ppxscal/embedding_network huggingface dataset:
Limitations of Pseudogenes in Identifying Gene Losses
Authors: James C. Costello, Mira V. Han, Matthew W. Hahn
Venue: Proceedings of the international workshop on Comparative Genomics (2008)

The loss of previously established genes has been proposed as a major force in evolutionary change. While the sequencing of many new species offers the opportunity to identify cases of gene loss, the best method to do this with is unclear. A number of methods to identify gene losses rely on the presence of a pseudogene for each loss. If genes are completely or largely removed from the genome, however, such methods will fail to identify these cases. As the fate of gene losses is still unclear, we attempt to identify losses using nine Drosophila genomes and determine whether these lost genes leave behind pseudogenes in the lineage leading to D. melanogaster. We were able to find 109 cases of unambiguous gene loss. Of these, a maximum of 18 have identifiable pseudogenes, while the other 91 do not. We were also able to identify a large number of previously unannotated genes in the D. melanogaster genome, most of which also had evidence for transcription. Though our results suggest that pseudogene-based methods for finding gene losses will miss a large proportion of these events, we discuss the dependence of these conclusions on the divergence times among the species considered.
Visual Tools for Accessible Computer Supported Collaboration
Authors: Antti Raike, Joanna Saad-Sulonen, Jürgen Scheible, Roman Suzi, Tarmo Toikkanen
Venue: Proceedings of the 11th international conference on Computers Helping People with Special Needs (2008)

This paper discusses device-agnostic technologies and the use of visual mashups in augmenting accessibility in computer supported collaboration. The principles of Design for All (DfA) could be easily taken into software development if participants are allowed to contribute with whatever devices they have at their disposal or are able to use. However, device-agnostic services should rely on open standards, agile development and accessibility guidelines to allow participation of diverse user communities. We present three cases for further considerations of DfA in software development. We aim to promote the learning dimension of the visual tools; the ability of peers to learn and let colleagues learn, collaborate and innovate.
Passive Location to Moving Emitter Using DOA and Its Rate of Change
Authors: Jiangang Wang, Xinglai Hua, Yuanqing Zhu, Qiushi Xi, Zhangheng
Venue: Proceedings of the 2008 Congress on Image and Signal Processing, Vol. 4 - Volume 04 (2008)

The theory of passive location to moving emitter on the ground using DOA (direction of arrival) and its rate of change is described. Expression of observability is obtained by Jacobi matrix and conditions of observability under different relative motion states are discussed. A location algorithm which involves DOA and its rate of change based on MGEKF (Modified Gain Extended Kalman Filter) is put forward, and comparisons with the location algorithm only using DOA and other classic algorithms------EKF ------ are also given respectively according to simulation results.
Graphs and Path Equilibria
Authors: Stéphane Roux
Venue: Proceedings of the 4th international conference on Algorithmic Aspects in Information and Management (2008)

The quest for optimal/stable paths in graphs concerns a few practical or theoretical areas. Taking part in the quest, this paper adopts an abstract, general, equilibrium-oriented approach: it uses (quasi-arbitrary) arc-labelled digraphs, and assumes little about the structure of the sought paths and the definition of equilibrium, i.e. optimality/stability. The paper gives both a sufficient condition and a necessary condition for equilibrium existence for every "graph", pinpoints the difference between these conditions, and shows coincidence when optimality relates to a total order. These results are applied to network routing.
Modeling Transfer Relationships Between Learning Tasks for Improved Inductive Transfer
Authors: Eric Eaton, Marie Desjardins, Terran Lane
Venue: Proceedings of the 2008 European Conference on Machine Learning and Knowledge Discovery in Databases - Part I (2008)

