Systems as diverse as genetic networks or the World Wide Web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This feature was found to be a consequence of two generic mechanisms: (i) networks expand continuously by the addition of new vertices, and (ii) new vertices attach preferentially to sites that are already well connected. A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.

https://arxiv.org/pdf/cond-mat/9910332.pdf

Emergence of Scaling in Random Networks

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

The increasing volume of data in modern business and science calls for more complex and sophisticated tools. Although advances in data mining technology have made extensive data collection much easier, it's still always evolving and there is a constant need for new techniques and tools that can help us transform this data into useful information and knowledge. Since the previous edition's publication, great advances have been made in the field of data mining. Not only does the third of edition of Data Mining: Concepts and Techniques continue the tradition of equipping you with an understanding and application of the theory and practice of discovering patterns hidden in large data sets, it also focuses on new, important topics in the field: data warehouses and data cube technology, mining stream, mining social networks, and mining spatial, multimedia and other complex data. Each chapter is a stand-alone guide to a critical topic, presenting proven algorithms and sound implementations ready to be used directly or with strategic modification against live data. This is the resource you need if you want to apply today's most powerful data mining techniques to meet real business challenges. * Presents dozens of algorithms and implementation examples, all in pseudo-code and suitable for use in real-world, large-scale data mining projects. * Addresses advanced topics such as mining object-relational databases, spatial databases, multimedia databases, time-series databases, text databases, the World Wide Web, and applications in several fields. *Provides a comprehensive, practical look at the concepts and techniques you need to get the most out of real business data

/pdf/data-mining-concepts-and-techniques-4dtvdfkvmi.pdf

Data Mining: Concepts and Techniques

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The emergence of order in natural systems is a constant source of inspiration for both physical and biological sciences. While the spatial order characterizing for example the crystals has been the basis of many advances in contemporary physics, most complex systems in nature do not offer such high degree of order. Many of these systems form complex networks whose nodes are the elements of the system and edges represent the interactions between them. 
Traditionally complex networks have been described by the random graph theory founded in 1959 by Paul Erdohs and Alfred Renyi. One of the defining features of random graphs is that they are statistically homogeneous, and their degree distribution (characterizing the spread in the number of edges starting from a node) is a Poisson distribution. In contrast, recent empirical studies, including the work of our group, indicate that the topology of real networks is much richer than that of random graphs. In particular, the degree distribution of real networks is a power-law, indicating a heterogeneous topology in which the majority of the nodes have a small degree, but there is a significant fraction of highly connected nodes that play an important role in the connectivity of the network. 
The scale-free topology of real networks has very important consequences on their functioning. For example, we have discovered that scale-free networks are extremely resilient to the random disruption of their nodes. On the other hand, the selective removal of the nodes with highest degree induces a rapid breakdown of the network to isolated subparts that cannot communicate with each other. 
The non-trivial scaling of the degree distribution of real networks is also an indication of their assembly and evolution. Indeed, our modeling studies have shown us that there are general principles governing the evolution of networks. Most networks start from a small seed and grow by the addition of new nodes which attach to the nodes already in the system. This process obeys preferential attachment: the new nodes are more likely to connect to nodes with already high degree. We have proposed a simple model based on these two principles wich was able to reproduce the power-law degree distribution of real networks. Perhaps even more importantly, this model paved the way to a new paradigm of network modeling, trying to capture the evolution of networks, not just their static topology.

/pdf/statistical-mechanics-of-complex-networks-1zfjpvxipu.pdf

Statistical mechanics of complex networks

Most networked systems of scientific interest are characterized by temporal links, meaning the network’s structure changes over time. Link temporality has been shown to hinder many dynamical processes, from information spreading to accessibility, by disrupting network paths. Considering the ubiquity of temporal networks in nature, we ask: Are there any advantages of the networks’ temporality? We use an analytical framework to show that temporal networks can, compared to their static counterparts, reach controllability faster, demand orders of magnitude less control energy, and have control trajectories, that are considerably more compact than those characterizing static networks. Thus, temporality ensures a degree of flexibility that would be unattainable in static networks, enhancing our ability to control them.

The fundamental advantages of temporal networks

Models for the topology or dynamics of various networks abound, but until now, there has been no single universal framework for complex networks that can separate factors contributing to the topology and dynamics of networks across biological and social systems.

/pdf/universality-in-network-dynamics-32gkn5w2dj.pdf

Universality in network dynamics

Controlling large natural and technological networks is an outstanding challenge. It is typically neither feasible nor necessary to control the entire network, prompting us to explore target control: the efficient control of a preselected subset of nodes. We show that the structural controllability approach used for full control overestimates the minimum number of driver nodes needed for target control. Here we develop an alternate ‘k-walk’ theory for directed tree networks, and we rigorously prove that one node can control a set of target nodes if the path length to each target node is unique. For more general cases, we develop a greedy algorithm to approximate the minimum set of driver nodes sufficient for target control. We find that degree heterogeneous networks are target controllable with higher efficiency than homogeneous networks and that the structure of many real-world networks are suitable for efficient target control.

/pdf/targeted-control-of-complex-networks-3n26u4oadx.pdf

Targeted Control of Complex Networks

Nature 530, 307–312 (2016); doi:10.1038/nature16948 In the last sentence of page 310 of this Letter, the parameter h should equal 2, rather than 1. In addition, after equation (4), the text should have stated ‘Aij > 0’ and ‘positive interactions’, to read “...the weighted connectivity matrix Aij > 0 captures the positive interactions between the nodes.

/pdf/erratum-universal-resilience-patterns-in-complex-networks-4od6pe45x2.pdf

Erratum: Universal resilience patterns in complex networks

We introduce the concept of control centrality to quantify the ability of a single node to control a directed weighted network. We calculate the distribution of control centrality for several real networks and find that it is mainly determined by the network’s degree distribution. We show that in a directed network without loops the control centrality of a node is uniquely determined by its layer index or topological position in the underlying hierarchical structure of the network. Inspired by the deep relation between control centrality and hierarchical structure in a general directed network, we design an efficient attack strategy against the controllability of malicious networks.

/pdf/control-centrality-and-hierarchical-structure-in-complex-4htrmkfem8.pdf

Albert-László Barabási

Papers

The fundamental advantages of temporal networks

Universality in network dynamics

Targeted Control of Complex Networks

Erratum: Universal resilience patterns in complex networks

Control Centrality and Hierarchical Structure in Complex Networks