ppxscal/embedding_network huggingface dataset:
Evaluation of Placement Techniques for DNA Probe Array Layout
Authors: Andrew B. Kahng, Ion Mandoiu, Sherief Reda, Xu Xu, Alex Z. Zelikovsky
Venue: Proceedings of the 2003 IEEE/ACM international conference on Computer-aided design (2003)

DNA probe arrays have emerged as a core genomic technology thatenables cost-effective gene expression monitoring, mutation detection,single nucleotide polymorphism analysis and other genomicanalyses. DNA chips are manufactured through a highly scalableprocess, Very Large-Scale Immobilized Polymer Synthesis (VL-SIPS),that combines photolithographic technologies adapted fromthe semiconductor industry with combinatorial chemistry. Commerciallyavailable DNA chips contain more than a half millionprobes and are expected to exceed one hundred million probes inthe next generation. This paper is one of the first attempts to applyVLSI CAD methods to the problem of probe placement in DNAchips, where the main objective is to minimize total border cost(i.e., the number of nucleotide mismatches between adjacent sites).We make the following contributions. First, we propose severalpartitioning-based algorithms for DNA probe placement thatimprove solution quality by over 4% compared to best previouslyknown methods. Second, we give a simple in-place probe re-embeddingalgorithm with solution quality better than previous"chessboard" and batched greedy algorithms. Third, we experimentallyevaluate scalability and suboptimality of existing and newlyproposed probe placement algorithms. Interestingly, we find thatDNA placement algorithms appear to have better suboptimalityproperties than those recently reported for VLSI placement algorithms.
Tuning before feedback: combining ranking discovery and blind feedback for robust retrieval
Authors: Weiguo Fan, Ming Luo, Li Wang, Wensi Xi, Edward A. Fox
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

Both ranking functions and user queries are very important factors affecting a search engine's performance. Prior research has looked at how to improve ad-hoc retrieval performance for existing queries while tuning the ranking function, or modify and expand user queries using a fixed ranking scheme using blind feedback. However, almost no research has looked at how to combine ranking function tuning and blind feedback together to improve ad-hoc retrieval performance. In this paper, we look at the performance improvement for ad-hoc retrieval from a more integrated point of view by combining the merits of both techniques. In particular, we argue that the ranking function should be tuned first, using user-provided queries, before applying the blind feedback technique. The intuition is that highly-tuned ranking offers more high quality documents at the top of the hit list, thus offers a stronger baseline for blind feedback. We verify this integrated model in a large scale heterogeneous collection and the experimental results show that combining ranking function tuning and blind feedback can improve search performance by almost 30% over the baseline Okapi system.
From Unordered Range Images to 3D Models: A Fully Automatic Multiview Correspondence Algorithm
Venue: Proceedings of the Theory and Practice of Computer Graphics 2004 (TPCG'04) (2004)

In this paper, we present a fully automatic multiviewcorrespondence algorithm based on our tensor representation.Our algorithm can automatically establish correspondencesbetween a set of unordered range images of an objectand register them in a common coordinate basis. Existingtechniques of correspondence are either manual or inefficientand require the ordering of range images accordingto their overlap. Our algorithm does not suffer from anysuch limitation. We also present a complete and fully automatic3D modeling framework by integrating our multiviewcorrespondence algorithm with a global registration, an integrationand a surface reconstruction algorithm. Our resultsshow that our algorithm is fully automatic, applicableto free-form objects, efficient and independent of the resolutionand sampling of the range images.
Unlabeled Data Classification via Support Vector Machines and k-means Clustering
Authors: Maokuan Li, Yusheng Cheng, Honghai Zhao
Venue: Proceedings of the International Conference on Computer Graphics, Imaging and Visualization (2004)

