ppxscal/embedding_network huggingface dataset:
Proceedings of the 2004 international symposium on Symbolic and algebraic computation
Venue: International Conference on Symbolic and Algebraic Computation (2004)

ISSAC 2004 is a continuation of a well-established series of the international conferences for the presentation of the latest advances in the field of Symbolic and Algebraic Computation. The first meeting of the series (1966) was held in Washington, and sponsored by Association for Computing Machinery (ACM). Since then, the abbreviated name of the meeting has evolved from SYMSAM, SYMSAC, EUROSAM, EUROCAL to finally settle on the present name ISSAC. This 29th meeting will be at the University of Cantabria in Santander, Spain from July 4th to July 7th.The topics of the conference includes, but are not limited to: Algorithmic mathematics. Algebraic, symbolic and symbolic-numeric algorithms. Simplification, function manipulation, equations, summation, integration, ODE/PDE, linear algebra, number theory, group and geometric computing. Computer Science. Theoretical and practical problems in symbolic computation. Systems, problem solving environments, user interfaces, software, libraries, parallel/distributed computing and programming languages for symbolic computation, concrete analysis, benchmarking, theoretical and practical complexity of computer algebra algorithms, automatic differentiation, code generation, mathematical data structures and exchange protocols. Applications. Problem treatments using algebraic, symbolic or symbolic-numeric computation in an essential or a novel way. Engineering, economics and finance, physical and biological sciences, computer science, logic, mathematics, statistics, education.Following the tradition, ISSAC 2004 features invited talks, contributed papers, tutorials, poster sessions, and software exhibitions. This volume contains all the contributed papers to be presented at the meeting as well as the abstracts of the invited talks.A total of 131 papers were submitted, and each was distributed to members of the program committee and external reviewers. An average of 3 referee reports were obtained for each submission, and finally 43 papers were selected for presentation. As a consequence, we are convinced that the contributions in these proceedings represent excellent and wide, though not complete, spectra of areas spanning most of symbolic and algebraic computation. It is a pleasure to acknowledge the contributions of all these persons, as well as all researchers and educators who submitted papers for consideration, and all those who assisted in the selection process. Unfortunately, due to the time constraint of three days without parallel sessions, many interesting papers could not be accepted for presentation and inclusion in these proceedings.
Mass production of individual feedback
Authors: David Heaney, Charlie Daly
Venue: ACM SIGCSE Bulletin (2004)

We describe a system to improve the quality of feedback provided to an Introductory Programming course. The system uses web technology to create a graphical tool that the tutors can use to produce student-friendly feedback. It was used during the first semester in Autumn 2002. Analysis of exam results show that there was a statistically significant improvement and student surveys showed that they enjoyed using the system.
Smarandache pseudo- ideals
Authors: W. B. Vasantha Kandasamy
Venue: Smarandache Notions Journal (2004)

In this paper we define Smarandache pseudo- ideals of a Smarandache ring. We prove every ideal is a Smarandache pseudo-ideal in a Smarandache ring but every Smarandache pseudo-ideal in general is not an ideal. Further we show that every polynomial ring over a field and group rings FG of the group G over any field are Smarandache rings. We pose some interesting problems about them.
Applications of Forman's Discrete Morse Theory to Topology Visualization and Mesh Compression
Authors: Thomas Lewiner, Helio Lopes, Geovan Tavares
Venue: IEEE Transactions on Visualization and Computer Graphics (2004)

Morse theory is a powerful tool for investigating the topology of smooth manifolds. It has been widely used by the computational topology, computer graphics, and geometric modeling communities to devise topology-based algorithms and data structures. Forman introduced a discrete version of this theory which is purely combinatorial. This work aims to build, visualize, and apply the basic elements of Forman's discrete Morse theory. It intends to use some of those concepts to visually study the topology of an object. As a basis, an algorithmic construction of optimal Forman's discrete gradient vector fields is provided. This construction is then used to topologically analyze mesh compression schemes, such as Edgebreaker and Grow&Fold. In particular, this paper proves that the complexity class of the strategy optimization of Grow&Fold is MAX-SNP hard.
Lossless Online Bayesian Bagging
Authors: Herbert K. H. Lee, Merlise A. Clyde
Venue: The Journal of Machine Learning Research (2004)

Bagging frequently improves the predictive performance of a model. An online version has recently been introduced, which attempts to gain the benefits of an online algorithm while approximating regular bagging. However, regular online bagging is an approximation to its batch counterpart and so is not lossless with respect to the bagging operation. By operating under the Bayesian paradigm, we introduce an online Bayesian version of bagging which is exactly equivalent to the batch Bayesian version, and thus when combined with a lossless learning algorithm gives a completely lossless online bagging algorithm. We also note that the Bayesian formulation resolves a theoretical problem with bagging, produces less variability in its estimates, and can improve predictive performance for smaller data sets.
Compressed Pattern Matching in DNA Sequences
Authors: Lei Chen, Shiyong Lu, Jeffrey Ram
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