In this paper, we propose a novel graph-based method for knowledge transfer. We model the transfer relationships between source tasks by embedding the set of learned source models in a graph using transferability as the metric. Transfer to a new problem proceeds by mapping the problem into the graph, then learning a function on this graph that automatically determines the parameters to transfer to the new learning task. This method is analogous to inductive transfer along a manifold that captures the transfer relationships between the tasks. We demonstrate improved transfer performance using this method against existing approaches in several real-world domains.
Designing human-computer multi-agent collaboration in productive multi-player games
Authors: Wenn-Chieh Tsai, Yuan-Hsiang Lee, Tsung-Hsiang Chang, Chien-Ju Ho, Jane Yung-jen Hsu
Venue: Proceedings of the 7th international joint conference on Autonomous agents and multiagent systems - Volume 3 (2008)

This research explores productive multi-player games as a platform for human-computer agent collaboration. A multiagent perspective is taken to examine the principles of both gameplay and mechanism design for productive games. To engage human players in sustained gameplay, the game agents are designed with the flow and dramatic principles. To ensure productivity, the game mechanism is designed such that rational agents, both human and software, will follow the target strategy to reach subgame perfect equilibrium. The design principles are demonstrated and evaluated using PhotoSlap, a multi-player productive game for photo annotation.
Enabling Networked Knowledge
Authors: Stefan Decker, Manfred Hauswirth
Venue: Proceedings of the 12th international workshop on Cooperative Information Agents XII (2008)

Despite the enormous amounts of information the Web has made accessible, we still lack means to interconnect and link this information in a meaningful way to lift it from the level of information to the level of knowledge. Additionally, new sources of information about the physical world become available through the emerging sensor technologies. This information needs to be integrated with the existing information on the Web and in information systems which requires (light-weight) semantics as a core building block. In this position paper we discuss the potential of a global knowledge space and which research and technologies are required to enable our vision of networked knowledge.
Statistical Assessment of MSigDB Gene Sets in Colon Cancer
Authors: Angela Distaso, Luca Abatangelo, Rosalia Maglietta, Teresa Maria Creanza, Ada Piepoli, Massimo Carella, Annarita D'Addabbo, Sayan Mukherjee, Nicola Ancona
Venue: Proceedings of the 12th international conference on Knowledge-Based Intelligent Information and Engineering Systems, Part II (2008)

Gene expression profiling offers a great opportunity for understanding the key role of genes in alterations which drive a normal cell to a cancer state. A deep understanding of the mechanisms of tumorigenesis can be reached focusing on deregulation of gene sets or pathways. We measure the amount of deregulation and assess the statistical significance of predefined pathways belonging to MSigDB collection in a colon cancer data set. To measure the relevance of the pathways we use two well-established methods: Gene Set Enrichment Analysis (GSEA) [7] and Gene List Analysis with Prediction Accuracy (GLAPA) [8]. We found that pathways associated to different diseases are strictly connected with colon cancer. Our study highlights the importance of using gene sets genes for understanding the main biological processes and pathways involved in colorectal cancer. Our analysis shows that many of the genes involved in these pathways are strongly associated to colorectal tumorigenesis.
Object-oriented development and application of a nonlinear structural analysis framework
Authors: Bo-Zhou Lin, Ming-Chieh Chuang, Keh-Chyuan Tsai
Venue: Advances in Engineering Software (2009)

