/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

The Lovasz local lemma (LLL)is a powerful tool that is increasingly playing a valuable role in computer science. The original lemma was nonconstructive; a breakthrough of Beck and its generalizations (due to Alon and Molloy and Reed)have led to constructive versions. However, these methods do not capture some classes of applications of the LLL. We make progress on this by providing algorithmic approaches to two families of applications of the LLL. The first provides constructive versions of certain applications of an extension of the LLL (modeling, e.g., hypergraph-partitioning and low-congestion routing problems); the second provides new algorithmic results on constructing disjoint paths in graphs. Our results can also be seen as constructive upper bounds on the integrality gap of certain packing problems. One common theme of our work is a "gradual rounding" approach.

New algorithmic aspects of the Local Lemma with applications to routing and partitioning

In this paper, we propose an energy efficient device discovery protocol, eDiscovery, as the first step to bootstrapping opportunistic communications for smartphones, the most popular mobile devices We chose Bluetooth over WiFi as the underlying wireless technology of device discovery, based on our measurement study of their energy consumption on smartphones eDiscovery adaptively changes the duration and interval of Bluetooth inquiry in dynamic environments, by leveraging history information of discovered peers We implement a prototype of eDiscovery on Nokia N900 smartphones and evaluate its performance in three different environments To the best of our knowledge, we are the first to conduct extensive performance evaluation of Bluetooth device discovery in the wild Our experimental results demonstrate that compared with a scheme with constant inquiry duration and interval, eDiscovery can save around 44% energy at the expense of discovering only about 21% less peers The results also show that eDiscovery performs better than other existing schemes, by discovering more peers and consuming less energy

/pdf/ediscovery-energy-efficient-device-discovery-for-mobile-2p0y3drczb.pdf

eDiscovery: Energy efficient device discovery for mobile opportunistic communications

The PAC learning of rectangles has been studied because they have been found experimentally to yield excellent hypotheses for severaf applied learning problems. Also, pseudorandom sets for rectangles have been actively studied recently because (i) they are a subpmblem common to the derandomization of depth-2 (DIW) circuits and derandotnizing Randomized Logspace, and (ii) they approximate the distribution of n independent multivalued random variables. We present improved upper bounds for a class of such problems of “approximating” highdlmensional rectangles that arise in PAC learning and pseudorandomness.

Approximating Hyper-Rectangles: Learning and Pseudo-random Sets

Equipping wireless nodes with multiple radios can significantly increase the capacity of wireless networks, by making these radios simultaneously transmit over multiple non-overlapping channels. However, due to the limited number of radios and available orthogonal channels, designing efficient channel assignment and scheduling algorithms in such networks is a major challenge. In this paper, we present provably-good distributed algorithms for simultaneous channel allocation of individual links and packet-scheduling, in software-defined radio (SDR) wireless networks. Our distributed algorithms are very simple to implement, and do not require any coordination even among neighboring nodes. A novel access hash function or random oracle methodology is one of the key drivers of our results. With this access hash function, each radio can know the transmitters' decisions for links in its interference set for each time slot without introducing any extra communication overhead between them. Further, by utilizing the inductive-scheduling technique, each radio can also backoff appropriately to avoid collisions. Extensive simulations demonstrate that our bounds are valid in practice.

/pdf/distributed-strategies-for-channel-allocation-and-scheduling-3ao4dmjyn0.pdf

Distributed Strategies for Channel Allocation and Scheduling in Software-Defined Radio Networks

We show that for all large n, every n-uniform hypergraph with at most 0.7/spl radic/(n/lnn)/spl times/2/sup n/ edges can be two-colored. We, in fact, present fast algorithms that output a proper two-coloring with high probability for such hypergraphs. We also derandomize and parallelize these algorithms, to derive NC/sup 1/ versions of these results. This makes progress on a problem of Erdos (1963), improving the previous-best bound of n/sup 1/3-0(1)//spl times/2/sup n/ due to Beck (1978). We further generalize this to a "local" version, improving on one of the first applications of the Lovasz Local Lemma.

Aravind Srinivasan

Papers

New algorithmic aspects of the Local Lemma with applications to routing and partitioning

eDiscovery: Energy efficient device discovery for mobile opportunistic communications

Approximating Hyper-Rectangles: Learning and Pseudo-random Sets

Distributed Strategies for Channel Allocation and Scheduling in Software-Defined Radio Networks

Improved bounds and algorithms for hypergraph two-coloring