ppxscal/embedding_network huggingface dataset:
Spatial Clusters of Cancers in Illinois 1986&ndash;2000
Authors: Fahui Wang
Venue: Journal of Medical Systems (2004)

Elevated cancer rates in some areas may arise simply by chance. The pattern generally warrants a study only when it is statistically significant. This research uses a recently developed spatial statistic, implemented in a Geographic Information System (GIS) environment, to detect spatial clusters of diagnostically specific cancers in Illinois. On the basis of the cancer incidence data (the 1986&ndash;1990 and 1996-2000 data sets) from the Illinois Cancer Registry, the study examines different clustering patterns of four leading types of cancer in Illinois, namely breast, lung, colorectal, and prostate cancers. The first part of the study uses the data at the county level, and the second part uses the data in zip code areas. The analysis using the zip code area data directly may be problematic since the rate estimates for rare events like cancer in small populations are susceptible to data errors. The spatial order method is used to group zip code areas so that the new geographic areas have sufficiently large base populations for estimates of reliable cancer rates. Results from the spatial cluster analysis may be valuable for other researchers to design follow-up case-control and retrospective cohort studies.
Alias analysis in Java with reference-set representation for high-performance computing
Authors: Jongwook Woo, Jean-Luc Gaudiot, Andrew L. Wendelborn
Venue: International Journal of Parallel Programming (2004)

In this paper, a flow-sensitive, context-insensitive alias analysis in Java is proposed. It is more efficient and precise than previous analyses for C++, and it does not negatively affect the safety of aliased references. To this end, we first present a reference-set alias representation. Second, data-flow equations based on the propagation rules for the reference-set alias representation are introduced. The equations compute alias information more efficiently and precisely than previous analyses for C++. Third, for the constant time complexity of the type determination, a type table is introduced with reference variables and all possible types for each reference variable. Fourth, an alias analysis algorithm is proposed, which uses a popular iterative loop method for an alias analysis. Finally, running times of benchmark codes are compared for reference-set and existing object-pair representation.
An Intelligent Digital Library System for Biologists
Authors: Jeffrey Stone, Xindong Wu, Marc Greenblatt
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

To aid researchers in obtaining, organizing and managing biological data, we have developed a sophisticated digital library system that utilizes advanced data mining techniques. Our digital library system is centralized with Web links to publicly accessible data repositories. Our digital library is based on a framework used for conventional libraries and an object-oriented paradigm, and will provide personalized user-centered services based on the userýs areas of interests and preferences. To make personalized service possible, a "user profile" that represents the preferences of an individual user is constructed based upon the userýs past activities, goals indicated by the user, and options. Utilizing these user profiles, our system will make relevant information available to the user in an appropriate form, amount, and level of detail with minimal user effort.
Transaction support for indexed summary views
Authors: Goetz Graefe, Michael Zwilling
Venue: Proceedings of the 2004 ACM SIGMOD international conference on Management of data (2004)

Materialized views have become a standard technique for performance improvement in decision support databases and for a variety of monitoring purposes. In order to avoid inconsistencies and thus unpredictable query results, materialized views and their indexes should be maintained immediately within user transaction just like indexes on ordinary tables. Unfortunately, the smaller a materialized view is, the higher the concurrency contention between queries and updates as well as among concurrent updates. Therefore, we have investigated methods that reduce contention without forcing users to sacrifice serializability and thus predictable application semantics. These methods extend escrow locking with multi-granularity (hierarchical) locking, snapshot transactions, multi-version concurrency control, key range locking, and system transactions, i.e., multiple proven database implementation techniques. The complete design eliminates all contention between pure read transactions and pure update transactions as well as contention among pure update transactions as well as contention among pure update transactions; it enables maximal concurrency of mixed read-write transactions with other transactions; it supports bulk operations such as data import and online index creation; and it provides recovery for transaction, media, and system failures.
Reusable anonymous return channels
Authors: Philippe Golle, Markus Jakobsson
Venue: Proceedings of the 2003 ACM workshop on Privacy in the electronic society (2003)

Mix networks are used to deliver messages anonymously to recipients, but do not straightforwardly allow the recipient of an anonymous message to reply to its sender. Yet the ability to reply one or more times, and to further reply to replies, is essential to a complete anonymous conversation. We propose a protocol that allows a sender of anonymous messages to establish a reusable anonymous return channel. This channel enables any recipient of one of these anonymous messages to send back one or more anonymous replies. Recipients who reply to different messages can not test whether two return channels are the same, and there-fore can not learn whether they are replying to the same person. Yet the fact that multiple recipients may send multiple replies through the same return channel helps defend against the counting attacks that defeated earlier proposals for return channels. In these attacks, an adversary traces the origin of a message by sending a specific number of replies and observing who collects the same number of messages. Our scheme resists these attacks because the replies sent by an attacker are mixed with other replies submitted by other recipients through the same return channel. Moreover, our protocol straightforwardly allows for replies to replies, etc. Our protocol is based upon a re-encryption mix network, and requires four times the amount of computation and communication of a basic mixnet.
Consistency-Preserving Neighbor Table Optimization for P2P Networks
Authors: Huaiyu Liu, Simon S. Lam
Venue: Proceedings of the Parallel and Distributed Systems, Tenth International Conference (2004)

