ppxscal/embedding_network huggingface dataset:
Automating the Biological Data Collection Process with Agents
Authors: Zoe Lacroix, Kaushal Parekh, Hasan Davulcu, I. V. Ramakrishnan, Nikeeta Julasana
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

Scientists spend significant amount of time accessing Web resources, extracting information of interest, filtering, and integrating relevant data from multiple heterogeneous Web sites to support their data collection needs. This tedious collection process is typically performed manually as available technology does not allow scientists to explore and control their data collection process step by step. However, most of the process can be automated. While scripts (e.g., Perl) may be written to retrieve, parse and extract data of interest, many scientists are not programmers and do not have IT support. In contrast we propose an approach based on Personal Information Agents (PIA) that provide scientists a user-friendly mechanism to automate their data collection processes without the need of any programming. This approach is currently being evaluated at the Brain Tumor Cancer Unit of the Translational Genomics Research Institute (TGen), Phoenix, Arizona.
Chiral Polyhedra in Ordinary Space, I
Authors: Egon Schulte
Venue: Discrete Computational Geometry (2004)

Chiral polyhedra in ordinary euclidean space E3 are nearly regular polyhedra; their geometric symmetry groups have two orbits on the flags, such that adjacent flags are in distinct orbits. This paper completely enumerates the discrete infinite chiral polyhedra in E3 with finite skew faces and finite skew vertex-figures. There are several families of such polyhedra of types {4,6}, {6,4} and {6,6}. Their geometry and combinatorics are discussed in detail. It is also proved that a chiral polyhedron in E3 cannot be finite. Part II of the paper will complete the classification of all chiral polyhedra in E3. All chiral polyhedra not described in Part I have infinite, helical faces and again occur in families. So, in effect, Part I enumerates all chiral polyhedra in E3 with finite faces.
Consistent and compact data management in distributed storage systems
Authors: Baruch Awerbuch, Christian Scheideler
Venue: Proceedings of the sixteenth annual ACM symposium on Parallelism in algorithms and architectures (2004)

In this paper we consider the problem of maintaining a consistent mapping of a virtual object space to a set of memory modules, i.e. the object space can be decomposed into a set of ranges where every module is responsible for exactly one range. A module owning some range R is responsible for storing all objects in R. Besides consistency, we require the mapping to be compact, i.e. any object or consecutive range of objects should be spread out over as few memory modules as possible. A compact mapping is important for many applications such as efficiently executing programs using a large amount of space or complex search queries such as semi-group range queries. Our main result assumes a static set of memory modules of uniform capacity, but we also show how to extend this to a dynamic set of memory modules of non-uniform capacity in a decentralized environment.In both settings, new objects may be added, old objects may be deleted, or objects may be modified over time. Each object consists of a set of data blocks of uniform size. So insert, delete, or modify operations on objects can be seen as insert or delete operations of data blocks. Each module can send or receive at most one data block in each unit of time and the injection of insert or delete requests for data blocks is under adversarial control. We prove asymptotically tight upper and lower bounds on the maximum rate at which the adversary can inject requests into the system so that a consistent and compact placement can be preserved without exceeding the capacity of a module at any time. Specifically, we show that in a (1-ε)-utilized system (i.e. the available space is used up to an ε fraction) the maximum injection rate that can be sustained is Θ(ε).
Meanshift Clustering for DNA Microarray Analysis
Authors: Danny Barash, Dorin Comaniciu
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

Meanshift clustering is a well established algorithm that has been applied successfully in image processing and computer vision. Cluster centers are derived by local mode seeking identifying maxima in the normalized density of the data set. Recently, quantum clustering that highly resembles mean shift clustering has been proposed for analyzing microarray expression data. Quantum clustering is based on physical intuition derived from quantum mechanics. By an iterative process using a gradient descent procedure, the potential energy V belonging to the Hamiltonian of the time-indepedent Schrodinger equation develops minima that are identified with cluster centers. The analogies between the wavefunction in quantum clustering and the multivariate kernel density estimator in meanshift clustering are leading to closely related formulations. However, the approach towards the minima of the potential in quantum clustering needs to be performed unrelatedly to the formulation, by gradient descent steps. In contrast, in meanshift clustering the approach towards the maxima of the normalized density is performed by the meanshift vector that is derived by the formulation of the methodology. It points towards the direction of the maximum increase in the underlying density. Based on these observations, we propose implementing meanshift clustering to improve the efficiency of local mode seeking in analyzing expression data.
Formation of an Online Community of Practice: An Inductive Study Unearthing Key Elements
Authors: Lori Baker-Eveleth, Suprateek Sarker, Daniel M. Eveleth
Venue: Proceedings of the Proceedings of the 38th Annual Hawaii International Conference on System Sciences - Volume 08 (2005)

