OpenRaiser/Intern-Atlas huggingface dataset:
Approximate analysis of biological systems by hybrid switching jump diffusion
Venue: arXiv cs.PF 2015
Year: 2015

In this paper we consider large state space continuous time Markov chains (MCs) arising in the field of systems biology. For density dependent families of MCs that represent the interaction of large groups of identical objects, Kurtz has proposed two kinds of approximations. One is based on ordinary differential equations, while the other uses a diffusion process. The computational cost of the deterministic approximation is significantly lower, but the diffusion approximation retains stochasticity and is able to reproduce relevant random features like variance, bimodality, and tail behavior. In a recent paper, for particular stochastic Petri net models, we proposed a jump diffusion approximation that aims at being applicable beyond the limits of Kurtz's diffusion approximation, namely when the process reaches the boundary with non-negligible probability. Other limitations of the diffusion approximation in its original form are that it can provide inaccurate results when the number of objects in some groups is often or constantly low and that it can be applied only to pure density dependent Markov chains. In order to overcome these drawbacks, in this paper we propose to apply the jump-diffusion approximation only to those components of the model that are in density dependent form and are associated with high population levels. The remaining components are treated as discrete quantities. The resulting process is a hybrid switching jump diffusion. We show that the stochastic differential equations that characterize this process can be derived automatically both from the description of the original Markov chains or starting from a higher level description language, like stochastic Petri nets. The proposed approach is illustrated on three models: one modeling the so called crazy clock reaction, one describing viral infection kinetics and the last considering transcription regulation.
Random Aerial Beamforming for Underlay Cognitive Radio with Exposed Secondary Users
Venue: arXiv cs.IT 2015
Year: 2015

In this paper, we introduce the exposed secondary users problem in underlay cognitive radio systems, where both the secondary-to-primary and primary-to-secondary channels have a Line-of-Sight (LoS) component. Based on a Rician model for the LoS channels, we show, analytically and numerically, that LoS interference hinders the achievable secondary user capacity when interference constraints are imposed at the primary user receiver. This is caused by the poor dynamic range of the interference channels fluctuations when a dominant LoS component exists. In order to improve the capacity of such system, we propose the usage of an Electronically Steerable Parasitic Array Radiator (ESPAR) antennas at the secondary terminals. An ESPAR antenna involves a single RF chain and has a reconfigurable radiation pattern that is controlled by assigning arbitrary weights to M orthonormal basis radiation patterns via altering a set of reactive loads. By viewing the orthonormal patterns as multiple virtual dumb antennas, we randomly vary their weights over time creating artificial channel fluctuations that can perfectly eliminate the undesired impact of LoS interference. This scheme is termed as Random Aerial Beamforming (RAB), and is well suited for compact and low cost mobile terminals as it uses a single RF chain. Moreover, we investigate the exposed secondary users problem in a multiuser setting, showing that LoS interference hinders multiuser interference diversity and affects the growth rate of the SU capacity as a function of the number of users. Using RAB, we show that LoS interference can actually be exploited to improve multiuser diversity via opportunistic nulling.
Semantic Graph for Zero-Shot Learning
Venue: arXiv cs.CV 2015
Year: 2015

Zero-shot learning aims to classify visual objects without any training data via knowledge transfer between seen and unseen classes. This is typically achieved by exploring a semantic embedding space where the seen and unseen classes can be related. Previous works differ in what embedding space is used and how different classes and a test image can be related. In this paper, we utilize the annotation-free semantic word space for the former and focus on solving the latter issue of modeling relatedness. Specifically, in contrast to previous work which ignores the semantic relationships between seen classes and focus merely on those between seen and unseen classes, in this paper a novel approach based on a semantic graph is proposed to represent the relationships between all the seen and unseen class in a semantic word space. Based on this semantic graph, we design a special absorbing Markov chain process, in which each unseen class is viewed as an absorbing state. After incorporating one test image into the semantic graph, the absorbing probabilities from the test data to each unseen class can be effectively computed; and zero-shot classification can be achieved by finding the class label with the highest absorbing probability. The proposed model has a closed-form solution which is linear with respect to the number of test images. We demonstrate the effectiveness and computational efficiency of the proposed method over the state-of-the-arts on the AwA (animals with attributes) dataset.
Analyzing Traffic Problem Model With Graph Theory Algorithms
Venue: arXiv cs.DS 2015
Year: 2015

