ppxscal/embedding_network huggingface dataset:
Visualizing the Gene Ontology-Annotated Clusters of Co-expressed Genes: A Two-Design Study
Authors: David C. Y. Fung, Seok-Hee Hong, Kai Xu, David Hart
Venue: Proceedings of the 2008 Fifth International Conference BioMedical Visualization: Information Visualization in Medical and Biomedical Informatics (2008)

In molecular biology, Gene Ontology (GO) has often been used for annotation and as a data mining dimension. A frequently performed step in microarray analytics is the clustering of co-expressed genes by their GO bioprocesses. Biological deductions are then made from the visual representation of the cluster pattern. Thus far, the question of how different representations of GO-annotated clusters affect biological interpretation and usability has not been investigated. In this paper, we evaluated two representations of GO-annotated clusters of co-expressed genes. Using a published cDNA microarray dataset, we tested the effect of each representation on biological interpretation. We also reported the results of the user evaluation conducted with bench biologists from different areas of expertise. Our study suggests that the bipartite graph may be more suitable for microarray analytics.
Principal Component Analysis for Large Scale Problems with Lots of Missing Values
Authors: Tapani Raiko, Alexander Ilin, Juha Karhunen
Venue: Proceedings of the 18th European conference on Machine Learning (2007)

Principal component analysis (PCA) is a well-known classical data analysis technique. There are a number of algorithms for solving the problem, some scaling better than others to problems with high dimensionality. They also differ in their ability to handle missing values in the data. We study a case where the data are high-dimensional and a majority of the values are missing. In case of very sparse data, overfitting becomes a severe problem even in simple linear models such as PCA. We propose an algorithm based on speeding up a simple principal subspace rule, and extend it to use regularization and variational Bayesian (VB) learning. The experiments with Netflix data confirm that the proposed algorithm is much faster than any of the compared methods, and that VB-PCA method provides more accurate predictions for new data than traditional PCA or regularized PCA.
Incremental Generation of Abductive Explanations for Tactical Behavior
Authors: Thomas Wagner, Tjorben Bogon, Carsten Elfers
Venue: RoboCup 2007: Robot Soccer World Cup XI (2008)

According to the expert literature on (human) soccer, e.g., the tactical behavior of a soccer team should differ significantly with respect to the tactics and strategy of the opponent team. In the offensive phase the attacking team is usually able to actively select an appropriate tactic with limited regard to the opponent strategy. In contrast, in the defensive phase the more passive recognition of tactical patterns of the behavior of the opponent team is crucial for success. In this paper we present a qualitative, formal, abductive approach, based on a uniform representation of soccer tactics that allows to recognize/explain the tactical and strategical behavior of opponent teams based on past (usually incomplete) observations.
Local coordination based routing and spectrum assignment in multi-hop cognitive radio networks
Authors: Zongkai Yang, Geng Cheng, Wei Liu, Wei Yuan, Wenqing Cheng
Venue: Mobile Networks and Applications (2008)

Although Cognitive Radio technology brings efficient spectrum usage and effective interference avoidance, it also brings new challenges to routing in multi-hop Cognitive Radio Networks. Firstly, spectrum assignment is required for each hop in routing; secondly, new delay is introduced during multi-frequency scheduling and frequency switching in each node; thirdly, the intersecting nodes serving multi-frequency traffic is easy to be bottleneck in neighborhood region. In this paper, we analysis and model the pernode delay and the path delay in multi-hop Cognitive Radio Network. Then we propose a framework of local coordination based routing and spectrum assignment to solve above problems, which consists of one protocol for routing path and one scheme for neighborhood region. A on-demand Routing and Spectrum Assignment Protocol is proposed to exchange the local spectrum information and interact with multi-frequency scheduling in each node. A local coordination scheme is presented to support flow redirection at an intersecting node and distribute heavy multi-frequency workload to its neighborhood. We prove the correctness and effectiveness of the protocol by thorough simulations, and find that the proposed solution provides good adaptability to varying spectrum distribution. The end-to-end delay when adaptive relay is cooperating with routing protocol outperforms traditional bare-routing solutions.
Object Oriented Software Architecture Design based on UML/Petri Net approach for deadlock prevention of Real Time Systems
Authors: Sílvio Bacalá Júnior, Stéphane Julia
Venue: Journal of Computational Methods in Sciences and Engineering (2005)

