ppxscal/embedding_network huggingface dataset:
A simple iterative approach to parameter optimization
Authors: Alexander Zein, Ralf Zimmer, Thomas Lengauer
Venue: Proceedings of the fourth annual international conference on Computational molecular biology (2000)

Various bioinformatics problems require optimizing several different properties simultaneously. For example, in the protein threading problem, a linear scoring function combines the values for different properties of possible sequence-to-structure alignments into a single score to allow for unambigous optimization. In this context, an essential question is how each property should be weighted. As the native structures are known for some sequences, the implied partial ordering on optimal alignments may be used to adjust the weights. To resolve the arising interdependence of weights and computed solutions, we propose a novel approach: iterating the computation of solutions (here: threading alignments) given the weights and the estimation of optimal weights of the scoring function given these solutions via a systematic calibration method. We show that this procedure converges to structurally meaningful weights, that also lead to significantly improved performance on comprehensive test data sets as measured in different ways. The latter indicates that the performance of threading can be improved in general.
Context interchange: new features and formalisms for the intelligent integration of information
Authors: Cheng Hian Goh, Stéphane Bressan, Stuart Madnick, Michael Siegel
Venue: ACM Transactions on Information Systems (TOIS) (1999)

The Context Interchange strategy presents a novel perspective for mediated data access in which semantic conflicts among heterogeneous systems are not identified a priori, but are detected and reconciled by a context mediator through comparison of contexts axioms corresponding to the systems engaged in data exchange. In this article, we show that queries formulated on shared views, export schema, and shared &ldquo;ontologies&rdquo; can be mediated in the same way using the Context Interchange framework. The proposed framework provides a logic-based object-oriented formalsim for representing and reasoning about data semantics in disparate systems, and has been validated in a prototype implementation providing mediated data access to both traditional and web-based information sources.
Push vs. pull: data movement for linked data structures
Authors: Chia-Lin Yang, Alvin R. Lebeck
Venue: Proceedings of the 14th international conference on Supercomputing (2000)

As the performance gap between the CPU and main memory continues to grow, techniques to hide memory latency are essential to deliver a high performance computer system. Prefetching can often overlap memory latency with computation for array-based numeric applications. However, prefetching for pointer-intensive applications still remains a challenging problem. Prefetching linked data structures (LDS) is difficult because the address sequence of LDS traversal does not present the same arithmetic regularity as array-based applications and the data dependence of pointer dereferences can serialize the address generation process.In this paper, we propose a cooperative hardware/software mechanism to reduce memory access latencies for linked data structures. Instead of relying on the past address history to predict future accesses, we identify the load instructions that traverse the LDS, and execute them ahead of the actual computation. To overcome the serial nature of the LDS address generation, we attach a prefetch controller to each level of the memory hierarchy and push, rather than pull, data to the CPU. Our simulations, using four pointer-intensive applications, show that the push model can achieve between 4% and 30% larger reductions in execution time compared to the pull model.
A Pascal-Based Decision Support System Model for Diagnosis and Treatment Processes in Urology
Authors: Serdar Müldür, İnan Güler
Venue: Journal of Medical Systems (1999)

This program is designed for a urologist as a Decision Support System to facilitate the pre-diagnosis and identify the definite diagnosis as quickly as possible with the help of symptoms and physical examination by taking into consideration all the possible diseases with cross-questioning. The aim is to enable the physician to display on the monitor all the possible diseases causing the arising symptoms by entering the symptoms and the physician's observations into the database with &ldquo;yes&rdquo; or &ldquo;no&rdquo; type answers.
Preparing the information technology workforce for the new millennium
Authors: Janet L. Bailey, Greg Stefaniak
Venue: Proceedings of the 2000 ACM SIGCPR conference on Computer personnel research (2000)

In an era when information technology (IT) is an integral part of society, many organizations are finding it difficult to hire adequate numbers of information technology personnel. Computer systems have permeated virtually every facet of organizations, creating a demand for individuals with IT skills at every level. The situation is complicated by the fact that finding personnel with the appropiate skills mix is even more problematic. As we move into the new millennium, IT roles are shifting at a rapidly increasing pace. Technical skills alone are no longer sufficient for success in the IT profession &mdash; soft skills like communication, problem solving, and teamwork are increasingly important. Recognizing that no curriculum can provide all training needed by every employee in every position, the issue then becomes to identify which specific sets of knowledge, skills, and abilities (KSAs) are most important to IT organizations. This paper presents the findings of an initial case study undertaken to indentify the necessary KSAs that can be used in the development of academic and industry training programs.
Positivity-Preserving Numerical Schemes for Lubrication-Type Equations
Authors: L. Zhornitskaya, A. L. Bertozzi
Venue: SIAM Journal on Numerical Analysis (1999)