Constructing and maintaining consistent neighbor tablesand optimizing neighbor tables to improve routing localityare two important issues in p2p networks. In this paper, weaddress the problem of preserving consistency while optimizingneighbor tables for p2p networks with node dynamics.We present a general strategy: identify a consistent subnetas large as possible and only replace a neighbor with acloser one if both of them belong to the subnet. We realizethe general strategy in the context of hypercube routing.First, we present a join protocol that enables the identificationof a large consistent subnet with very low cost whennew nodes join. Next, we define an optimization rule to constrainneighbor replacements to preserve consistency, andpresent a set of optimization heuristics to optimize neighbortables with low cost. The join protocol is then integratedwith a failure recovery protocol. By evaluating the protocolsthrough simulation experiments, we found our protocols andoptimization heuristics to be effective, efficient, and scalableto a large number of network nodes.
An experimental analysis of GAME: a generic automated marking environment
Authors: Michael Blumenstein, Steven Green, Ann Nguyen, Vallipuram Muthukkumarasamy
Venue: Proceedings of the 9th annual SIGCSE conference on Innovation and technology in computer science education (2004)

This paper describes the Generic Automated Marking Environment (GAME) and provides a detailed analysis of its performance in assessing student programming projects and exercises. GAME has been designed to automatically assess programming assignments written in a variety of languages based on the "structure" of the source code and the correctness of the program's output. Currently, the system is able to mark programs written in Java, C++ and the C language. To use the system, instructors are required to provide a simple "marking schema" for any given assessment item, which includes pertinent information such as the location of files and the model solution. In this research, GAME has been tested on a number of student programming exercises and assignments. The results obtained, have been analysed and compared against a human marker providing encouraging results.
Multilingual debugging with the SWAT high-level debugger
Authors: James R. Cardell
Venue: ACM SIGPLAN Notices (1983)

The SWAT (TM) debugger, Data General Corporation's Source Language Debugger, is an interactive, high-level, symbolic debugging tool. It offers its users a full complement of standard high-level debugging features with a simple command format modeled after that of Data General's AOS and AOS/VS operating system Command Line Interpreter. Multilingual capability was a primary design goal and this has resulted in the benefits of both wide user acceptance and product extensibility. This paper presents a summary of SWAT functionality and relates some of the experience of adding support for Data General Information Systems Division's recently announced AOS/VS Pascal and AOS/VS C languages.
On Benchmarking the Dependability of Automotive Engine Control Applications
Authors: Juan-Carlos Ruiz, Pedro Yuste, Pedro Gil, Lenin Lemus
Venue: Proceedings of the 2004 International Conference on Dependable Systems and Networks (2004)

The pervasive use of ECUs (Electronic ControlUnits) in automotive systems motivates the interest ofthe community in methodologies for quantifying theirdependability in a reproducible and cost-effective way.Although the core of modern vehicle engines ismanaged by the control software embedded in engineECUs, no practical approach has been proposed so farto characterise the impact of faults on the behaviour ofthis software. This paper proposes a dependabilitybenchmark for engine control applications. Theessential features of such type of applications are firstcaptured in a general model, which is then exploited inorder to specify a standard procedure to assessdependability measures. These measures are definedtaking into account the expectations of industrialspurchasing engine ECUs with integration purposes.The benchmark also considers the current set oftechnological limitations that the manufacturing ofmodern engine ECUs imposes to the experimentalprocess. The approach is exemplified on two enginecontrol applications.
Social presence and group attraction: exploring the effects of awareness systems in the home
Authors: C. A. G. J. Huijnen, W. A. IJsselsteijn, P. Markopoulos, B. de Ruyter
Venue: Cognition, Technology and Work (2004)

This paper describes an experimental assessment of affective user benefits that may result from adding peripheral awareness information while remote friends share an activity in a home environment. The experiment has shown that providing awareness information increases the social presence and the group attraction felt by individuals towards remote partners.
CORDS: automatic discovery of correlations and soft functional dependencies
Authors: Ihab F. Ilyas, Volker Markl, Peter Haas, Paul Brown, Ashraf Aboulnaga
Venue: Proceedings of the 2004 ACM SIGMOD international conference on Management of data (2004)

