OpenRaiser/Intern-Atlas huggingface dataset:
Software Mutational Robustness
Venue: arXiv cs.SE 2013
Year: 2013

Neutral landscapes and mutational robustness are believed to be important enablers of evolvability in biology. We apply these concepts to software, defining mutational robustness to be the fraction of random mutations that leave a program's behavior unchanged. Test cases are used to measure program behavior and mutation operators are taken from genetic programming. Although software is often viewed as brittle, with small changes leading to catastrophic changes in behavior, our results show surprising robustness in the face of random software mutations. The paper describes empirical studies of the mutational robustness of 22 programs, including 14 production software projects, the Siemens benchmarks, and 4 specially constructed programs. We find that over 30% of random mutations are neutral with respect to their test suite. The results hold across all classes of programs, for mutations at both the source code and assembly instruction levels, across various programming languages, and are only weakly related to test suite coverage. We conclude that mutational robustness is an inherent property of software, and that neutral variants (i.e., those that pass the test suite) often fulfill the program's original purpose or specification. Based on these results, we conjecture that neutral mutations can be leveraged as a mechanism for generating software diversity. We demonstrate this idea by generating a population of neutral program variants and showing that the variants automatically repair unknown bugs with high probability. Neutral landscapes also provide a partial explanation for recent results that use evolutionary computation to automatically repair software bugs.
Extended master equation models for molecular communication networks
Venue: arXiv cs.CE 2013
Year: 2013

We consider molecular communication networks consisting of transmitters and receivers distributed in a fluidic medium. In such networks, a transmitter sends one or more signalling molecules, which are diffused over the medium, to the receiver to realise the communication. In order to be able to engineer synthetic molecular communication networks, mathematical models for these networks are required. This paper proposes a new stochastic model for molecular communication networks called reaction-diffusion master equation with exogenous input (RDMEX). The key idea behind RDMEX is to model the transmitters as time series of signalling molecule counts, while diffusion in the medium and chemical reactions at the receivers are modelled as Markov processes using master equation. An advantage of RDMEX is that it can readily be used to model molecular communication networks with multiple transmitters and receivers. For the case where the reaction kinetics at the receivers is linear, we show how RDMEX can be used to determine the mean and covariance of the receiver output signals, and derive closed-form expressions for the mean receiver output signal of the RDMEX model. These closed-form expressions reveal that the output signal of a receiver can be affected by the presence of other receivers. Numerical examples are provided to demonstrate the properties of the model.
On Budgeted Influence Maximization in Social Networks
Venue: arXiv cs.SI 2013
Year: 2013

Given a budget and arbitrary cost for selecting each node, the budgeted influence maximization (BIM) problem concerns selecting a set of seed nodes to disseminate some information that maximizes the total number of nodes influenced (termed as influence spread) in social networks at a total cost no more than the budget. Our proposed seed selection algorithm for the BIM problem guarantees an approximation ratio of (1 - 1/sqrt(e)). The seed selection algorithm needs to calculate the influence spread of candidate seed sets, which is known to be #P-complex. Identifying the linkage between the computation of marginal probabilities in Bayesian networks and the influence spread, we devise efficient heuristic algorithms for the latter problem. Experiments using both large-scale social networks and synthetically generated networks demonstrate superior performance of the proposed algorithm with moderate computation costs. Moreover, synthetic datasets allow us to vary the network parameters and gain important insights on the impact of graph structures on the performance of different algorithms.
A Tight Combinatorial Algorithm for Submodular Maximization Subject to a Matroid Constraint
Venue: arXiv cs.DS 2013
Year: 2013

We present an optimal, combinatorial 1-1/e approximation algorithm for monotone submodular optimization over a matroid constraint. Compared to the continuous greedy algorithm (Calinescu, Chekuri, Pal and Vondrak, 2008), our algorithm is extremely simple and requires no rounding. It consists of the greedy algorithm followed by local search. Both phases are run not on the actual objective function, but on a related non-oblivious potential function, which is also monotone submodular. Our algorithm runs in randomized time O(n^8u), where n is the rank of the given matroid and u is the size of its ground set. We additionally obtain a 1-1/e-eps approximation algorithm running in randomized time O (eps^-3n^4u). For matroids in which n = o(u), this improves on the runtime of the continuous greedy algorithm. The improvement is due primarily to the time required by the pipage rounding phase, which we avoid altogether. Furthermore, the independence of our algorithm from pipage rounding techniques suggests that our general approach may be helpful in contexts such as monotone submodular maximization subject to multiple matroid constraints. Our approach generalizes to the case where the monotone submodular function has restricted curvature. For any curvature c, we adapt our algorithm to produce a (1-e^-c)/c approximation. This result complements results of Vondrak (2008), who has shown that the continuous greedy algorithm produces a (1-e^-c)/c approximation when the objective function has curvature c. He has also proved that achieving any better approximation ratio is impossible in the value oracle model.
Robust Geometric Spanners
Venue: arXiv cs.CG 2013
Year: 2013