Lubrication equations are fourth order degenerate diffusion equations of the form $h_t + \nabla \cdot (f(h) \nabla \Delta h) = 0$, describing thin films or liquid layers driven by surface tension. Recent studies of singularities in which $h\to 0$ at a point, describing rupture of the fluid layer, show that such equations exhibit complex dynamics which can be difficult to simulate accurately. In particular, one must ensure that the numerical approximation of the interface does not show a false premature rupture. Generic finite difference schemes have the potential to manifest such instabilities especially when underresolved. We present new numerical methods, in one and two space dimensions, that preserve positivity of the solution, regardless of the spatial resolution, whenever the PDE has such a property. We also show that the schemes can preserve positivity even when the PDE itself is only known to be nonnegativity preserving. We prove that positivity-preserving finite difference schemes have unique positive solutions at all times. We prove stability and convergence of both positivity-preserving and generic methods, in one and two space dimensions, to positive solutions of the PDE, showing that the generic methods also preserve positivity and have global solutions for sufficiently fine meshes. We generalize the positivity-preserving property to a finite element framework and show, via concrete examples, how this leads to the design of other positivity-preserving schemes.
The forum
Authors: Andrew McGrath
Venue: ACM SIGGROUP Bulletin (1998)

Working collaboratively over networks is ultimately about communication, if the interface between people communicating is not transparent enough then the event is affected and 'navigation' starts to replace the communication. The Forum is a two-part communication environment designed to transparently foster communication between colleagues who cannot be together but who work together. Combining virtual environments and agent technology and using implied navigation we have created a prototype environment that we will be using with customers in the near future.
Parallel Distributive Join Algorithm on the Intel Paragon
Authors: Soon M. Chung, Arindam Chatterjee
Venue: The Journal of Supercomputing (1999)

In this paper, we analyze the performance of the parallel Distributive Join algorithm that we proposed in Chung and Yang 1995. We implemented the algorithm on an Intel Paragon machine and analyzed the effect of the number of processors and the join selectivity on the performance of the algorithm. We also compared the performance of the Distributive Join (DJ) algorithm with that of the Hybrid-Hash(HH) join algorithm. Our results show that the DJ performs comparably with the HH over the entire range of number of processors used and different join selectivities. A big advantage of the parallel DJ algorithm over the HH join algorithm is that it can easily support non-equijoin operations. The results can also be used to estimate the performance of file I/O intensive applications to be implemented on the Intel Paragon machine.
Resettable vector clocks
Authors: Anish Arora, Sandeep Kulkarni, Murat Demirbas
Venue: Proceedings of the nineteenth annual ACM symposium on Principles of distributed computing (2000)

Vector clocks (VC) are an inherent component of a rich class of distributed applications. In this paper, we consider the problem of realistic &mdash;more specifically, bounded-space and fault-tolerant&mdash; implementation of these client applications. To this end, we generalize the notion of VC to resettable vector clocks (RVC), and provide a realistic implementation of RVC. Further, we identify an interface contract under which our RVC implementation can be substituted for VC in client applications, without affecting the client's correctness. Based on such substitution, we show how to transform the client so that it is itself realistically implemented; we demonstrate our method in the context of Ricart-Agrawala's mutual exclusion program.
Implementing digital libraries (panel session)
Authors: Dan Greenstein, David Millman, Margery Tibbetts, Gregory Zick
Venue: Proceedings of the fifth ACM conference on Digital libraries (2000)

This panel will address some of the practical issues of implementing digital libraries. Everyone seems to agree that digital libraries are in their infancy. Many of us watch in amazement as new developments occur. In the year 2000 building a production digital library means analyzing tradeoffs between stability, innovation, and costs/benefits. In this panel we will address some of the more interesting issues of digital library implementation.One of the critical challenges is the economics of digital libraries. Institutions are forming consortia out of necessity and this raises issues of trust, cooperation and commitment. In order for institutions to deliver web-based resources effectively sophisticated cross-organizational access management tools are needed to authenticate and authorize.Institutions are developing new tools and exporting them from research departments into libraries. How well does this collaboration work?The above issues are only a sampling of the challenges this panel will explore.
Minimizing a Sum of Norms Subject to Linear Equality Constraints
Authors: Knud D. Andersen, Edmund Christiansen
Venue: Computational Optimization and Applications (1998)

