/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

The mapping of large-scale human movements is important for urban planning, traffic forecasting and epidemic prevention. Work in animals had suggested that their foraging might be explained in terms of a random walk, a mathematical rendition of a series of random steps, or a Levy flight, a random walk punctuated by occasional larger steps. The role of Levy statistics in animal behaviour is much debated — as explained in an accompanying News Feature — but the idea of extending it to human behaviour was boosted by a report in 2006 of Levy flight-like patterns in human movement tracked via dollar bills. A new human study, based on tracking the trajectory of 100,000 cell-phone users for six months, reveals behaviour close to a Levy pattern, but deviating from it as individual trajectories show a high degree of temporal and spatial regularity: work and other commitments mean we are not as free to roam as a foraging animal. But by correcting the data to accommodate individual variation, simple and predictable patterns in human travel begin to emerge. The cover photo (by Cesar Hidalgo) captures human mobility in New York's Grand Central Station. This study used a sample of 100,000 mobile phone users whose trajectory was tracked for six months to study human mobility patterns. Displacements across all users suggest behaviour close to the Levy-flight-like pattern observed previously based on the motion of marked dollar bills, but with a cutoff in the distribution. The origin of the Levy patterns observed in the aggregate data appears to be population heterogeneity and not Levy patterns at the level of the individual. Despite their importance for urban planning1, traffic forecasting2 and the spread of biological3,4,5 and mobile viruses6, our understanding of the basic laws governing human motion remains limited owing to the lack of tools to monitor the time-resolved location of individuals. Here we study the trajectory of 100,000 anonymized mobile phone users whose position is tracked for a six-month period. We find that, in contrast with the random trajectories predicted by the prevailing Levy flight and random walk models7, human trajectories show a high degree of temporal and spatial regularity, each individual being characterized by a time-independent characteristic travel distance and a significant probability to return to a few highly frequented locations. After correcting for differences in travel distances and the inherent anisotropy of each trajectory, the individual travel patterns collapse into a single spatial probability distribution, indicating that, despite the diversity of their travel history, humans follow simple reproducible patterns. This inherent similarity in travel patterns could impact all phenomena driven by human mobility, from epidemic prevention to emergency response, urban planning and agent-based modelling.

/pdf/understanding-individual-human-mobility-patterns-3k1tyob274.pdf

Understanding individual human mobility patterns

We present Tor, a circuit-based low-latency anonymous communication service. This second-generation Onion Routing system addresses limitations in the original design by adding perfect forward secrecy, congestion control, directory servers, integrity checking, configurable exit policies, and a practical design for location-hidden services via rendezvous points. Tor works on the real-world Internet, requires no special privileges or kernel modifications, requires little synchronization or coordination between nodes, and provides a reasonable tradeoff between anonymity, usability, and efficiency. We briefly describe our experiences with an international network of more than 30 nodes. We close with a list of open problems in anonymous communication.

/pdf/tor-the-second-generation-onion-router-2qfrg0ppqb.pdf

Tor: the second-generation onion router

NetworkX is a Python language package for exploration and analysis of networks and network algorithms. The core package provides data structures for representing many types of networks, or graphs, including simple graphs, directed graphs, and graphs with parallel edges and self-loops. The nodes in NetworkX graphs can be any (hashable) Python object and edges can contain arbitrary data; this flexibility makes NetworkX ideal for representing networks found in many dierent scientific fields. In addition to the basic data structures many graph algorithms are implemented for calculating network properties and structure measures: shortest paths, betweenness centrality, clustering, and degree distribution and many more. NetworkX can read and write various graph formats for easy exchange with existing data, and provides generators for many classic graphs and popular graph models, such as the Erdos-Renyi, Small World, and Barabasi-Albert models. The ease-of-use and flexibility of the Python programming language together with connection to the SciPy tools make NetworkX a powerful tool for scientific computations. We discuss some of our recent work studying synchronization of coupled oscillators to demonstrate how NetworkX enables research in the field of computational networks.

/pdf/exploring-network-structure-dynamics-and-function-using-2isdfk9y1h.pdf

Exploring Network Structure, Dynamics, and Function using NetworkX

Here we present a highly resolved agent-based simulation tool (EpiSims), which combines realistic estimates of population mobility,based on census and land-use data, with parameterized models for simulating the progress of a disease within a host and of transmission between hosts10. The simulation generates a largescale,dynamic contact graph that replaces the differential equations of the classic approach. EpiSims is based on the Transportation Analysis and Simulation System (TRANSIMS) developed at Los Alamos National Laboratory, which produces estimates of social networks based on the assumption that the transportation infrastructure constrains people’s choices about where and when to perform activities11. TRANSIMS creates a synthetic population endowed with demographics such as age and income, consistent with joint distributions in census data. It then estimates positions and activities of all travellers on a second-by-second basis. For more information on TRANSIMS and its availability, see Supplementary Information. The resulting social network is the best extant estimate of the physical contact patterns among large groups of people—alternative methodologies are limited to physical contacts among hundreds of people or non-physical contacts (such as e-mail or citations) among large groups.