The objective of this article is to present an approach based on UML dynamic diagrams and on Petri Net Objects for the deadlock prevention of Real Time Systems. The main idea consists of translating the sequence diagrams which express the initial specifications of the system in a unique Petri Net model which represents the global behaviour of the entire system and which belongs to the special class of Petri Nets called Simple Sequential Process with Resources. After the detection of possible unmarked siphons in the structure of the global model, a deadlock prevention strategy based on the addition of local control places is applied in order to remove structural deadlocks. The augmented Petri Net model is then translated into a set of collaboration and state-transition diagrams which represent the final deadlock free UML specification. Finally, a software architecture free of deadlocks based on an object which contains the global behaviour of the system and which centralises all the interactions between the software objects is presented. The approach is illustrated through an example of Real Time System used at the global coordination level of a Batch System.
Better Perception of 3D-Spatial Relations by Viewport Variations
Authors: Markus Jobst, Jürgen Döllner
Venue: Proceedings of the 10th international conference on Visual Information Systems: Web-Based Visual Information Search and Management (2008)

Computer-graphics and especially virtual 3D worlds evolve to important tools for digital cartography, where the main aim of efficient spatial communication rules processes of conception, design and dissemination. This paper investigates the enhancement of visual spatial relations in virtual 3D worlds, which's limitation on standard displays is a main drawback of digital cartography. The main limitations of digital cartography concern the extension of viewing plane and its resolution, which have impact on information depth of the map content, transmitting an overview, thus the highlighting of spatial relations and additional request for cognitive load. These drawbacks are not only limited to 2D maps, but are also existing in virtual 3D environments, where additional geometric characteristics, like perspective distortions, multiple scales or overriding, may influence a correct extraction of spatial-related content. On the other hand these specific geometric disadvantages should be formulated as benefit of 3D, especially when infinite numbers of scale can be combined in a "natural way" or spatial content becomes extracted by naïve interaction. One main limitation of digital presentations generally persists: the limitation of the presentation area on standard displays, which leads to a very restricted overview and fewer visible relations of spatial content. View-port variations that modify perspective and/or orthographic projections are one possibility to enhance rendering methods in a way that the main disadvantages of regular perspective views become decreased and the perceptibility for an overview and spatial relations expanded. These variations cover progressive and degressive central-perspectives as well as progressive and degressive "parallel-perspectives", which provide very specific characteristics in use with spatial information transmission. This contribution focuses on enhancing virtual spatial relations in 3D environments by using view-port variations, that modify perspective and orthographic views in a progressive and degressive way. Provided that standard displays deliver significant limitations for effective and expressive geo-communication with virtual 3D environments, offers by 3D cartography are discussed. An exemplary comparison of actual 3D city models allows to identify "dead values" and gives one clue for the requested modification. The description and exemplary visualization of view-port varia-tions lead to their theoretical communication aspects, which will guide pragmatic (user) studies in future.
Proceedings of the 7th international joint conference on Autonomous agents and multiagent systems: demo papers
Venue: International Conference on Autonomous Agents (2008)

The AAMAS conference is the premier international forum for research in autonomous agents and multi-agent systems. Since its first edition in 2002, it has featured a demonstration session where live interactive demos are given. The goal of the AAMAS demonstration session is to give participants, from industry and academia alike, an opportunity to present their latest developments on software and robotic systems. In 2006, the demonstration track featured 17 demos, followed in 2007 by 11 demos coming primarily from academic (software) contributors, as well as a some research labs and industry. In the 2008 edition, demonstrations were invited for three different categories: academic software, industrial software, and robotics. Another change we introduced this year is that the winners of the "best demo" awards will be chosen by public vote, and there will separate awards for each of the demo categories. Also, the demonstrations will be presented in a plenary session for the first time this year. We were delighted to receive an unusually high number of excellent submissions, each one of them attesting to the clear maturity of current Agents technology. Due to space constraints, we have been able to accept only 34 demos from the many strong submissions we received. However, the vast majority of them are still academic, although some with apparent industrial links. In particular, the accepted demos were 23 in the academic software category, 5 in industrial software, and 6 in robotics. Examples of demo topics of interest included, but were not limited to: &bull; Multi-agent software systems &bull; Industrial and military applications (including prototypes) &bull; Agent-based games &bull; Agent platforms and development environments &bull; Open-source software tools &bull; Robotic systems (single and multi-agent) &bull; Virtual agents and interactive virtual environments &bull; Simulation environments This section of the proceedings includes 2-page papers describing each demo presentation at AAMAS'08. Taken together, we believe these articles showcase the amazing recent progress in the area of Autonomous Agents and Multi-Agent Systems, and we look forward for a very exciting demo session at AAMAS'08. We hope that these articles will promote discussion and future research, as well as encourage the AAMAS community to get involved in implementing, deploying, and popularising novel Agents technology. 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
Classes of Submodular Constraints Expressible by Graph Cuts
Authors: Stanislav Živný, Peter G. Jeavons
Venue: Proceedings of the 14th international conference on Principles and Practice of Constraint Programming (2008)