We propose derivative Boyer-Moore (d-BM), a new compressed pattern matching algorithm in DNA sequences. This algorithm is based on the Boyer-Moore method, which is one of the most popular string matching algorithms. In this approach, we compress both DNA sequences and patterns by using two bits to represent each A, T, C, G character. Experiments indicate that this compressed pattern matching algorithm searches long DNA patterns (length > 50) more than 10 times faster than the exact match routine of the software package Agrep, which is known as the fastest pattern matching tool. Moreover, compression of DNA sequences by this method gives a guaranteed space saving of 75%. In part the enhanced speed of the algorithm is due to the increased efficiency of the Boyer-Moore method resulting from an increase in alphabet size from 4 to 256.
Focused online discussions, moments of difficulty, and student understanding
Authors: Caroline Hodges Persell
Venue: Social Science Computer Review (2004)

How might computing technologies be used to help address critical problems in the teaching of sociology and other disciplines? This article discusses a qualitative case study designed to illuminate this question. It examines how a very simple computing technology, namely online discussion groups, was designed and structured to address certain pedagogical problems. Qualitative analysis of student postings and observations of the process reveals that focused, web-based discussions made student thinking visible to peers and teacher, created an electronic archive, and provided feedback to instructors. The moments-of-difficulty approach helped to identify and address lacunae in background knowledge or skills that interfere with learning, highlight new concepts needing clarification or statistical relationships requiring explanation, and helped students construct new interpretations and questions. The article discusses threshold conditions for using technology, suggests questions for further research, and considers how computing technologies may increase our understanding of teaching and learning more generally.
Moving to CC2001 at a small college
Authors: John F. Dooley
Venue: ACM SIGCSE Bulletin (2004)

In this paper, we describe the process, problems, and successes of moving a Computer Science major at a small liberal arts college from CC1991[1] to CC2001[3]. Our current computer science major is largely based on CC1991 and on A Revised Model Curriculum for a Liberal Arts Degree in Computer Science[2]. We discuss issues with the number of required courses, the mathematics requirement, staffing, and transitioning to the new curricular model within a small department.
A Framework for Designing Reusable Analog Circuits
Authors: Dean Liu, Stefanos Sidiropoulos, Mark Horowitz
Venue: Proceedings of the 2003 IEEE/ACM international conference on Computer-aided design (2003)

Recent analog design tools have started to allow designers to archivenot only the sized schematics but also some of the objectives thatthe circuit is trying to achieve. This paper first describes STAR(Schematic Tool for Analog Reuse), a system that captures designer'sknowledge as part of the archival circuit representation,and then describes how this system can be used to create portabledesign modules. Creating portable analog modules require morethan just the optimization criteria for the cell. It must also includethe constraints on the cellýs environment (for proper operation), andhow these constraints should scale with technology. Furthermore,the system must help the designer in the current task of creatingthe design, since it is rare that a designer thinks about creating IPfor someone else. We demonstrate the capability and utility of thissystem by examining the reuse of a phase-locked loop.
Approximate factorization of multivariate polynomials via differential equations
Authors: Shuhong Gao, Erich Kaltofen, John May, Zhengfeng Yang, Lihong Zhi
Venue: Proceedings of the 2004 international symposium on Symbolic and algebraic computation (2004)

The input to our algorithm is a multivariate polynomial, whose complex rational coefficients are considered imprecise with an unknown error that causes f to be irreducible over the complex numbers C. We seek to perturb the coefficients by a small quantitity such that the resulting polynomial factors over C. Ideally, one would like to minimize the perturbation in some selected distance measure, but no efficient algorithm for that is known. We give a numerical multivariate greatest common divisor algorithm and use it on a numerical variant of algorithms by W. M. Ruppert and S. Gao. Our numerical factorizer makes repeated use of singular value decompositions. We demonstrate on a significant body of experimental data that our algorithm is practical and can find factorizable polynomials within a distance that is about the same in relative magnitude as the input error, even when the relative error in the input is substantial (10-3).
Feedback-based Real-time Scheduling in Autonomous Vehicle Systems
Venue: Proceedings of the 10th IEEE Real-Time and Embedded Technology and Applications Symposium (2004)