This paper will contribute to a practical problem, Urban Traffic. We will investigate those features, try to simplify the complexity and formulize this dynamic system. These contents mainly contain how to analyze a decision problem with combinatorial method and graph theory algorithms; how to optimize our strategy to gain a feasible solution through employing other principles of Computer Science.
Large System Analysis of the Energy Consumption Distribution in Multi-User MIMO Systems with Mobility
Venue: arXiv cs.IT 2015
Year: 2015

In this work, we consider the downlink of a single-cell multi-user MIMO system in which the base station (BS) makes use of $N$ antennas to communicate with $K$ single-antenna user equipments (UEs). The UEs move around in the cell according to a random walk mobility model. We aim at determining the energy consumption distribution when different linear precoding techniques are used at the BS to guarantee target rates within a finite time interval $T$. The analysis is conducted in the asymptotic regime where $N$ and $K$ grow large with fixed ratio under the assumption of perfect channel state information (CSI). Both recent and standard results from large system analysis are used to provide concise formulae for the asymptotic transmit powers and beamforming vectors for all considered schemes. These results are eventually used to provide a deterministic approximation of the energy consumption and to study its fluctuations around this value in the form of a central limit theorem. Closed-form expressions for the asymptotic means and variances are given. Numerical results are used to validate the accuracy of the theoretical analysis and to make comparisons. We show how the results can be used to approximate the probability that a battery-powered BS runs out of energy and also to design the cell radius for minimizing the energy consumption per unit area. The imperfect CSI case is also briefly considered.
Unimodal Bandits without Smoothness
Venue: arXiv cs.LG 2015
Year: 2015

We consider stochastic bandit problems with a continuous set of arms and where the expected reward is a continuous and unimodal function of the arm. No further assumption is made regarding the smoothness and the structure of the expected reward function. For these problems, we propose the Stochastic Pentachotomy (SP) algorithm, and derive finite-time upper bounds on its regret and optimization error. In particular, we show that, for any expected reward function $μ$ that behaves as $μ(x)=μ(x^\star)-C|x-x^\star|^ξ$ locally around its maximizer $x^\star$ for some $ξ, C>0$, the SP algorithm is order-optimal. Namely its regret and optimization error scale as $O(\sqrt{T\log(T)})$ and $O(\sqrt{\log(T)/T})$, respectively, when the time horizon $T$ grows large. These scalings are achieved without the knowledge of $ξ$ and $C$. Our algorithm is based on asymptotically optimal sequential statistical tests used to successively trim an interval that contains the best arm with high probability. To our knowledge, the SP algorithm constitutes the first sequential arm selection rule that achieves a regret and optimization error scaling as $O(\sqrt{T})$ and $O(1/\sqrt{T})$, respectively, up to a logarithmic factor for non-smooth expected reward functions, as well as for smooth functions with unknown smoothness.
Coalition Formation and Combinatorial Auctions; Applications to Self-organization and Self-management in Utility Computing
Venue: arXiv cs.MA 2015
Year: 2015

In this paper we propose a two-stage protocol for resource management in a hierarchically organized cloud. The first stage exploits spatial locality for the formation of coalitions of supply agents; the second stage, a combinatorial auction, is based on a modified proxy-based clock algorithm and has two phases, a clock phase and a proxy phase. The clock phase supports price discovery; in the second phase a proxy conducts multiple rounds of a combinatorial auction for the package of services requested by each client. The protocol strikes a balance between low-cost services for cloud clients and a decent profit for the service providers. We also report the results of an empirical investigation of the combinatorial auction stage of the protocol.
Validity of altmetrics data for measuring societal impact: A study using data from Altmetric and F1000Prime
Venue: arXiv cs.DL 2015
Year: 2015

