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

Scalable Molecular Dynamics with NAMD

An important part of our information-gathering behavior has always been to find out what other people think. With the growing availability and popularity of opinion-rich resources such as online review sites and personal blogs, new opportunities and challenges arise as people now can, and do, actively use information technologies to seek out and understand the opinions of others. The sudden eruption of activity in the area of opinion mining and sentiment analysis, which deals with the computational treatment of opinion, sentiment, and subjectivity in text, has thus occurred at least in part as a direct response to the surge of interest in new systems that deal directly with opinions as a first-class object.

This survey covers techniques and approaches that promise to directly enable opinion-oriented information-seeking systems. Our focus is on methods that seek to address the new challenges raised by sentiment-aware applications, as compared to those that are already present in more traditional fact-based analysis. We include material on summarization of evaluative text and on broader issues regarding privacy, manipulation, and economic impact that the development of opinion-oriented information-access services gives rise to. To facilitate future work, a discussion of available resources, benchmark datasets, and evaluation campaigns is also provided.

/pdf/opinion-mining-and-sentiment-analysis-3v5ya3qqiw.pdf

Opinion Mining and Sentiment Analysis

Many tasks in computer vision involve assigning a label (such as disparity) to every pixel. A common constraint is that the labels should vary smoothly almost everywhere while preserving sharp discontinuities that may exist, e.g., at object boundaries. These tasks are naturally stated in terms of energy minimization. The authors consider a wide class of energies with various smoothness constraints. Global minimization of these energy functions is NP-hard even in the simplest discontinuity-preserving case. Therefore, our focus is on efficient approximation algorithms. We present two algorithms based on graph cuts that efficiently find a local minimum with respect to two types of large moves, namely expansion moves and swap moves. These moves can simultaneously change the labels of arbitrarily large sets of pixels. In contrast, many standard algorithms (including simulated annealing) use small moves where only one pixel changes its label at a time. Our expansion algorithm finds a labeling within a known factor of the global minimum, while our swap algorithm handles more general energy functions. Both of these algorithms allow important cases of discontinuity preserving energies. We experimentally demonstrate the effectiveness of our approach for image restoration, stereo and motion. On real data with ground truth, we achieve 98 percent accuracy.

/pdf/fast-approximate-energy-minimization-via-graph-cuts-3usqtddnkx.pdf

Fast approximate energy minimization via graph cuts

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

Methods used to sequence the transcriptome often produce more than 200 million short sequences. We introduce StringTie, a computational method that applies a network flow algorithm originally developed in optimization theory, together with optional de novo assembly, to assemble these complex data sets into transcripts. When used to analyze both simulated and real data sets, StringTie produces more complete and accurate reconstructions of genes and better estimates of expression levels, compared with other leading transcript assembly programs including Cufflinks, IsoLasso, Scripture and Traph. For example, on 90 million reads from human blood, StringTie correctly assembled 10,990 transcripts, whereas the next best assembly was of 7,187 transcripts by Cufflinks, which is a 53% increase in transcripts assembled. On a simulated data set, StringTie correctly assembled 7,559 transcripts, which is 20% more than the 6,310 assembled by Cufflinks. As well as producing a more complete transcriptome assembly, StringTie runs faster on all data sets tested to date compared with other assembly software, including Cufflinks.

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Models for the processes by which ideas and influence propagate through a social network have been studied in a number of domains, including the diffusion of medical and technological innovations, the sudden and widespread adoption of various strategies in game-theoretic settings, and the effects of "word of mouth" in the promotion of new products. Recently, motivated by the design of viral marketing strategies, Domingos and Richardson posed a fundamental algorithmic problem for such social network processes: if we can try to convince a subset of individuals to adopt a new product or innovation, and the goal is to trigger a large cascade of further adoptions, which set of individuals should we target?We consider this problem in several of the most widely studied models in social network analysis. The optimization problem of selecting the most influential nodes is NP-hard here, and we provide the first provable approximation guarantees for efficient algorithms. Using an analysis framework based on submodular functions, we show that a natural greedy strategy obtains a solution that is provably within 63% of optimal for several classes of models; our framework suggests a general approach for reasoning about the performance guarantees of algorithms for these types of influence problems in social networks.We also provide computational experiments on large collaboration networks, showing that in addition to their provable guarantees, our approximation algorithms significantly out-perform node-selection heuristics based on the well-studied notions of degree centrality and distance centrality from the field of social networks.

/pdf/maximizing-the-spread-of-influence-through-a-social-network-3nnj0jic76.pdf

Maximizing the spread of influence through a social network

/pdf/maximizing-the-spread-of-influence-through-a-social-network-47y1ehuvwi.pdf

Maximizing the Spread of Influence through a Social Network

We consider the problem of routing traffic to optimize the performance of a congested network. We are given a network, a rate of traffic between each pair of nodes, and a latency function for each edge specifying the time needed to traverse the edge given its congestion; the objective is to route traffic such that the sum of all travel times---the total latency---is minimized.In many settings, it may be expensive or impossible to regulate network traffic so as to implement an optimal assignment of routes. In the absence of regulation by some central authority, we assume that each network user routes its traffic on the minimum-latency path available to it, given the network congestion caused by the other users. In general such a "selfishly motivated" assignment of traffic to paths will not minimize the total latency; hence, this lack of regulation carries the cost of decreased network performance.In this article, we quantify the degradation in network performance due to unregulated traffic. We prove that if the latency of each edge is a linear function of its congestion, then the total latency of the routes chosen by selfish network users is at most 4/3 times the minimum possible total latency (subject to the condition that all traffic must be routed). We also consider the more general setting in which edge latency functions are assumed only to be continuous and nondecreasing in the edge congestion. Here, the total latency of the routes chosen by unregulated selfish network users may be arbitrarily larger than the minimum possible total latency; however, we prove that it is no more than the total latency incurred by optimally routing twice as much traffic.

/pdf/how-bad-is-selfish-routing-g644vu88rg.pdf

How bad is selfish routing

Algorithm Design introduces algorithms by looking at the real-world problems that motivate them. The book teaches students a range of design and analysis techniques for problems that arise in computing applications. The text encourages an understanding of the algorithm design process and an appreciation of the role of algorithms in the broader field of computer science.

Éva Tardos

Papers

Maximizing the spread of influence through a social network

Maximizing the Spread of Influence through a Social Network

How bad is selfish routing

Algorithm Design

Algorithmic Game Theory: Quantifying the Inefficiency of Equilibria