Support vector machines(SVMS), a powerful machine method developed from statistical learning and have made significant achievement in some field. Introduced in the early 90ýs, they led to an explosion of interest in machine learning. However, like most machine learning algorithms, they are generally applied using a selected training set classified in advance. With the repaid development of the internet and telecommunication, huge of information has been produced as digital data format, generally the data is unlabeled. It is impossible to classify the data with oneýs own hand one by one in many realistic problems, so that the research on unlabeled data classification has been grown. Improvements in databases technology, computing performance and artificial intelligence have contributed to the development of intelligent data analysis. In this paper, a SVMs classifier based on k-means algorithm is presented for the classification of unlabeled data.
Números felizes e sucessões de Smarandache: digressões com o Maple
Authors: Delfim F. M. Torres
Venue: Smarandache Notions Journal (2004)

Dando jus à matemática experimental, mostramos como o Maple pode ser usado na investigação matemática de algumas questões actualmente sem resposta na Teoria dos Números. A tese defendida é que os alunos de um curso de Matemática podem facilmente usar o computador como tun lugar onde se excita e exercita a imaginação.
Obsessive compulsive font disorder: the challenge of supporting pupils writing with the computer
Authors: Sasha Matthewman, Pat Triggs
Venue: Computers Education (2004)

Writing with the computer provokes and enables pupils to engage with aspects of multimodal design [Multiliteracies: Literacy Learning and the Design of Social Futures, Routledge, London, 2000]. At the same time the traditional stages of the writing process become much more fluid and integrated [Aust. J. Language Literacy 17(3) (1994) 183]. These consequences of technology are not recognised within the curriculum, the assessment system or current models of teaching the writing process in the UK. Using examples from current classroom research this paper argues that the significance of pupils' uses of the 'available designs' of digital experience [Multiliteracies: Literacy Learning and the Design of Social Futures, Routledge, London, 2000] is undervalued. Furthermore it suggests that this undervaluing leaves teachers without well-developed pedagogic models of literacy when computers are involved.
GridSphere: An Advanced Portal Framework
Authors: Jason Novotny, Michael Russell, Oliver Wehrens
Venue: Proceedings of the 30th EUROMICRO Conference (2004)

In traditional web application development, very few libraries exist to make portal development easy. In general, many homegrown and vertical solutions exist and very little code is shared or reused. Finally with the emergence of some critical new web technologies, web application development is focusing more on reusable solutions and software. The GridSphere portal framework provides a standards based portal for the easy development of modular web components, called portlets. Portlets are defined by a standard API and provide a model for developing new portal components that can be shared and exchanged by various portlet containers. GridSphere provides both a portlet container, a collection of core portlets and an advanced user interface library that makes developing new portlets easier for application developers. This paper discusses brie y the the GridSphere portal architecture including the layout engine, support for two portlet API implementations and the portlet services model.
HybridTreeMiner: An Efficient Algorithm for Mining Frequent Rooted Trees and Free Trees Using Canonical Forms
Authors: Yun Chi, Yirong Yang, Richard R. Muntz
Venue: Proceedings of the 16th International Conference on Scientific and Statistical Database Management (2004)

Tree structures are used extensively in domains suchas computational biology, pattern recognition, XMLdatabases, computer networks, and so on. In this paper,we present HybridTreeMiner, a computationally efficientalgorithm that discovers all frequently occurringsubtrees in a database of rooted unordered trees. The algorithmmines frequent subtrees by traversing an enumerationtree that systematically enumerates all subtrees. The enumerationtree is defined based on a novel canonicalform for rooted unordered trees-the breadth-first canonicalform (BFCF). By extending the definitions of our canonicalform and enumeration tree to free trees, our algorithmcan efficiently handle databases of free trees as well.We study the performance of our algorithms through extensiveexperiments based on both synthetic data and datasetsfrom real applications. The experiments show that our algorithmis competitive in comparison to known rooted treemining algorithms and is faster by one to two orders ofmagnitudes compared to a known algorithm for mining frequentfree trees.
Generalized Bhaskar Rao designs and dihedral groups
Authors: R. J. R. Abel, D. Combe, W. D. Palmer
Venue: Journal of Combinatorial Theory Series A (2004)