Highly connected and yet sparse graphs (such as expanders or graphs of high treewidth) are fundamental, widely applicable and extensively studied combinatorial objects. We initiate the study of such highly connected graphs that are, in addition, geometric spanners. We define a property of spanners called robustness. Informally, when one removes a few vertices from a robust spanner, this harms only a small number of other vertices. We show that robust spanners must have a superlinear number of edges, even in one dimension. On the positive side, we give constructions, for any dimension, of robust spanners with a near-linear number of edges.
Regret in Online Combinatorial Optimization
Venue: arXiv cs.LG 2013
Year: 2013

We address online linear optimization problems when the possible actions of the decision maker are represented by binary vectors. The regret of the decision maker is the difference between her realized loss and the best loss she would have achieved by picking, in hindsight, the best possible action. Our goal is to understand the magnitude of the best possible (minimax) regret. We study the problem under three different assumptions for the feedback the decision maker receives: full information, and the partial information models of the so-called "semi-bandit" and "bandit" problems. Combining the Mirror Descent algorithm and the INF (Implicitely Normalized Forecaster) strategy, we are able to prove optimal bounds for the semi-bandit case. We also recover the optimal bounds for the full information setting. In the bandit case we discuss existing results in light of a new lower bound, and suggest a conjecture on the optimal regret in that case. Finally we also prove that the standard exponentially weighted average forecaster is provably suboptimal in the setting of online combinatorial optimization.
Dynamic Planar Point Location with Sub-Logarithmic Local Updates
Venue: arXiv cs.CG 2013
Year: 2013

We study planar point location in a collection of disjoint fat regions, and investigate the complexity of \emph {local updates}: replacing any region by a different region that is "similar" to the original region. (i.e., the size differs by at most a constant factor, and distance between the two regions is a constant times that size). We show that it is possible to create a linear size data structure that allows for insertions, deletions, and queries in logarithmic time, and allows for local updates in sub-logarithmic time on a pointer machine.
Regenerating Codes: A System Perspective
Venue: arXiv cs.DC 2013
Year: 2013

The explosion of the amount of data stored in cloud systems calls for more efficient paradigms for redundancy. While replication is widely used to ensure data availability, erasure correcting codes provide a much better trade-off between storage and availability. Regenerating codes are good candidates for they also offer low repair costs in term of network bandwidth. While they have been proven optimal, they are difficult to understand and parameterize. In this paper we provide an analysis of regenerating codes for practitioners to grasp the various trade-offs. More specifically we make two contributions: (i) we study the impact of the parameters by conducting an analysis at the level of the system, rather than at the level of a single device; (ii) we compare the computational costs of various implementations of codes and highlight the most efficient ones. Our goal is to provide system designers with concrete information to help them choose the best parameters and design for regenerating codes.
Time and Space Efficient Lempel-Ziv Factorization based on Run Length Encoding
Venue: arXiv cs.DS 2013
Year: 2013

We propose a new approach for calculating the Lempel-Ziv factorization of a string, based on run length encoding (RLE). We present a conceptually simple off-line algorithm based on a variant of suffix arrays, as well as an on-line algorithm based on a variant of directed acyclic word graphs (DAWGs). Both algorithms run in $O(N+n\log n)$ time and O(n) extra space, where N is the size of the string, $n\leq N$ is the number of RLE factors. The time dependency on N is only in the conversion of the string to RLE, which can be computed very efficiently in O(N) time and O(1) extra space (excluding the output). When the string is compressible via RLE, i.e., $n = o(N)$, our algorithms are, to the best of our knowledge, the first algorithms which require only o(N) extra space while running in $o(N\log N)$ time.
Multi-agent Path Planning and Network Flow
Venue: arXiv cs.DS 2013
Year: 2013

This paper connects multi-agent path planning on graphs (roadmaps) to network flow problems, showing that the former can be reduced to the latter, therefore enabling the application of combinatorial network flow algorithms, as well as general linear program techniques, to multi-agent path planning problems on graphs. Exploiting this connection, we show that when the goals are permutation invariant, the problem always has a feasible solution path set with a longest finish time of no more than $n + V - 1$ steps, in which $n$ is the number of agents and $V$ is the number of vertices of the underlying graph. We then give a complete algorithm that finds such a solution in $O(nVE)$ time, with $E$ being the number of edges of the graph. Taking a further step, we study time and distance optimality of the feasible solutions, show that they have a pairwise Pareto optimal structure, and again provide efficient algorithms for optimizing two of these practical objectives.
Minimum Description Length Principle for Maximum Entropy Model Selection
Venue: arXiv cs.IT 2013
Year: 2013