This paper describes the framework and application of numerical simulation software on earthquake engineering research and practice. The analysis kernel is developed at the National Center for Research on Earthquake Engineering (NCREE) and is entitled as ''Platform of Inelastic Structural Analysis for 3D systems (PISA3D)''. The design of PISA3D framework adopts the Design Pattern and the Unified Process. PISA3D provides structural modeling and high computational efficiency for engineers and researchers to simulate the responses of nonlinear systems under various kinds of load effects. It includes static or cyclic loads, displacements, earthquake ground accelerations, and earthquake aftershocks. PISA3D is easy to extend and maintain due to its object-oriented nature. Advanced users can derive or compose its objects' libraries to perform different types of structural analyses. Based on object-oriented techniques, VISA3D (Visualization of Inelastic Structural Analysis for 3D systems) has been implemented with usage of OpenGL for 3D graphics and MFC for graphical user interface (GUI). Its framework allows further extension on new input formats and new element types. VISA3D has been mainly developed as a post-processor to examine the analytical results of PISA3D through 2D/3D static or dynamic graphic approaches. It includes graphical checking of the structural model, mode shapes, deformations, extents and locations of plastic hinges, plotting of nodal velocity, acceleration, and energy distribution time histories. This paper then introduces NCREE's recent development on the pre-processing framework GISA3D (Graphical Interface of Inelastic Structural Analysis for 3D systems). The GISA3D does not only supply features as a ''post-processor'', but also fully supports operations of ''model generation'' via mouse motion. Users can create, remove, modify and set elements/nodes through mouse clicking, dragging and selecting. Finally, this paper illustrates the networked sub-structural pseudo dynamic tests using PISA3D as the analysis engine, and concludes with several successful applications of PISA3D/VISA3D/GISA3D on various researches and actual structural engineering projects.
Towards Interoperability in Component Based Development with a Family of DSLs
Authors: Ileana Ober, Ali Abou Dib, Louis Féraud, Christian Percebois
Venue: Proceedings of the 2nd European conference on Software Architecture (2008)

In this paper we address interoperability between components specified using various languages within a same family of DSLs. Our approach consists in applying results of the category theory in order to merge the languages into a unification one, automatically obtained. For this, we use the category of formal specifications of each DSL in the family. Using colimits on the category of algebraic specifications that implements the semantics of the DSLs in the family, we construct a language that unifies the family. Additionally we obtain translation morphisms from individual DSLs to the resulting unified one. By application of the translation morphisms, one can translate each component specifications into a specification written in the unification language. Moreover, properties established in the context of a DSL are transferred to the unifying language. In this paper, we illustrate the unification and the preservation of a property on an example.
Image Processing Applications with a PCNN
Authors: Mario I. Chacon M., Alejandro Zimmerman S., Pablo Rivas P.
Venue: Proceedings of the 4th international symposium on Neural Networks: Advances in Neural Networks, Part III (2007)

This paper illustrates the potentials of the PCNN for image processing. A description of three schemes for image processing using the PCNN is presented in this paper. The first scheme is related to image segmentation, the second to automatic target location, ATL, and the third to face recognition. The first scheme was developed in order to obtain an insight of the behavior of the PCNN as a preprocessor element, the second one is an application to test the performance of the PCNN in an ATL problem. The third is a feature extraction method for face recogiton. The segmentation scheme showed great potentials to perform pixel grouping. The second scheme turned into a system with an ATL performance as good as other systems reported in the literature. And the third scheme seems to improve the performance of a face recognition system.
CTC: An Alternative to Extract Explanation from Bagging
Authors: Ibai Gurrutxaga, Jesús Ma Pérez, Olatz Arbelaitz, Javier Muguerza, José I. Martín, Ander Ansuategi
Venue: Current Topics in Artificial Intelligence: 12th Conference of the Spanish Association for Artificial Intelligence, CAEPIA 2007, Salamanca, Spain, November 12-16, 2007. Selected Papers (2007)

Being aware of the importance of classifiers to be comprehensible when using machine learning to solve real world problems, bagging needs a way to be explained. This work compares Consolidated Tree's Construction (CTC) algorithm with the Combined Multiple Models (CMM) method proposed by Domingos when used to extract explanation of the classification made by bagging. The comparison has been done from two main points of view: accuracy, and quality of the provided explanation. From the experimental results we can conclude that it is recommendable the use of CTC rather than the use of CMM. From the accuracy point of view, the behaviour of CTC is nearer the behaviour of bagging than CMM's one. And, analysing the complexity of the obtained classifiers, we can say that Consolidated Trees (CT trees) will give simpler and, therefore, more comprehensible explanation than CMM classifiers. And besides, looking to the stability of the structure of the built trees, we could say that the explanation given by CT trees is steadier than the one given by CMM classifiers. As a consequence, the user of the classifier will feel more confident using CTC than using CMM.
Secure RFID Cross Certification Protocol Based on One-Time Random Number
Authors: Seung-Min Lee, Jeong-Jai Kim, Moon-Seog Jun
Venue: Proceedings of the 2008 International Conference on Convergence and Hybrid Information Technology (2008)

