OpenRaiser/Intern-Atlas huggingface dataset:
Efficient Two-Stage Group Testing Algorithms for DNA Screening
Venue: arXiv cs.DM 2011
Year: 2011

Group testing algorithms are very useful tools for DNA library screening. Building on recent work by Levenshtein (2003) and Tonchev (2008), we construct in this paper new infinite classes of combinatorial structures, the existence of which are essential for attaining the minimum number of individual tests at the second stage of a two-stage disjunctive testing algorithm.
SSA-Caterpillar in Group Anonymity
Venue: arXiv cs.CR 2011
Year: 2011

Nowadays, it is a common practice to protect various types of statistical data before publishing them for different researches. For instance, when conducting extensive demographic surveys such as national census, the collected data should be at least depersonalized to guarantee proper level of privacy preservation. In practice, even more complicated methods of data protection need to be used. All these methods can be generally divided into two classes. The first ones aim at providing individual data anonymity, whereas the other ones are focused on protecting information about a group of respondents. In this paper, we propose a novel technique of providing group anonymity in statistical data using singular spectrum analysis (SSA).Also, we apply SSA to defining hidden patterns in demographic data distribution.
Convex Geometry and Stoichiometry
Venue: arXiv cs.CG 2011
Year: 2011

We demonstrate the benefits of a convex geometric perspective for questions on chemical stoichiometry. We show that the balancing of chemical equations, the use of "mixtures" to explain multiple stoichiometry, and the half-reaction for balancing redox actions all yield nice convex geometric interpretations. We also relate some natural questions on reaction mechanisms with the enumeration of lattice points in polytopes. Lastly, it is known that a given reaction mechanism imposes linear constraints on observed stoichiometries. We consider the inverse question of deducing reaction mechanism consistent with a given set of linear stoichiometric restrictions.
Group Codes and the Schreier matrix form
Venue: arXiv cs.IT 2011
Year: 2011

In a group trellis, the sequence of branches that split from the identity path and merge to the identity path form two normal chains. The Schreier refinement theorem can be applied to these two normal chains. The refinement of the two normal chains can be written in the form of a matrix, called the Schreier matrix form, with rows and columns determined by the two normal chains. Based on the Schreier matrix form, we give an encoder structure for a group code which is an estimator. The encoder uses the important idea of shortest length generator sequences previously explained by Forney and Trott. In this encoder the generator sequences are shown to have an additional property: the components of the generators are coset representatives in a chain coset decomposition of the branch group B of the code. Therefore this encoder appears to be a natural form for a group code encoder. The encoder has a register implementation which is somewhat different from the classical shift register structure. This form of the encoder can be extended. We find a composition chain of the branch group B and give an encoder which uses coset representatives in the composition chain of B. When B is solvable, the generators are constructed using coset representatives taken from prime cyclic groups.
Refinement for Probabilistic Systems with Nondeterminism
Venue: arXiv cs.SE 2011
Year: 2011

Before we combine actions and probabilities two very obvious questions should be asked. Firstly, what does "the probability of an action" mean? Secondly, how does probability interact with nondeterminism? Neither question has a single universally agreed upon answer but by considering these questions at the outset we build a novel and hopefully intuitive probabilistic event-based formalism. In previous work we have characterised refinement via the notion of testing. Basically, if one system passes all the tests that another system passes (and maybe more) we say the first system is a refinement of the second. This is, in our view, an important way of characterising refinement, via the question "what sort of refinement should I be using?" We use testing in this paper as the basis for our refinement. We develop tests for probabilistic systems by analogy with the tests developed for non-probabilistic systems. We make sure that our probabilistic tests, when performed on non-probabilistic automata, give us refinement relations which agree with for those non-probabilistic automata. We formalise this property as a vertical refinement.
Complexity Classes and Theories for the Comparator Circuit Value Problem
Venue: arXiv cs.CC 2011
Year: 2011

