OpenRaiser/Intern-Atlas huggingface dataset:
Bidimensionality and EPTAS
Venue: arXiv cs.DS 2011
Year: 2011

Bidimensionality theory is a powerful framework for the development of metaalgorithmic techniques. It was introduced by Demaine et al. as a tool to obtain sub-exponential time parameterized algorithms for problems on H-minor free graphs. Demaine and Hajiaghayi extended the theory to obtain PTASs for bidimensional problems, and subsequently improved these results to EPTASs. Fomin et. al related the theory to the existence of linear kernels for parameterized problems. In this paper we revisit bidimensionality theory from the perspective of approximation algorithms and redesign the framework for obtaining EPTASs to be more powerful, easier to apply and easier to understand. Two of the most widely used approaches to obtain PTASs on planar graphs are the Lipton-Tarjan separator based approach, and Baker's approach. Demaine and Hajiaghayi strengthened both approaches using bidimensionality and obtained EPTASs for a multitude of problems. We unify the two strenghtened approaches to combine the best of both worlds. At the heart of our framework is a decomposition lemma which states that for "most" bidimensional problems, there is a polynomial time algorithm which given an H-minor-free graph G as input and an e > 0 outputs a vertex set X of size e * OPT such that the treewidth of G n X is f(e). Here, OPT is the objective function value of the problem in question and f is a function depending only on e. This allows us to obtain EPTASs on (apex)-minor-free graphs for all problems covered by the previous framework, as well as for a wide range of packing problems, partial covering problems and problems that are neither closed under taking minors, nor contractions. To the best of our knowledge for many of these problems including cycle packing, vertex-h-packing, maximum leaf spanning tree, and partial r-dominating set no EPTASs on planar graphs were previously known.
Image Characterization and Classification by Physical Complexity
Venue: arXiv cs.CC 2011
Year: 2011

We present a method for estimating the complexity of an image based on Bennett's concept of logical depth. Bennett identified logical depth as the appropriate measure of organized complexity, and hence as being better suited to the evaluation of the complexity of objects in the physical world. Its use results in a different, and in some sense a finer characterization than is obtained through the application of the concept of Kolmogorov complexity alone. We use this measure to classify images by their information content. The method provides a means for classifying and evaluating the complexity of objects by way of their visual representations. To the authors' knowledge, the method and application inspired by the concept of logical depth presented herein are being proposed and implemented for the first time.
A Note on Element-wise Matrix Sparsification via a Matrix-valued Bernstein Inequality
Venue: arXiv cs.DS 2011
Year: 2011

Given an n x n matrix A, we present a simple, element-wise sparsification algorithm that zeroes out all sufficiently small elements of A and then retains some of the remaining elements with probabilities proportional to the square of their magnitudes. We analyze the approximation accuracy of the proposed algorithm using a recent, elegant non-commutative Bernstein inequality, and compare our bounds with all existing (to the best of our knowledge) element-wise matrix sparsification algorithms.
Geodesic diameter of a polygonal domain in O(n^4 log n) time
Venue: arXiv cs.CG 2011
Year: 2011

We show that the geodesic diameter of a polygonal domain with n vertices can be computed in O(n^4 log n) time by considering O(n^3) candidate diameter endpoints; the endpoints are a subset of vertices of the overlay of shortest path maps from vertices of the domain.
Attack--Defense Trees and Two-Player Binary Zero-Sum Extensive Form Games Are Equivalent - Technical Report with Proofs
Venue: arXiv cs.CR 2011
Year: 2011

Attack--defense trees are used to describe security weaknesses of a system and possible countermeasures. In this paper, the connection between attack--defense trees and game theory is made explicit. We show that attack--defense trees and binary zero-sum two-player extensive form games have equivalent expressive power when considering satisfiability, in the sense that they can be converted into each other while preserving their outcome and their internal structure.
Diversity Embedded Streaming Erasure Codes (DE-SCo): Constructions and Optimality
Venue: arXiv cs.IT 2011
Year: 2011