Model selection is central to statistics, and many learning problems can be formulated as model selection problems. In this paper, we treat the problem of selecting a maximum entropy model given various feature subsets and their moments, as a model selection problem, and present a minimum description length (MDL) formulation to solve this problem. For this, we derive normalized maximum likelihood (NML) codelength for these models. Furthermore, we prove that the minimax entropy principle is a special case of maximum entropy model selection, where one assumes that complexity of all the models are equal. We apply our approach to gene selection problem and present simulation results.
Generalising unit-refutation completeness and SLUR via nested input resolution
Venue: arXiv cs.LO 2013
Year: 2013

We introduce two hierarchies of clause-sets, SLUR_k and UC_k, based on the classes SLUR (Single Lookahead Unit Refutation), introduced in 1995, and UC (Unit refutation Complete), introduced in 1994. The class SLUR, introduced in [Annexstein et al, 1995], is the class of clause-sets for which unit-clause-propagation (denoted by r_1) detects unsatisfiability, or where otherwise iterative assignment, avoiding obviously false assignments by look-ahead, always yields a satisfying assignment. It is natural to consider how to form a hierarchy based on SLUR. Such investigations were started in [Cepek et al, 2012] and [Balyo et al, 2012]. We present what we consider the "limit hierarchy" SLUR_k, based on generalising r_1 by r_k, that is, using generalised unit-clause-propagation introduced in [Kullmann, 1999, 2004]. The class UC, studied in [Del Val, 1994], is the class of Unit refutation Complete clause-sets, that is, those clause-sets for which unsatisfiability is decidable by r_1 under any falsifying assignment. For unsatisfiable clause-sets F, the minimum k such that r_k determines unsatisfiability of F is exactly the "hardness" of F, as introduced in [Ku 99, 04]. For satisfiable F we use now an extension mentioned in [Ansotegui et al, 2008]: The hardness is the minimum k such that after application of any falsifying partial assignments, r_k determines unsatisfiability. The class UC_k is given by the clause-sets which have hardness <= k. We observe that UC_1 is exactly UC. UC_k has a proof-theoretic character, due to the relations between hardness and tree-resolution, while SLUR_k has an algorithmic character. The correspondence between r_k and k-times nested input resolution (or tree resolution using clause-space k+1) means that r_k has a dual nature: both algorithmic and proof theoretic. This corresponds to a basic result of this paper, namely SLUR_k = UC_k.
Generative Maximum Entropy Learning for Multiclass Classification
Venue: arXiv cs.IT 2013
Year: 2013

Maximum entropy approach to classification is very well studied in applied statistics and machine learning and almost all the methods that exists in literature are discriminative in nature. In this paper, we introduce a maximum entropy classification method with feature selection for large dimensional data such as text datasets that is generative in nature. To tackle the curse of dimensionality of large data sets, we employ conditional independence assumption (Naive Bayes) and we perform feature selection simultaneously, by enforcing a `maximum discrimination' between estimated class conditional densities. For two class problems, in the proposed method, we use Jeffreys ($J$) divergence to discriminate the class conditional densities. To extend our method to the multi-class case, we propose a completely new approach by considering a multi-distribution divergence: we replace Jeffreys divergence by Jensen-Shannon ($JS$) divergence to discriminate conditional densities of multiple classes. In order to reduce computational complexity, we employ a modified Jensen-Shannon divergence ($JS_{GM}$), based on AM-GM inequality. We show that the resulting divergence is a natural generalization of Jeffreys divergence to a multiple distributions case. As far as the theoretical justifications are concerned we show that when one intends to select the best features in a generative maximum entropy approach, maximum discrimination using $J-$divergence emerges naturally in binary classification. Performance and comparative study of the proposed algorithms have been demonstrated on large dimensional text and gene expression datasets that show our methods scale up very well with large dimensional datasets.
Lower Bounds for Existential Pebble Games and k-Consistency Tests
Venue: arXiv cs.LO 2013
Year: 2013

The existential k-pebble game characterizes the expressive power of the existential-positive k-variable fragment of first-order logic on finite structures. The winner of the existential k-pebble game on two given finite structures can be determined in time O(n2k) by dynamic programming on the graph of game configurations. We show that there is no O(n(k-3)/12)-time algorithm that decides which player can win the existential k-pebble game on two given structures. This lower bound is unconditional and does not rely on any complexity-theoretic assumptions. Establishing strong k-consistency is a well-known heuristic for solving the constraint satisfaction problem (CSP). By the game characterization of Kolaitis and Vardi our result implies that there is no O(n(k-3)/12)-time algorithm that decides if strong k-consistency can be established for a given CSP-instance.
Parameter Tracking via Optimal Distributed Beamforming in an Analog Sensor Network
Venue: arXiv cs.IT 2013
Year: 2013