Numerical analysis of a class of nonlinear duality problems is presented. One side of the duality is to minimize a sum of Euclidean norms subject to linear equality constraints (the constrained MSN problem). The other side is to maximize a linear objective function subject to homogeneous linear equality constraints and quadratic inequalities. Large sparse problems of this form result from the discretization of infinite dimensional duality problems in plastic collapse analysis.The solution method is based on the l_1 penalty function approach to the constrained MSN problem. This can be formulated as an unconstrained MSN problem for which the first author has recently published an efficient Newton barrier method, and for which new methods are still being developed.Numerical results are presented for plastic collapse problems with up to 180000 variables, 90000 terms in the sum of norms and 90000 linear constraints. The obtained accuracy is of order 10^{-8} measured in feasibility and duality gap.
An integrated cost model for software reuse
Authors: A. Mili, S. Fowler Chmiel, R. Gottumukkala, L. Zhang
Venue: Proceedings of the 22nd international conference on Software engineering (2000)

Several cost models have been proposed in the past for estimating, predicting, and analyzing the costs of software reuse. In this paper we analyze existing models, explain their variance, and propose a tool-supported comprehensive model that encompasses most of the existing models.
On the Sizes of Extended Fibonacci Cubes
Authors: Vittorio Scarano
Venue: IEEE Transactions on Parallel and Distributed Systems (1999)

Hypercube is a popular interconnection network whose size must be a power of 2. Several interconnection networks have been proposed that do not suffer this limitation. Among them the Extended Fibonacci Cubes [13] are based on the same sequence of the Fibonacci Cubes and share many appealing structural properties. In this paper, we show how Extended Fibonacci Cubes can be seen as (Cartesian) product graphs whose components are hypercubes and Fibonacci Cubes. By exposing this property, we prove a conjecture in [13] that there are no distinct Extended Fibonacci Cubes (except the trivial ones) with the same number of nodes. Our result further validates the motivations behind the proposal of this interconnection network as a flexible alternative to hypercubes.
Simulation of Complete Binary Tree Structures in a Faulty Flexible Hypercube
Authors: Huan-Chao Keh, Jen-Chih Lin
Venue: Journal of Scientific Computing (1999)

The Flexible Hypercube is a generalization of binary hypercube networks in that the number of nodes can be arbitrary in contrast to a strict power of 2. Restated, the Flexible Hypercube retains the connectivity and diameter properties of the corresponding hypercube. Although the embedding of complete binary trees in faulty hypercubes has received considerable attention, to our knowledge, no paper has demonstrated how to embed a complete binary tree in a faulty Flexible Hypercube. Therefore, this investigation presents a novel algorithm to facilitate the embedding job when the Flexible Hypercube contains faulty nodes. Of particular concern are the network structures of the Flexible Hypercube that balance the load before as well as after faults start to degrade the performance of the Flexible Hypercube. Furthermore, to obtain the replaceable node of the faulty node, 2-expansion is permitted such that up to (n &minus; 2) faults can be tolerated with congestion 1, dilation 4 and load 1. That is, (n &minus; 1) is the dimension of a Flexible Hypercube. Results presented herein demonstrate that embedding methods are optimized.
An experimental configuration for the evaluation of CAC algorithms
Authors: Andrew Moore, Simon Crosby
Venue: ACM SIGMETRICS Performance Evaluation Review (1999)

Interest in Connection Admission Control (CAC) algorithms stems from the need for a network user and a network provider to forge an agreement on the Quality of Service (QoS) for a new network connection. Traditional evaluation of CAC algorithms has been through simulation studies. We present an alternative approach: an evaluation environment for CAC algorithms that is based around an experimental test-rig. This paper presents the architecture of the test-rig and an evaluation of its performance.
Realizable reduction for RC interconnect circuits
Authors: Anirudh Devgan, Peter R. O'Brien
Venue: Proceedings of the 1999 IEEE/ACM international conference on Computer-aided design (1999)

Interconnect reduction is an important step in the design and analysis of complex interconnects found in present-day integrated circuits. This paper presents techniques for obtaining realizable and accurate reduced models for two-port and multi-port RC circuits. The proposed method is also particularly suitable for interconnect reduction for nonlinear circuit simulation and for interconnect post-processing in a parasitic extractor. The method has two limitations. First, it only considers the first few moments of the transfer function; however, that is accurate enough for RC circuits. Second, the amount of interconnect reduction is topology dependent. Although, most on-chip interconnect topologies are well suited for the method proposed. Accuracy and efficiency of the proposed method is demonstrated for various realistic examples.
Image mining in IRIS: integrated retinal information system
Authors: Wynne Hsu, Mong Li Lee, Kheng Guan Goh
Venue: ACM SIGMOD Record (2000)

There is an increasing demand for systems that can automatically analyze images and extract semantically meaningful information. IRIS, an Integrated Retinal Information system, has been developed to provide medical professionals easy and unified access to the screening, trend and progression of diabetic-related eye diseases in a diabetic patient database. This paper shows how mining techniques can be used to accurately extract features in the retinal images. In particular, we apply a classification approach to determine the conditions for tortuousity in retinal blood vessels.
Trends in Hospital Efficiency Among Metropolitan Markets
Authors: Bill Binglong Wang, Yasar A. Ozcan, Thomas T. H. Wan, Jeff Harrison
Venue: Journal of Medical Systems (1999)