Streaming erasure codes guarantee that each source packet is recovered within a fixed delay at the receiver over a burst-erasure channel. This paper introduces a new class of streaming codes: Diversity Embedded Streaming Erasure Codes (DE-SCo), that provide a flexible tradeoff between the channel quality and receiver delay. When the channel conditions are good, the source stream is recovered with a low delay, whereas when the channel conditions are poor the source stream is still recovered, albeit with a larger delay. Information theoretic analysis of the underlying burst-erasure broadcast channel reveals that DE-SCo achieve the minimum possible delay for the weaker user, without sacrificing the single-user optimal performance of the stronger user. Our constructions are explicit, incur polynomial time encoding and decoding complexity and outperform random linear codes over burst-erasure channels.
Privacy-Preserving Access of Outsourced Data via Oblivious RAM Simulation
Venue: arXiv cs.DS 2011
Year: 2011

Suppose a client, Alice, has outsourced her data to an external storage provider, Bob, because he has capacity for her massive data set, of size n, whereas her private storage is much smaller--say, of size O(n^{1/r}), for some constant r > 1. Alice trusts Bob to maintain her data, but she would like to keep its contents private. She can encrypt her data, of course, but she also wishes to keep her access patterns hidden from Bob as well. We describe schemes for the oblivious RAM simulation problem with a small logarithmic or polylogarithmic amortized increase in access times, with a very high probability of success, while keeping the external storage to be of size O(n). To achieve this, our algorithmic contributions include a parallel MapReduce cuckoo-hashing algorithm and an external-memory dataoblivious sorting algorithm.
Parameterizing by the Number of Numbers
Venue: arXiv cs.DS 2011
Year: 2011

The usefulness of parameterized algorithmics has often depended on what Niedermeier has called, "the art of problem parameterization". In this paper we introduce and explore a novel but general form of parameterization: the number of numbers. Several classic numerical problems, such as Subset Sum, Partition, 3-Partition, Numerical 3-Dimensional Matching, and Numerical Matching with Target Sums, have multisets of integers as input. We initiate the study of parameterizing these problems by the number of distinct integers in the input. We rely on an FPT result for ILPF to show that all the above-mentioned problems are fixed-parameter tractable when parameterized in this way. In various applied settings, problem inputs often consist in part of multisets of integers or multisets of weighted objects (such as edges in a graph, or jobs to be scheduled). Such number-of-numbers parameterized problems often reduce to subproblems about transition systems of various kinds, parameterized by the size of the system description. We consider several core problems of this kind relevant to number-of-numbers parameterization. Our main hardness result considers the problem: given a non-deterministic Mealy machine M (a finite state automaton outputting a letter on each transition), an input word x, and a census requirement c for the output word specifying how many times each letter of the output alphabet should be written, decide whether there exists a computation of M reading x that outputs a word y that meets the requirement c. We show that this problem is hard for W[1]. If the question is whether there exists an input word x such that a computation of M on x outputs a word that meets c, the problem becomes fixed-parameter tractable.
Polyominoes and Polyiamonds as Fundamental Domains of Isohedral Tilings with Rotational Symmetry
Venue: arXiv cs.CG 2011
Year: 2011

We describe computer algorithms that produce the complete set of isohedral tilings by n-omino or n-iamond tiles in which the tiles are fundamental domains and the tilings have 3-, 4-, or 6-fold rotational symmetry. The symmetry groups of such tilings are of types p3, p31m, p4, p4g, and p6. There are no isohedral tilings with symmetry groups p3m1, p4m, or p6m that have polyominoes or polyiamonds as fundamental domains. We display the algorithms' output and give enumeration tables for small values of n. This expands on our earlier works (Fukuda et al 2006, 2008).
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
Venue: arXiv cs.CE 2011
Year: 2011