Submodular constraints play an important role both in theory and practice of valued constraint satisfaction problems (VCSPs). It has previously been shown, using results from the theory of combinatorial optimisation, that instances of VCSPs with submodular constraints can be minimised in polynomial time. However, the general algorithm is of order O(n 6) and hence rather impractical. In this paper, by using results from the theory of pseudo-Boolean optimisation, we identify several broad classes of submodular constraints over a Boolean domain which are expressible using binary submodular constraints, and hence can be minimised in cubic time. We also discuss the question of whether all submodular constraints of bounded arity over a Boolean domain are expressible using only binary submodular constraints, and can therefore be minimised efficiently.
Auditing Categorical SUM, MAX and MIN Queries
Authors: Francesco M. Malvestuto
Venue: Proceedings of the UNESCO Chair in data privacy international conference on Privacy in Statistical Databases (2008)

Auditing consists in logging answered queries and checking, each time that a new query is submitted, that no sensitive information is disclosed by combining responses to answered queries with the response to the current query. Such a method for controlling data disclosure naturally raises the following inference problem: Given a set Q of answered queries and a query q, is the information asked by q determined by responses to queries in Q? We solve this inference problem for sum-queries (of real type and nonnegative real type), max-queries and min-queries and provide tests running in polynomial time. To achieve this, we introduce an inference model which, unlike previous inference models, is sound and complete in that the answer to the question of the inference problem comes out to be affirmative if and only if the information asked by q coincides exactly with the value of q determined by Q.
Efficient Fuzzy Predictive Economic Set---Point Optimizer
Authors: Piotr M. Marusak
Venue: Proceedings of the 9th international conference on Artificial Intelligence and Soft Computing (2006)

A fuzzy predictive set---point optimizer which uses a nonlinear, fuzzy dynamic process model is proposed in the paper. The algorithm of the optimizer is formulated in such a way that only a numerically efficient, quadratic optimization problem must be solved at each algorithm iteration. It is demonstrated, using an example of a control system of a nonlinear MIMO control plant, that application of the optimizer based on a fuzzy model instead of a linear one can result in substantial improvement of control system operation. The fuzzy control plant model, the optimizer is based on, consists of local models in the form of control plant step responses. Thus, the model is easy to obtain and the proposed optimizer easy to design. 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
Sub-tree Swapping Crossover, Allele Diffusion and GP Convergence
Authors: Stephen Dignum, Riccardo Poli
Venue: Proceedings of the 10th international conference on Parallel Problem Solving from Nature: PPSN X (2008)

We provide strong evidence that sub-tree swapping crossover when applied to tree-based representations will cause alleles (node labels) to diffuse within length classes. For a-ary trees we provide further confirmation that all programs are equally likely to be sampled within any length class when sub-tree swapping crossover is applied in the absence of selection and mutation. Therefore, we propose that this form of search is unbiased - within length classes - for a-ary trees. Unexpectedly, however, for mixed-arity trees this is not found and a more complicated form of search is taking place where certain tree shapes, hence programs, are more likely to be sampled than others within each class. We examine the reasons for such shape bias in mixed arity representations and provide the practitioner with a thorough examination of sub-tree swapping crossover bias. The results of this, when combined with crossover length bias research, explain Genetic Programming's lack of structural convergence during later stages of an experimental run. Several operators are discussed where a broader form of convergence may be detected in a similar way to that found in Genetic Algorithm experimentation.
Ignoble Trails - Where Crossover Is Provably Harmful
Authors: J. Neal Richter, Alden Wright, John Paxton
Venue: Proceedings of the 10th international conference on Parallel Problem Solving from Nature: PPSN X (2008)

Beginning with the early days of the genetic algorithm and the schema theorem it has often been argued that the crossover operator is the more important genetic operator. The early Royal Road functions were put forth as an example where crossover would excel, yet mutation based EAs were subsequently shown to experimentally outperform GAs with crossover on these functions. Recently several new Royal Roads have been introduced and proved to require expected polynomial time for GAs with crossover, while needing exponential time to optimize for mutation-only EAs. This paper does the converse, showing proofs that GAs with crossover require exponential optimization time on new Ignoble Trail functions while mutation based EAs optimize them efficiently.
An Analysis of Case-Based Value Function Approximation by Approximating State Transition Graphs
Authors: Thomas Gabel, Martin Riedmiller
Venue: Proceedings of the 7th international conference on Case-Based Reasoning: Case-Based Reasoning Research and Development (2007)

