ppxscal/embedding_network huggingface dataset:
Preface: life sciences and cyberinfrastructure: dual and interacting revolutions that will drive future science
Authors: Peter W. Arzberger, Abbas Farazdel, Akihiko Konagaya, Larry Ang, Shinji Shimojo, Rick L. Stevens
Venue: New Generation Computing (2004)

Over the past quarter century, two revolutions, one in biomedicine, the other in computing and information technology leading to cyberinfrastructure, have made the largest advances and the most significant impacts on science, technology, and society. The interface between these areas is rich with opportunity for major advances. The Life Sciences Grid Research Group (LSG-RG) of the Global Grid Forum recognized the opportunities and needs to bring the communities together to ensure the cyberinfrastructure will be constructed for the benefit of science. This article gives an overview of the area, the activities of the LSG-RG, and the minisymposium organized by LSG-RG, and introduces the papers in this Special Issue of New Generation Computing.
Debugging methodology: session summary
Authors: Wayne C. Gramlich
Venue: ACM SIGPLAN Notices (1983)

Two sessions were held on the general topic of debugging methodology. Both were moderated by R. Stockton Gaines. During the first session five speakers presented short talks on their workshop submissions. Each talk was followed by a brief question and answer period. The format of the second session was that of an open discussion. The talks presented in the first session have been briefly summarized. The remaining notes of these two sessions have been arranged topically rather than chronologically.
Optimal algorithms for semi-online preemptive scheduling problems on two uniform machines
Authors: Yong He, Yiwei Jiang
Venue: Acta Informatica (2004)

This paper investigates two preemptive semi-online scheduling problems to minimize makespan on two uniform machines. In the first semi-online problem, we know in advance that all jobs have their processing times in between p and rp $(p > 0,r\geq 1)$. In the second semi-online problem, we know the size of the largest job in advance. We design an optimal semi-online algorithm which is optimal for every combination of machine speed ratio $s\geq 1$ and job processing time ratio $r\geq 1$ for the first problem, and an optimal semi-online algorithm for every machine speed ratio $s\geq 1$ for the second problem.
A Study of Forest Fire Danger Prediction System in Japan
Authors: Kohyu Satoh, Song Weiguo, K. T. Yang
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

All over the world, forest fires cause severe damages to valuable natural environment and loss of human lives. The fire statistics showed that the number of Japanese forest fires remains high at 3,000 per year, most fires are caused by human activities and occur in the populated area, although the forest fires are of course mainly affected by weather conditions.Based on the analyzed fundamentals of the weather conditions together with the city related data in relation to the fire occurence, we have developed a system to predict forest fire danger.The fire danger simulations were made, using not only previous weather conditions, but also population density data and others.The comparison between the map of predicted fire danger and the locations of real fire occurrence indicated almost reasonable agreement.In addition, CFD simulations were conducted to examine the fire progression behavior and the suppression.
Scalar-field-guided adaptive shape deformation and animation
Authors: Jing Hua, Hong Qin
Venue: The Visual Computer: International Journal of Computer Graphics (2004)

In this paper, we propose a novel scalar-field-guided adaptive shape deformation (SFD) technique founded on PDE-based flow constraints and scalar fields of implicit functions. Scalar fields are used as embedding spaces. Upon deformation of the scalar field, a corresponding displacement/velocity field will be generated accordingly, which results in a shape deformation of the embedded object. In our system, the scalar field creation, sketching, and manipulation are both natural and intuitive. The embedded model is further enhanced with self-optimization capability. During the deformation we can also enforce various constraints on embedded models. In addition, this technique can be used to ease the animation design. Our experiments demonstrate that the new SFD technique is powerful, efficient, versatile, and intuitive for shape modeling and animation.
Introductory paper
Authors: S. Purushothaman Iyer, David Hislop, Paul L. Jones, Jaime Lee, Frederick Pearce, Stephen Van Albert
Venue: International Journal on Software Tools for Technology Transfer (STTT) (2004)