Subramanian defined the complexity class CC as the set of problems log-space reducible to the comparator circuit value problem. He proved that several other problems are complete for CC, including the stable marriage problem, and finding the lexicographical first maximal matching in a bipartite graph. We suggest alternative definitions of CC based on different reducibilities and introduce a two-sorted theory VCC* based on one of them. We sharpen and simplify Subramanian's completeness proofs for the above two problems and formalize them in VCC*.
Similarity-based Browsing over Linked Open Data
Venue: arXiv cs.DL 2011
Year: 2011

An increasing amount of data is published on the Web according to the Linked Open Data (LOD) principles. End users would like to browse these data in a flexible manner. In this paper we focus on similarity-based browsing and we introduce a novel method for computing the similarity between two entities of a given RDF/S graph. The distinctive characteristics of the proposed metric is that it is generic (it can be used to compare nodes of any kind), it takes into account the neighborhoods of the nodes, and it is configurable (with respect to the accuracy vs computational complexity tradeoff). We demonstrate the behavior of the metric using examples from an application over LOD. Finally, we generalize and elaborate on implementation approaches harmonized with the distributed nature of LOD which can be used for computing the most similar entities using neighborhood-based similarity metrics.
A Novel Attack against Android Phones
Venue: arXiv cs.CR 2011
Year: 2011

In the first quarter of 2011, Android has become the top-selling operating system for smartphones. In this paper, we present a novel, highly critical attack that allows unprompted installation of arbitrary applications from the Android Market. Our attack is based on a single malicious application, which, in contrast to previously known attacks, does not require the user to grant it any permissions.
Machine Learning Markets
Venue: arXiv cs.AI 2011
Year: 2011

Prediction markets show considerable promise for developing flexible mechanisms for machine learning. Here, machine learning markets for multivariate systems are defined, and a utility-based framework is established for their analysis. This differs from the usual approach of defining static betting functions. It is shown that such markets can implement model combination methods used in machine learning, such as product of expert and mixture of expert approaches as equilibrium pricing models, by varying agent utility functions. They can also implement models composed of local potentials, and message passing methods. Prediction markets also allow for more flexible combinations, by combining multiple different utility functions. Conversely, the market mechanisms implement inference in the relevant probabilistic models. This means that market mechanism can be utilized for implementing parallelized model building and inference for probabilistic modelling.
PDDL2.1: An Extension to PDDL for Expressing Temporal Planning Domains
Venue: arXiv cs.AI 2011
Year: 2011

In recent years research in the planning community has moved increasingly toward s application of planners to realistic problems involving both time and many typ es of resources. For example, interest in planning demonstrated by the space res earch community has inspired work in observation scheduling, planetary rover ex ploration and spacecraft control domains. Other temporal and resource-intensive domains including logistics planning, plant control and manufacturing have also helped to focus the community on the modelling and reasoning issues that must be confronted to make planning technology meet the challenges of application. The International Planning Competitions have acted as an important motivating fo rce behind the progress that has been made in planning since 1998. The third com petition (held in 2002) set the planning community the challenge of handling tim e and numeric resources. This necessitated the development of a modelling langua ge capable of expressing temporal and numeric properties of planning domains. In this paper we describe the language, PDDL2.1, that was used in the competition. We describe the syntax of the language, its formal semantics and the validation of concurrent plans. We observe that PDDL2.1 has considerable modelling power --- exceeding the capabilities of current planning technology --- and presents a number of important challenges to the research community.
An Efficient Partitioning Oracle for Bounded-Treewidth Graphs
Venue: arXiv cs.DS 2011
Year: 2011