We identify two fundamental points of utilizing CBR for an adaptive agent that tries to learn on the basis of trial and error without a model of its environment. The first link concerns the utmost efficient exploitation of experience the agent has collected by interacting within its environment, while the second relates to the acquisition and representation of a suitable behavior policy. Combining both connections, we develop a state-action value function approximation mechanism that relies on case-based, approximate transition graphs and forms the basis on which the agent improves its behavior. We evaluate our approach empirically in the context of dynamic control tasks.
Applying Dynamic Fuzzy Model in Combination with Support Vector Machine to Explore Stock Market Dynamism
Authors: Deng-Yiv Chiu, Ping-Jie Chen
Venue: Proceedings of the 8th international conference on Adaptive and Natural Computing Algorithms, Part II (2007)

In the study, a new dynamic fuzzy model is proposed in combination with support vector machine (SVM) to explore stock market dynamism. The fuzzy model integrates various factors with influential degree as the input variables, and the genetic algorithm (GA) adjusts the influential degree of each input variable dynamically. SVM then serves to predict stock market dynamism in the next phase. In the meanwhile, the multiperiod experiment method is designed to simulate the volatility of stock market. Then, we compare it with other methods. The model from the study does generate better results than others.
An Improved Safety Solver in Go Using Partial Regions
Authors: Xiaozhen Niu, Martin Müller
Venue: Proceedings of the 6th international conference on Computers and Games (2008)

Previous safety-of-territory solvers for the game of Go have worked on whole regions surrounded by stones of one color. Their applicability is limited to small to medium-size regions. We describe a new technique that is able to prove that parts of large regions are safe. By using pairs of dividing points, even huge regions can be divided into smaller partial regions that can be proven much easier and faster. Our experimental results show that the new technique significantly improves the performance of our previous state of the art safety-of-territory solver. Especially in earlier game phases, the solver utilizing the new technique outperforms the previous solver by a large margin.
A Symbolic Model Checking Framework for Safety Analysis, Diagnosis, and Synthesis
Authors: Piergiorgio Bertoli, Marco Bozzano, Alessandro Cimatti
Venue: Model Checking and Artificial Intelligence: 4th Workshop, MoChArt IV, Riva del Garda, Italy, August 29, 2006, Revised Selected and Invited Papers (2007)

Modern reactive control system are typically very complex entities, and their design poses substantial challenges. In addition to ensuring functional correctness, other steps may be required: with safety analysis, the behavior is analyzed, and proved compliant to some requirements considering possible faulty behaviors; diagnosis and diagnosability are forms of reasoning on the run-time explanation of faulty behaviors; planning and synthesis allow the automated construction of controllers that implement desired behaviors. Symbolic Model Checking (SMC) is a formal technique for ensuring functional correctness that has achieved a substantial industrial penetration in the last decade. In this paper, we show how SMC can be used as a convenient framework to express safety analysis, diagnosis and diagnosability, and synthesis. We also discuss how model checking tools can be used and extended to solve the resulting computational challenges.
Improved Algorithm for Image Processing in TCON of TFT-LCD
Authors: Feng Ran, Lian-Zhou Wang, Mei-Hua Xu
Venue: Proceedings of the 5th international symposium on Neural Networks: Advances in Neural Networks, Part II (2008)

In order to satisfy the special demand for image display in TFT-LCD, this paper presents a synthesis algorithm for image processing in TCON of TFT-LCD. The algorithm includes contrast adjustment, Gama correction and dithering technique which is improved to deal with the zoomed image, and at the same time, matches the real-time requirements. All the modules are simulated and verified using MATLAB, and then described in RTL. The experimental results show that the design achieves the anticipative effects.
4th International Workshop on Language Engineering (ATEM 2007)
Authors: Jean-Marie Favre, Dragan Gašević, Ralf Lämmel, Andreas Winter
Venue: Models in Software Engineering: Workshops and Symposia at MoDELS 2007, Nashville, TN, USA, September 30 - October 5, 2007, Reports and Revised Selected Papers (2008)

Following the great success of previous editions, ATEM2007 is the 4th edition of the ATEM workshop series. The first two editions were held with WCRE in 2003 and 2004, while the 3rd one was held with MoDELS 2006. ATEM has always been focused on engineering of language descriptions. In order to cover as many aspects of language descriptions important for greater success and adoption of model-driven engineering, ATEM has been evolving so as its scope:The first edition was about metamodels and schemas. The second about was metamodels, schemas and grammars.The third edition was about metamodels, schemas, grammars and ontologies.