The computer-assisted resuscitation algorithm (CARA) is the software component of an automatic infusion pump system being designed by US Army&#x2019;s Walter Reed Institute of Research (WRAIR) to be used in the battlefields of tomorrow. Such medical devices are safety critical, and their use needs to be approved by the US Food and Drug Administration (FDA) &#x2013; a process on which formal methods can have a great impact. In this special section, six papers on the analysis of CARA&#x2019;s requirements are presented. In the rest of this introduction, we present the framework and summary of results from those papers.
Data Extraction from Web Data Sources
Authors: Jerome Robinson
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

An explanation is given of the basic data structures used in a new page analysis technique to create wrappers (data extractors) for the result pages produced by web sites in response to user qeries via web page forms. The key structure called a tpGrid is a representation of the web page, which is easier to analyse than the raw html code. The analysis looks for repetition patterns of sets of tagSets, which are defined in the paper.
A m-fold-decimation-based technique for model validation using a single system output data set
Authors: Dimosthenis Anagnostopoulos, Vassilis Dalakas, Mara Nikolaidou
Venue: Mathematics and Computers in Simulation (2004)

Using simulation to support making decisions imposes that models are thoroughly validated. We discuss widely adopted techniques for testing the validity of simulation results against real observations, as various techniques may be employed depending on the statistical features and the number of the available system/model data sets. Confidence-interval-based comparison provides certain advantages, but cannot be employed when a single system output data set is available. We propose an effective validation technique, performing confidence-interval-based comparison using a single system data set and multiple model data sets. The system data set is considered as a discrete signal and m-fold decimation is used, according to signal processing theory, fulfilling the essential requirements imposed to retain the statistical features of the original data set. We have evaluated both the effectiveness and the applicability of this technique, and thus have experimented with various data sets (both test and real-world). Results and conclusions are discussed to indicate the potential of the technique.
Bose-Mesner algebras attached to invertible Jones pairs
Authors: Ada Chan, Chris Godsil
Venue: Journal of Combinatorial Theory Series A (2004)

In 1989, Vaughan Jones introduced spin models and showed that they could be used to form link invariants in two different ways--by constructing representations of the braid group, or by constructing partition functions. These spin models were subsequently generalized to the so-called four-weight spin models by Bannai and Bannai; these could be used to construct partition functions, but did not lead to braid group representations in any obvious way. Jaeger showed that spin models were intimately related to certain association schemes. Yamada gave a construction of a symmetric spin model on 4n vertices from each four-weight spin model on n vertices.In this paper, we build on recent work with Munemasa to give a different proof to Yamada's result, and we analyze the structure of the association scheme attached to this spin model.
Adaptive Fuzzy Approach to Estimate Supplier's Competitiveness in Open E-Bidding
Authors: Trung T. Pham, Simone K. Fuchter, Guanrong Chen
Venue: Proceedings of the E-Commerce Technology for Dynamic E-Business, IEEE International Conference (2004)

This paper presents an adaptive fuzzy approach to estimate the competition of the suppliers in an open electronic bidding. The competition is formulated as the supply curve relating pricing against requested quantity. A set of supply curves, each from a competitor, is formulated into fuzzy expression to allow flexibility for a supplier to prepare an optimal pricing policy that deals with the fact that other competitors are also adapting at some unknown rate. The pricing policy is formulated into a mathematical expression that is easily adjusted as new information on the competitors becomes available. A revision of pricing policy for a supplier to compete on the pricing basis while maintaining an optimal profit margin is derived as an application. Computer simulations are provided to demonstrate the workability of this approach.
Using GIS to Monitor Emergency Room Use in a Large Urban Hospital in Chicago
Authors: Edward Rafalski, Leslie Zun
Venue: Journal of Medical Systems (2004)

