ppxscal/embedding_network huggingface dataset:
Visualization-Driven Structural and Statistical Analysis of Turbulent Flows
Authors: Kenny Gruchalla, Mark Rast, Elizabeth Bradley, John Clyne, Pablo Mininni
Venue: Proceedings of the 8th International Symposium on Intelligent Data Analysis: Advances in Intelligent Data Analysis VIII (2009)

Knowledge extraction from data volumes of ever increasing size requires ever more flexible tools to facilitate interactive query. Interactivity enables real-time hypothesis testing and scientific discovery, but can generally not be achieved without some level of data reduction. The approach described in this paper combines multi-resolution access, region-of-interest extraction, and structure identification in order to provide interactive spatial and statistical analysis of a terascale data volume. Unique aspects of our approach include the incorporation of both local and global statistics of the flow structures, and iterative refinement facilities, which combine geometry, topology, and statistics to allow the user to effectively tailor the analysis and visualization to the science. Working together, these facilities allow a user to focus the spatial scale and domain of the analysis and perform an appropriately tailored multivariate visualization of the corresponding data. All of these ideas and algorithms are instantiated in a deployed visualization and analysis tool called VAPOR, which is in routine use by scientists internationally. In data from a 10243 simulation of a forced turbulent flow, VAPOR allowed us to perform a visual data exploration of the flow properties at interactive speeds, leading to the discovery of novel scientific properties of the flow, in the form of two distinct vortical structure populations. These structures would have been very difficult (if not impossible) to find with statistical overviews or other existing visualization-driven analysis approaches. This kind of intelligent, focused analysis/refinement approach will become even more important as computational science moves towards petascale applications.
Investigating Temporal-Spatial Characteristics of Mouse and Touch Input
Authors: Christian Müller-Tomfelde
Venue: Proceedings of the 12th IFIP TC 13 International Conference on Human-Computer Interaction: Part I (2009)

This paper explores differences between user actions employing mouse and touch input devices when performing a collaborative task on a tabletop interface. We explore temporal and spatial characteristics of drag actions of users through mouse (indirect) and touch input (direct) devices. Our analysis is based on system-logged interaction data we collected in an exploratory study. The analysis reveals that touch users performed more drag actions than mouse users. Furthermore, touch users dragged artefacts on a tabletop for a shorter period of time than mouse users. At the same time, touch users dragged objects in the workspace shorter distances than mouse users. We also identify differences based on the temporal-spatial histograms of the drag actions. We discuss our findings based on observations we made during the collaborative task and interviews with participants after the study. The results may be related to the performed task and to ergonomic design issues of the setup. We describe the possible implications on co-located and remote collaboration.
A Parallel Memory System Model for Multi-core Processor
Authors: Mengxiao Liu, Weixing Ji, Xing Pu, Jiaxin Li
Venue: Proceedings of the 2009 IEEE International Conference on Networking, Architecture, and Storage (2009)

Modern multi-core processors are predominant in improving performance of parallel applications. This paper discusses a triple-based multi-core architecture which provides native support for object-oriented methodology and applications in hardware level. The model explicitly represents objects and supports messaging-based communication, which maps well to the standard style of interaction in object oriented languages. However, the Memory Wall is still the bottleneck which should be resolved to decrease the disparity between how fast a CPU can operate on data and how fast it can get data. A hierarchy shared memory system (HSM) working with the partially-inclusive cache mapping policy is proposed. And a new object management model is presented, which use object table and recycle stack scheme to supports explicit dynamic object management. Our cache design presents an innovative solution to handling the costs of cache coherence by allowing applications to control the amount of sharing between cores. Experimental analysis based on comparisons between our objects management and other common link structured object organization methods shows that our method is predominant in spatial and temporal aspects on memory parallel access efficiency and costs less storage space to organize objects.
PROMISE
Authors: Stan Pounds, Cheng Cheng, Xueyuan Cao, Kristine R. Crews, William Plunkett, Varsha Gandhi, Jeffrey Rubnitz, Raul C. Ribeiro, James R. Downing, Jatinder Lamba
Venue: Bioinformatics (2009)

