ppxscal/embedding_network huggingface dataset:
A Lagrangean based branch-and-cut algorithm for global optimization of nonconvex mixed-integer nonlinear programs with decomposable structures
Authors: Ramkumar Karuppiah, Ignacio E. Grossmann
Venue: Journal of Global Optimization (2008)

In this work we present a global optimization algorithm for solving a class of large-scale nonconvex optimization models that have a decomposable structure. Such models, which are very expensive to solve to global optimality, are frequently encountered in two-stage stochastic programming problems, engineering design, and also in planning and scheduling. A generic formulation and reformulation of the decomposable models is given. We propose a specialized deterministic branch-and-cut algorithm to solve these models to global optimality, wherein bounds on the global optimum are obtained by solving convex relaxations of these models with certain cuts added to them in order to tighten the relaxations. These cuts are based on the solutions of the sub-problems obtained by applying Lagrangean decomposition to the original nonconvex model. Numerical examples are presented to illustrate the effectiveness of the proposed method compared to available commercial global optimization solvers that are based on branch and bound methods.
Toward Verified Biological Models
Authors: Avital Sadot, Jasmin Fisher, Dan Barak, Yishai Admanit, Michael J. Stern, E. Jane Albert Hubbard, David Harel
Venue: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (2008)

The last several decades have witnessed a vast accumulation of biological data and data analysis. Many of these data sets represent only a small fraction of the system's behavior, making the visualization of full system behavior difficult. A more complete understanding of a biological system is gained when different types of data (and/or conclusions drawn from the data) are integrated into a larger-scale representation or model of the system. Ideally, this type of model is consistent with all available data about the system, and it is then used to generate additional hypotheses to be tested. Computer-based methods intended to formulate models that integrate various events and to test the consistency of these models with respect to the laboratory-based observations on which they are based are potentially very useful. In addition, in contrast to informal models, the consistency of such formal computer-based models with laboratory data can be tested rigorously by methods of formal verification. We combined two formal modeling approaches in computer science that were originally developed for non-biological system design. One is the inter-object approach using the language of live sequence charts (LSCs) with the Play-Engine tool, and the other is the intra-object approach using the language of statecharts and Rhapsody as the tool. Integration is carried out using InterPlay, a simulation engine coordinator. Using these tools, we constructed a combined model comprising three modules. One module represents the early lineage of the somatic gonad of C. elegans in LSCs, while a second more detailed module in statecharts represents an interaction between two cells within this lineage that determine their developmental outcome. Using the advantages of the tools, we created a third module representing a set of key experimental data using LSCs. We tested the combined statechart-LSC model by showing that the simulations were consistent with the set of experimental LSCs. This small-scale modular example demonstrates the potential for using similar approaches for verification by exhaustive testing of models by LSCs. It also shows the advantages of these approaches for modeling biology.
Adaptabilty of a GP Based IDS on Wireless Networks
Authors: Adetokunbo Makanju, Nur Zincir-Heywood, Evangelos Milios
Venue: Proceedings of the 2008 Third International Conference on Availability, Reliability and Security (2008)

Abstract—Security and Intrusion detection in WiFi networks is currently an active area of research where WiFi specific Data Link layer attacks are an area of focus; particularly recent work has focused on producing machine learning based IDSs for these WiFi specific attacks. These proposed machine learning based IDSs come in addition to the already deployed signatures which are already in use in conventional intrusion detection systems like Snort-Wireless and Kismet. In this paper, we compare the detection capability of Snort-Wireless and a Genetic Programming (GP) based intrusion detector, based on the ability to adapt to modified attacks, ability to adapt to similar unknown attacks and infrastructure independent detection. Our results show that the GP based detection system is much more robust against modified attacks compared to Snort-Wireless. Moreover, by focusing on the method(s) used in feature preprocessing for presentation to learning algorithms, GP based IDSs can achieve infrastructure independent detection and can adapt to similar unknown attacks too. On the other hand, even though Snort-Wireless is an infrastructure independent detector, it cannot adapt to unknown attacks even if they are similar to others for which it has signatures on.
Scalable network distance browsing in spatial databases
Authors: Hanan Samet, Jagan Sankaranarayanan, Houman Alborzi
Venue: Proceedings of the 2008 ACM SIGMOD international conference on Management of data (2008)

