ppxscal/embedding_network huggingface dataset:
Comparative study on ChIP-seq data
Authors: Cenny Taslim, Jiejun Wu, Pearlly Yan, Greg Singer, Jeffrey Parvin, Tim Huang, Shili Lin, Kun Huang
Venue: Bioinformatics (2009)

Motivation: Antibody-based Chromatin Immunoprecipitation assay followed by high-throughput sequencing technology (ChIP-seq) is a relatively new method to study the binding patterns of specific protein molecules over the entire genome. ChIP-seq technology allows scientist to get more comprehensive results in shorter time. Here, we present a non-linear normalization algorithm and a mixture modeling method for comparing ChIP-seq data from multiple samples and characterizing genes based on their RNA polymerase II (Pol II) binding patterns. Results: We apply a two-step non-linear normalization method based on locally weighted regression (LOESS) approach to compare ChIP-seq data across multiple samples and model the difference using an Exponential-NormalK mixture model. Fitted model is used to identify genes associated with differential binding sites based on local false discovery rate (fdr). These genes are then standardized and hierarchically clustered to characterize their Pol II binding patterns. As a case study, we apply the analysis procedure comparing normal breast cancer (MCF7) to tamoxifen-resistant (OHT) cell line. We find enriched regions that are associated with cancer (P < 0.0001). Our findings also imply that there may be a dysregulation of cell cycle and gene expression control pathways in the tamoxifen-resistant cells. These results show that the non-linear normalization method can be used to analyze ChIP-seq data across multiple samples. Availability: Data are available at http://www.bmi.osu.edu/~khuang/Data/ChIP/RNAPII/ Contact:taslim.2@osu.edu; khuang@bmi.osu.edu Supplementary information:Supplementary data are available at Bioinformatics online.
A Plot-Manipulation Algebra to Support Digital Storytelling
Authors: Börje Karlsson, Simone D. Barbosa, Antonio L. Furtado, Marco A. Casanova
Venue: Proceedings of the 8th International Conference on Entertainment Computing (2009)

Plot composition is examined here at a logic design level, an intermediate stage that comes next to the conceptual level wherein the intended narrative genre is specified. An abstract data structure is proposed to represent plots, together with an algebra for manipulating the data structure. Our purpose is to adapt for narratives the strategy applied to databases by Codd's relational model. The basic operators of our Plot-Manipulation Algebra (PMA) are introduced in view of the four fundamental relations between events that we identified in a previous work. A logic programming prototype was implemented in order to run examples using the algebra.
New Semantic Similarity Based Model for Text Clustering Using Extended Gloss Overlaps
Authors: Walaa K. Gad, Mohamed S. Kamel
Venue: Proceedings of the 6th International Conference on Machine Learning and Data Mining in Pattern Recognition (2009)

Most text clustering techniques are based on words and/or phrases weights in the text. Such representation is often unsatisfactory because it ignores the relationships between terms, and considers them as independent features.In this paper, a new semantic similarity based model (SSBM) is proposed. The semantic similarity based model computes semantic similarities by utilizing WordNet as an ontology. The proposed model captures the semantic similarities between documents that contain semantically similar terms but unnecessarily syntactically identical.The semantic similarity based model assigns a new weight to document terms reflecting the semantic relationships between terms that co-occur literally in the document. Our model in conjunction with the extended gloss overlaps measure and the adapted Lesk algorithm solves ambiguity, synonymy problems that are not detected using traditional term frequency based text mining techniques.The proposed model is evaluated on the Reuters-21578 and the 20-Newsgroups text collections datasets. The performance is assessed in terms of the Fmeasure, Purity and Entropy quality measures. The obtained results show promising performance improvements compared to the traditional term based vector space model (VSM) as well as other existing methods that include semantic similarity measures in text clustering.
System building cost vs. output quality in data-to-text generation
Authors: Anja Belz, Eric Kow
Venue: Proceedings of the 12th European Workshop on Natural Language Generation (2009)

Data-to-text generation systems tend to be knowledge-based and manually built, which limits their reusability and makes them time and cost-intensive to create and maintain. Methods for automating (part of) the system building process exist, but do such methods risk a loss in output quality? In this paper, we investigate the cost/quality trade-off in generation system building. We compare four new data-to-text systems which were created by predominantly automatic techniques against six existing systems for the same domain which were created by predominantly manual techniques. We evaluate the ten systems using intrinsic automatic metrics and human quality ratings. We find that increasing the degree to which system building is automated does not necessarily result in a reduction in output quality. We find furthermore that standard automatic evaluation metrics underestimate the quality of handcrafted systems and over-estimate the quality of automatically created systems.
Characteristic Polynomial Analysis on Matrix Representations of Graphs
Authors: Peng Ren, Richard C. Wilson, Edwin R. Hancock
Venue: Proceedings of the 7th IAPR-TC-15 International Workshop on Graph-Based Representations in Pattern Recognition (2009)