Informal conversations occur all day long among employees. These conversations allow employees to share experience such as innovative ideas for performing a task. Internalizing those experiences enables sharing of tacit knowledge. Tacit knowledge is valuable to business because it embodies expertise. Shared with others as storytelling or "war" stories, tacit knowledge is difficult to catalog and store. A model for connecting and sharing tacit knowledge is a community of practice. Information systems can be used to create, support, and maintain communities of practice in a variety of settings. Analogies can be drawn in the development of informal, learning communities in distance education to the creation of online communities of practice. Qualitative investigations of online interactions in a distance course highlight the development of an online community of practice. Implications of this study are discussed as well as the lessons learned.
Model checking XML manipulating software
Authors: Xiang Fu, Tevfik Bultan, Jianwen Su
Venue: ACM SIGSOFT Software Engineering Notes (2004)

The use of XML as the de facto data exchange standard has allowed integration of heterogeneous web based software systems regardless of implementation platforms and programming languages. On the other hand, the rich tree-structured data representation, and the expressive XML query languages (such as XPath) make formal specification and verification of software systems that manipulate XML data a challenge. In this paper, we present our initial efforts in automated verification of XML data manipulation operations using the SPIN model checker. We present algorithms for translating (bounded) XML data and XPath expressions to Promela, the input language of SPIN. The techniques presented in this paper constitute the basis of our Web Service Analysis Tool (WSAT) which verifies LTL properties of composite web services.
Visualizing multiple network perspectives
Authors: Misja N. Hoebe, Rien Bosma
Venue: Proceedings of the conference on Dutch directions in HCI (2004)

In this paper, we describe a tool for displaying multiple network perspectives, where each perspective is a relation in which resources on the network are linked to others via a shared property. Every change or addition of perspective can be seen as a context switch, providing the actor with various navigation paths through a complex, multidimensional information space. This tool will attempt to capture and visualize the increasing amount of information coming available through the tools and standards currently being developed for the semantic web. As such, it may provide the learner means to explore, get to know and interact with her environment, fitting very well in a (social) constructivist approach of learning.
Crest Lines for Surface Segmentation and Flattening
Authors: Georgios Stylianou, Gerald Farin
Venue: IEEE Transactions on Visualization and Computer Graphics (2004)

We present a method for extracting feature curves called crest lines from a triangulated surface. Then, we calculate the geodesic Voronoi diagram of crest lines to segment the surface into several regions. Afterward, barycentric surface flattening using theory from graph embeddings is implemented and, using the Geodesic Voronoi diagram, we develop a faster surface flattening algorithm.
Optimal Control of Bilateral Obstacle Problems
Authors: Maïtine Bergounioux, Suzanne Lenhart
Venue: SIAM Journal on Control and Optimization (2004)

We consider an optimal control problem where the state satisfies a bilateral elliptic variational inequality and the control functions are the upper and lower obstacles. We seek a state that is close to a desired profile and the H2 norms of the obstacles are not too large. Existence results are given and an optimality system is derived. A particular case is studied that needs no compactness assumption, via a monotonicity method.
Retrieval evaluation with incomplete information
Authors: Chris Buckley, Ellen M. Voorhees
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

This paper examines whether the Cranfield evaluation methodology is robust to gross violations of the completeness assumption (i.e., the assumption that all relevant documents within a test collection have been identified and are present in the collection). We show that current evaluation measures are not robust to substantially incomplete relevance judgments. A new measure is introduced that is both highly correlated with existing measures when complete judgments are available and more robust to incomplete judgment sets. This finding suggests that substantially larger or dynamic test collections built using current pooling practices should be viable laboratory tools, despite the fact that the relevance information will be incomplete and imperfect.
The Effect of Testing on Reliability of Fault-Tolerant Software
Authors: Peter Popov, Bev Littlewood
Venue: Proceedings of the 2004 International Conference on Dependable Systems and Networks (2004)

Previous models have investigated the impact upondiversity - and hence upon the reliability of fault-tolerantsoftware built from 'diverse' versions - of the variation in'difficulty' of demands over the demand space. Thesemodels are essentially static, taking a single snapshotview of the system. In this paper we consider ageneralisation in which the individual versions areallowed to evolve - and their reliability to grow - throughdebugging. In particular, we examine the trade-off thatoccurs in testing between, on the one hand, the increasingreliability of individual versions, and on the other handthe possible diminution of diversity.
On a Generalization of R&#x00e9;dei&#x2019;s Theorem
Authors: Andr&#x00e1;s G&#x00e1;cs
Venue: Combinatorica (2003)