We solve the existence problem for generalized Bhaskar Rao designs of block size 3 for an infinite family of non-abelian groups, the dihedral groups Dn, of order 2n. In our main result we show that for n ≥ 1 and v ≥ 3 the following set of conditions is necessary and sufficient for the existence of a GBRD(v, 3, λ Dn): 1. λ ≡ 0 (mod 2n): 2. λ v(v - 1) ≡ 0 (mod 24).
Understanding combination of evidence using generative probabilistic models for information retrieval (abstract only)
Authors: Paul Ogilvie
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

Structured documents, rich information needs, and detailed information about users are becoming more pervasive within everyday computing usage. Applications such as Question Answering, reading tutors, and XML retrieval demand more robust retrieval on richly annotated documents. In order to effectively serve these applications, the community will need a better understanding of the combination of evidence. In this work, I propose that the use of simple generative probabilistic models will be an effective framework for these problems. Statistical language models, which are a special case of generative probabilistic models, have been used extensively within recent Information Retrieval research. Their flexibility has been very effective in adapting to numerous tasks and problems. I propose to extend the statistical language modeling framework to handle rich information needs and documents with structural and linguistic annotations. Much of the prior work on combination of evidence has had few well-studied theoretical contributions, so I also propose to develop a sounder theoretical basis which gives more predictable results.
Service Selection Algorithms for Web Services with End-to-End QoS Constraints
Authors: Tao Yu, Kwei-Jay Lin
Venue: Proceedings of the IEEE International Conference on E-Commerce Technology (2004)

Web services are new forms of Internet software that can be universally deployed and invoked using standard protocol. Services from different providers can be integrated to provide composite services. In this paper, we study the end-to-end QoS issues of composite service by utilizing a QoS broker that is responsible for coordinating the individual service component to meet the quality constraint. We design the service selection algorithms used by QoS brokers to meet end-to-end QoS constraints. The objective of the algorithms is to maximize the user-defined utility while meeting the end-to-end delay constraint. We model the problem as the Multiple Choice Knapsack Problem (MCKP) and provide efficient solutions. The algorithms are tested for their performance.
Policy migration for sensitive credentials in trust negotiation
Authors: Ting Yu, Marianne Winslett
Venue: Proceedings of the 2003 ACM workshop on Privacy in the electronic society (2003)

Trust negotiation is an approach to establishing trust between strangers through the bilateral, iterative disclosure of digital credentials. Under automated trust negotiation, access control policies are associated with sensitive credentials to control under what circumstances those credentials can be disclosed. Ideally, the information in a user's sensitive credential should not be known by others unless the corresponding policy is satisfied. However, the original model for user interaction in trust negotiation has pitfalls which can be easily exploited to infer one's private information, even if access control policies are strictly enforced. To preserve one's privacy, a more flexible interaction model for trust negotiation is required. On the other hand, it is also desirable for two parties to be able to establish trust whenever possible. There is potentially a conflict between privacy preservation and the assurance of a successful trust negotiation. In this paper, we identify the situation where sensitive information can be inferred through observing one's behavior in trust negotiation. Then we propose policy migration as one approach to preventing such inference. Compared to previously proposed approaches, policy migration has a low management overhead, and provides a nice balance between inference prevention and guarantees of success in trust establishment. We also discuss the limitations of policy migration, and possible directions for more comprehensive solutions.
Adaptive Cache Compression for High-Performance Processors
Authors: Alaa R. Alameldeen, David A. Wood
Venue: Proceedings of the 31st annual international symposium on Computer architecture (2004)