Motivation: In some applications, prior biological knowledge can be used to define a specific pattern of association of multiple endpoint variables with a genomic variable that is biologically most interesting. However, to our knowledge, there is no statistical procedure designed to detect specific patterns of association with multiple endpoint variables. Results: Projection onto the most interesting statistical evidence (PROMISE) is proposed as a general procedure to identify genomic variables that exhibit a specific biologically interesting pattern of association with multiple endpoint variables. Biological knowledge of the endpoint variables is used to define a vector that represents the biologically most interesting values for statistics that characterize the associations of the endpoint variables with a genomic variable. A test statistic is defined as the dot-product of the vector of the observed association statistics and the vector of the most interesting values of the association statistics. By definition, this test statistic is proportional to the length of the projection of the observed vector of correlations onto the vector of most interesting associations. Statistical significance is determined via permutation. In simulation studies and an example application, PROMISE shows greater statistical power to identify genes with the interesting pattern of associations than classical multivariate procedures, individual endpoint analyses or listing genes that have the pattern of interest and are significant in more than one individual endpoint analysis. Availability: Documented R routines are freely available from www.stjuderesearch.org/depts/biostats and will soon be available as a Bioconductor package from www.bioconductor.org. Contact: stanley.pounds@stjude.org Supplementary information:Supplementary data are available at Bioinformatics online.
Partially supervised coreference resolution for opinion summarization through structured rule learning
Authors: Veselin Stoyanov, Claire Cardie
Venue: Proceedings of the 2006 Conference on Empirical Methods in Natural Language Processing (2006)

Combining fine-grained opinion information to produce opinion summaries is important for sentiment analysis applications. Toward that end, we tackle the problem of source coreference resolution -- linking together source mentions that refer to the same entity. The partially supervised nature of the problem leads us to define and approach it as the novel problem of partially supervised clustering. We propose and evaluate a new algorithm for the task of source coreference resolution that outperforms competitive baselines.
New Perspectives on Adobe Dreamweaver CS4: Thomson Course Technology, 1st edition
Authors: Kelly Hart, Mitch Geller
Venue:  (2009)

NEW PERSPECTIVES ON ADOBE DREAMWEAVER CS4, COMPREHENSIVE offers a critical-thinking approach to teaching and learning Adobe Dreamweaver CS4.
Faster and Active Surveillance of Hospital-Acquired Infections: A Model for Settings with High Sensitivity Predictors
Authors: Yaowen Chung, Yu-Sheng Lo, Wen-Sen Lee, Min-Huei Hsu, Chien-Tsai Liu
Venue: Proceedings of the 2009 Ninth IEEE International Conference on Bioinformatics and Bioengineering (2009)

Background: At present, passive alarm system from culture reports and announced from groups outbreak events make cases investigate delayed. Is there any predict factor can be used to suggest active high capture sensitivity surveillance and alarm outbreak early? Objectives: Is there any predict factor can be used to get active high capture sensitivity surveillance of hospital-acquired infections (HAI) in acute hospitals. Can it give alarm of outbreak early? Can it decrease the number for direct patient examination or chart review. Methods : We performed three months retrospective study to identify predictors(urine routine, device as catheter or cystoscope, antibiotics, culture, etc.) about major HAI (urinary tract infections), as defined by the Centers for Disease Control and Prevention (CDC) criteria in a medical center (733 beds). We compared patients list of predictor(s) positive collected from electronic medical record by medical information department members with confirmed nosocomial UTI cases list given from infection control department. Results: 5533 admission patients were screened. The overall prevalence of HAI was 2.5% (141/5533); 1.4% (77/5533) of patients was nosocomial UTI. At presence of urine routine examination and devices guarantees 100% capture sensitivity in detecting nosocomial UTI but requires an assessment of 2763 patients (49.9%) of the population. At presence of antibiotics and devices guarantees 98.7% capture sensitivity and requires an assessment of 1921 patients (34.7%) of the population, whereas presence of antibiotics and urine routine examination has 98.7% capture sensitivity but requires an assessment of 3019 patients (54.7%) of the population. Conclusion: A capture system based on daily list of newly order about antibiotics, devices, urine routine examination, urine culture, blood culture, infection control department of hospital can decide which high predict value criteria suggesting checklist from medical information department for infection control department member to perform active patient examination and decrease the number of direct patient examination and chart review, but still keep high capture sensitivity
About A New Kind Of Autonomous, Self-Adapting Agents And The Library Game Environment
Authors: Herwig Unger, Daniel Berg
Venue: Journal of Integrated Design Process Science (2008)