An algorithm is presented for finding the k nearest neighbors in a spatial network in a best-first manner using network distance. The algorithm is based on precomputing the shortest paths between all possible vertices in the network and then making use of an encoding that takes advantage of the fact that the shortest paths from vertex u to all of the remaining vertices can be decomposed into subsets based on the first edges on the shortest paths to them from u. Thus, in the worst case, the amount of work depends on the number of objects that are examined and the number of links on the shortest paths to them from q, rather than depending on the number of vertices in the network. The amount of storage required to keep track of the subsets is reduced by taking advantage of their spatial coherence which is captured by the aid of a shortest path quadtree. In particular, experiments on a number of large road networks as well as a theoretical analysis have shown that the storage has been reduced from O(N3) to O(N1.5) (i.e., by an order of magnitude equal to the square root). The precomputation of the shortest paths along the network essentially decouples the process of computing shortest paths along the network from that of finding the neighbors, and thereby also decouples the domain S of the query objects and that of the objects from which the neighbors are drawn from the domain V of the vertices of the spatial network. This means that as long as the spatial network is unchanged, the algorithm and underlying representation of the shortest paths in the spatial network can be used with different sets of objects.
Automating spoken dialogue management design using machine learning: An industry perspective
Authors: Tim Paek, Roberto Pieraccini
Venue: Speech Communication (2008)

In designing a spoken dialogue system, developers need to specify the actions a system should take in response to user speech input and the state of the environment based on observed or inferred events, states, and beliefs. This is the fundamental task of dialogue management. Researchers have recently pursued methods for automating the design of spoken dialogue management using machine learning techniques such as reinforcement learning. In this paper, we discuss how dialogue management is handled in industry and critically evaluate to what extent current state-of-the-art machine learning methods can be of practical benefit to application developers who are deploying commercial production systems. In examining the strengths and weaknesses of these methods, we highlight what academic researchers need to know about commercial deployment if they are to influence the way industry designs and practices dialogue management.
Efficient computation of Euclidean shortest paths in the plane
Authors: J. Hershberger, S. Suri
Venue: Proceedings of the 1993 IEEE 34th Annual Foundations of Computer Science (1993)

We propose a new algorithm for a classical problem in plane computational geometry: computing a shortest path between two points in the presence of polygonal obstacles. Our algorithm runs in worst-case time O(nlog/sup 2/ n) and requires O(nlog n) space, where n is the total number of vertices in the obstacle polygons. Our algorithm actually computes a planar map that encodes shortest paths from a fixed source point to all other points of the plane; the map can be used to answer single-source shortest path queries in O(log n) time. The time complexity of our algorithm is a significant improvement over all previous results known for the shortest path problem.
A practical approach of memory access parallelization to exploit multiple off-chip DDR memories
Authors: Woo-Cheol Kwon, Sungjoo Yoo, Sung-Min Hong, Byeong Min, Kyu-Myung Choi, Soo-Kwan Eo
Venue: Proceedings of the 45th annual Design Automation Conference (2008)

3D stacked memory enables more off-chip DDR memories. Redesigning existing IPs to exploit the increased memory parallelism will be prohibitively costly. In our work, we propose a practical approach to exploit the increased bandwidth and reduced latency of multiple off-chip DDR memories while reusing existing IPs without modification. The proposed approach is based on two new concepts: transaction id renaming and distributed soft arbitration. We present two on-chip network components, request parallelizer and read data serializer, to realize the concepts. Experiments with synthetic test cases and an industrial strength DTV SoC design show that the proposed approach gives significant improvements in total execution cycle (21.6%) and average memory access latency (31.6%) in the DTV case with a small area overhead (30.1% in the on-chip network, and less than 1.4% in the entire chip).
Numerical predictions of short-pulsed laser transport in absorbing and scattering media. I-A time-based approach with flux limiters
Authors: D. R. Rousse
Venue: International Journal of Computational Fluid Dynamics (2007)

