, national, and international economies. We find that the worldwide air transportation network is a scale-free small-world network. In contrast to the prediction of scale-free network models, however, we find that the most connected cities are not necessarily the most central, resulting in anomalous values of the centrality. We demonstrate that these anomalies arise because of the multicommunity structure of the network. We identify the communities in the air transportation network and show that the community structure cannot be explained solely based on geographical constraints and that geopolitical considerations have to be taken into account. We identify each citys global role based on its pattern of intercommunity and intracommunity connections, which enables us to obtain scale-specific representations of the network.

Universal and Nonuniversal Properties of Cross Correlations in Financial Time Series

We use methods of random matrix theory to analyze the cross-correlation matrix C of price changes of the largest 1000 US stocks for the 2-year period 1994-95. We find that the statistics of most of the eigenvalues in the spectrum of C agree with the predictions of random matrix theory, but there are deviations for a few of the largest eigenvalues. We find that C has the universal properties of the Gaussian orthogonal ensemble of random matrices. Furthermore, we analyze the eigenvectors of C through their inverse participation ratio and find eigenvectors with large inverse participation ratios at both edges of the eigenvalue spectrum--a situation reminiscent of results in localization theory.

Scaling of the distribution of fluctuations of financial market indices

We study the distribution of fluctuations of the S&P 500 index over a time scale deltat by analyzing three distinct databases. Database (i) contains approximately 1 200 000 records, sampled at 1-min intervals, for the 13-year period 1984-1996, database (ii) contains 8686 daily records for the 35-year period 1962-1996, and database (iii) contains 852 monthly records for the 71-year period 1926-1996. We compute the probability distributions of returns over a time scale deltat, where deltat varies approximately over a factor of 10(4)-from 1 min up to more than one month. We find that the distributions for deltat<or= 4 d (1560 min) are consistent with a power-law asymptotic behavior, characterized by an exponent alpha approximately 3, well outside the stable Lévy regime 0<alpha<2. To test the robustness of the S&P result, we perform a parallel analysis on two other financial market indices. Database (iv) contains 3560 daily records of the NIKKEI index for the 14-year period 1984-1997, and database (v) contains 4649 daily records of the Hang-Seng index for the 18-year period 1980-1997. We find estimates of alpha consistent with those describing the distribution of S&P 500 daily returns. One possible reason for the scaling of these distributions is the long persistence of the autocorrelation function of the volatility. For time scales longer than (deltat)x approximately 4 d, our results are consistent with a slow convergence to Gaussian behavior.

Modularity from fluctuations in random graphs and complex networks

The mechanisms by which modularity emerges in complex networks are not well understood but recent reports have suggested that modularity may arise from evolutionary selection. We show that finding the modularity of a network is analogous to finding the ground-state energy of a spin system. Moreover, we demonstrate that, due to fluctuations, stochastic network models give rise to modular networks. Specifically, we show both numerically and analytically that random graphs and scale-free networks have modularity. We argue that this fact must be taken into consideration to define statistically significant modularity in complex networks.

Scaling of the distribution of price fluctuations of individual companies.

We present a phenomenological study of stock price fluctuations of individual companies. We systematically analyze two different databases covering securities from the three major U.S. stock markets: (a) the New York Stock Exchange, (b) the American Stock Exchange, and (c) the National Association of Securities Dealers Automated Quotation stock market. Specifically, we consider (i) the trades and quotes database, for which we analyze 40 million records for 1000 U.S. companies for the 2-yr period 1994-95; and (ii) the Center for Research and Security Prices database, for which we analyze 35 million daily records for approximately 16,000 companies in the 35-yr period 1962-96. We study the probability distribution of returns over varying time scales Delta t, where Delta t varies by a factor of approximately 10(5), from 5 min up to approximately 4 yr. For time scales from 5 min up to approximately 16 days, we find that the tails of the distributions can be well described by a power-law decay, characterized by an exponent 2.5 < proportional to < 4, well outside the stable Lévy regime 0 < alpha < 2. For time scales Delta t >> (Delta t)(x) approximately equal to 16 days, we observe results consistent with a slow convergence to Gaussian behavior. We also analyze the role of cross correlations between the returns of different companies and relate these correlations to the distribution of returns for market indices.

Inverse cubic law for the distribution of stock price variations

Abstract:The probability distribution of stock price changes is studied by analyzing a database (the Trades and Quotes Database) documenting every trade for all stocks in three major US stock markets, for the two year period January 1994 - December 1995. A sample of 40 million data points is extracted, which is substantially larger than studied hitherto. We find an asymptotic power-law behavior for the cumulative distribution with an exponent