Geographic Information System (GIS) technology is being used at Mount Sinai Hospital in Chicago to better understand utilization patterns by the city's fire department and the subsequent effects on the rates of trauma cases who leave without being treated (LWOT) and throughput times. In this process, opportunities for process improvement in data capture, categorization, and analysis are being realized. Further, to more intelligently apply resources, a surge protocol has been developed calling for deploying physician assistants, which is having a positive effect on throughput times and LWOT rates. Finally, opportunities for GIS application in urban mass casualty planning are offered for consideration.
A basic characteristic of twin primes and its generalization
Authors: Sebastián Martín Ruiz, Azmy Ariff
Venue: Smarandache Notions Journal (2004)

The sum of powers of positive divisors of an integer, expressed in terms of the floor function, provides the basis for another characterization of twin primes in particular, and of prime k-tuples generally. This elementary characterization is deployed in a software test for prime k-tuples using Mathematica.
Small Complete Arcs in Projective Planes
Authors: H. Kim, H. Vu
Venue: Combinatorica (2003)

In the late 1950&#x2019;s, B. Segre introduced the fundamental notion of arcs and complete arcs [48,49]. An arc in a &#xfb01;nite projective plane is a set of points with no three on a line and it is complete if cannot be extended without violating this property. Given a projective plane $${\user1{P}}$$, determining $$n{\left( {\user1{P}} \right)}$$, the size of its smallest complete arc, has been a major open question in finite geometry for several decades. Assume that $${\user1{P}}$$ has order q, it was shown by Lunelli and Sce [41], more than 40 years ago, that $${\left( {\user1{P}} \right)} \geqslant {\sqrt {2q} }$$. Apart from this bound, practically nothing was known about $$n{\left( {\user1{P}} \right)}$$, except for the case $${\user1{P}}$$ is the Galois plane. For this case, the best upper bound, prior to this paper, was O(q3/4) obtained by Sz&#x0151;nyi using the properties of the Galois field GF(q).In this paper, we prove that $$n{\left( {\user1{P}} \right)} \leqslant {\sqrt q }{\kern 1pt} \log^{c} q$$ for any projective plane $${\user1{P}}$$ of order q, where c is a universal constant. Together with Lunelli-Sce&#x2019;s lower bound, our result determines $$n{\left( {\user1{P}} \right)}$$ up to a polylogarithmic factor. Our proof uses a probabilistic method known as the dynamic random construction or R&#x00f6;dl&#x2019;s nibble. The proof also gives a quick randomized algorithm which produces a small complete arc with high probability.The key ingredient of our proof is a new concentration result, which applies for non-Lipschitz functions and is of independent interest.
East of Neuchâtel: A Universal Model for the Representation of Statistical Taxonomy Systems
Authors: Michaela Denk, Karl A. Froeschl
Venue: Proceedings of the 16th International Conference on Scientific and Statistical Database Management (2004)

The Neuchâtel data model for statistical classificationsystems can be regarded as a standard for classificationmanagement in official statistics. However, despite itsunquestioned benefits, the model remains rather informal.For computational use, the semantics of modelstructures have to be specified more accurately. Focussingon formal underpinnings of the model required tosupport automated processing of classification structures,this paper proposes an alternative approach. The Neuchâtelconcepts are simplified and generalized, leading toa universal model of hierarchical-taxonomic classificationstructures featuring precise semantics and supportingtypical algebraic transformations related to classificationsystems.
The 18th British HCI Group annual conference
Authors: Marisa Campbell
Venue: interactions (2004)

The 18th British HCI Group Annual Conference<br>September 6-10, 2004<br>Leeds Metropolitan University, UK
Scaki - The Scaffolding Wiki
Authors: Alejandro Fernandez
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