Partitioning oracles were introduced by Hassidim et al. (FOCS 2009) as a generic tool for constant-time algorithms. For any epsilon > 0, a partitioning oracle provides query access to a fixed partition of the input bounded-degree minor-free graph, in which every component has size poly(1/epsilon), and the number of edges removed is at most epsilon*n, where n is the number of vertices in the graph. However, the oracle of Hassidimet al. makes an exponential number of queries to the input graph to answer every query about the partition. In this paper, we construct an efficient partitioning oracle for graphs with constant treewidth. The oracle makes only O(poly(1/epsilon)) queries to the input graph to answer each query about the partition. Examples of bounded-treewidth graph classes include k-outerplanar graphs for fixed k, series-parallel graphs, cactus graphs, and pseudoforests. Our oracle yields poly(1/epsilon)-time property testing algorithms for membership in these classes of graphs. Another application of the oracle is a poly(1/epsilon)-time algorithm that approximates the maximum matching size, the minimum vertex cover size, and the minimum dominating set size up to an additive epsilon*n in graphs with bounded treewidth. Finally, the oracle can be used to test in poly(1/epsilon) time whether the input bounded-treewidth graph is k-colorable or perfect.
Verifying Eiffel Programs with Boogie
Venue: arXiv cs.SE 2011
Year: 2011

Static program verifiers such as Spec#, Dafny, jStar, and VeriFast define the state of the art in automated functional verification techniques. The next open challenges are to make verification tools usable even by programmers not fluent in formal techniques. This paper presents AutoProof, a verification tool that translates Eiffel programs to Boogie and uses the Boogie verifier to prove them. In an effort to be usable with real programs, AutoProof fully supports several advanced object-oriented features including polymorphism, inheritance, and function objects. AutoProof also adopts simple strategies to reduce the amount of annotations needed when verifying programs (e.g., frame conditions). The paper illustrates the main features of AutoProof's translation, including some whose implementation is underway, and demonstrates them with examples and a case study.
Bound Propagation
Venue: arXiv cs.AI 2011
Year: 2011

In this article we present an algorithm to compute bounds on the marginals of a graphical model. For several small clusters of nodes upper and lower bounds on the marginal values are computed independently of the rest of the network. The range of allowed probability distributions over the surrounding nodes is restricted using earlier computed bounds. As we will show, this can be considered as a set of constraints in a linear programming problem of which the objective function is the marginal probability of the center nodes. In this way knowledge about the maginals of neighbouring clusters is passed to other clusters thereby tightening the bounds on their marginals. We show that sharp bounds can be obtained for undirected and directed graphs that are used for practical applications, but for which exact computations are infeasible.
Wrapper Maintenance: A Machine Learning Approach
Venue: arXiv cs.AI 2011
Year: 2011

The proliferation of online information sources has led to an increased use of wrappers for extracting data from Web sources. While most of the previous research has focused on quick and efficient generation of wrappers, the development of tools for wrapper maintenance has received less attention. This is an important research problem because Web sources often change in ways that prevent the wrappers from extracting data correctly. We present an efficient algorithm that learns structural information about data from positive examples alone. We describe how this information can be used for two wrapper maintenance applications: wrapper verification and reinduction. The wrapper verification system detects when a wrapper is not extracting correct data, usually because the Web source has changed its format. The reinduction algorithm automatically recovers from changes in the Web source by identifying data on Web pages so that a new wrapper may be generated for this source. To validate our approach, we monitored 27 wrappers over a period of a year. The verification algorithm correctly discovered 35 of the 37 wrapper changes, and made 16 mistakes, resulting in precision of 0.73 and recall of 0.95. We validated the reinduction algorithm on ten Web sources. We were able to successfully reinduce the wrappers, obtaining precision and recall values of 0.90 and 0.80 on the data extraction task.
The All Relevant Feature Selection using Random Forest
Venue: arXiv cs.AI 2011
Year: 2011