Different problems from several areas like network routing, traffic control in urban environments or economic optimization problems seem to have a similar theoretical background, especially in case, that somebody looks on strategies to solve them. Due to a high amount of input data and the high complexity of most of these tasks, it usually is very difficult or even impossible to find optimal solutions. Humans may be able to solve those problems still faster and better by using their intuition and by their ability to learn from their experience. The authors intend to show that a new approach to let an individual find sufficient solutions in a human-like manner is to rely on incremental exploration and on the adaptation of processes. Such a solution is not necessarily optimal but although it may satisfy the needs of the individual or a group of them. The individuals' decisions on what activities have to be performed to reach a certain goal are derived from previously successfully applied activity-sequences in combination with a trial-and-error-approach. Like the brain of a growing child, our algorithm is able to become more intelligent during time, i.e. the kept activity-sequences may consider more conditions by getting longer when the individual gains more experience. That also includes, that partial mistakes are made, learnt and that sequences must be erased after they have been identified to be inefficient in comparison to other strategies. The Library Game, introduced in this article, is a model related to the above-cited problems. It provides an environment to analyze and to proof the practicability and efficiency of our suggested solution.
Relevance Feedback on Keyword Space for Interactive Information Retrieval
Authors: Xiao-Gang Wang, Yue Li
Venue: Proceedings of the 2009 IITA International Conference on Services Science, Management and Engineering (2009)

The relevance feedback techniques have been studied in the field of document retrieval, aiming to generate appropriate queries for users’ information needs. Conventional relevance feedback techniques are performed on document space, while the resultant queries should be represented in keyword space. In this paper, it is proposed to perform relevance feedback on keyword space. The relevance feedback is supposed to work with interactive keyword map system, which visualizes the relationship between keywords extracted from retrieved results. As the first step for realizing relevance feedback based on interactive keyword map, this paper also proposes the algorithm for extracting the pair of keywords that reflects a user’s interest from the keyword map. Experimental results are given for showing how the algorithm works on the keyword map that is modified by the user.
Quality Indicators on Global Software Development Projects: Does "Getting to Know You" Really Matter?
Authors: Olly Gotel, Vidya Kulkarni, Moniphal Say, Christelle Scharff, Thanwadee Sunetnanta
Venue: Proceedings of the 2009 Fourth IEEE International Conference on Global Software Engineering (2009)

In Spring 2008, five student teams were put into competition to develop software for a Cambodian client. Each extended team comprised students distributed across a minimum of three locations, drawn from the US, India, Thailand and Cambodia. This paper describes a couple of exercises conducted with students to examine their basic awareness of the countries of their collaborators and competitors, and to assess their knowledge of their own extended team members during the course of the project. The results from these exercises are examined in conjunction with the high-level communication patterns exhibited by the participating teams and provisional findings are drawn with respect to quality, as measured through a final product selection process. Initial implications for practice are discussed.
Cluster Based Modeling and Remote Visualization of Virtual Geographical Space
Authors: Victor Bacu, Lucian Muresan, Dorian Gorgan
Venue: Proceedings of the 2008 10th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (2008)