In 1970 R&#x00e9;dei and Megyesi proved that a set of p points in AG(2,p), p prime, is a line, or it determines at least $$\frac{{p + 3}} {2}$$ directions. In &#x2019;81 Lov&#x00e1;sz and Schrijver characterized the case of equality. Here we prove that the number of determined directions cannot be between $$\frac{{p + 5}} {2}$$ and $$2\frac{{p - 1}} {3}$$. The upper bound obtained is one less than the smallest known example.
Dynamic Semantics for a Controlled Natural Language
Authors: Rolf Schwitter
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

In this paper I present a dynamic approach for constructing an unambiguous semantic representation for a text written in a controlled natural language called PENG. The semantic representation is built up incrementally - in left-to-right order - while the user of the PENG system writes the text. For each word form that the user types, the language processor creates a partial logical structure that is analysed in the context of a given information state and then either updates that information state or delays this process if necessary. After each processing step, the language processor reports what kind of syntactic categories can follow the current input. These predictive grammatical hints guide the writing process of the user and enforce the rules of the controlled language. The result is an unambiguous text in controlled natural language that has first-order equivalent properties and that can be further processed by a computer.
Some results in dynamic model theory
Authors: Dexter Kozen
Venue: Science of Computer Programming (2004)

First-order structures over a fixed signature Σ give rise to a family of trace-based and relational Kleene algebras with tests defined in terms of Tarskian frames. A Tarskian frame is a Kripke frame whose states are valuations of program variables and whose atomic actions are state changes effected by variable assignments x := e, where e is a Σ-term. The Kleene algebras with tests that arise in this way play a role in dynamic model theory akin to the role played by Lindenbaum algebras in classical first-order model theory. Given a first-order theory T over Σ, we exhibit a Kripke frame U whose trace algebra TrU is universal for the equational theory of Tarskian trace algebras over Σ satisfying T, although U itself is not Tarskian in general. The corresponding relation algebra RelU is not universal for the equational theory of relation algebras of Tarskian frames, but it is so modulo observational equivalence.
Model-Driven Development of Recursive CORBA Component Assemblies
Authors: Gernot Schmoelzer, Egon Teiniker, Stefan Mitterdorfer, Christian Kreiner, Zsolt Kovacs, Reinhold Weiss
Venue: Proceedings of the 30th EUROMICRO Conference (2004)

Software applications can be described as compositions of software components at an abstract level. In this paper we present a component modeling process which allows to design, model and implement recursive component compositions. We model nested components in a platform independent manner and provide a transformation to the CORBA Component Model (CCM), one example of a Platform Specific Model (PSM). Furthermore, an implementation technique of recursive component assembling compliant to the CCM standard is described, where the components structure is automatically generated by code generation tools.
Scene Management Models and Overlap Tests for Tile-Based Rendering
Authors: I. Antochi, B. Juurlink, S. Vassiliadis, P. Liuha
Venue: Proceedings of the Digital System Design, EUROMICRO Systems (2004)

Tile-based rendering (also called chunk rendering or bucket rendering) is a promising technique for low-power, 3D graphics platforms. This technique decomposes a scene into smaller regions called tiles and renders the tiles one-by-one.The advantage of this scheme is that a small memory integrated on the graphics accelerator can be used to store the color components and z values of one tile, so that accesses to the frame and z buffer are local, on-chip accesses which consume significantly less power than off-chip accesses. Tile-based rendering, however, requires that the primitives (commonly triangles) are sorted into bins corresponding to the tiles. This paper describes several algorithms for sorting the primitives into bins and evaluates their computational complexity and memory requirements. In addition, we present and evaluate several tests for determining if a triangle and a tile overlap. Experimental results obtained using several suitable 3D graphics workloads show that various trade-offs can be made and that, usually, better performance can be obtained by trading it for memory. This information allows the designer to select the appropriate method depending on the amount of memory available and the computational power.
ACCEL-RATE: a faster mechanism for memory efficient per-flow traffic estimation
Authors: Fang Hao, Murali Kodialam, T. V. Lakshman
Venue: Proceedings of the joint international conference on Measurement and modeling of computer systems (2004)

Per-flow network traffic measurement is an important component of network traffic management, network performance assessment, and detection of anomalous network events such as incipient DoS attacks. In [1], the authors developed a mechanism called RATE where the focus was on developing a memory efficient scheme for estimating per-flow traffic rates to a specified level of accuracy. The time taken by RATE to estimate the per-flow rates is a function of the specified estimation accuracy and this time is acceptable for several applications. However some applications, such as quickly detecting worm related activity or the tracking of transient traffic, demand faster estimation times. The main contribution of this paper is a new scheme called ACCEL-RATE that, for a specified level of accuracy, can achieve orders of magnitude decrease in per-flow rate estimation times. It achieves this by using a hashing scheme to split the incoming traffic into several sub-streams, estimating the per-flow traffic rates in each of the substreams and then relating it back to the original per-flow traffic rates. We show both theoretically and experimentally that the estimation time of ACCEL-RATE is at least one to two orders of magnitude lower than RATE without any significant increase in the memory size.
A haptic feedback device based on an active mesh
Authors: Andrea Mazzone, Christian Spagno, Andreas Kunz
Venue: Proceedings of the ACM symposium on Virtual reality software and technology (2003)