Can altmetric data be validly used for the measurement of societal impact? The current study seeks to answer this question with a comprehensive dataset (about 100,000 records) from very disparate sources (F1000, Altmetric, and an in-house database based on Web of Science). In the F1000 peer review system, experts attach particular tags to scientific papers which indicate whether a paper could be of interest for science or rather for other segments of society. The results show that papers with the tag "good for teaching" do achieve higher altmetric counts than papers without this tag - if the quality of the papers is controlled. At the same time, a higher citation count is shown especially by papers with a tag that is specifically scientifically oriented ("new finding"). The findings indicate that papers tailored for a readership outside the area of research should lead to societal impact. If altmetric data is to be used for the measurement of societal impact, the question arises of its normalization. In bibliometrics, citations are normalized for the papers' subject area and publication year. This study has taken a second analytic step involving a possible normalization of altmetric data. As the results show there are particular scientific topics which are of especial interest for a wide audience. Since these more or less interesting topics are not completely reflected in Thomson Reuters' journal sets, a normalization of altmetric data should not be based on the level of subject categories, but on the level of topics.
Covering the Boundary of a Simple Polygon with Geodesic Unit Disks
Venue: arXiv cs.CG 2015
Year: 2015

We consider the problem of covering the boundary of a simple polygon on n vertices using the minimum number of geodesic unit disks. We present an O(n \log^2 n+k) time 2-approximation algorithm for finding the centers of the disks, with k denoting the number centers found by the algorithm.
Synchronization of finite-state pulse-coupled oscillators
Venue: arXiv cs.SY 2015
Year: 2015

We propose a novel generalized cellular automaton(GCA) model for discrete-time pulse-coupled oscillators and study the emergence of synchrony. Given a finite simple graph and an integer $n\ge 3$, each vertex is an identical oscillator of period $n$ with the following weak coupling along the edges: each oscillator inhibits its phase update if it has at least one neighboring oscillator at a particular "blinking" state and if its state is ahead of this blinking state. We obtain conditions on initial configurations and on network topologies for which states of all vertices eventually synchronize. We show that our GCA model synchronizes arbitrary initial configurations on paths, trees, and with random perturbation, any connected graph. In particular, our main result is the following local-global principle for tree networks: for $n\in \{3,4,5,6\}$, any $n$-periodic network on a tree synchronizes arbitrary initial configuration if and only if the maximum degree of the tree is less than the period $n$.
Cooperative Slotted Aloha for Multi-Base Station Systems
Venue: arXiv cs.IT 2015
Year: 2015

We introduce a framework to study slotted Aloha with cooperative base stations. Assuming a geographic-proximity communication model, we propose several decoding algorithmswith different degrees of base stations' cooperation (non-cooperative, spatial, temporal, and spatio-temporal). With spatial cooperation, neighboring base stations inform each other whenever they collect a user within their coverage overlap; temporal cooperation corresponds to (temporal) successive interference cancellation done locally at each station. We analyze the four decoding algorithms and establish several fundamental results. With all algorithms, the peak throughput (average number of decoded users per slot, across all base stations) increases linearly with the number of base stations. Further, temporal and spatio-temporal cooperations exhibit a threshold behavior with respect to the normalized load (number of users per station, per slot). There exists a positive load $G^\star$, such that, below $G^\star$, the decoding probability is asymptotically maximal possible, equal the probability that a user is heard by at least one base station; with non-cooperative decoding and spatial cooperation, we show that $G^\star$ is zero. Finally, with spatio-temporal cooperation, we optimize the degree distribution according to which users transmit their packet replicas; the optimum is in general very different from the corresponding optimal distribution of the single-base station system.
A Bit-Parallel Russian Dolls Search for a Maximum Cardinality Clique in a Graph
Venue: arXiv cs.DS 2015
Year: 2015

