Handling editor: Evelyn Sander

Complex Networks in Biology and Engineering: From Principles to Applications

Eshel Ben-Jacob, School of Physics and Astronomy, Tel-Aviv University, Israel,
Vito Latora, Dipartimento di Fisica, Universita di Catania & INFN Sezione, Italy,
and Stefano Boccaletti, Embassy of Italy in Tel Aviv, Israel

An illustration of a complex network.

The first Italian-Israeli meeting on "Complex Networks in Biology and Engineering: From Principles to Applications" took place in Israel, at the Tel Aviv University, on October 24-25, 2007. The conference was sponsored by the Italian Embassy in Israel and by the Tel Aviv University. The study of complex networks is currently viewed as a hot topic in science, both for its multi-disciplinary nature and for its innovative applications. Complex networks appear in several systems from biology to computer science, tuning and ruling most of the life activities of organisms and the functioning of technological networks. Consequently, complex networks theory has become an essential ingredient in the background of any scientist. The main purpose of the meeting was to bring together a small group of about thirty Italian and Israeli experts in complex networks from many different fields (physics, computer science, biology and engineering) to discuss the current techniques and applications of network theory.

The Italian group was coordinated by Vito Latora, from the University of Catania, Italy, and included researchers from CNR, INFN, ENEA, ICTP (Trieste), ISI (Torino) and the universities of Roma, Padova, Catania and Palermo, as well as from leading industries such as STmicrolectronics. The Israeli participants were coordinated by Eshel Ben-Jacobs from the Tel Aviv University, and included researchers from the Technion, Tel-Aviv University, Haifa University, Ben Gurion University, Hebrew University and the Weizmann Institute as well as industrial participants from leading companies in the field.

The Marcel Gordon University Club.

The lectures were held at the The Marcel Gordon University Club (the Green House) at Tel Aviv University which provided a very special warm atmosphere for interactive lectures and discussions. There were many exciting topics at the forefront of research in complex networks, such as the principles of gene networks regulation, memory and learning in neural networks, information processing by the immune network, modeling of epidemic spreading, information flow and information mining in the Internet, and synchronization phenomena in biological and social networks. All the speakers were asked to present part of their lectures in a more popular manner to be accessible to students and scientists with different backgrounds and goals.

The first day of work started with the opening and welcoming remarks of the Italian Ambassador in Israel, His Excellency Sandro De Bernardin, who described to the audience the huge body of cooperation in science and technology that exists between Italy and Israel, and how the Italian Government considers strategic to boost cooperation in science and technology between the two countries.

His Excellency Sandro De Bernardin.

During the Opening Ceremony both the President and the Rector of the Tel Aviv University stated how important are the ties between the scientists of the University and the Italian system of research and innovation. The Rector of the Tel Aviv University then signed a Memorandum of Understanding between the Tel Aviv University and the University of Catania that is intended to promote a strong future collaboration between these two Organisms. The Memorandum was countersigned by the Dean of the Faculty of Engineering at the University of Catania, Prof. Luigi Fortuna.

Following the opening remarks, the first lecture was given by the science attaché of Italy in Israel Stefano Boccaletti, who explained how the intimate interplay between network topology and functionality may lead to the emergence of collective phenomena such as synchronization in connection with specific statistical properties characterizing the graph connectivity. He was followed by Sorin Solomon, who illustrated how understanding the fundamental principles of complex networks can play a crucial role in extracting information from systems such as WWW, Wikipedia, peer-to-peer, biological and cognitive networks.

Irun Cohen (WIS) discussed how the immune system maintains the human body by computing its current state through a network of interactions of distributed cells and molecules. In particular, Cohen presented two examples of the many system elements involved in immune computation: the architecture of cytokine mediated cell connectivity and the immunological homunculus (a dynamic representation of body biomarkers inherent in one's repertoire of auto-antibodies).

Massimo Marchiori (University of Padova) spoke on social search engines. Marchiori showed how society and technological progress have changed the rules of the World Wide Web, introducing good but also bad components, and how the social flows can be used to make up for a better generation of search engines. Rosario Mantegna (University of Palermo) discussed how one can construct networks of financial stocks, based on the correlation between their time series. He also discussed how such networks can be characterized in terms of minimum spanning trees, and planar maximally filtered graphs.

There were three lectures on biological systems. Andrea Giansanti (University of Roma La Sapienza) used hydrophobicity scales to construct in various ways a protein network from the information contained in the protein sequences. In particular, he showed how the network metaphor can shed some light on the problem of the stability and aggregation properties of acyl-phossphateses and of a class of viral neuraminidases. Martin Kupiec talked about network perspective of telomeres control. The importance of this question is related to the fact that in multi-cellular organisms, telomere shortening acts as a tumor suppressive mechanism. Replenishing telomeres is one of the few essential steps that a normal human fibroblast cell must take on its way to become malignant. He presented two complementary approaches: computational and experimental ones that were employed to identify the various pathways that regulate telomere length, with focusing on genetic interactions that connect TLM genes to the telomeres machinery. The third talk was that of Yitzhak Pilpel (WIS), on coping with genetic and non-genetic perturbations. The lecture was devoted to genetic circuits that allow them to respond more efficiently to their environment, and to control the internal stochastic fluctuation and genetic backup against external and internal variability. New results about the structure of redundancy-based circuits that provide cellular solution to genetic and non-genetic fluctuations were presented.