We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model, as well as the BIBEE approximation to BEM. The hardware acceleration is achieved through graphics processors, GPUs. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. The applications demonstrated include the electrostatics of protein--drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of lysozyme molecules. The parallel scalability of the software was studied in a cluster at the Nagasaki Advanced Computing Center, using 128 nodes, each with 4 GPUs. Delicate tuning has resulted in strong scaling with parallel efficiency of 0.8 for 256 and 0.5 for 512 GPUs. The largest application run, with over 20 million atoms and one billion unknowns, required only one minute on 512 GPUs. We are currently adapting our BEM software to solve the linearized Poisson-Boltzmann equation for dilute ionic solutions, and it is also designed to be flexible enough to be extended for a variety of integral equation problems, ranging from Poisson problems to Helmholtz problems in electromagnetics and acoustics to high Reynolds number flow.
Applications of Belief Propagation in CSMA Wireless Networks
Venue: arXiv cs.NI 2011
Year: 2011

The belief propagation (BP) algorithm is an efficient way to solve "inference" problems in graphical models, such as Bayesian networks and Markov random fields. The system-state probability distribution of CSMA wireless networks is a Markov random field. An interesting question is how BP can help the analysis and design of CSMA wireless networks. This paper explores three such applications. First, we show how BP can be used to compute the throughputs of different links in the network given their access intensities, defined as the mean packet transmission time divided by the mean backoff countdown time. Second, we propose an inverse-BP algorithm to solve the reverse problem: how to set the access intensities of different links to meet their target throughputs? Third, we introduce a BP-adaptive CSMA algorithm to find the link access intensities that can achieve optimal system utility. BP solves the three problems with exact results in tree networks. It may, however, lose accuracy in networks with a loopy contention graph. We show how a generalized version of BP, GBP, can be designed to solve the three problems with high accuracy for networks with a loopy contention graph. Importantly, we show how the BP and GBP algorithms in this paper can be implemented in a distributed manner, making them useful in practical CSMA network opera-tion.
When Both Transmitting and Receiving Energies Matter: An Application of Network Coding in Wireless Body Area Networks
Venue: arXiv cs.NI 2011
Year: 2011

A network coding scheme for practical implementations of wireless body area networks is presented, with the objective of providing reliability under low-energy constraints. We propose a simple network layer protocol for star networks, adapting redundancy based on both transmission and reception energies for data and control packets, as well as channel conditions. Our numerical results show that even for small networks, the amount of energy reduction achievable can range from 29% to 87%, as the receiving energy per control packet increases from equal to much larger than the transmitting energy per data packet. The achievable gains increase as a) more nodes are added to the network, and/or b) the channels seen by different sensor nodes become more asymmetric.
Novel Modifications of Parallel Jacobi Algorithms
Venue: arXiv cs.NA 2011
Year: 2011

We describe two main classes of one-sided trigonometric and hyperbolic Jacobi-type algorithms for computing eigenvalues and eigenvectors of Hermitian matrices. These types of algorithms exhibit significant advantages over many other eigenvalue algorithms. If the matrices permit, both types of algorithms compute the eigenvalues and eigenvectors with high relative accuracy. We present novel parallelization techniques for both trigonometric and hyperbolic classes of algorithms, as well as some new ideas on how pivoting in each cycle of the algorithm can improve the speed of the parallel one-sided algorithms. These parallelization approaches are applicable to both distributed-memory and shared-memory machines. The numerical testing performed indicates that the hyperbolic algorithms may be superior to the trigonometric ones, although, in theory, the latter seem more natural.
High-resolution scalar quantization with Rényi entropy constraint
Venue: arXiv cs.IT 2011
Year: 2011