Support for documenting and managing work processes is valuable for any distributed software development team. Existing tools for process documentation and enactment are complex and expensive. Scaffolding is a simple approach to describe practices. WikiWikiWeb is a simple and inexpensive collaborative publication tool. This paper proposes extensions to exploit the simplicity of WikiWikiWeb to create and tailor scaffoldings of work processes that can be enacted.
Specifying and analyzing early requirements in Tropos
Authors: Ariel Fuxman, Lin Liu, John Mylopoulos, Marco Pistore, Marco Roveri, Paolo Traverso
Venue: Requirements Engineering (2004)

We present a framework that supports the formal verification of early requirements specifications. The framework is based on Formal Tropos, a specification language that adopts primitive concepts for modeling early requirements (such as actor, goal, and strategic dependency), along with a rich temporal specification language. We show how existing formal analysis techniques, and in particular model checking, can be adapted for the automatic verification of Formal Tropos specifications. These techniques have been implemented in a tool, called the T-Tool, that maps Formal Tropos specifications into a language that can be handled by the NuSMV model checker. Finally, we evaluate our methodology on a course-exam management case study. Our experiments show that formal analysis reveals gaps and inconsistencies in early requirements specifications that are by no means trivial to discover without the help of formal analysis tools.
Intra-individual information behaviour in daily life
Authors: Heidi Julien, David Michels
Venue: Information Processing and Management: an International Journal (2004)

This study addresses the lack of attention in the literature paid to detailed analysis of individuals' information behaviour in daily life contexts. In particular, the study characterizes one individual's information behaviour across different daily life situations, to seek behavioural patterns that might be associated with various aspects of each information seeking situation. Data was collected through participant diaries, and subsequent oral interviews. This study reports on source selection, and influence of various aspects of the situations described. These aspects were identified from analysis of the interview transcripts, and include time constraints and pressures, motivation for the information need, context of the information need, type of initiating event, location of information seeking activities, intended application of the information found, and source type.
Time and space optimization for processing groups of multi-dimensional scientific queries
Authors: Suresh Aryangat, Henrique Andrade, Alan Sussman
Venue: Proceedings of the 18th annual international conference on Supercomputing (2004)

Data analysis applications in areas as diverse as remote sensing and telepathology require operating on and processing very large datasets. For such applications to execute efficiently, careful attention must be paid to the storage, retrieval, and manipulation of the datasets. This paper addresses the optimizations performed by a high performance database system that processes groups of data analysis requests for these applications, which we call queries. The system performs end-to-end processing of the requests, formulated as PostgreSQL declarative queries. The queries are converted into imperative descriptions, multiple imperative descriptions are merged into a single execution plan, the plan is optimized to decrease execution time via common compiler optimization techniques, and, finally, the plan is optimized to decrease memory consumption. The last two steps are experimentally shown to effectively reduc the amount of time required while conserving memory space as a group of queries is processed by the database.
Processes of consciousness
Authors: Flavian Vasile
Venue: Smarandache Notions Journal (2004)

This paper presents consciousness as the sum of describable processes, without limiting it only to verbal understanding. Consciousness is presented as a buffer space of the unconscious, accessed by any mental decision-taking processes. Consciousness is composed of sequential outputs of non-conscious processes that form, as frames in a picture, the impression of our ego continuity. The functional consequences on real-life information fusion problems are then further discussed.
TicToc
Venue: ACM SIGGRAPH 2003 video review on Animation theater program: part 1 - Volume 145 (2003)

Two naughty girls have a night out. They dance and have to cope with strange guys, and a handsome shark. Tic falls in love. Copyright held by creator.
Parallel Implementation of WAP-Tree Mining Algorithm
Authors: Ming Wu, Moon Jung Chung, H. D. K. Moonesinghe
Venue: Proceedings of the Parallel and Distributed Systems, Tenth International Conference (2004)

