ppxscal/embedding_network huggingface dataset:
Coclustering of Human Cancer Microarrays Using Minimum Sum-Squared Residue Coclustering
Authors: Hyuk Cho, Inderjit S. Dhillon
Venue: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (2008)

It is a consensus in microarray analysis that identifying potential local patterns, characterized by coherent groups of genes and conditions, may shed light on the discovery of previously undetectable biological cellular processes of genes as well as macroscopic phenotypes of related samples. In order to simultaneously cluster genes and conditions, we have previously developed a fast co-clustering algorithm, Minimum Sum-Squared Residue Co-clustering (MSSRCC), which employs an alternating minimization scheme and generates what we call co-clusters in a checkerboard structure. In this paper, we propose specific strategies that enable MSSRCC to escape poor local minima and resolve the degeneracy problem in partitional clustering algorithms. The strategies include binormalization, deterministic spectral initialization, and incremental local search. We assess the effects of various strategies on both synthetic gene expression datasets and real human cancer microarrays and provide empirical evidence that MSSRCC with the proposed strategies performs better than existing co-clustering and clustering algorithms. In particular, the combination of all the three strategies leads to the best performance. Furthermore, we illustrate coherence of the resulting co-clusters in a checkerboard structure, where genes in a co-cluster manifest the phenotype structure of corresponding specific samples, and evaluate the enrichment of functional annotations in Gene Ontology (GO).
Utilization of Soft Computing Techniques for Making Environmental Games More Exciting ---Toward an Effective Utilization of the COMMONS GAME
Authors: Norio Baba, Kenta Nagasawa, Hisashi Handa
Venue: Proceedings of the 12th international conference on Knowledge-Based Intelligent Information and Engineering Systems, Part II (2008)

We have suggested that utilization of soft computing techniques such as GAs and EAs could contribute a lot for making the original COMMONS GAME much more exciting. In this paper, we try to find an answer concerning to the question "Which game is the best for letting people consider seriously about the commons among the three games (the original COMMONS GAME, the modified COMMONS GAME utilizing GAs NNs , and the modified COMMONS GAME utilizing EAs NNs) ?". Several game playing by our students confirm that the modified COMMONS GAME utilizing EAs NNs can provide the best chance for letting players consider seriously about the commons.
Robustness design of nonlinear systems: fuzzy Lyapunov approach
Authors: Ken Yeh, Meng-Lung Lin, Chen-Yuan Chen, Cheng-Wu Chen
Venue: Proceedings of the 7th WSEAS International Conference on Application of Electrical Engineering (2008)

This study addresses a fuzzy Lyapunov method for the stability analysis of time-delay fuzzy systems subject to external disturbances. The Takagi-Sugeno (T-S) fuzzy model and parallel distributed compensation (PDC) scheme are first employed to design a nonlinear fuzzy controller in order to stabilize the time-delay fuzzy systems. According to the controlled system, the H infinity criterion is derived based on the fuzzy Lyapunov method, which is defined in terms of fuzzy blending quadratic Lyapunov functions. Based on the stability criterion, the time-delay fuzzy systems are guaranteed to be stable.
A Model-Driven Measurement Approach
Authors: Martin Monperrus, Jean-Marc Jézéquel, Joël Champeau, Brigitte Hoeltzener
Venue: Proceedings of the 11th international conference on Model Driven Engineering Languages and Systems (2008)

Companies using domain specific languages in a model-driven development process need to measure their models. However, developing and maintaining a measurement software for each domain specific modeling language is costly. Our contribution is a model-driven measurement approach. This measurement approach is model-driven from two viewpoints: 1) it measures models of a model-driven development process; 2) it uses models as unique and consistent metric specifications, w.r.t a metric specification metamodel. This declarative specification of metrics is then used to generate a fully fledged implementation. The benefit from applying the approach is evaluated by two applications. They indicate that this approach reduces the domain-specific measurement software development cost.
Flexible Querying of Fuzzy RDF Annotations Using Fuzzy Conceptual Graphs
Authors: Patrice Buche, Juliette Dibie-Barthélemy, Gaëlle Hignette
Venue: Proceedings of the 16th international conference on Conceptual Structures: Knowledge Visualization and Reasoning (2008)

This paper presents a flexible querying system of fuzzy RDF annotations which consists in translating fuzzy RDF annotations into fuzzy conceptual graphs and using an "approximate"-projection operation in order to compare fuzzy query graphs with fuzzy annotation graphs. The fuzzy sets in the query graphs having a semantic of preferences are compared with the fuzzy sets in the annotation graphs having a semantic of similarity or imprecision. These comparisons deliver several scores which are used by our flexible querying system to sort the answers according to a total order even if these scores are not commensurable.
Toward Emotional E-Commerce: The Customer Agent
Authors: Nicolae Jascanu, Veronica Jascanu, Severin Bumbaru
Venue: Proceedings of the 12th international conference on Knowledge-Based Intelligent Information and Engineering Systems, Part I (2008)