Finding the clique of maximum cardinality in an arbitrary graph is an NP-Hard problem that has many applications, which has motivated studies to solve it exactly despite its difficulty. The great majority of algorithms proposed in the literature are based on the Branch and Bound method. In this paper, we propose an exact algorithm for the maximum clique problem based on the Russian Dolls Search method. When compared to Branch and Bound, the main difference of the Russian Dolls method is that the nodes of its search tree correspond to decision subproblems, instead of the optimization subproblems of the Branch and Bound method. In comparison to a first implementation of this Russian Dolls method from the literature, several improvements are presented. Some of them are adaptations of techniques already employed successfully in Branch and Bound algorithms, like the use of approximate coloring for pruning purposes and bit-parallel operations. Two different coloring heuristics are tested: the standard greedy and the greedy with recoloring. Other improvements are directly related to the Russian Dolls scheme: the adoption of recursive calls where each subproblem (doll) is solved itself via the same principles than the Russian Dolls Search and the application of an elimination rule allowing not to generate a significant number of dolls. Results of computational experiments show that the algorithm outperforms the best exact combinatorial algorithms in the literature for the great majority of the dense graphs tested, being more than twice faster in several cases.
Single Pass Spectral Sparsification in Dynamic Streams
Venue: arXiv cs.DS 2015
Year: 2015

We present the first single pass algorithm for computing spectral sparsifiers of graphs in the dynamic semi-streaming model. Given a single pass over a stream containing insertions and deletions of edges to a graph G, our algorithm maintains a randomized linear sketch of the incidence matrix of G into dimension O((1/epsilon^2) n polylog(n)). Using this sketch, at any point, the algorithm can output a (1 +/- epsilon) spectral sparsifier for G with high probability. While O((1/epsilon^2) n polylog(n)) space algorithms are known for computing "cut sparsifiers" in dynamic streams [AGM12b, GKP12] and spectral sparsifiers in "insertion-only" streams [KL11], prior to our work, the best known single pass algorithm for maintaining spectral sparsifiers in dynamic streams required sketches of dimension Omega((1/epsilon^2) n^(5/3)) [AGM14]. To achieve our result, we show that, using a coarse sparsifier of G and a linear sketch of G's incidence matrix, it is possible to sample edges by effective resistance, obtaining a spectral sparsifier of arbitrary precision. Sampling from the sketch requires a novel application of ell_2/ell_2 sparse recovery, a natural extension of the ell_0 methods used for cut sparsifiers in [AGM12b]. Recent work of [MP12] on row sampling for matrix approximation gives a recursive approach for obtaining the required coarse sparsifiers. Under certain restrictions, our approach also extends to the problem of maintaining a spectral approximation for a general matrix A^T A given a stream of updates to rows in A.
A Universal Parallel Two-Pass MDL Context Tree Compression Algorithm
Venue: arXiv cs.IT 2015
Year: 2015

Computing problems that handle large amounts of data necessitate the use of lossless data compression for efficient storage and transmission. We present a novel lossless universal data compression algorithm that uses parallel computational units to increase the throughput. The length-$N$ input sequence is partitioned into $B$ blocks. Processing each block independently of the other blocks can accelerate the computation by a factor of $B$, but degrades the compression quality. Instead, our approach is to first estimate the minimum description length (MDL) context tree source underlying the entire input, and then encode each of the $B$ blocks in parallel based on the MDL source. With this two-pass approach, the compression loss incurred by using more parallel units is insignificant. Our algorithm is work-efficient, i.e., its computational complexity is $O(N/B)$. Its redundancy is approximately $B\log(N/B)$ bits above Rissanen's lower bound on universal compression performance, with respect to any context tree source whose maximal depth is at most $\log(N/B)$. We improve the compression by using different quantizers for states of the context tree based on the number of symbols corresponding to those states. Numerical results from a prototype implementation suggest that our algorithm offers a better trade-off between compression and throughput than competing universal data compression algorithms.
Learning Discriminative Stein Kernel for SPD Matrices and Its Applications
Venue: arXiv cs.CV 2015
Year: 2015