The rich dependency structure found in the columns of real-world relational databases can be exploited to great advantage, but can also cause query optimizers---which usually assume that columns are statistically independent---to underestimate the selectivities of conjunctive predicates by orders of magnitude. We introduce CORDS, an efficient and scalable tool for automatic discovery of correlations and soft functional dependencies between columns. CORDS searches for column pairs that might have interesting and useful dependency relations by systematically enumerating candidate pairs and simultaneously pruning unpromising candidates using a flexible set of heuristics. A robust chi-squared analysis is applied to a sample of column values in order to identify correlations, and the number of distinct values in the sampled columns is analyzed to detect soft functional dependencies. CORDS can be used as a data mining tool, producing dependency graphs that are of intrinsic interest. We focus primarily on the use of CORDS in query optimization. Specifically, CORDS recommends groups of columns on which to maintain certain simple joint statistics. These "column-group" statistics are then used by the optimizer to avoid naive selectivity estimates based on inappropriate independence assumptions. This approach, because of its simplicity and judicious use of sampling, is relatively easy to implement in existing commercial systems, has very low overhead, and scales well to the large numbers of columns and large table sizes found in real-world databases. Experiments with a prototype implementation show that the use of CORDS in query optimization can speed up query execution times by an order of magnitude. CORDS can be used in tandem with query feedback systems such as the LEO learning optimizer, leveraging the infrastructure of such systems to correct bad selectivity estimates and ameliorating the poor performance of feedback systems during slow learning phases.
Introduction: Geographic Information Systems in Public Health and Medicine
Authors: Ross M. Mullner, Kyusuk Chung, Kevin G. Croke, Edward K. Mensah
Venue: Journal of Medical Systems (2004)

Geographic information systems (GIS) are increasingly being used in public health and medicine. Advances in computer technology, the encouragement of its use by the federal government, and the wide availability of academic and commercial courses on GIS are responsible for its growth. Some view GIS as only a tool for spatial research and policy analysis, while others believe it is part of a larger emerging new science including geography, cartography, geodesy, and remote sensing. The specific advantages and problems of GIS are discussed. The greatest potential of GIS is its ability to clearly show the results of complex analyses through maps. Problems in using GIS include its costs, the need to adequately train staff, the use of appropriate spatial units, and the risk it poses to violating patient confidentiality. Lastly, the fourteen articles in this special issue devoted to GIS are introduced and briefly discussed.
A Java Program to Create Simulated Microarray Images
Authors: Bill Martin, Robert M. Horton
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

We have developed a microarray image generation program to create customized sets of images representing "virtual microarray experiments" to teach microarray technology in undergraduate biology courses.
Sharing Metadata - Problems and Potential Solutions
Authors: Simone Stumpf, Janet McDonnell
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

This paper investigates the level of agreement in applying metadata and highlights results from the analysis of agreement between and within user communities. Problems in applying and sharing metadata are diagnosed by examining the reliability of metadata application by domain experts, especially when contrasted to researchers. Three main problems are discussed: issues pertaining to data, the metadata and the application process. Strategies are proposed to resolve these issues. Our research highlights the need for diagnostic tools that identify the sources of poor agreement and therefore guide steps to improve metadata application and sharing.
Subquadrangles of order s of generalized quadrangles of order (s, s2), Part II
Authors: M. R. Brown, J. A. Thas
Venue: Journal of Combinatorial Theory Series A (2004)

In this paper, subquadrangles of order s of generalized quadrangles (GQ) of order (s, s2), with s odd, are investigated. The even case was considered in Part I. In the case where O is an egg good at an element π and the translation generalized quadrangle Y = T(O) has order (s, s2), with s odd, we prove that if Y' is a subquadrangle of order s of Y, then Y' is the classical GQ Q(4, s) and either Y is the classical GQ Q(5, s) or Y' is one of the s3 + s2 subquadrangles of order s containing the line π of Y. Further, some characterizations of particular eggs are obtained. Finally, it is shown that if Y is a flock GQ of order (s2, s), s odd, with base point (∞) and Y' is a subquadrangle of order s of Y containing the point (∞), then Y is a Kantor semifield flock GQ, Y' is isomorphic to the classical GQ W(s) and either Y is isomorphic to the classical GQ H(3, s2) or Y' is one of the s3 + s2 subquadrangles of order s containing the point (∞). As an application there is a characterization of the Kantor semifield flock GQ in terms of the net defined by the regular point (∞) of the flock GQ.
Symbolic summation with single-nested sum extensions
Authors: Carsten Schneider
Venue: Proceedings of the 2004 international symposium on Symbolic and algebraic computation (2004)