Modern processors use two or more levels ofcache memories to bridge the rising disparity betweenprocessor and memory speeds. Compression canimprove cache performance by increasing effectivecache capacity and eliminating misses. However,decompressing cache lines also increases cache accesslatency, potentially degrading performance.In this paper, we develop an adaptive policy thatdynamically adapts to the costs and benefits of cachecompression. We propose a two-level cache hierarchywhere the L1 cache holds uncompressed data and the L2cache dynamically selects between compressed anduncompressed storage. The L2 cache is 8-way set-associativewith LRU replacement, where each set can storeup to eight compressed lines but has space for only fouruncompressed lines. On each L2 reference, the LRUstack depth and compressed size determine whethercompression (could have) eliminated a miss or incurs anunnecessary decompression overhead. Based on thisoutcome, the adaptive policy updates a single globalsaturating counter, which predicts whether to allocatelines in compressed or uncompressed form.We evaluate adaptive cache compression usingfull-system simulation and a range of benchmarks. Weshow that compression can improve performance formemory-intensive commercial workloads by up to 17%.However, always using compression hurts performancefor low-miss-rate benchmarks-due to unnecessarydecompression overhead-degrading performance byup to 18%. By dynamically monitoring workload behavior,the adaptive policy achieves comparable benefitsfrom compression, while never degrading performanceby more than 0.4%.
Developing for windows on Linux
Authors: Joey Bernard
Venue: Linux Journal (2004)

Use these tools from the MinGW Project to write, maintain and test Win32 apps on any GNU system. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Long cycles in triangle-free graphs with prescribed independence number and connectivity
Authors: Hikoe Enomoto, Atsushi Kaneko, Akira Saito, Bing Wei
Venue: Journal of Combinatorial Theory Series B (2004)

The Chvátal-Erdös theorem says that a 2-connected graph with α(G)≤κ(G) is hamiltonian. We extend this theorem for triangle-free graphs. We prove that if G is a 2-connected triangle-free graph of order n with α(G)≤2κ(G) - 2, then every longest cycle in G is dominating, and G has a cycle of length at least min{n - α(G) + κ(G), n}.
Constant-Time Navigation in Four-Dimensional Nested Simplicial Meshes
Venue: Proceedings of the Shape Modeling International 2004 (2004)

We consider a recursive decomposition of a four-dimensionalhypercube into a hierarchy of nested 4-dimensional simplexes,that we call pentatopes. The paper presents an algorithm for findingthe neighbors of a pentatope along its five tetrahedral facesin constant time. To this aim, we develop a labeling techniquefor nested pentatopes that enables their identification by usinglocation codes. The constant-time behavior is achieved throughbit manipulation operations, thus avoiding traversing the simplicialhierarchy via pointer following. We discuss an applicationof this representation to multi-resolution representations of four-dimensionalscalar fields. Extracting adaptive continuous approximationsof the scalar field from such a model requires generatingconforming meshes, i.e., meshes in which the pentatopes matchalong their tetrahedral faces. Our neighbor finding algorithm enablescomputing face-adjacent pentatopes efficiently.
Prenatal Care Need and Access: A GIS Analysis
Authors: Sara McLafferty, Sue Grady
Venue: Journal of Medical Systems (2004)

Many municipalities provide special prenatal care services targeted to low-income women whose access to prenatal care is constrained. For such services to be successful and effective, they must be geographically targeted to the places where low-income, high-need mothers live. This paper presents a GIS analysis of prenatal care need and clinic services for low-income mothers in Brooklyn, NY. We analyze fine-grained geographic variation in need using data on the residential locations of recent mothers who lack health insurance or are covered by Medicaid. Spatial statistical methods are used to create spatially smoothed maps of the density of mothers and corresponding maps of the density of prenatal clinics. For these mothers, clinic density is positively associated with early initiation of prenatal care. Although clinic locations conform relatively well to the residential concentrations of high-need women, we identify several underserved areas with large numbers of needy women and few clinics available.
Constraint-based XML query rewriting for data integration
Authors: Cong Yu, Lucian Popa
Venue: Proceedings of the 2004 ACM SIGMOD international conference on Management of data (2004)