Matrix representations for graphs play an important role in combinatorics. In this paper, we investigate four matrix representations for graphs and carry out an characteristic polynomial analysis upon them. The first two graph matrices are the adjacency matrix and Laplacian matrix. These two matrices can be obtained straightforwardly from graphs. The second two matrix representations, which are newly introduced [9][3], are closely related with the Ihara zeta function and the discrete time quantum walk. They have a similar form and are established from a transformed graph, i.e. the oriented line graph of the original graph. We make use of the characteristic polynomial coefficients of the four matrices to characterize graphs and construct pattern spaces with a fixed dimensionality. Experimental results indicate that the two matrices in the transformed domain perform better than the two matrices in the original graph domain whereas the matrix associated with the Ihara zeta function is more efficient and effective than the matrix associated with the discrete time quantum walk and the remaining methods.
Recovering temporal integrity with Data Driven Time Synchronization
Authors: Martin Lukac, Paul Davis, Robert Clayton, Deborah Estrin
Venue: Proceedings of the 2009 International Conference on Information Processing in Sensor Networks (2009)

Data Driven Time Synchronization (DDTS) provides synchronization across sensors by using underlying characteristics of data collected by an embedded sensing system. We apply the concept of Data Driven Time Synchronization through a seismic deployment consisting of 100 seismic sensors to repair data that was not time synchronized correctly. This deployment used GPS for time synchronization, but due to system faults common to environmental sensing systems, data was collected with large time offsets. In seismic deployments, offset data is often never used, but we show that Data Driven Time Synchronization can recover the synchronization and make the data usable. To implement Data Driven Time Synchronization to repair the time offsets we use microseisms as the underlying characteristics. Microseisms are waves that travel through the earth's crust and are independent of the seismic events used for the study of the earth's structure. We have developed a model of microseism propagation through a linear seismic array and use the model to obtain time correction shifts. By simulating time offsets in real data which does not have offsets, we determined that this method is able to repair the offset to between 0.05 and 0.2 seconds. Our ongoing work will attempt to refine the model to correct the offsets to less than 0.05 seconds and evaluate how errors in the correction affect seismic results such as event location. Data Driven Time Synchronization may be applicable to other high data rate embedded sensing applications such as acoustic source localization.
Tile Percolation: An OpenMP Tile Aware Parallelization Technique for the Cyclops-64 Multicore Processor
Authors: Ge Gan, Xu Wang, Joseph Manzano, Guang R. Gao
Venue: Proceedings of the 15th International Euro-Par Conference on Parallel Processing (2009)

Programming a multicore processor is difficult. It is even more difficult if the processor has software-managed memory hierarchy, e.g. the IBM Cyclops-64 (C64). A widely accepted parallel programming solution for multicore processor is OpenMP. Currently, all OpenMP directives are only used to decompose computation code (such as loop iterations, tasks, code sections, etc.). None of them can be used to control data movement, which is crucial for the C64 performance. In this paper, we propose a technique called tile percolation. This method provides the programmer with a set of OpenMP pragma directives. The programmer can use these directives to annotate their program to specify where and how to perform data movement. The compiler will then generate the required code accordingly. Our method is a semi-automatic code generation approach intended to simplify a programmer's work. The paper provides (a) an exploration of the possibility of developing pragma directives for semi-automatic data movement code generation in OpenMP; (b) an introduction of techniques used to implement tile percolation including the programming API, the code generation in compiler, and the required runtime support routines; (c) and an evaluation of tile percolation with a set of benchmarks. Our experimental results show that tile percolation can make the OpenMP programs run on the C64 chip more efficiently.
A New Kind of Non-contact Stress Sensor Based on Magnetoelastic Effect
Authors: Yanping Shi, Yifei Shi
Venue: Proceedings of the 2009 International Conference on Measuring Technology and Mechatronics Automation - Volume 01 (2009)

at present the non-contact stress sensor which can be choose are not many, so it is necessary to develop the new non-contact stress sensor. A new kind of the non-contact stress sensor based on magnetoelastic effect with three magnetic poles is designed in this paper. The author first discussed the structure and the operation principle of the sensor, then derived its induced voltage output equation, finally through the experiment, analyzed the exciting current intensity, the frequency as well as the test magnet gap and so on to its input level influence. The results of the test have showed that the sensor has high measuring precision and sensitivity and it can meet the demands of the general practical application.
The Learning Effectiveness of Blended and Embodied Interactive Video Game on Kindergarten Students
Authors: Chih-Min Tsai, Jon-Chao Hong, Ya-Jiuan Ho
Venue: Proceedings of the 4th International Conference on E-Learning and Games: Learning by Playing. Game-based Education System Design and Development (2009)