This study evaluates trends in efficiency among American hospital markets. A total of 6010 hospitals were identified for use in the analysis from the American Hospital Association's Annual Surveys for 1989 and 1993. Using data envelopment analysis (DEA), a longitudinal study of hospital efficiency was conducted on all 314 metropolitan markets in the United States. Results suggest that large hospital markets generally demonstrated higher inefficiency. The major inefficiencies exist in the availability of hospital services, the number of operating beds, the utilization of hospital staffing and operating expenses. Consequently, the large hospital market had a significant excess of health manpower that resulted in inefficiency that amounted to approximately &dollar;23 billion. From a policy perspective, this study has shed some light on the need to establish more specific policies to address inefficiency in the health care industry.
Parallel Strategies for Solving SURE Models with Variance Inequalities and Positivity of Correlations Constraints
Authors: Erricos J. Kontoghiorghes
Venue: Computational Economics (2000)

The problem of computing estimates of parameters in SURE models with variance inequalities and positivity of correlations constraints is considered. Efficient algorithms that exploit the block bi-diagonal structure of the data matrix are presented. The computational complexity of the main matrix factorizations is analyzed. A compact method to solve the model with proper subset regressors is proposed.
Dynamic Translinear Circuits&mdash;An Overview
Authors: Jan Mulder, Wouter A. Serdijn, Albert C. van der Woerd, Arthur H. M. van Roermund
Venue: Analog Integrated Circuits and Signal Processing (2000)

Dynamic translinear circuits and log-domain filters form a promising and challenging approach to meet the dynamic range limitations that conventional analog implementation techniques are facing due to ever lower supply voltages, low power consumption and high-frequency demands. This paper aims to give an overview of this young, yet rapidly developing, circuit paradigm. Emphasis is placed on methods for analysis and synthesis and on state-of-the-art results obtained for both linear and non-linear applications.
Cache-conscious structure layout
Authors: Trishul M. Chilimbi, Mark D. Hill, James R. Larus
Venue: ACM SIGPLAN Notices (1999)

Hardware trends have produced an increasing disparity between processor speeds and memory access times. While a variety of techniques for tolerating or reducing memory latency have been proposed, these are rarely successful for pointer-manipulating programs.This paper explores a complementary approach that attacks the source (poor reference locality) of the problem rather than its manifestation (memory latency). It demonstrates that careful data organization and layout provides an essential mechanism to improve the cache locality of pointer-manipulating programs and consequently, their performance. It explores two placement techniques---clustering and coloring---that improve cache performance by increasing a pointer structure's spatial and temporal locality, and by reducing cache-conflicts.To reduce the cost of applying these techniques, this paper discusses two strategies---cache-conscious reorganization and cache-conscious allocation---and describes two semi-automatic tools---ccmorph and ccmalloc---that use these strategies to produce cache-conscious pointer structure layouts. ccmorph is a transparent tree reorganizer that utilizes topology information to cluster and color the structure. ccmalloc is a cache-conscious heap allocator that attempts to co-locate contemporaneously accessed data elements in the same physical cache block. Our evaluations, with microbenchmarks, several small benchmarks, and a couple of large real-world applications, demonstrate that the cache-conscious structure layouts produced by ccmorph and ccmalloc offer large performance benefits---in most cases, significantly outperforming state-of-the-art prefetching.
A theory of type qualifiers
Authors: Jeffrey S. Foster, Manuel Fähndrich, Alexander Aiken
Venue: ACM SIGPLAN Notices (1999)

We describe a framework for adding type qualifiers to a language. Type qualifiers encode a simple but highly useful form of subtyping. Our framework extends standard type rules to model the flow of qualifiers through a program, where each qualifier or set of qualifiers comes with additional rules that capture its semantics. Our framework allows types to be polymorphic in the type qualifiers. We present a const-inference system for C as an example application of the framework. We show that for a set of real C programs, many more consts can be used than are actually present in the original code.
Scenario-Based Hypersequential Programming
Authors: Naoshi Uchihira, Hideji Kawata, Fumitaka Tamura
Venue: International Journal of Parallel Programming (2000)

Hypersequential programming is a new paradigm of concurrent programming. The original concurrent program is first serialized, then the sequential version is tested and debugged, and finally the target concurrent program is synthesized by parallelizing the debugged sequential version. In hypersequential programming, testing and debugging are performed on the sequential version of the program and the correctness is preserved in the subsequent parallelization process. Therefore, it offers both higher productivity and enhanced reliability. This paper describes a practical approach to hypersequential programming using the execution history called scenario. It also formalizes the parallelization process using a new equivalence relation called scenario graph equivalence, and gives the parallelization algorithm.