We study the problem of answering queries through a target schema, given a set of mappings between one or more source schemas and this target schema, and given that the data is at the sources. The schemas can be any combination of relational or XML schemas, and can be independently designed. In addition to the source-to-target mappings, we consider as part of the mapping scenario a set of target constraints specifying additional properties on the target schema. This becomes particularly important when integrating data from multiple data sources with overlapping data and when such constraints can express data merging rules at the target. We define the semantics of query answering in such an integration scenario, and design two novel algorithms, basic query rewrite and query resolution, to implement the semantics. The basic query rewrite algorithm reformulates target queries in terms of the source schemas, based on the mappings. The query resolution algorithm generates additional rewritings that merge related information from multiple sources and assemble a coherent view of the data, by incorporating target constraints. The algorithms are implemented and then evaluated using a comprehensive set of experiments based on both synthetic and real-life data integration scenarios.
Batch codes and their applications
Authors: Yuval Ishai, Eyal Kushilevitz, Rafail Ostrovsky, Amit Sahai
Venue: Proceedings of the thirty-sixth annual ACM symposium on Theory of computing (2004)

A batch code encodes a string x into an m-tuple of strings, called buckets, such that each batch of k bits from x can be decoded by reading at most one (more generally, t) bits from each bucket. Batch codes can be viewed as relaxing several combinatorial objects, including expanders and locally decodable codes. We initiate the study of these codes by presenting some constructions, connections with other problems, and lower bounds. We also demonstrate the usefulness of batch codes by presenting two types of applications: trading maximal load for storage in certain load-balancing scenarios, and amortizing the computational cost of private information retrieval (PIR) and related cryptographic protocols.
Conservative multi-implicit spectral deferred correction methods for reacting gas dynamics
Authors: Anita T. Layton, Michael L. Minion
Venue: Journal of Computational Physics (2004)

In most models of reacting gas dynamics, the characteristic time scales of chemical reactions are much shorter than the hydrodynamic and diffusive time scales, rendering the reaction part of the model equations stiff. Moreover, non-linear forcings may introduce into the solutions sharp gradients or shocks, the robust behavior and correct propagation of which require the use of specialized spatial discretization procedures. This study presents high-order conservative methods for the temporal integration of model equations of reacting flows. By means of a method of lines discretization on the flux difference form of the equations, these methods compute approximations to the cell-averaged or finite-volume solution. The temporal discretization is based on a multi-implicit generalization of spectral deferred correction methods. The advection term is integrated explicitly, and the diffusion and reaction terms are treated implicitly but independently, with the splitting errors reduced via the spectral deferred correction procedure. To reduce computational cost, different time steps may be used to integrate processes with widely-differing time scales. Numerical results show that the conservative nature of the methods allows a robust representation of discontinuities and sharp gradients; the results also demonstrate the expected convergence rates for the methods of orders three, four, and five for smooth problems.
PoPS: A Computational Tool for Modeling and Predicting Protease Specificity
Authors: Sarah E. Boyd, Maria Garcia de la Banda, Robert N. Pike, James C. Whisstock, George B. Rudy
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

Proteases play a fundamental role in the control of intra- and extracellular processes by binding and cleaving specific amino acid sequences. Identifying these targets is extremely challenging. Current computational attempts to predict cleavage sites are limited, representing these amino acid sequences as patterns or frequency matrices. Here we present PoPS, a publicly accessible bioinformatics tool (http://pops.csse.monash.edu.au/) which provides a novel method for building computational models of protease specificity that, while still being based on these amino acid sequences, can be built from any experimental data or expert knowledge available to the user. PoPS specificity models can be used to predict and rank likely cleavages within a single substrate, and within entire proteomes. Other factors, such as the secondary or tertiary structure of the substrate, can be used to screen unlikely sites. Furthermore, the tool also provides facilities to infer, compare and test models, and to store them in a publicly accessible database.