In this paper we examine the application of the random forest classifier for the all relevant feature selection problem. To this end we first examine two recently proposed all relevant feature selection algorithms, both being a random forest wrappers, on a series of synthetic data sets with varying size. We show that reasonable accuracy of predictions can be achieved and that heuristic algorithms that were designed to handle the all relevant problem, have performance that is close to that of the reference ideal algorithm. Then, we apply one of the algorithms to four families of semi-synthetic data sets to assess how the properties of particular data set influence results of feature selection. Finally we test the procedure using a well-known gene expression data set. The relevance of nearly all previously established important genes was confirmed, moreover the relevance of several new ones is discovered.
Four-Dimensional Gallant-Lambert-Vanstone Scalar Multiplication
Venue: arXiv cs.CR 2011
Year: 2011

The GLV method of Gallant, Lambert and Vanstone (CRYPTO 2001) computes any multiple $kP$ of a point $P$ of prime order $n$ lying on an elliptic curve with a low-degree endomorphism $Φ$ (called GLV curve) over $\mathbb{F}_p$ as [kP = k_1P + k_2Φ(P), \quad\text{with} \max{|k_1|,|k_2|}\leq C_1\sqrt n] for some explicit constant $C_1>0$. Recently, Galbraith, Lin and Scott (EUROCRYPT 2009) extended this method to all curves over $\mathbb{F}_{p^2}$ which are twists of curves defined over $\mathbb{F}_p$. We show in this work how to merge the two approaches in order to get, for twists of any GLV curve over $\mathbb{F}_{p^2}$, a four-dimensional decomposition together with fast endomorphisms $Φ, Ψ$ over $\mathbb{F}_{p^2}$ acting on the group generated by a point $P$ of prime order $n$, resulting in a proved decomposition for any scalar $k\in[1,n]$ $$ kP=k_1P+ k_2Φ(P)+ k_3Ψ(P) + k_4ΨΦ(P)\quad \text{with} \max_i (|k_i|)< C_2\, n^{1/4} $$ for some explicit $C_2>0$. Furthermore, taking the best $C_1, C_2$, we get $C_2/C_1<408$, independently of the curve, ensuring a constant relative speedup. We also derive new families of GLV curves, corresponding to those curves with degree 3 endomorphisms.
The Contest Between Simplicity and Efficiency in Asynchronous Byzantine Agreement
Venue: arXiv cs.DC 2011
Year: 2011

In the wake of the decisive impossibility result of Fischer, Lynch, and Paterson for deterministic consensus protocols in the aynchronous model with just one failure, Ben-Or and Bracha demonstrated that the problem could be solved with randomness, even for Byzantine failures. Both protocols are natural and intuitive to verify, and Bracha's achieves optimal resilience. However, the expected running time of these protocols is exponential in general. Recently, Kapron, Kempe, King, Saia, and Sanwalani presented the first efficient Byzantine agreement algorithm in the asynchronous, full information model, running in polylogarithmic time. Their algorithm is Monte Carlo and drastically departs from the simple structure of Ben-Or and Bracha's Las Vegas algorithms. In this paper, we begin an investigation of the question: to what extent is this departure necessary? Might there be a much simpler and intuitive Las Vegas protocol that runs in expected polynomial time? We will show that the exponential running time of Ben-Or and Bracha's algorithms is no mere accident of their specific details, but rather an unavoidable consequence of their general symmetry and round structure. We define a natural class of "fully symmetric round protocols" for solving Byzantine agreement in an asynchronous setting and show that any such protocol can be forced to run in expected exponential time by an adversary in the full information model. We assume the adversary controls $t$ Byzantine processors for $t = cn$, where $c$ is an arbitrary positive constant $< 1/3$. We view our result as a step toward identifying the level of complexity required for a polynomial-time algorithm in this setting, and also as a guide in the search for new efficient algorithms.
A Game Theoretical Approach to Broadcast Information Diffusion in Social Networks
Venue: arXiv cs.SI 2011
Year: 2011