We developed an embodied interactive video game (EIVG) that is both educational and entertaining in the hope of using such system to explore the differences that exist in learning effectiveness between blended and pure digital learning. Apart from conducting experiments by having the children learned using the EIVG, we also involved teachers as part of the study helping us observe the emotional aspect of the children. The results of the study can be summarized into the following: 1 The effectiveness of blended learning is much better comparing to that of pure digital learning. 2 The effectiveness of EIVG learning of boys is better than girls. However there is no significant difference between them. 3 The EIVG is highly entertaining which results in learning objects remain highly interested and focused throughout the study. Both types of learning can effectively improve the learning outcomes of the objects.
PaMGIS: A Framework for Pattern-Based Modeling and Generation of Interactive Systems
Authors: Jürgen Engel, Christian Märtin
Venue: Proceedings of the 13th International Conference on Human-Computer Interaction. Part I: New Trends (2009)

This paper introduces the PaMGIS framework for pattern-based modeling, generation and usability evaluation of interactive systems. It describes the structural aspects of HCI pattern languages and how such languages and patterns for various modeling stages (e.g. task modeling) and abstraction levels can be exploited to automate part of the software development process for interactive applications. The main components and the general functionality of the framework are discussed. The remaining part of the paper focuses on the low-level automation component of the framework and illustrates how the code for concrete interaction objects is generated from semi-abstract user interface patterns.
Data Management for Federated Biobanks
Authors: Johann Eder, Claus Dabringer, Michaela Schicho, Konrad Stark
Venue: Proceedings of the 20th International Conference on Database and Expert Systems Applications (2009)

Biobanks store and manage collections of biological material (tissue, blood, cell cultures, etc.) and manage the medical and biological data associated with this material. Biobanks are invaluable resources for medical research. The diversity, heterogeneity and volatility of the domain make information systems for biobanks a challenging application domain. The European project BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) has the mission to network European biobanks, to improve resources for biomedical research, an thus contribute to improve the prevention, diagnosis and treatment of diseases. We present the challenges and discuss some architectures for interconnecting European biobanks and harmonizing their data.
Study on Hoisting Speed Control for the 7500T Full Revolving Floating Crane
Authors: Yijian Liu, Shilong Xue
Venue: Proceedings of the 2009 International Conference on Measuring Technology and Mechatronics Automation - Volume 01 (2009)

The full revolving floating crane is one of the most key equipment in the large floating ocean engineering ship. With the highly speed development of ocean oil, it was need rapidly. In this paper, the 7500T large full revolving floating crane was regarded as the study object, and the field-bus technology T-LINK, MICREX-SX series PLC and Inverter VG7S was adopted to build control system. T-LINK network for control system was introduced. The hoisting control programs such as control logic, interlock logic and speed control under heavy loading had been worked out designed with D300win software, which makes it possible to monitor and control the large floating crane effectively.
Interpolatory quad/triangle subdivision schemes for surface design
Authors: Qingtang Jiang, Baobin Li, Weiwei Zhu
Venue: Computer Aided Geometric Design (2009)

Recently the study and construction of quad/triangle subdivision schemes have attracted attention. The quad/triangle subdivision starts with a control net consisting of both quads and triangles and produces finer and finer meshes with quads and triangles. The use of the quad/triangle structure for surface design is motivated by the fact that in CAD modelling, the designers often want to model certain regions with quad meshes and others with triangle meshes to get better visual quality of subdivision surfaces. Though the smoothness analysis tool for regular quad/triangle vertices has been established and C^1 and C^2 quad/triangle schemes (for regular vertices) have been constructed, there is no interpolatory quad/triangle schemes available in the literature. The problem for this is probably that since the template sizes of the local averaging rules of interpolatory schemes for either quad subdivision or triangle subdivision are big, an interpolatory quad/triangle scheme will have large sizes of local averaging rule templates. In this paper we consider matrix-valued interpolatory quad/triangle schemes. In this paper, first we show that both scalar-valued and matrix-valued quad/triangle subdivision scheme can be derived from a nonhomogeneous refinement equation. This observation enables us to treat polynomial reproduction of scalar-valued and matrix-valued quad/triangle schemes in a uniform way. Then, with the result on the polynomial reproduction of matrix-valued quad/triangle schemes provided in our accompanying paper, we obtain in this paper a smoothness estimate for matrix-valued quad/triangle schemes, which extends the smoothness analysis of Levin-Levin from the scalar-valued setting to the matrix-valued setting. Finally, with this smoothness estimate established in this paper, we construct C^1 matrix-valued interpolatory quad/triangle scheme (for regular vertices) with the same sizes of local averaging rule templates as those of Stam-Loop's quad/triangle scheme. We also obtain C^2 matrix-valued interpolatory quad/triangle scheme (for regular vertices) with reasonable sizes of local averaging rule templates.
What's in a Link? From Document Importance to Topical Relevance
Authors: Marijn Koolen, Jaap Kamps
Venue: Proceedings of the 2nd International Conference on Theory of Information Retrieval: Advances in Information Retrieval Theory (2009)