In this paper, we present parallel algorithms forweb log mining and the performance prediction model.The algorithm, based on WAP-tree, scans dataset onlytwice and avoids candidate generation process. Weparallelized mining part of WAP tree. To balance theworkload among processors, we developed a taskscheduling strategy. A performance model of parallelweb mining algorithm is also developed to predict theperformance of parallel implementation. This modelshows that we can get linear speedup for a smallnumber of processors, and a slow down of speedup asthe number of processors increases. Using theperformance model, we can also estimate themaximum speed up. We implemented the algorithm ona Pittsburg Super Computer Center Lemieux using upto 48 processors. Our benchmark results showed thatthe performance model correctly predicts theperformance of the parallel implementation. We haveachieved a good speedup as the size of the dataset is increased.
On the simple numbers and the mean value properties
Authors: Liu Hongyan, Zhang Wenpeng
Venue: Smarandache Notions Journal (2004)

A number n is called simple number if the product of its proper divisors is less than or equal to n. In this paper, we study the mean value properties of the sequence of the simple numbers, and give several interesting asymptotic formulae.
Automatic Prediction of Functional Site Regions in Low-Resolution Protein Structures
Authors: Jaspreet Singh Sodhi, Liam J. McGuffin, Kevin Bryson, Jonathan J. Ward, Lorenz Wernisch, David T. Jones
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of generating at least low resolution structural models of target proteins. Accurate detection and classification of functional sites within both solved and modelled protein structures therefore represents an important challenge. We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. The method is designed primarily to require only backbone residue positions without the need for specific side-chain atoms to be present. In order to highlight effective site detection in low resolution structural models FuncSite was used to screen model proteins generated using mGenTHREADER on a set of newly released structures. We found effective metal site detection even for moderate quality protein models illustrating the robustness of the method.
Test input generation with java PathFinder
Authors: Willem Visser, Corina S. Pǎsǎreanu, Sarfraz Khurshid
Venue: Proceedings of the 2004 ACM SIGSOFT international symposium on Software testing and analysis (2004)

We show how model checking and symbolic execution can be used to generate test inputs to achieve structural coverage of code that manipulates complex data structures. We focus on obtaining branch-coverage during unit testing of some of the core methods of the red-black tree implementation in the Java TreeMap library, using the Java PathFinder model checker. Three different test generation techniques will be introduced and compared, namely, straight model checking of the code, model checking used in a black-box fashion to generate all inputs up to a fixed size, and lastly, model checking used during white-box test input generation. The main contribution of this work is to show how efficient white-box test input generation can be done for code manipulating complex data, taking into account complex method preconditions.
COFI approach for mining frequent itemsets revisited
Authors: Mohammad El-Hajj, Osmar R. Zaïane
Venue: Proceedings of the 9th ACM SIGMOD workshop on Research issues in data mining and knowledge discovery (2004)

The COFI approach for mining frequent itemsets, introduced recently, is an efficient algorithm that was demonstrated to outperform state-of-the-art algorithms on synthetic data. For instance, COFI is not only one order of magnitude faster and requires significantly less memory than the popular FP-Growth, it is also very effective with extremely large datasets, better than any reported algorithm. However, COFI has a significant drawback when mining dense transactional databases which is the case with some real datasets. The algorithm performs poorly in these cases because it ends up generating too many local candidates that are doomed to be infrequent. In this paper, we present a new algorithm COFI* for mining frequent itemsets. This novel algorithm uses the same data structure COFI-tree as its predecessor, but partitions the patterns in such a way to avoid the drawbacks of COFI. Moreover, its approach uses a pseudo-Oracle to pinpoint the maximal itemsets, from which all frequent itemsets are derived and counted, avoiding the generation of candidates fated infrequent. Our implementation tested on real and synthetic data shows that COFI* algorithm outperforms state-of-the-art algorithms, among them COFI itself.
A simple implementation of a queue with a circularly linked list
Authors: David B. Sher
Venue: Proceedings of the 9th annual SIGCSE conference on Innovation and technology in computer science education (2004)

This Tips and Techniques sections will demonstrate that teaching about queues implemented as circularly linked lists becomes easy when an extra link is used.