We present a streamlined and refined version of Karr's summation algorithm. Karr's original approach constructively decides the telescoping problem in ΠΣ-fields, a very general class of difference fields that can describe rational terms of arbitrarily nested indefinite sums and products. More generally, our new algorithm can decide constructively if there exists a so called single-nested ΠΣ-extension over a given ΠΣ-field in which the telescoping problem for f can be solved in terms that are not more nested than f itself. This allows to eliminate an indefinite sum over f by expressing it in terms of additional sums that are not more nested than f. Moreover, our refined algorithm contributes to definite summation: it can decide constructively if the creative telescoping problem for a fixed order can be solved in single-nested Σ*-extensions that are less nested than the definite sum itself.
Asymmetric k-center is log* n-hard to approximate
Authors: Julia Chuzhoy, Sudipto Guha, Eran Halperi, Sanjeev Khanna, Guy Kortsarz, Joseph (Seffi) Nao
Venue: Proceedings of the thirty-sixth annual ACM symposium on Theory of computing (2004)

In the Asymmetric k-Center problem, the input is an integer k and a complete digraph over n points together with a distance function obeying the directed triangle inequality. The goal is to choose a set of k points to serve as centers and to assign all the points to the centers, so that the maximum distance of any point to its center is as small as possible. We show that the Asymmetric k-Center problem is hard to approximate up to a factor of log* n - Θ(1) unless NP ⊆ DTIME(nlog log n). Since an O(log* n)-approximation algorithm is known for this problem, this essentially resolves the approximability of this problem. This is the first natural problem whose approximability threshold does not polynomially relate to the known approximation classes. We also resolve the approximability threshold of the metric k-Center problem with costs.
The impact of BGP dynamics on intra-domain traffic
Authors: Sharad Agarwal, Chen-Nee Chuah, Supratik Bhattacharyya, Christophe Diot
Venue: Proceedings of the joint international conference on Measurement and modeling of computer systems (2004)

Recent work in network traffic matrix estimation has focused on generating router-to-router or PoP-to-PoP (Point-of-Presence) traffic matrices within an ISP backbone from network link load data. However, these estimation techniques have not considered the impact of inter-domain routing changes in BGP (Border Gateway Protocol). BGP routing changes have the potential to introduce significant errors in estimated traffic matrices by causing traffic shifts between egress routers or PoPs within a single backbone network. We present a methodology to correlate BGP routing table changes with packet traces in order to analyze how BGP dynamics affect traffic fan-out within a large "tier-1" network. Despite an average of 133 BGP routing updates per minute, we find that BGP routing changes do not cause more than 0.03% of ingress traffic to shift between egress PoPs. This limited impact is mostly due to the relative stability of network prefixes that receive the majority of traffic -- 0.05% of BGP routing table changes affect intra-domain routes for prefixes that carry 80% of the traffic. Thus our work validates an important assumption underlying existing techniques for traffic matrix estimation in large IP networks.
A shock model for the maintenance problem of a repairable system
Authors: Yeh Lam, Yuan Lin Zhang
Venue: Computers and Operations Research (2004)

In this paper, a shock model for the maintenance problem of a repairable system is studied. Assume that shocks will arrive according to a Poisson process. If the interarrival time of two successive shocks is less than a threshold, then the system will fail. For a deteriorating system, we assume that the successive threshold values are geometrically nondecreasing after repair, and the consecutive repair times after failure form an increasing geometric process. For an improving system, we assume that the successive threshold values are geometrically decreasing after repair, and the consecutive repair times after failure form a decreasing geometric process. A replacement policy N is adopted by which we shall replace the system by an identical new one at the time following the Nth failure. Then for each of the deteriorating system and improving system, an optimal policy N for minimizing the long-run average cost per unit time is determined explicitly.
Large-Scale Testing of Chemical Shift Prediction Algorithms and Improved Machine Learning-Based Approaches to Shift Prediction
Authors: K. Arun, Christopher James Langmead
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

The resonant frequencies, or chemical shifts, of nuclear magnetic resonance (NMR) active nuclei in proteins are determined by covalent and through-space interactions and, more generally, the electronic environment surrounding each nucleus. However, the precise nature of the correlation between protein three-dimensional (3D) structure and chemical shift remains largely unsolved. Thus, chemical shift prediction is a non-trivial task. This study tests the accuracy of three existing structure-based chemical shift prediction algorithms (SHIFTS, SHIFTX, PROSHIFT) against REFDB, a large database of experimentally determined, and manually re-referenced ¹H, ¹³C, and ¹¿N chemical shifts.We report that the accuracy of backbone chemical shift predictions for each program is lower than that originally reported. This suggests these programs over-fit the data used in their construction. We then compare two novel methods for chemical shift prediction based on support vector machines (SVM) and bagging respectively. Each method was trained on REFDB using predictions made by SHIFTS, SHIFTX, and PROSHIFT as features. In cross-validated experiments, bagging is shown to be superior to SVMs, while both methods are substantially better than SHIFTS, SHIFTX, and PROSHIFT. Our results suggest that meta-methods for chemical shift prediction yield increased accuracy for chemical shift prediction.