We consider the problem of optimal distributed beamforming in a sensor network where the sensors observe a dynamic parameter in noise and coherently amplify and forward their observations to a fusion center (FC). The FC uses a Kalman filter to track the parameter using the observations from the sensors, and we show how to find the optimal gain and phase of the sensor transmissions under both global and individual power constraints in order to minimize the mean squared error (MSE) of the parameter estimate. For the case of a global power constraint, a closed-form solution can be obtained. A numerical optimization is required for individual power constraints, but the problem can be relaxed to a semidefinite programming problem (SDP), and we show how the optimal solution can be constructed from the solution to the SDP. Simulation results show that compared with equal power transmission, the use of optimized power control can significantly reduce the MSE.
RIPless compressed sensing from anisotropic measurements
Venue: arXiv cs.IT 2013
Year: 2013

Compressed sensing is the art of reconstructing a sparse vector from its inner products with respect to a small set of randomly chosen measurement vectors. It is usually assumed that the ensemble of measurement vectors is in isotropic position in the sense that the associated covariance matrix is proportional to the identity matrix. In this paper, we establish bounds on the number of required measurements in the anisotropic case, where the ensemble of measurement vectors possesses a non-trivial covariance matrix. Essentially, we find that the required sampling rate grows proportionally to the condition number of the covariance matrix. In contrast to other recent contributions to this problem, our arguments do not rely on any restricted isometry properties (RIP's), but rather on ideas from convex geometry which have been systematically studied in the theory of low-rank matrix recovery. This allows for a simple argument and slightly improved bounds, but may lead to a worse dependency on noise (which we do not consider in the present paper).
Faster arithmetic for number-theoretic transforms
Venue: arXiv cs.SC 2013
Year: 2013

We show how to improve the efficiency of the computation of fast Fourier transforms over F_p where p is a word-sized prime. Our main technique is optimisation of the basic arithmetic, in effect decreasing the total number of reductions modulo p, by making use of a redundant representation for integers modulo p. We give performance results showing a significant improvement over Shoup's NTL library.
A Partially Ordered Structure and a Generalization of the Canonical Partition for General Graphs with Perfect Matchings
Venue: arXiv cs.DM 2013
Year: 2013

This paper is concerned with structures of general graphs with perfect matchings. We first reveal a partially ordered structure among factor-components of general graphs with perfect matchings. Our second result is a generalization of Kotzig's canonical partition to a decomposition of general graphs with perfect matchings. It contains a short proof for the theorem of the canonical partition. These results give decompositions which are canonical, that is, unique to given graphs. We also show that there are correlations between these two and that these can be computed in polynomial time.
The Role of Weight Shrinking in Large Margin Perceptron Learning
Venue: arXiv cs.LG 2013
Year: 2013

We introduce into the classical perceptron algorithm with margin a mechanism that shrinks the current weight vector as a first step of the update. If the shrinking factor is constant the resulting algorithm may be regarded as a margin-error-driven version of NORMA with constant learning rate. In this case we show that the allowed strength of shrinking depends on the value of the maximum margin. We also consider variable shrinking factors for which there is no such dependence. In both cases we obtain new generalizations of the perceptron with margin able to provably attain in a finite number of steps any desirable approximation of the maximal margin hyperplane. The new approximate maximum margin classifiers appear experimentally to be very competitive in 2-norm soft margin tasks involving linear kernels.
Automorphism groups of Cayley graphs generated by connected transposition sets
Venue: arXiv cs.DM 2013
Year: 2013

Let $S$ be a set of transpositions that generates the symmetric group $S_n$, where $n \ge 3$. The transposition graph $T(S)$ is defined to be the graph with vertex set $\{1,\ldots,n\}$ and with vertices $i$ and $j$ being adjacent in $T(S)$ whenever $(i,j) \in S$. We prove that if the girth of the transposition graph $T(S)$ is at least 5, then the automorphism group of the Cayley graph $\Cay(S_n,S)$ is the semidirect product $R(S_n) \rtimes \Aut(S_n,S)$, where $\Aut(S_n,S)$ is the set of automorphisms of $S_n$ that fixes $S$. This strengthens a result of Feng on transposition graphs that are trees. We also prove that if the transposition graph $T(S)$ is a 4-cycle, then the set of automorphisms of the Cayley graph $\Cay(S_4,S)$ that fixes a vertex and each of its neighbors is isomorphic to the Klein 4-group and hence is nontrivial. We thus identify the existence of 4-cycles in the transposition graph as being an important factor in causing a potentially larger automorphism group of the Cayley graph.