This paper introduces a preliminary study about the Smart-Mesh, a novel type of active structure capable of deforming actively its shape and thus being able to form objects. It is a new approach to find a solution to the difficulties that are encountered in the field of haptic interaction in virtual environments. The paper describes the basic working principles of the structure, which allow the generation of overhanging surfaces. A first prototype based on 16 nodes and 48 linkages with prismatic joints is presented. The SmartMesh can be embedded into a table, into walls, ceilings and floors. The resolution of the SmartMesh depends on the amount of nodes and the length of the linkages. The linkages can be replaced by linear actuators.
Estimating the weight of metric minimum spanning trees in sublinear-time
Authors: Artur Czumaj, Christian Sohler
Venue: Proceedings of the thirty-sixth annual ACM symposium on Theory of computing (2004)

In this paper we present a sublinear time (1 + ε)-approximation randomized algorithm to estimate the weight of the minimum spanning tree of an n-point metric space. The running time of the algorithm is Û(n/εO(1)). Since the full description of an n-point metric space is of size Θ(n2), the complexity of our algorithm is sublinear with respect to the input size. Our algorithm is almost optimal as it is not possible to approximate in o(n) time the weight of the minimum spanning tree to within any factor. Furthermore, it has been previously shown that no o(n2) algorithm exists that returns a spanning tree whose weight is within a constant times the optimum.
An optimization method for integrating two kinds of preference information in group decision-making
Authors: Zhi-Ping Fan, Si-Han Xiao, Guo-Fen Hu
Venue: Computers and Industrial Engineering (2004)

The purpose of this paper is to study a group decision-making (GDM) problem in which the preference information about the alternative provided by the decision makers can be of a diverse nature. A new method is presented to deal with the GDM problem with two different formats of preference information on alternatives: fuzzy preference relations and multiplicative preference relations. A two-objective optimization model is constructed to integrate the two formats of preference relations and compute the ranking values of alternatives. Using this method, the ranking of alternatives or selection of the most desirable alternatives is directly done based on the obtained ranking values. A numerical example is also used to illustrate the use of the proposed method.
Bipartite structure of all complex networks
Authors: Jean-Loup Guillaume, Matthieu Latapy
Venue: Information Processing Letters (2004)

The analysis and modelling of various complex networks has received much attention in the last few years. Some such networks display a natural bipartite structure: two kinds of nodes coexist with links only between nodes of different kinds. This bipartite structure has not been deeply studied until now, mainly because it appeared to be specific to only a few complex networks. However, we show here that all complex networks can be viewed as bipartite structures sharing some important statistics, like degree distributions. The basic properties of complex networks can be viewed as consequences of this underlying bipartite structure. This leads us to propose the first simple and intuitive model for complex networks which captures the main properties met in practice.
Generalized pattern searches with derivative information
Authors: Mark A. Abramson, Charles Audet, J. E. Dennis,  Jr.
Venue: Mathematical Programming: Series A and B (2004)

A common question asked by users of direct search algorithms is how to use derivative information at iterates where it is available. This paper addresses that question with respect to Generalized Pattern Search (GPS) methods for unconstrained and linearly constrained optimization. Specifically, this paper concentrates on the GPS pollstep. Polling is done to certify the need to refine the current mesh, and it requires O(n) function evaluations in the worst case. We show that the use of derivative information significantly reduces the maximum number of function evaluations necessary for pollsteps, even to a worst case of a single function evaluation with certain algorithmic choices given here. Furthermore, we show that rather rough approximations to the gradient are sufficient to reduce the pollstep to a single function evaluation. We prove that using these less expensive pollsteps does not weaken the known convergence properties of the method, all of which depend only on the pollstep.
Rapid prototyping of interactive information systems
Authors: Anthony I. Wasserman, David T. Shewmake
Venue: Proceedings of the workshop on Rapid prototyping (1982)

The User Software Engineering methodology is a set of techniques, supported by automated tools (Unified Support Environment), to support the specification and implementation of interactive information systems. The methodology advocates construction of a prototype of the user/program dialogue as an aid to the analysis process, and suggests the construction of a functional prototype as an aid to the specification. The USE tool RAPID (RApid Prototypes of Interactive Dialogues) supports the construction of prototypes and partial systems. RAPID builds upon two automated tools, the Transition Diagram Interpreter (TDI) and a relational database management system (Troll). This paper describes the role of prototypes in the USE methodology and the function and use of RAPID, TDI, and Troll.