A one-dimensional transient radiative transfer problem in the Cartesian coordinate system involving an absorbing and scattering medium illuminated by a short laser pulse has computationally been solved by use of a finite volume method (FVM). Previous works have shown that first order spatial interpolation schemes cannot represent the physics of the problem adequately as transmitted fluxes emerge before the minimal physical time required to leave the medium. In this paper, the Van Leer and Superbee flux limiters, combined with the second order Lax-Wendroff scheme, are used in an attempt to prevent this. Results presented in this work show that, despite significant improvement, flux limiters fail to completely eliminate the physically unrealistic behaviour. Therefore, a numerical approach into which temporal variables are transformed into frequency-dependent variables is presented in the companion paper to this work.
Incorporating transformations into jflap for enhanced understanding of automata
Authors: Joan M. Lucas, Jonathan Jarvis
Venue: Proceedings of the 39th SIGCSE technical symposium on Computer science education (2008)

This paper describes our experience extending the educational software program JFLAP. JFLAP enables students to design and simulate automata such as Finite State Machines, push-down automata, and Turing Machines. It is a valuable aid in any Automata Theory course. We modified JFLAP so that students could write Java programs that alter the actual automaton itself. This utility greatly increases the students' ability to grasp such fundamental topics as the Church-Turing thesis and the theory of undecidability.
SDSOA 2008: second international workshop on systems development in SOA environments
Authors: Kostas Kontogiannis, Grace A. Lewis, Dennis B. Smith, Marin Litoiu
Venue: Companion of the 30th international conference on Software engineering (2008)

The key objective of this workshop is to provide researchers and practitioners an opportunity to discuss open SOA research challenges. An SOA research agenda that has been developed by SEI and a group of collaborators over the past year will be presented as a framework for obtaining feedback and new ideas from researchers and practitioners who do work and research in this area.
Reconfigurable hardware for high-security/high-performance embedded systems: the SAFES perspective
Authors: Guy Gogniat, Tilman Wolf, Wayne Burleson, Jean-Philippe Diguet, Lilian Bossuet, Romain Vaslin
Venue: IEEE Transactions on Very Large Scale Integration (VLSI) Systems (2008)

Embedded systems present significant security challenges due to their limited resources and power constraints. This paper focuses on the issues of building secure embedded systems on reconfigurable hardware and proposes a security architecture for embedded systems (SAFES). SAFES leverages the capabilities of reconfigurable hardware to provide efficient and flexible architectural support for security standards and defenses against a range of hardware attacks. The SAFES architecture is based on three main ideas: 1) reconfigurable security primitives; 2) reconfigurable hardware monitors; and 3) a hierarchy of security controllers at the primitive, system and executive level. Results are presented for reconfigurable AES and RC6 security primitives and highlight the value of such an architecture. This paper also emphasizes that re-configurable hardware is not just a technology for hardware accelerators dedicated to security primitives as has been focused on by most studies but a real solution to provide high-security and high-performance for a system.
Processing effects on the dissolution properties of thin chemically amplified photoresist films
Authors: D. Drygiannakis, I. Raptis, G. P. Patsis, A. Boudouvis, K. vanWerden
Venue: Microelectronic Engineering (2008)

Resist film thickness is anticipated to be 60nm in the 22nm technology node setting significant processing challenges due to resist non-bulk behavior. The changes in the dissolution rate of a positive DUV polymer based chemically amplified resist due to various processing conditions such as film thickness, exposure dose, and thermal processing conditions, are experimentally investigated. It is quantified among others, the way an increase of PAB temperature deteriorates dissolution rate at low exposure dose, while in higher exposure doses increasing PAB temperature enhances dissolution rate. Also, an analytic model for the dissolution rate is imported on a stochastic lithography simulator and first quantitative results for thin films are reported.
An adjusted boxplot for skewed distributions
Authors: M. Hubert, E. Vandervieren
Venue: Computational Statistics Data Analysis (2008)