One major function of social networks (e.g., massive online social networks) is the dissemination of information, such as scientific knowledge, news, and rumors. Information can be propagated by the users of the network via natural connections in written, oral or electronic form. The information passing from a sender to receivers and back (in the form of comments) involves all of the actors considering their knowledge, trust, and popularity, which shape their publishing and commenting strategies. To understand such human aspects of the information dissemination, we propose a game theoretical model of a one-way information forwarding and feedback mechanism in a star-shaped social network that takes into account the personalities of the communicating actors.
AltAltp: Online Parallelization of Plans with Heuristic State Search
Venue: arXiv cs.AI 2011
Year: 2011

Despite their near dominance, heuristic state search planners still lag behind disjunctive planners in the generation of parallel plans in classical planning. The reason is that directly searching for parallel solutions in state space planners would require the planners to branch on all possible subsets of parallel actions, thus increasing the branching factor exponentially. We present a variant of our heuristic state search planner AltAlt, called AltAltp which generates parallel plans by using greedy online parallelization of partial plans. The greedy approach is significantly informed by the use of novel distance heuristics that AltAltp derives from a graphplan-style planning graph for the problem. While this approach is not guaranteed to provide optimal parallel plans, empirical results show that AltAltp is capable of generating good quality parallel plans at a fraction of the cost incurred by the disjunctive planners.
Towards an IO intensive Grid application instrumentation in MedioGRID
Venue: arXiv cs.DC 2011
Year: 2011

Obtaining high performance in IO intensive applications requires systems that support reliable fast transfer, data replication, and caching. In this paper we present an architecture designed for supporting IO intensive applications in MedioGRID, a system for real-time processing of satellite images, operating in a Grid environment. The solution ensures that applications which are processing geographical data have uniform access to data and is based on continuous monitoring of the data transfers using MonALISA and its extensions. The MedioGRID architecture is also built on Globus, Condor and PBS and based on this middleware we aim to extract information about the running systems. The results obtained in testing MedioGRID system for large data transfers show that monitoring system provides a very good view of system evolution.
Resource CoAllocation for Scheduling Tasks with Dependencies, in Grid
Venue: arXiv cs.DC 2011
Year: 2011

Scheduling applications on wide-area distributed systems is useful for obtaining quick and reliable results in an efficient manner. Optimized scheduling algorithms are fundamentally important in order to achieve optimized resources utilization. The existing and potential applications include many fields of activity like satellite image processing and medicine. The paper proposes a scheduling algorithm for tasks with dependencies in Grid environments. CoAllocation represents a strategy that provides a schedule for task with dependencies, having as main purpose the efficiency of the schedule, in terms of load balancing and minimum time for the execution of the tasks.
Pose Estimation from a Single Depth Image for Arbitrary Kinematic Skeletons
Venue: arXiv cs.CV 2011
Year: 2011

We present a method for estimating pose information from a single depth image given an arbitrary kinematic structure without prior training. For an arbitrary skeleton and depth image, an evolutionary algorithm is used to find the optimal kinematic configuration to explain the observed image. Results show that our approach can correctly estimate poses of 39 and 78 degree-of-freedom models from a single depth image, even in cases of significant self-occlusion.
Reconstruction and Estimation of Scattering Functions of Overspread Radar Targets
Venue: arXiv cs.IT 2011
Year: 2011

In many radar scenarios, the radar target or the medium is assumed to possess randomly varying parts. The properties of a target are described by a random process known as the spreading function. Its second order statistics under the WSSUS assumption are given by the scattering function. Recent developments in the operator identification theory suggest a channel sounding procedure that allows to determine the spreading function given complete statistical knowledge of the operator echo. We show that in a continuous model it is indeed theoretically possible to identify a scattering function of an overspread target given full statistics of a received echo from a single sounding by a custom weighted delta train. Our results apply whenever the scattering function is supported on a set of area less than one. Absent such complete statistics, we construct and analyze an estimator that can be used as a replacement of the averaged periodogram estimator in case of poor geometry of the support set of the scattering function.