Modelling disease outbreaks in realistic urban social networks.

3G networks are currently overloaded, due to the increasing popularity of various applications for smartphones. Offloading mobile data traffic through opportunistic communications is a promising solution to partially solve this problem, because there is almost no monetary cost for it. We propose to exploit opportunistic communications to facilitate information dissemination in the emerging Mobile Social Networks (MoSoNets) and thus reduce the amount of mobile data traffic. As a case study, we investigate the target-set selection problem for information delivery. In particular, we study how to select the target set with only k users, such that we can minimize the mobile data traffic over cellular networks. We propose three algorithms, called Greedy, Heuristic, and Random, for this problem and evaluate their performance through an extensive trace-driven simulation study. Our simulation results verify the efficiency of these algorithms for both synthetic and real-world mobility traces. For example, the Heuristic algorithm can offload mobile data traffic by up to 73.66 percent for a real-world mobility trace. Moreover, to investigate the feasibility of opportunistic communications for mobile phones, we implement a proof-of-concept prototype, called Opp-off, on Nokia N900 smartphones, which utilizes their Bluetooth interface for device/service discovery and content transfer.

/pdf/mobile-data-offloading-through-opportunistic-communications-cx402sq928.pdf

Mobile Data Offloading through Opportunistic Communications and Social Participation

We present a fairly general method for finding deterministic constructions obeying what we call k-restrictions; this yields structures of size not much larger than the probabilistic bound. The structures constructed by our method include (n,k)-universal sets (a collection of binary vectors of length n such that for any subset of size k of the indices, all 2/sup k/ configurations appear) and families of perfect hash functions. The near-optimal constructions of these objects imply the very efficient derandomization of algorithms in learning, of fixed-subgraph finding algorithms, and of near optimal /spl Sigma/II/spl Sigma/ threshold formulae. In addition, they derandomize the reduction showing the hardness of approximation of set cover. They also yield deterministic constructions for a local-coloring protocol, and for exhaustive testing of circuits.

/pdf/splitters-and-near-optimal-derandomization-3z9xxkmysh.pdf

Splitters and near-optimal derandomization

Chernoff-Hoeffding bounds are fundamental tools used in bounding the tail probabilities of the sums of bounded and independent random variables. We present a simple technique which gives slightly better bounds than these and which, more importantly, requires only limited independence among the random variables, thereby importing a variety of standard results to the case of limited independence for free. Additional methods are also presented, and the aggregate results are very sharp and provide a better understanding of the proof techniques behind these bounds. They also yield improved bounds for various tail probability distributions and enable improved approximation algorithms for jobshop scheduling. The ``limited independence'''' result implies that weaker sources of randomness are sufficient for randomized algorithms whose analyses use the Chernoff-Hoeffding bounds; further, it leads to algorithms that require a reduced amount of randomness for any analysis which uses the Chernoff-Hoeffding bounds, e.g., the analysis of randomized algorithms for random sampling and oblivious packet routing.

Chernoff-Hoeffding bounds for applications with limited independence

Certain types of routing, scheduling, and resource-allocation problems in a distributed setting can be modeled as edge-coloring problems We present fast and simple randomized algorithms for edge coloring a graph in the synchronous distributed point-to-point model of computation Our algorithms compute an edge coloring of a graph $G$ with $n$ nodes and maximum degree $\Delta$ with at most $16 \Delta + O(\log^{1+ \delta} n)$ colors with high probability (arbitrarily close to 1) for any fixed $\delta > 0$; they run in polylogarithmic time The upper bound on the number of colors improves upon the $(2 \Delta - 1)$-coloring achievable by a simple reduction to vertex coloring
To analyze the performance of our algorithms, we introduce new techniques for proving upper bounds on the tail probabilities of certain random variables The Chernoff--Hoeffding bounds are fundamental tools that are used very frequently in estimating tail probabilities However, they assume stochastic independence among certain random variables, which may not always hold Our results extend the Chernoff--Hoeffding bounds to certain types of random variables which are not stochastically independent We believe that these results are of independent interest and merit further study

/pdf/randomized-distributed-edge-coloring-via-an-extension-of-the-4appgao60l.pdf

Aravind Srinivasan

Papers

Modelling disease outbreaks in realistic urban social networks.

Mobile Data Offloading through Opportunistic Communications and Social Participation

Splitters and near-optimal derandomization

Chernoff-Hoeffding bounds for applications with limited independence

Randomized Distributed Edge Coloring via an Extension of the Chernoff--Hoeffding Bounds