The use of feedback control techniques has been gainingimportance in the context of scheduling in real-time systemsas a means to provide predictable performance in the faceof uncertain workload. In this paper, we propose a novelfeedback-based scheduling approach for task scheduling inreal-time systems. We focus on a system with a mobile node,where the mobility characteristics affect task parameters.The objective is to achieve low miss ratio and high CPUutilization. This objective is achieved by feeding back systemperformances and adapting the node' mobility parameters.We study the new approach in a selective herbicidespraying problem in the agricultural production wherein thespeed of an autonomous vehicle (and hence task parameters)is adapted based on weed distribution in the given farmfield. Simulations and analysis show that our approach canachieve low miss ratio and high CPU utilization.
Bringing skeletons out of the closet: a pragmatic manifesto for skeletal parallel programming
Authors: Murray Cole
Venue: Parallel Computing (2004)

Skeleton and pattern based parallel programming promise significant benefits but remain absent from mainstream practice. We consider why this situation has arisen and propose a number of design principles which may help to redress it. We sketch the eSkel library, which represents a concrete attempt to apply these principles, eSkel is based on C and MPI, thereby embedding its skeletons in a conceptually familiar framework. We present an application of eSkel and analyse it as a response to our manifesto.
Bounding Volumes for Linearly Interpolated Shapes
Authors: Tobias Klug, Marc Alexa
Venue: Proceedings of the Computer Graphics International (2004)

Bounding volumes are crucial for culling in interactivegraphics applications. For dynamic shapes, computing abounding volume for each frame could be very expensive.We analyze the situation for a particular class of dynamicgeometry, namely, shapes resulting from the linear interpolationof several base shapes. The space of weights for thelinear combination can be decomposed into cells so that ineach cell a particular vertex is maximal (resp. minimal) in agiven direction. This cell decomposition of the weight spaceallows deriving bounding volumes from the weight vectorsrather than the generated geometry. We present algorithmsto generate the cell decomposition, to map from weights tocells, and to efficiently compute the necessary data structures.This approach to computing bounding volumes fordynamic shapes proves to be beneficial if the geometry representationis large compared to the number of base shapes.
Separation of Ion Types in Tandem Mass Spectrometry Data Interpretation " A Graph-Theoretic Approach
Authors: Bo Yan, Chongle Pan, Victor N. Olman, Robert L. Hettich, Ying Xu
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

Mass spectrometry is one of the most popular analytical techniques for identification of individual proteins in a protein mixture, one of the basic problems in proteomics. It identifies a protein through identifying its unique mass spectral pattern. While the problem is theoretically solvable, it remains a challenging problem computationally. One of the key challenges comes from the difficulty in distinguishing the N- and C-terminus ions, mostly b- and y-ions respectively. In this paper, we present a graph algorithm for solving the problem of separating bfrom y-ions in a set of mass spectra. We represent each spectral peak as a node and consider two types of edges: a type-1 edge connects two peaks possibly of the same ion types and a type-2 edge connects two peaks possibly of different ion types, predicted based on local information. The ion-separation problem is then formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, namely b-, y-ions and others respectively, so to maximize the total weight of type-1 edges while minimizing the total weight of type-2 edges within each subgraph. We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME. We have tested PRIME on 18 data sets of high accurate FT-ICR tandem mass spectra and found that it achieved ~90% accuracy for separation of b- and y- ions.
Parameterized generation of labeled datasets for text categorization based on a hierarchical directory
Authors: Dmitry Davidov, Evgeniy Gabrilovich, Shaul Markovitch
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

Although text categorization is a burgeoning area of IR research, readily available test collections in this field are surprisingly scarce. We describe a methodology and system (named ACCIO) for automatically acquiring labeled datasets for text categorization from the World Wide Web, by capitalizing on the body of knowledge encoded in the structure of existing hierarchical directories such as the Open Directory. We define parameters of categories that make it possible to acquire numerous datasets with desired properties, which in turn allow better control over categorization experiments. In particular, we develop metrics that estimate the difficulty of a dataset by examining the host directory structure. These metrics are shown to be good predictors of categorization accuracy that can be achieved on a dataset, and serve as efficient heuristics for generating datasets subject to user's requirements. A large collection of automatically generated datasets are made available for other researchers to use.
The Computational Complexity of the Chow Form
Authors: Gabriela Jeronimo, Teresa Krick, Juan Sabia, Mart&#x00ed;n Sombra
Venue: Foundations of Computational Mathematics (2004)