Experiencing and expressing emotions are integral parts of our life. In the retail area of commerce, emotion plays a fundamental role. When we choose or buy a commodity, our choice has a profound emotional dimension. We are social beings, we are influenced by others opinions, we have our opinions and we like to bargain for everything. This paper proposes a novel model, based on dimensional models of emotion, able to capture and interpret the customer emotional knowledge.
A framework for detecting and diagnosing configuration faults in web applications
Authors: Atif Memon
Venue:  (2007)

Software portability is a key concern when target operational environments are highly configurable; variations in configuration settings can significantly impact software correctness. While portability is key for a wide range of software types, it is a significant challenge in web application development. The client configuration used to navigate and interact with web content is known to be an important factor in the subsequent quality of deployed web applications. With the widespread use of diverse, heterogeneous web client configurations, the results of web application deployment can vary unpredictably among users. Given existing approaches and limited development resources, attempting to develop web applications that are viewable, functional, and portable for the vast web configuration space is a significant undertaking. As a result, faults that only surface in precise configurations, termed configuration faults, have the potential to escape detection until web applications are fielded. This dissertation presents an automated, model-based framework that uses static analysis to detect and diagnose web configuration faults. This approach overcomes the limitations of current techniques by featuring an extensible model of the configuration space that enables efficient portability analysis across the vast array of client environments. The basic idea behind this approach is that source code fragments (i.e., HTML tags and CSS rules) embedded in web application source code adversely impact portability of web applications when they are unsupported in target client configurations; without proper support, the source code is either processed incorrectly or ignored, resulting in configuration faults. Using static analysis, configuration fault detection is performed by applying a model of the web application source against knowledge of support criteria; any unsupported source code detected is considered an index to potential configuration faults. In the effort to fully exploit this approach, improve practicality, and maximize fault detection efficiency, manual and automated approaches to knowledge acquisition have been implemented, variations of web application and client support knowledge models have been investigated, and visualization of configuration fault detection results has been explored. To optimize the automated acquisition of support knowledge, alternate learning strategies have been empirically investigated and provisions for capturing tag interaction have been integrated into the process.
A queueing approach to optimal resource replication in wireless sensor networks
Authors: Christopher R. Mann, Rusty O. Baldwin, Jeffrey P. Kharoufeh, Barry E. Mullins
Venue: Performance Evaluation (2008)

We develop a queueing model for analyzing resource replication strategies in wireless sensor networks. The model can be used to minimize either the total transmission rate of the network (an energy-centric approach) or to ensure the proportion of query failures does not exceed a predetermined threshold (a failure-centric approach). The model explicitly considers the limited availability of network resources, as well as the frequency of resource requests and query deadlines, to determine the optimal replication strategy for a network resource. While insufficient resource replication increases query failures and transmission rates, replication levels beyond the optimum result in only marginal decreases in the proportion of query failures at a cost of higher total energy expenditure and network traffic.
A Joint Segmenting and Labeling Approach for Chinese Lexical Analysis
Authors: Xinhao Wang, Jiazhong Nie, Dingsheng Luo, Xihong Wu
Venue: Proceedings of the European conference on Machine Learning and Knowledge Discovery in Databases - Part II (2008)

This paper introduces an approach which jointly performs a cascade of segmentation and labeling subtasks for Chinese lexical analysis, including word segmentation, named entity recognition and part-of-speech tagging. Unlike the traditional pipeline manner, the cascaded subtasks are conducted in a single step simultaneously, therefore error propagation could be avoided and the information could be shared among multi-level subtasks. In this approach, Weighted Finite State Transducers (WFSTs) are adopted. Within the unified framework of WFSTs, the models for each subtask are represented and then combined into a single one. Thereby, through one-pass decoding the joint optimal outputs for multi-level processes will be reached. The experimental results show the effectiveness of the presented joint processing approach, which significantly outperforms the traditional method in pipeline style.
Some Conceptual Links between Dynamic Physical Systems and Operator Theory Issues Concerning Energy Balances and Stability
Authors: M. De la Sen
Venue: Informatica (2005)

This paper relates properties of operators with the well-known concepts of positive realness and passivity properties in dynamic systems and their associate transfer functions. Those concepts together with very close related ones are first examined from a physical point of view. Then, they are related with hyperstability and properties of transfer functions while the hyperstability theorem is revisited and interpreted. Finally, the above concepts are compared to the mathematical concepts of positivity and closely related ones in operator theory in Hilbert spaces.
At Issue
Authors: Bill Feiereisen, George K. Thiruvathukal
Venue: Computing in Science and Engineering (2008)