Stein kernel has recently shown promising performance on classifying images represented by symmetric positive definite (SPD) matrices. It evaluates the similarity between two SPD matrices through their eigenvalues. In this paper, we argue that directly using the original eigenvalues may be problematic because: i) Eigenvalue estimation becomes biased when the number of samples is inadequate, which may lead to unreliable kernel evaluation; ii) More importantly, eigenvalues only reflect the property of an individual SPD matrix. They are not necessarily optimal for computing Stein kernel when the goal is to discriminate different sets of SPD matrices. To address the two issues in one shot, we propose a discriminative Stein kernel, in which an extra parameter vector is defined to adjust the eigenvalues of the input SPD matrices. The optimal parameter values are sought by optimizing a proxy of classification performance. To show the generality of the proposed method, three different kernel learning criteria that are commonly used in the literature are employed respectively as a proxy. A comprehensive experimental study is conducted on a variety of image classification tasks to compare our proposed discriminative Stein kernel with the original Stein kernel and other commonly used methods for evaluating the similarity between SPD matrices. The experimental results demonstrate that, the discriminative Stein kernel can attain greater discrimination and better align with classification tasks by altering the eigenvalues. This makes it produce higher classification performance than the original Stein kernel and other commonly used methods.
A Multivariate Framework for Weighted FPT Algorithms
Venue: arXiv cs.DS 2015
Year: 2015

We introduce a novel multivariate approach for solving weighted parameterized problems. In our model, given an instance of size $n$ of a minimization (maximization) problem, and a parameter $W \geq 1$, we seek a solution of weight at most (or at least) $W$. We use our general framework to obtain efficient algorithms for such fundamental graph problems as Vertex Cover, 3-Hitting Set, Edge Dominating Set and Max Internal Out-Branching. The best known algorithms for these problems admit running times of the form $c^W n^{O(1)}$, for some constant $c>1$. We improve these running times to $c^s n^{O(1)}$, where $s\leq W$ is the minimum size of a solution of weight at most (at least) $W$. If no such solution exists, $s=\min\{W,m\}$, where $m$ is the maximum size of a solution. Clearly, $s$ can be substantially smaller than $W$. In particular, the running times of our algorithms are (almost) the same as the best known $O^*$ running times for the unweighted variants. Thus, we solve the weighted versions of * Vertex Cover in $1.381^s n^{O(1)}$ time and $n^{O(1)}$ space. * 3-Hitting Set in $2.168^s n^{O(1)}$ time and $n^{O(1)}$ space. * Edge Dominating Set in $2.315^s n^{O(1)}$ time and $n^{O(1)}$ space. * Max Internal Out-Branching in $6.855^s n^{O(1)}$ time and space. We further show that Weighted Vertex Cover and Weighted Edge Dominating Set admit fast algorithms whose running times are of the form $c^t n^{O(1)}$, where $t \leq s$ is the minimum size of a solution.
Strategy Derivation for Small Progress Measures
Venue: arXiv cs.LO 2015
Year: 2015

Small Progress Measures is one of the most efficient parity game solving algorithms. The original algorithm provides the full solution (winning regions and strategies) in $O(dm \cdot (n/\lceil d / 2 \rceil)^{\lceil d/2 \rceil})$ time, and requires a re-run of the algorithm on one of the winning regions. We provide a novel operational interpretation of progress measures, and modify the algorithm so that it derives the winning strategies for both players in one pass. This reduces the upper bound on strategy derivation for SPM to $O(dm \cdot (n/\lfloor d / 2 \rfloor)^{\lfloor d/2 \rfloor})$.
Discovery of Important Crossroads in Road Network using Massive Taxi Trajectories
Venue: arXiv cs.AI 2015
Year: 2015

A major problem in road network analysis is discovery of important crossroads, which can provide useful information for transport planning. However, none of existing approaches addresses the problem of identifying network-wide important crossroads in real road network. In this paper, we propose a novel data-driven based approach named CRRank to rank important crossroads. Our key innovation is that we model the trip network reflecting real travel demands with a tripartite graph, instead of solely analysis on the topology of road network. To compute the importance scores of crossroads accurately, we propose a HITS-like ranking algorithm, in which a procedure of score propagation on our tripartite graph is performed. We conduct experiments on CRRank using a real-world dataset of taxi trajectories. Experiments verify the utility of CRRank.