We consider optimal scalar quantization with $r$th power distortion and constrained Rényi entropy of order $α$. For sources with an absolutely continuous distribution the high rate asymptotics of the quantizer distortion has long been known for $α=0$ (fixed-rate quantization) and $\al pha=1$ (entropy-constrained quantization). For a large class of absolutely continuous source distributions we determine the sharp asymptotics of the optimal quantization distortion for $α\in [-\infty,0)\cup (0,1)$. The achievability proof is based on finding (asymptotically) optimal quantizers via the companding approach, and is thus constructive.
Constraint Propagation for First-Order Logic and Inductive Definitions
Venue: arXiv cs.LO 2011
Year: 2011

Constraint propagation is one of the basic forms of inference in many logic-based reasoning systems. In this paper, we investigate constraint propagation for first-order logic (FO), a suitable language to express a wide variety of constraints. We present an algorithm with polynomial-time data complexity for constraint propagation in the context of an FO theory and a finite structure. We show that constraint propagation in this manner can be represented by a datalog program and that the algorithm can be executed symbolically, i.e., independently of a structure. Next, we extend the algorithm to FO(ID), the extension of FO with inductive definitions. Finally, we discuss several applications.
Shortest paths between shortest paths and independent sets
Venue: arXiv cs.CC 2011
Year: 2011

We study problems of reconfiguration of shortest paths in graphs. We prove that the shortest reconfiguration sequence can be exponential in the size of the graph and that it is NP-hard to compute the shortest reconfiguration sequence even when we know that the sequence has polynomial length. Moreover, we also study reconfiguration of independent sets in three different models and analyze relationships between these models, observing that shortest path reconfiguration is a special case of independent set reconfiguration in perfect graphs, under any of the three models. Finally, we give polynomial results for restricted classes of graphs (even-hole-free and $P_4$-free graphs).
The Degrees of Freedom of MIMO Interference Channels without State Information at Transmitters
Venue: arXiv cs.IT 2011
Year: 2011

This paper fully determines the degree-of-freedom (DoF) region of two-user interference channels with arbitrary number of transmit and receive antennas and isotropic fading, where the channel state information is available to the receivers but not to the transmitters. The result characterizes the capacity region to the first order of the logarithm of the signal-to-noise ratio (SNR) in the high-SNR regime. The DoF region is achieved using random Gaussian codebooks independent of the channel states. Hence the DoF gain due to beamforming and interference alignment is completely lost in absence of channel state information at the transmitters (CSIT).
Statistical mechanical assessment of a reconstruction limit of compressed sensing: Toward theoretical analysis of correlated signals
Venue: arXiv cs.IT 2011
Year: 2011

We provide a scheme for exploring the reconstruction limit of compressed sensing by minimizing the general cost function under the random measurement constraints for generic correlated signal sources. Our scheme is based on the statistical mechanical replica method for dealing with random systems. As a simple but non-trivial example, we apply the scheme to a sparse autoregressive model, where the first differences in the input signals of the correlated time series are sparse, and evaluate the critical compression rate for a perfect reconstruction. The results are in good agreement with a numerical experiment for a signal reconstruction.
How to obtain efficient GPU kernels: an illustration using FMM & FGT algorithms
Venue: arXiv cs.MS 2011
Year: 2011

Computing on graphics processors is maybe one of the most important developments in computational science to happen in decades. Not since the arrival of the Beowulf cluster, which combined open source software with commodity hardware to truly democratize high-performance computing, has the community been so electrified. Like then, the opportunity comes with challenges. The formulation of scientific algorithms to take advantage of the performance offered by the new architecture requires rethinking core methods. Here, we have tackled fast summation algorithms (fast multipole method and fast Gauss transform), and applied algorithmic redesign for attaining performance on gpus. The progression of performance improvements attained illustrates the exercise of formulating algorithms for the massively parallel architecture of the gpu. The end result has been gpu kernels that run at over 500 Gigaflops on one nvidia Tesla C1060 card, thereby reaching close to practical peak. We can confidently say that gpu computing is not just a vogue, it is truly an irresistible trend in high-performance computing.
Multiplicative Attribute Graph Model of Real-World Networks
Venue: arXiv cs.SI 2011
Year: 2011