In this installment of At Issue, two of CiSE's editorial board members describe the magazine's current and future Web presence. We start with Bill Feiereisen's discussion of science on the Web and what it could mean for CiSE ("Are We There Yet?") and end with George Thiruvathukal's discussion of the challenges therein ("If We Build It, Will They Come?"). CiSE's official homepage is www.computer.org/cise; we gladly welcome comments with suggestions or feedback. You can contact lead editor (Jenny Stout; jstout@computer.org) or write to either Bill or George (their email addresses appear at the end of their respective essays).
Universal Execution of Parallel Processes: Penetrating NATs over the Grid
Authors: Insoon Jo, Hyuck Han, Heon Y. Yeom, Ohkyoung Kwon
Venue: Proceedings of the 7th international conference on Computational Science, Part II (2007)

Today, clusters are very important computing resources and many computing centers manage their clusters in private networks. But parallel programs may not work in private clusters. Because hosts in private clusters are not globally reachable, hosts behind different private clusters cannot be reached directly in order to communicate. It will certainly be a huge loss of resources if private clusters are excluded from the computing due to this reason. There has been much research on this issue, but most of them concentrate on user-level relaying because it is a general and easily-implementable solution. However, even well-implemented, user-level solutions result in much longer communication latency than kernel-level solutions. This paper adopted a novel kernel-level solution and applied it to MPICH-G2. Our scheme is generally applicable, simple and efficient. The experimental results show that our scheme incurs very little overhead except when small messages are transmitted. That is, it supports a more universal computing environment by including private clusters with remarkably little overhead.
Testing Concurrent Objects with Application-Specific Schedulers
Authors: Rudolf Schlatte, Bernhard Aichernig, Frank Boer, Andreas Griesmayer, Einar Broch Johnsen
Venue: Proceedings of the 5th international colloquium on Theoretical Aspects of Computing (2008)

In this paper, we propose a novel approach to testing executable models of concurrent objects under application-specific scheduling regimes. Method activations in concurrent objects are modeled as a composition of symbolic automata; this composition expresses all possible interleavings of actions. Scheduler specifications, also modeled as automata, are used to constrain the system execution. Test purposes are expressed as assertions on selected states of the system, and weakest precondition calculation is used to derive the test cases from these test purposes. Our new testing technique is based on the assumption that we have full control over the (application-specific) scheduler, which is the case in our executable models under test. Hence, the enforced scheduling policy becomes an integral part of a test case. This tackles the problem of testing non-deterministic behavior due to scheduling.
A Java Tool for the Management of Chemical Databases and Similarity Analysis Based on Molecular Graphs Isomorphism
Authors: Irene Luque Ruiz, Miguel Ángel Gómez-Nieto
Venue: Proceedings of the 8th international conference on Computational Science, Part II (2008)

This paper describes a computational chemistry solution for the management of large chemical databases of molecules and the performing of isomorphism calculation for the analysis of database similarity and diversity. The system has been fully developed using Java language and it uses other free and standard Java library. The system allows to the user the building of databases of molecules, store information about the molecules, the matching among molecules using different isomorphism paradigms and the similarity/diversity analysis of databases through a wide number of similarity indices.
A New Upper Bound for Max-2-SAT: A Graph-Theoretic Approach
Authors: Daniel Raible, Henning Fernau
Venue: Proceedings of the 33rd international symposium on Mathematical Foundations of Computer Science (2008)

In MaxSat, we ask for an assignment which satisfies the maximum number of clauses for a boolean formula in CNF. We present an algorithm yielding a run time upper bound of ${\mathcal{O}}^*({2^{\frac{K}{6.2158}}})$ for Max-2-Sat (each clause contains at most 2 literals), where K is the number of clauses. The run time has been achieved by using heuristic priorities on the choice of the variable on which we branch. The implementation of these heuristic priorities is rather simple, though they have a significant effect on the run time. Also the analysis uses a non-standard measure.
The ORDVAC
Authors: R. E. Meagher, J. P. Nash
Venue: Papers and discussions presented at the Dec. 10-12, 1951, joint AIEE-IRE computer conference: Review of electronic digital computers (1951)

The ORDVAC is a general purpose machine which has been built by the University of Illinois for the Ballistic Research Laboratories at Aberdeen, Maryland. The design has followed in a general way that of the computing machine discussed by Burks, Goldstine, and von Neumann in the "Preliminary Discussion of the Logical Design of an Electronic Computing Instrument" issued in 1946 by the Institute for Advanced Study.
Coreference Resolution for Questions and Answer Merging by Validation
Authors: Sven Hartrumpf, Ingo Glöckner, Johannes Leveling
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)