The graphical modeling and visualization of the virtual geographical space require high power computation and distributed massive spatial databases. The paper presents a few experiments on the solutions supported by the Chromium graphics cluster to provide fast distributed processing and remote visualization. The performance is evaluated for various cluster configurations and spatial data models. The research concerns as well with accessing the cluster based processing by Web applications through grid and Web services.
Comparison of Spectra in Unsequenced Species
Authors: Freddy Cliquet, Guillaume Fertin, Irena Rusu, Dominique Tessier
Venue: Proceedings of the 4th Brazilian Symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology (2009)

We introduce a new algorithm for the mass spectrometric identification of proteins. Experimental spectra obtained by tandem MS/MS are directly compared to theoretical spectra generated from proteins of evolutionarily closely related organisms. This work is motivated by the need of a method that allows the identification of proteins of unsequenced species against a database containing proteins of related organisms. The idea is that matching spectra of unknown peptides to very similar MS/MS spectra generated from this database of annotated proteins can lead to annotate unknown proteins. This process is similar to ortholog annotation in protein sequence databases. The difficulty with such an approach is that two similar peptides, even with just one modification (i.e. insertion, deletion or substitution of one or several amino acid(s)) between them, usually generate very dissimilar spectra. In this paper, we present a new dynamic programming based algorithm: PacketSpectralAlignment. Our algorithm is tolerant to modifications and fully exploits two important properties that are usually not considered: the notion of inner symmetry, a relation linking pairs of spectrum peaks, and the notion of packet inside each spectrum to keep related peaks together. Our algorithm, PacketSpectralAlignment is then compared to SpectralAlignment [1] on a dataset of simulated spectra. Our tests show that PacketSpectralAlignment behaves better, in terms of results and execution time.
A Term-Graph Syntax for Algebras over Multisets
Authors: Fabio Gadducci
Venue: Recent Trends in Algebraic Development Techniques: 19th International Workshop, WADT 2008, Pisa, Italy, June 13-16, 2008, Revised Selected Papers (2009)

Earlier papers argued that term graphs play for the specification of relation-based algebras the same role that standard terms play for total algebras. The present contribution enforces the claim by showing that term graphs are a sound and complete representation for multiset algebras, i.e., algebras whose operators are interpreted over multisets.
On Mesh Editing, Manifold Learning, and Diffusion Wavelets
Authors: R. M. Rustamov
Venue: Proceedings of the 13th IMA International Conference on Mathematics of Surfaces XIII (2009)

We spell out a formal equivalence between the naive Laplacian editing and semi-supervised learning by bi-Laplacian Regularized Least Squares. This allows us to write the solution to Laplacian mesh editing in a `closed' form, based on which we introduce the Generalized Linear Editing (GLE). GLE has both naive Laplacian editing and gradient based editing as special cases. GLE allows using diffusion wavelets for mesh editing. We present preliminary experiments, and shortly discuss connections to segmentation. 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
Some Domain Theory and Denotational Semantics in Coq
Authors: Nick Benton, Andrew Kennedy, Carsten Varming
Venue: Proceedings of the 22nd International Conference on Theorem Proving in Higher Order Logics (2009)

We present a Coq formalization of constructive ¿-cpos (extending earlier work by Paulin-Mohring) up to and including the inverse-limit construction of solutions to mixed-variance recursive domain equations, and the existence of invariant relations on those solutions. We then define operational and denotational semantics for both a simply-typed CBV language with recursion and an untyped CBV language, and establish soundness and adequacy results in each case.
Progressive Geometry-Driven Compression for Triangle Mesh Based on Binary Tree
Authors: Liu Hongnian, Liu Bo, Zhang Hongbin
Venue: Proceedings of the 2009 Second International Conference in Visualisation (2009)