The prior studies made on RFID certification protocol are still lack of location tracking, reply attack, and spoofing attack. Differentiated from the existing protocols that imposes heavy load on the hardware by generating random number in reader and tag, in this thesis, secure protocol has been designed for location tracking, reply attack, spoofing attack. It generates one time random number at back-end DB and utilize it in the cross certification.
Language support for model-driven software development
Authors: Vasian Cepa, Mira Mezini
Venue: Science of Computer Programming (2008)

This paper is about language technology for facilitating model-driven software development. We argue that two features are important for this purpose: (a) support for explicit meta-representation of programs as an AST-like structure (AST stands for abstract syntax tree) accessible in a programmatic way before and beyond the compilation, and (b) support for user-defined annotations of program elements. That is, we argue for language platforms organized around a Generalized Annotated AST, or GAAST languages for short. We outline the problems with a model-driven development process based on languages without such a support and show how GAAST language technology addresses these problems.
Scalable Architecture for Prefix Preserving Anonymization of IP Addresses
Authors: Anthony Blake, Richard Nelson
Venue: Proceedings of the 8th international workshop on Embedded Computer Systems: Architectures, Modeling, and Simulation (2008)

This paper describes a highly scalable architecture based on field-programmable gate-array (FPGA) technology for prefix-preserving anonymization of IP addresses at increasingly high network line rates. The Crypto-PAn technique, with the Advanced Encryption Standard (AES) as the underlying pseudo-random function, is fully mapped into reconfigurable hardware. A 32 Gb/s fully-pipelined AES engine was developed and used to prototype the Crypto-PAn architecture. The prototype was implemented on a Xilinx Virtex-4 device achieving a worst-case Ethernet throughput of 8 Gb/s using 141 block RAM's and 4262 logic cells. This is considerably faster than software implementations which generally achieve much less than 100 Mb/s throughput. A technology-independent analysis is presented to explore the scalability of the architecture to higher multi-gigabit line-rates.
Representation of Uncertain Knowledge in Probabilistic OLAP Model
Authors: Maciej Kiewra
Venue: Proceedings of the 12th international conference on Knowledge-Based Intelligent Information and Engineering Systems, Part II (2008)

The probabilistic OLAP model has been presented in this paper. It permits uncertain knowledge to be represented in data warehouse systems. There are two types of uncertainty that can be expressed in this model: imprecise facts and uncertain facts. The former are facts that have occurred but their characteristics are not certain. The latter are facts whose occurrences are uncertain. Typical OLAP algebra operators (set operators, restriction, projection etc.) are included in this model.
Symmetric Multiprocessor Design for Hybrid CPU/FPGA SoCs
Authors: Shane Santner, Wesley Peck, Jason Agron, David Andrews
Venue: Proceedings of the 4th international workshop on Reconfigurable Computing: Architectures, Tools and Applications (2008)

This paper presents the design of a Symmetric Multiprocessor (SMP) hybridthreads (hthreads) system that allows multiple threads to execute in parallel across multiple processors controlled by a single hardware scheduler. This approach increases the performance of software at a minimal cost to hardware. The issues that must be addressed for extending a uniprocessor kernel include system initialization, processor identification, context switching and concurrency control. As a proof of concept this paper shows how hthreads, an existing hardware/software co-designed kernel can be extended to control multiple processors from a single, centralized hardware scheduler. Analysis results from executing on hardware reveal that for computationally intensive programs the typical speedup is in the range of 1.65x. This shows improvement in system performance while also illustrating issues associated with bus arbitration and memory access times.
Massh!: a web-based collective music mashup system
Authors: Nao Tokui
Venue: Proceedings of the 3rd international conference on Digital Interactive Media in Entertainment and Arts (2008)