Luigi Fortuna (University of Catania) showed how the synchronization of dynamical networks of multiplexed chaotic systems with smooth nonlinearities can be achieved, while Mattia Frasca (University of Catania) studied how local interaction rules in a system of mobile agents can be used to obtain a form of coordinated behavior and how motion can influence epidemic spreading in such systems. In the final talk of the day, Remo Pareschi (University of Molise) showed how to model a situation where two networks come into contact and effectively compose into a larger network, as it may happen, for instance, when two enterprises are merged and the underlying communities of people become a single one.

Yuval Shavit (TAU) gave the opening lecture of the second day, presenting the first results of DIMES, a project to map the topology of the Internet. The DIMES project is based on a light-weight software measurement agent to be downloaded by volunteers around the world. The DIMES agent can be executed on every PC and allows mapping the Internet and tracking its evolution in time in several levels of granularity from the fine router level to the coarse Autonomous System (AS) level. In his lecture, Santo Fortunato (ISI Foundation, Torino) concentrates on the problem of how to detect community structures in a complex network. He discusses three main aspects of the problem: the definition(s) of community, the evaluation of partitions and the issue of hierarchies.

Shlomo Havlin talked about a central question in epidemics that is how to minimize the number of immunized nodes (people, computers etc) and still stop the spreading of epidemics. He reviewed and compared several efficient immunization methods recently developed. Vittoria Colizza (ISI Foundation, Torino) discussed the results of large-scale computational approaches for the study of global epidemics, showing the effect of complex real world transportation networks in the spreading pattern and in the forecast of emerging diseases.

Jesus Gomez-Gardenes (Scuola Superiore di Catania) lecture was on evolutionary game theory models on complex topologies. In particular Gomez-Gardenes showed how scale-free networks allow the survival of cooperative behavior even when selfish actions provide higher fitness (reproductive success). Ginestra Bianconi (ICTP, Trieste) discussed how to introduce the concept of entropy to characterize network ensembles with the same degree distribution, the same degree-correlations or the same community structure of any given real network. One main result is that the ensembles with fixed scale-free degree distribution have smaller entropy than the ensembles with homogeneous degree distribution, indicating a higher level of order in scale-free networks.

David Horn (TAU) talked about new approach to analyze enzymatic profiles of metagenomes. Recent genomic studies of microbial communities have become an important research trend, displaying results that turn out to be characteristic to the environments in which these communities are found. Thus networks of organisms are represented by their overall genetic content. It was shown that Applying the new Specific Peptides (SPs)method to metagenomes, it is possible to identify large numbers of putative enzymes, allowing us to construct an Enzymatic Profile for the metagenome in question which is, a step toward capturing relevant metaproteomic information.

Ron Meir (Technion) talked about optimal dynamic state estimation by neural networks based on recursive spike train decoding. Organisms acting in uncertain dynamical environments often employ exact or approximate Bayesian statistical calculations in order to continuously estimate the environmental state, integrate information from multiple sensory modalities, form predictions and choose actions. It was shown that such computations can be implemented using a network of neurons whose activity directly represents a probability distribution across the possible "world states." In this lecture rigorous mathematical results from the theory of continuous time point process filtering were used to show how optimal real-time state estimation and prediction may be implemented and relate the required network properties to the statistical nature of the environment, thereby quantifying the compatibility of a given network with its environment. Yael Hanein (TAU) talked of a set of novel neural network engineering tools suited for studying function-from relationship in neural networks. In particular he discussed a recently developed carbon nanotube based scheme to engineer neural networks with pre-defined geometries and to facilitate very high resolution electrical recordings and stimulations from these systems.

Vittorio Rosato (ENEA, Roma) focused on critical infrastructure networks, such as the electrical power transmission networks and the Internet He showed how such networks often display effects which are seldom predictable on the basis of their normal behavior, and how infrastructures are also strongly interdependent, as the operability of one of them depends on the correct operability of the others. Matteo Lo Presti (STMicroelectronics) presented some of the activities of the STMicroelectronics, one of the world's largest semiconductor companies, related with complex networks. In particular he discussed examples of STMicroelectronics activities such as: energy saving in home appliances, efficient solutions in factory automation, new sensors for medical image diagnosis, high scale integration and remote monitoring on cardiac applications, new solutions for industrial and service robotics.

The meeting ended with two more general public lectures. Uri Alon's (WIS) talk highlighted one of the aspects of simplicity in system biology: biological regulation networks appear to be built of a small set of recurring interaction patterns, called network motifs. In particular, Alon discussed how complicated biological networks made of interconnected motifs can be understood in terms of the dynamics of individual network motifs. Finally, Shimon Marom (Technion) discussed how measurements from large-scale recurrent networks of biological neurons provide a unique opportunity to observe and define issues pertaining to representation of environmental objects.

The meeting provided a unique forum for exchanging new ideas for initiating joint projects between Italian and Israeli scientists and also between academia and industry, and for strengthening scientific cooperation.