Efficient algorithms for compressing three-dimensional (3D) triangle meshes have been widely developed in recent years, but most of them are designed to deal with manifold meshes. A progressive geometry-driven 3D triangle meshes algorithm is proposed in this work which can be easily extended to non-manifold mesh compression and polygon mesh compression. Different from connectivity-driven algorithms; our method starts with the geometry; it encodes the geometry data into a symbol sequence consisting of only three kinds of symbols. Edge collapse and vertex unification operator are used to encode the connectivity, and the symbol sequences can be further encoded by arithmetic coding.
Compositional, Dynamic Cache Management for Embedded Chip Multiprocessors
Authors: Anca M. Molnos, Sorin D. Cotofana, Marc J. Heijligers, Jos T. Eijndhoven
Venue: Journal of Signal Processing Systems (2009)

This paper proposes a dynamic cache repartitioning technique that enhances compositionality on platforms executing media applications with multiple utilization scenarios. Because the repartitioning between scenarios requires a cache flush, two undesired effects may occur: (1) in particular, the execution of critical tasks may be disturbed and (2) in general, a performance penalty is involved. To cope with these effects we propose a method which: (1) determines, at design time, the cache footprint of each tasks, such that it creates the premises for critical tasks safety, and minimum flush in general, and (2) enforces, at run-time, the design time determined cache footprints and further decreases the flush penalty. We implement our dynamic cache management strategy on a CAKE multiprocessor with 4 Trimedia cores. The experimental workload consists of 6 multimedia applications, each of which formed by multiple tasks belonging to an extended MediaBench suite. We found on average that: (1) the relative variations of critical tasks execution time are less than 0.1%, regardless of the scenario switching frequency, (2) for realistic scenario switching frequencies the inter-task cache interference is at most 4% for the repartitioned cache, whereas for the shared cache it reaches 68%, and (3) the off-chip memory traffic reduces with 60%, and the performance (in cycles per instruction) enhances with 10%, when compared with the shared cache.
Update Maps - A New Abstraction for High-Throughput Batch Processing
Authors: Steffen Viken Valvag, Dag Johansen
Venue: Proceedings of the 2009 IEEE International Conference on Networking, Architecture, and Storage (2009)

Key/value databases are popular abstractions for applications that require synchronous single-key look-ups.However, such databases invariably have a random I/O access pattern, which is inefficient on traditional storage media. To maximize throughput, an alternative is to rely on asynchronous batch processing of requests. As applications evolve, changing requirements with regard to scale or load may thus lead to a redesign to increase the use of batch processing. We present a new abstraction that we have found useful in making such transitions:the update map. It aims to combine the convenience of a key/value database with the performance of abatch-oriented approach. The interface resembles that of an ordinary key/value database, but its implementation can rely on batch processing and sequential I/O, for improved throughput. We evaluate our new abstraction by comparing three different implementations and their performance trade-offs. Specifically, we identify some conditions under which update maps significantly outperform commonly deployed key/value databases. Finally,we discuss ways to improve generic batch processing systems like MapReduce as well as traditional key/value databases based on our findings.
Using Non-blocking I/O Operations in High Performance Computing to Reduce Execution Times
Authors: David Buettner, Julian Kunkel, Thomas Ludwig
Venue: Proceedings of the 16th European PVM/MPI Users' Group Meeting on Recent Advances in Parallel Virtual Machine and Message Passing Interface (2009)

As supercomputers become faster, the I/O part of applications can become a real problem in regard to overall execution times. System administrators and developers of hardware or software components reduce execution times by creating new and optimized parts for the supercomputers. While this helps a lot in the struggle to minimize I/O times, adjustment of the execution environment is not the only option to improve overall application behavior.In this paper we examine if the application programmer can also contribute by making use of non-blocking I/O operations. After an analysis of non-blocking I/O operations and their potential for shortening execution times we present a benchmark which was created and run in order to see if the theoretical promises also hold in practice.