Massh! is an online music software, which enables users to use any portions (i.e., loops) of sound data found on the Internet and mix them to make their own versions of songs (i.e., Mashup). Mashups made on this system can be also published as "blueprints" containing descriptions enough to reproduce the same result on other users' computers. Its distinctive visual user interface also provides highly interactive user experience, so that people with little music knowledge and experience can join the creative process of making music.
Fronto-temporal interactions during overt verbal initiation and suppression
Authors: Paul Allen, Andrea Mechelli, Klaas E. Stephan, Fern Day, Jeffery Dalton, Steven Williams, Philip K. McGuire
Venue: Journal of Cognitive Neuroscience (2008)

The Hayling Sentence Completion Task (HSCT) is known to activate left hemisphere frontal and temporal language regions. However, the effective connectivity between frontal and temporal language regions associated with the task has yet to be examined. The aims of the study were to examine activation and effective connectivity during the HSCT using a functional magnetic resonance imaging (fMRI) paradigm in which participants made overt verbal responses. We predicted that producing an incongruent response (response suppression), compared to a congruent one (response initiation), would be associated with greater activation in the left prefrontal cortex and an increase in the effective connectivity between temporal and frontal regions. Fifteen participants were scanned while completing 80 sentence stems. The congruency and constraint of sentences varied across trials. Dynamic Causal Modeling (DCM) and Bayesian Model Selection (BMS) were used to compare a set of alternative DCMs of fronto-temporal connectivity. The HSCT activated regions in the left temporal and prefrontal cortices, and the cuneus. Response suppression was associated with greater activation in the left middle and orbital frontal gyri and the bilateral precuneus than response initiation. Left middle temporal and frontal regions identified by the conventional fMRI analyses were entered into the DCM analysis. Using a systematic BMS procedure, the optimal DCM showed that the connection from the left middle temporal gyrus, which was driven by verbal stimuli per se, was significantly increased in strength during response suppression compared to initiation. Greater effective connectivity between left temporal and prefrontal regions during response suppression may reflect the transfer of information from posterior temporal regions where semantic and lexical information is stored to prefrontal regions where it is manipulated in preparation for an appropriate response.
What Happened to Esfinge in 2007?
Authors: Luís Miguel Cabral, Luís Fernando Costa, Diana Santos
Venue: Advances in Multilingual and Multimodal Information Retrieval: 8th Workshop of the Cross-Language Evaluation Forum, CLEF 2007, Budapest, Hungary, September 19-21, 2007, Revised Selected Papers (2008)

Esfinge is a general domain Portuguese question answering system which uses the information available on the Web as an additional resource when searching for answers. Other external resources and tools used are a broad coverage parser, a morphological analyser, a named entity recognizer and a Web-based database of word co-occurrences.In this fourth participation in CLEF, in addition to the new challenges posed by the organization (topics and anaphors in questions and the use of Wikipedia to search and support answers), we experimented with a multiple question and multiple answer approach in QA.
Muller message-passing automata and logics
Authors: Benedikt Bollig, Dietrich Kuske
Venue: Information and Computation (2008)

We study nonterminating message-passing automata whose behavior is described by infinite message sequence charts. As a first result, we show that Muller, Buchi, and termination-detecting Muller acceptance are equivalent for these devices. To describe the expressive power of these automata, we give a logical characterization. More precisely, we show that they have the same expressive power as the existential fragment of a monadic second-order logic featuring a first-order quantifier to express that there are infinitely many elements satisfying some property. This result is based on Vinner's extension of the classical Ehrenfeucht-Fraisse game to cope with the infinity quantifier.