Web information retrieval is best known for its use of the Web's link structure as a source of evidence. Global link evidence is by nature query-independent, and is therefore no direct indicator of the topical relevance of a document for a given search request. As a result, link information is usually considered to be useful to identify the `importance' of documents. Local link evidence, in contrast, is query-dependent and could in principle be related to the topical relevance. We analyse the link evidence in Wikipedia using a large set of ad hoc retrieval topics and relevance judgements to investigate the relation between link evidence and topical relevance.
A Distributed Control System Communication Mode Based on UDP Datagram and Dual-Port Memory
Authors: Zhang Haibo, Sun Ping, Yu Feng, Gao Shenyong, Li Daqing
Venue: Proceedings of the 2009 International Forum on Information Technology and Applications - Volume 01 (2009)

This paper try to promote a data exchange mode based on dual-port RAM and UDP datagram to achieve high-speed data communications in distributed control system. The purpose is to explore a high-performance, low CPU occupancy, high-speed, reliable exchanging mechanism for any amount of data. The model proposed a Dual-port RAM that one port connects the local CPU and the other port connects specific control logic that have reading and writing the Dual-port RAM and net communications functions, the control logic undertakes organizing, sending and receiving and analyzing UDP datagram and achieves the dual-port RAM reading and writing and sends interrupt requirement to the local processor. This model can not only implement efficient data exchange but also provide of interruption mechanism of real-time responding. The paper discusses the needed function modules for achieving these aims and expounds system composing and technical advantages. The paper also analyzes the system developing feasibility, and demonstrates that this model is an advanced, high-performance and promising communication program of distributed control system.
Prediction of Mechanical Lung Parameters Using Gaussian Process Models
Authors: Steven Ganzert, Stefan Kramer, Knut Möller, Daniel Steinmann, Josef Guttmann
Venue: Proceedings of the 12th Conference on Artificial Intelligence in Medicine: Artificial Intelligence in Medicine (2009)

Mechanical ventilation can cause severe lung damage by inadequate adjustment of the ventilator. We introduce a Machine Learning approach to predict the pressure-dependent, non-linear lung compliance, a crucial parameter to estimate lung protective ventilation settings. Features were extracted by fitting a generally accepted lumped parameter model to time series data obtained from ARDS (adult respiratory distress syndrome) patients. Numerical prediction was performed by use of Gaussian processes, a probabilistic, non-parametric modeling approach for non-linear functions.
History-Based Email Prioritization
Authors: Ronald Nussbaum, Abdol-Hossein Esfahanian, Pang-Ning Tan
Venue: Proceedings of the 2009 International Conference on Advances in Social Network Analysis and Mining (2009)

The rise of email as a communication medium raises several issues. A majority of email messages sent are spam. Also, the amount of legitimate email received by many users is overwhelming. In this paper, we propose two new methods of performing email prioritization. Both techniques rank users inboxes using models created from email history. With them, lower priority email messages may be dealt with so that the use of email remains a net productivity gain.
Incremental deployment of network monitors based on Group Betweenness Centrality
Authors: Shlomi Dolev, Yuval Elovici, Rami Puzis, Polina Zilberman
Venue: Information Processing Letters (2009)

In many applications we are required to increase the deployment of a distributed monitoring system on an evolving network. In this paper we present a new method for finding candidate locations for additional deployment in the network. This method is based on the Group Betweenness Centrality (GBC) measure that is used to estimate the influence of a group of nodes over the information flow in the network. The new method assists in finding the location of k additional monitors in the evolving network, such that the portion of additional traffic covered is at least (1-1/e) of the optimal.
An agent-based stochastic ruler approach for a stochastic knapsack problem with sequential competition
Authors: Matthew R. Gibson, Jeffrey W. Ohlmann, Michael J. Fry
Venue: Computers and Operations Research (2010)

We examine a situation in which a decision-maker executes a sequence of resource allocation decisions over time, but the availability of the indivisible resources at future epochs is uncertain due to actions of competitors. We cast this problem as a specialized type of stochastic knapsack problem in which the uncertainty of item (resource) availability is induced by competitors concurrently filling their own respective knapsacks. Utilizing a multi-period bounded multiple-choice knapsack framework, we introduce a general discrete stochastic optimization model that allows a nonlinear objective function, cardinality constraints, and a knapsack capacity constraint. Utilizing a set of greedy selection rules and agent-based modeling to simulate the competitors' actions, we solve the problem with a stochastic ruler approach that incorporates beam search to determine item selection of the types specified by the solution representation. We illustrate the computational effectiveness of our approach on instances motivated by a sports league draft as well as generic problem instances based on the knapsack literature.