The boxplot is a very popular graphical tool for visualizing the distribution of continuous unimodal data. It shows information about the location, spread, skewness as well as the tails of the data. However, when the data are skewed, usually many points exceed the whiskers and are often erroneously declared as outliers. An adjustment of the boxplot is presented that includes a robust measure of skewness in the determination of the whiskers. This results in a more accurate representation of the data and of possible outliers. Consequently, this adjusted boxplot can also be used as a fast and automatic outlier detection tool without making any parametric assumption about the distribution of the bulk of the data. Several examples and simulation results show the advantages of this new procedure.
On connectivity in graphs with given clique number
Authors: Angelika Hellwig, Lutz Volkmann
Venue: Journal of Graph Theory (2006)

We consider finite, undirected, and simple graphs G of order n(G) and minimum degree &delta;(G). The connectivity &kappa;(G) for a connected graph G is defined as the minimum cardinality over all vertex-cuts. If &kappa;(G)&thinsp;<&thinsp;&delta;(G), then Topp and Volkmann [7] showed in 1993 for p-partite graphs G that $$\kappa (G)\geq 2p\delta (G)-n(G)(2p-3).$$ As a simple consequence, Topp and Volkmann obtained for p-partite graphs G the identity &kappa;(G)&thinsp;=&thinsp;&delta;(G), if $$\delta (G)\geq {2p-3 \over 2p-1}n(G).$$ In this article, we will show that these results remain true for graphs G with &omega;(G)&thinsp;&le;&thinsp;p, where &omega;(G) denotes the clique number of G. Since each p-partite graph G satisfies &omega;(G)&thinsp;&le;&thinsp;p, this generalizes the results of Topp and Volkmann. &copy; 2006 Wiley Periodicals, Inc. J Graph Theory 52: 7&ndash;14, 2006
The asymptotics of semi-supervised learning in discriminative probabilistic models
Authors: Nataliya Sokolovska, Olivier Cappé, François Yvon
Venue: Proceedings of the 25th international conference on Machine learning (2008)

Semi-supervised learning aims at taking advantage of unlabeled data to improve the efficiency of supervised learning procedures. For discriminative models however, this is a challenging task. In this contribution, we introduce an original methodology for using unlabeled data through the design of a simple semi-supervised objective function. We prove that the corresponding semi-supervised estimator is asymptotically optimal. The practical consequences of this result are discussed for the case of the logistic regression model.
Pooling spaces associated with finite geometry
Authors: Tayuan Huang, Kaishun Wang, Chih-wen Weng
Venue: European Journal of Combinatorics (2008)

Motivated by the works of Ngo and Du [H. Ngo, D. Du, A survey on combinatorial group testing algorithms with applications to DNA library screening, DIMACS Series in Discrete Mathematics and Theoretical Computer Science 55 (2000) 171-182], the notion of pooling spaces was introduced [T. Huang, C. Weng, Pooling spaces and non-adaptive pooling designs, Discrete Mathematics 282 (2004) 163-169] for a systematic way of constructing pooling designs; note that geometric lattices are among pooling spaces. This paper attempts to draw possible connections from finite geometry and distance regular graphs to pooling spaces: including the projective spaces, the affine spaces, the attenuated spaces, and a few families of geometric lattices associated with the orbits of subspaces under finite classical groups, and associated with d-bounded distance-regular graphs.
Properties of tree convex constraints
Authors: Yuanlin Zhang, Eugene C. Freuder
Venue: Artificial Intelligence (2008)

It is known that a tree convex network is globally consistent if it is path consistent. However, if a tree convex network is not path consistent, enforcing path consistency on it may not make it globally consistent. In this paper, we investigate the properties of some tree convex constraints under intersection and composition. As a result, we identify a sub-class of tree convex networks that are locally chain convex and strictly union closed. This class of problems can be made globally consistent by arc and path consistency and thus is tractable. Interestingly, we also find that some scene labeling problems can be modeled by tree convex constraints in a natural and meaningful way.
Loss Recovery in Application-Layer Multicast
Authors: Xing Jin, W. -P. Ken Yiu, S. -H. Gary Chan
Venue: IEEE MultiMedia (2008)