Large scale real-world network data such as social and information networks are ubiquitous. The study of such social and information networks seeks to find patterns and explain their emergence through tractable models. In most networks, and especially in social networks, nodes have a rich set of attributes (e.g., age, gender) associated with them. Here we present a model that we refer to as the Multiplicative Attribute Graphs (MAG), which naturally captures the interactions between the network structure and the node attributes. We consider a model where each node has a vector of categorical latent attributes associated with it. The probability of an edge between a pair of nodes then depends on the product of individual attribute-attribute affinities. The model yields itself to mathematical analysis and we derive thresholds for the connectivity and the emergence of the giant connected component, and show that the model gives rise to networks with a constant diameter. We analyze the degree distribution to show that MAG model can produce networks with either log-normal or power-law degree distributions depending on certain conditions.
Free inductive K-semialgebras
Venue: arXiv cs.FL 2011
Year: 2011

We consider rational power series over an alphabet $Σ$ with coefficients in a ordered commutative semiring $K$ and characterize them as the free ordered $K$-semialgebras in various classes of ordered $K$-semialgebras equipped with a star operation satisfying the least pre-fixed point rule and/or its dual. The results are generalizations of Kozen's axiomatization of regular languages.
The Need to Support of Data Flow Graph Visualization of Forensic Lucid Programs, Forensic Evidence, and their Evaluation by GIPSY
Venue: arXiv cs.PL 2011
Year: 2011

Lucid programs are data-flow programs and can be visually represented as data flow graphs (DFGs) and composed visually. Forensic Lucid, a Lucid dialect, is a language to specify and reason about cyberforensic cases. It includes the encoding of the evidence (representing the context of evaluation) and the crime scene modeling in order to validate claims against the model and perform event reconstruction, potentially within large swaths of digital evidence. To aid investigators to model the scene and evaluate it, instead of typing a Forensic Lucid program, we propose to expand the design and implementation of the Lucid DFG programming onto Forensic Lucid case modeling and specification to enhance the usability of the language and the system and its behavior. We briefly discuss the related work on visual programming an DFG modeling in an attempt to define and select one approach or a composition of approaches for Forensic Lucid based on various criteria such as previous implementation, wide use, formal backing in terms of semantics and translation. In the end, we solicit the readers' constructive, opinions, feedback, comments, and recommendations within the context of this short discussion.
Characterizing perfect recall using next-step temporal operators in S5 and sub-S5 Epistemic Temporal Logic
Venue: arXiv cs.LO 2011
Year: 2011

We review the notion of perfect recall in the literature on interpreted systems, game theory, and epistemic logic. In the context of Epistemic Temporal Logic (ETL), we give a (to our knowledge) novel frame condition for perfect recall, which is local and can straightforwardly be translated to a defining formula in a language that only has next-step temporal operators. This frame condition also gives rise to a complete axiomatization for S5 ETL frames with perfect recall. We then consider how to extend and consolidate the notion of perfect recall in sub-S5 settings, where the various notions discussed are no longer equivalent.
Sequences of Inequalities Among New Divergence Measures
Venue: arXiv cs.IT 2011
Year: 2011

There are three classical divergence measures exist in the literature on information theory and statistics. These are namely, Jeffryes-Kullback-Leiber J-divergence. Sibson-Burbea-Rao Jensen-Shannon divegernce and Taneja arithemtic-geometric mean divergence. These three measures bear an interesting relationship among each other and are based on logarithmic expressions. The divergence measures like Hellinger discrimination, symmetric chi-square divergence, and triangular discrimination are also known in the literature and are not based on logarithmic expressions. Past years Dragomir et al., Kumar and Johnson and Jain and Srivastava studied different kind of divergence measures. In this paper, we have presented some more new divergence measures and obtained inequalities relating these new measures and also made connections with previous ones. The idea of exponential divergence is also introduced.