For its fourth participation at QA@CLEF, the German question answering (QA) system InSicht was improved for CLEF 2007 in the following main areas: questions containing pronominal or nominal anaphors are treated by a coreference resolver; the shallow QA methods are improved; and a specialized module is added for answer merging. Results showed a performance drop compared to last year mainly due to problems in handling the newly added Wikipedia corpus. However, dialog treatment by coreference resolution delivered very accurate results so that follow-up questions can be handled similarly to isolated questions.
Motion Capture and Emotion: Affect Detection in Whole Body Movement
Authors: Elizabeth Crane, Melissa Gross
Venue: Proceedings of the 2nd international conference on Affective Computing and Intelligent Interaction (2007)

Bodily expression of felt emotion was associated with emotion-specific changes in gait parameters and kinematics. The emotions angry, sad, content, joy and no emotion at all were elicited in forty-two undergraduates (22 female, 20 male; 20.1±2.7 yrs) while video and whole body motion capture data (120 Hz) were acquired. Participants completed a self-report of felt emotion after each trial. To determine whether the walkers' felt emotions were recognizable in their body movements, video clips of the walkers were shown to 60 undergraduates (29 female, 31 male; 20.9±2.7 yrs). After viewing each video clip, observers selected one of 10 emotions that they thought the walker experienced during the trial. This study provides evidence that emotions can be successfully elicited in the laboratory setting, emotions can be recognized in the body movements of others, and that body movements are affected by felt emotions.
Designing multimedia learning objects for PDAs
Authors: Claire Bradley, Richard Haynes, Tom Boyle
Venue: International Journal of Mobile Learning and Organisation (2008)

This paper discusses the design of rich multimedia learning objects for Personal Digital Assistants (PDAs). It shows how successful design principles developed for web-based learning objects have been adapted for the PDA. A prototype object and technical design guidelines have been developed, and these are outlined. The prototype was evaluated with a small number of target students, to give initial feedback on the prototype and their views of using the PDA as a learning tool. The work has produced a proof of concept, which illustrates that rich multimedia learning objects can be developed for the PDA, and it informs our future work in mobile learning.
A Rational Reconstruction of a System for Experimental Mathematics
Authors: Jacques Carette, William M. Farmer, Volker Sorge
Venue: Proceedings of the 14th symposium on Towards Mechanized Mathematical Assistants: 6th International Conference (2007)

In previous papers we described the implementation of a system which combines mathematical object generation, transformation and filtering, conjecture generation, proving and disproving for mathematical discovery in non-associative algebra. While the system has generated novel, fully verified theorems, their construction involved a lot of ad hoc communication between disparate systems. In this paper we carefully reconstruct a specification of a sub-process of the original system in a framework for trustable communication between mathematics systems put forth by us. It employs the concept of biform theories that enables the combined formalisation of the axiomatic and algorithmic theories behind the generation process. This allows us to gain a much better understanding of the original system, and exposes clear generalisation opportunities.
Explanatory Style for Socially Interactive Agents
Authors: Sejin Oh, Jonathan Gratch, Woontack Woo
Venue: Proceedings of the 2nd international conference on Affective Computing and Intelligent Interaction (2007)

Recent years have seen an explosion of interest in computational models of socio-emotional processes, both as a mean to deepen understanding of human behavior and as a mechanism to drive a variety of training and entertainment applications. In contrast with work on emotion, where research groups have developed detailed models of emotional processes, models of personality have emphasized shallow surface behavior. Here, we build on computational appraisal models of emotion to better characterize dispositional differences in how people come to understand social situations. Known as explanatory style, this dispositional factor plays a key role in social interactions and certain socio-emotional disorders, such as depression. Building on appraisal and attribution theories, we model key conceptual variables underlying the explanatory style, and enable agents to exhibit different explanatory tendencies according to their personalities. We describe an interactive virtual environment that uses the model to allow participants to explore individual differences in the explanation of social events, with the goal of encouraging the development of perspective taking and emotion-regulatory skills.
Reducing Temporary Trees in XQuery
Authors: David Bednárek
Venue: Proceedings of the 12th East European conference on Advances in Databases and Information Systems (2008)

The creation, maintenance and disposal of tree fragments during XQuery execution form a significant issue in the design of XQuery processors. The problem is further complicated by the definition of node identity which violates the functional nature of the XQuery language. This paper presents a novel mathematical model of XQuery execution that reflects temporary tree construction and manipulation, including navigation. Using this model as reference, an efficient algorithm of static analysis is presented that determines the level of information required at a particular place of the XQuery program. As a side effect, the algorithm also decides on the ordered/unordered context as defined by the XQuery language. Based on this algorithm, the amount of information stored during the execution as well as the complexity of operations may be significantly reduced.