Application-layer multicast, sometimes called overlay multicast, can help circumvent the limitations in IP multicast and unicast.
Memory tagging in Charm++
Authors: Filippo Gioachin, Laxmikant V. Kalé
Venue: Proceedings of the 6th workshop on Parallel and distributed systems: testing, analysis, and debugging (2008)

Many scientific applications are logically decomposed into modules. each module performing a different type of computation. These modules are then linked together inside the same executable. While these modules are logically independent, they are not physically independent: a faulty module can corrupt the state of another one. By identifying the different modules inside an application, tagging the memory according to the different modules, and performing extra runtime checks, we can automatically detect certain type of errors. We implemented our idea inside the Charm++ runtime system, where modules can be easily identified. We illustrate the validity of our approach, and evaluate its overhead.
Route recovery in vertex-disjoint multipath routing for many-to-one sensor networks
Authors: Wei Cheng, Kai Xing, Xiuzhen Cheng, Xicheng Lu, Zexin Lu, Jinshu Su, Baosheng Wang, Yujun Liu
Venue: Proceedings of the 9th ACM international symposium on Mobile ad hoc networking and computing (2008)

Multipath routing is attractive for load-balancing, fault-tolerance, and security enhancement. However, constructing and maintaining a set of node-disjoint paths between the data source and sink is non-trivial in a dynamic environment. In this paper, we study the problem of route recovery in vertex-disjoint multipath routing for sensor networks with many-to-one traffic patterns. We identify the sufficient conditions for multipaths to be recovered when the existing node-disjoint paths are broken, and provide a simple framework for multipath maintenance. This framework is very efficient in time when multipath source routing is employed. Our findings can help to conserve network resource by not launching any route discovery when the data source realizes that a new route may not exist, to guide mobile data sources to relocate themselves in order to reconstruct the new multipaths, and to help newly-deployed data sources quickly determine whether the required number of multipaths exist for sure or not and then compute them. The technique proposed in this paper is a good complement to the classic max-flow algorithm when node-disjoint multipaths are needed.
Continuum redundancy-PLS regression: A simple continuum approach
Authors: S. Bougeard, M. Hanafi, E. M. Qannari
Venue: Computational Statistics Data Analysis (2008)

The relationships between two data sets are investigated. The aim is to predict one data set from the other. New formulations of Redundancy Analysis and Partial Least Square Regression (PLS) are discussed, clearly showing the connexions between these two popular methods. Moreover, it is shown that the Redundancy Analysis and PLS regression are the two end points of a continuum approach. Properties related to this continuum approach are discussed, showing how the multicolinearity problem is handled. The interest of the general strategy of analysis is illustrated on the basis of a data set pertaining to epidemiology.
Splitting extrapolation method for solving second-order parabolic equations with curved boundaries by using domain decomposition and d-quadratic isoparametric finite elements
Authors: Xiaoming He, Tao Lü
Venue: International Journal of Computer Mathematics (2007)

This article discusses a splitting extrapolation method for solving second-order parabolic equations with curved boundaries by using domain decomposition and d-quadratic isoparametric finite elements. This method possesses superconvergence, a high order of accuracy and a high degree of parallelism. First, we prove the multi-variable asymptotic expansion of fully discrete d-quadratic isoparametric finite element errors. Based on the expansion, we generate splitting extrapolation formulas. These formulas generate a numerical solution on a globally fine grid with higher accuracy by solving only a set of smaller discrete subproblems on different coarser grids. Therefore, a large-scale multidimensional problem with a curved boundary is turned into a set of smaller discrete subproblems on a polyhedron. Because these subproblems are independent of each other and have similar scales, our algorithm possesses a high degree of parallelism. In addition, this method is effective for solving discontinuous problems if we regard the interfaces of the problems as the interfaces of the initial domain decomposition. Our numerical results also show that the algorithm is effective for solving nonlinear parabolic equations.