We present a bounded probability algorithm for the computation of the Chowforms of the equidimensional components of an algebraic variety. In particular, this gives an alternative procedure for the effective equidimensional decomposition of the variety, since each equidimensional component is characterized by its Chow form. The expected complexity of the algorithm is polynomial in the size and the geometric degree of the input equation system defining the variety. Hence it improves (or meets in some special cases) the complexity of all previous algorithms for computing Chow forms. In addition to this, we clarify the probability and uniformity aspects, which constitutes a further contribution of the paper. The algorithm is based on elimination theory techniques, in line with the geometric resolution algorithm due to M. Giusti, J. Heintz, L. M. Pardo, and their collaborators. In fact, ours can be considered as an extension of their algorithm for zero-dimensional systems to the case of positive-dimensional varieties. The key element for dealing with positive-dimensional varieties is a new Poisson-type product formula. This formula allows us to compute the Chow form of an equidimensional variety from a suitable zero-dimensional fiber. As an application, we obtain an algorithm to compute a subclass of sparse resultants, whose complexity is polynomial in the dimension and the volume of the input set of exponents. As another application, we derive an algorithm for the computation of the (unique) solution of a generic overdetermined polynomial equation system.
Faster constraint solving with subtypes
Authors: Jonathan Edwards, Daniel Jackson, Emina Torlak, Vincent Yeung
Venue: ACM SIGSOFT Software Engineering Notes (2004)

Constraints in predicate or relational logic can be translated into boolean logic and solved with a SAT solver. For faster solving, it is common to exploit the typing of predicates or relations, in order to reduce the number of boolean variables needed to encode the constraint. Here we show how to extend this idea to constraints expressed in a language with subtyping. Our technique, called atomization, refactors the type hierarchy into a flat collection of disjoint atomic types. The constraints are then decomposed into equivalent constraints involving smaller relations or predicates over these new types, which can then be solved in the normal fashion. Experiments with an implementation of this technique within the Alloy Analyzer show improved performance on practical software checking problems.
Real-Time Watercolor Painting on a Distributed Paper Model
Authors: Tom Van Laerhoven, Jori Liesenborgs, Frank Van Reeth
Venue: Proceedings of the Computer Graphics International (2004)

Current watercolor painting systems produce convincingresults, but trade this quality for a simulation that is muchtoo slow for interactive use. We describe the implementationof a paper model that allows for real-time creation ofwatercolor images by simulating the mechanics of pigmentand water throughout a three-layer paper model. In orderto keep the simulation real-time while painting on large surfaces,we adopt a distributed paper canvas by dividing it ina grid of subpapers, each of which is delegated to a remoteprocess.
Assigning Gene Ontology Categories (GO) to Yeast Genes Using Text-Based Supervised Learning Methods
Authors: Tomonori Izumitani, Hirotoshi Taira, Hideto Kazawa, Eisaku Maeda
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

We propose a method for assigning upper level Gene Ontology terms (GO categories) to genes using relevant documents. This method represents each gene as a vector using relevant documents to the gene. Then, binary classifiers are made for the GO categories using such supervised learning methods as support vector machines and maximum entropy method.We applied this method for assigning GO categories to yeast genes and achieved an average F-measure of 0.67, which is > 0.3 higher than the existing method developed by Raychaudhuri et al. We also applied this method to genome-wide annotation for yeast by all GO Slim categories provided by SGD and achieved average F-measures of 0.58, 0.72, and 0.60, respectively, for the three GO parts: cellular component, molecular function, and biological process.
The origins of network server latency & the myth of connection scheduling
Authors: Yaoping Ruan, Vivek S. Pai
Venue: ACM SIGMETRICS Performance Evaluation Review (2004)

We investigate the origins of server-induced latency to understand how to improve latency optimization techniques. Using the Flash Web server [4], we analyze latency behavior under various loads. Despite latency profiles that suggest standard queuing delays, we find that most latency actually originates from negative interactions between the application and the locking and blocking mechanisms in the kernel. Modifying the server and kernel to avoid these problems yields both qualitative and quantitative changes in the latency profiles -- latency drops by more than an order of magnitude, and the effective service discipline also improves.We find our modifications also mitigate service burstiness in the application, reducing the event queue lengths dramatically and eliminating any benefit from application-level connection scheduling. We identify one remaining source of unfairness, related to competition in the networking stack. We show that adjusting the TCP congestion window size addresses this problem, reducing latency by an additional factor of three.
Project oriented student work: learning & examination
Authors: Ulf Melin, Stefan Cronholm
Venue: ACM SIGCSE Bulletin (2004)

This paper evaluates students' experiences from learning and examination when using a project oriented work approach in an undergraduate information systems development course. The result in this paper shows that students' has an overall positive attitude towards project oriented work. It provides students with an arena for discussing different perspectives, peer-to-peer learning, social interaction and a dynamic work setting. Motivating factors are that the work is authentic, prepare students for working life and last but not least considered as fun. There is however an anxiety about unfair grading that needs to be dealt with. The individual performance must be measured and be a central part of examination and grading. The students must be provided with opportunities to demonstrate what they are able to do on a course, and get genuine feedback on that. This is a way of reducing the free rider syndrome.