ppxscal/embedding_network huggingface dataset:
Visualization of multi-dimensional data of bioactive chemicals using a hierarchical data visualization technique "Heiankyo view"
Authors: Takayuki Itoh, Fumiyoshi Yamashita
Venue: Proceedings of the 2006 Asia-Pacific Symposium on Information Visualisation - Volume 60 (2006)

In the age of combinatorial chemistry and high throughput screening, large-scale data of bioactive chemicals oriented to drug development are being accumulated. Due to the difficulties inherent in understanding such large quantities of data, information visualization techniques are increasingly attractive. Authors apply "Heiankyo View", which is the technique for the representation of large-scale hierarchical data, for the visualization of multi-dimensional data of bioactive chemicals. In the present study, we investigated applicability of the visualization technique to the structure-activity relationship (SAR) analyses. The study first classifies chemicals according to similarity in their biological actions through self-organizing map analysis. It then applies a recursive partitioning method to find the relationship between biologically based categories and chemical structure, and finally it stores the drugs as hierarchical data. HeiankyoView is suitable for the visualization of such hierarchical data. This paper first describes the algorithmic overview of Heiankyo View, and then provides some example of visualization of multi-dimensional data of bioactive chemicals.
A Novel Two-Relay Collaborative Multihop Inter-Vehicle Communication Systems
Authors: Xiaojian Xu, Qingmin Meng, Hanying Hu
Venue: Proceedings of the First International Conference on Innovative Computing, Information and Control - Volume 2 (2006)

A novel collaborative strategy employing two relays is developed for the multihop inter-vehicle communication (IVC) systems in this paper, which has great complexity degradation. Instead of the traditional terminal collaboration or relay tier spacetime coding (STC), a relay tier interaction is proposed. Considering time division multiple access (TDMA) scheme, two spatial adjacent vehicles are conjoined by an interaction radio link to create a virtual antenna array (VAA). Then the collaborative two-relay is integrated into a multihop IVC network mentioned above, which enables a single-antenna terminal to share its antenna with other terminals easily, and avoids the synchronization or other complicated requirements in terminal collaboration or STC systems. Furthermore, except the low complexity in hardware implementation, the proposed method also can enhance the performance of the IVC systems over both the quasi-static fading channel and time varying Rayleigh fading relay channel, which is verified through the Monte-Carlo simulations
Feature instability as a criterion for selecting potential style markers: Special Topic Section on Computational Analysis of Style
Authors: Moshe Koppel, Navot Akiva, Ido Dagan
Venue: Journal of the American Society for Information Science and Technology (2006)

We introduce a new measure on linguistic features, called stability, which captures the extent to which a language element such as a word or a syntactic construct is replaceable by semantically equivalent elements. This measure may be perceived as quantifying the degree of available &ldquo;synonymy&rdquo; for a language item. We show that frequent, but unstable, features are especially useful as discriminators of an author's writing style. &copy; 2006 Wiley Periodicals, Inc.
A Strategy for Verification of Decomposable SCR Models
Authors: Dejan Desovski, Bojan Cukic
Venue: Proceedings of the 12th Pacific Rim International Symposium on Dependable Computing (2006)

Formal methods for verification of software systems often face the problem of state explosion and complexity. We propose a divide and conquer methodology which leads to component-based verification and analysis of formal requirements specifications expressed using Software Cost Reduction (SCR) models. This paper presents a novel decomposition methodology which identifies components in the given SCR specification and automates related abstraction methods. Further, we propose a verification strategy for modular and decomposable software models. Efficient verification of SCR models is achieved through the use of invariants and proof compositions. Experimental validation of our methodology brought to light the importance of modularity, encapsulation, information hiding and the avoidance of global variables in the context of formal specification models. The advantages of the compositional verification strategy are demonstrated in the analysis of the Personnel Access Control System. Our approach offers significant savings in terms of time and memory requirements needed to perform formal system verification.
On Basic Principles of Intelligent Systems Design
Authors: Victor Korotkikh, Galina Korotkikh
Venue: Proceedings of the Sixth International Conference on Hybrid Intelligent Systems (2006)

In the paper we present results of computational experiments to suggest the possibility of a general optimality condition of complex systems: a system demonstrates the optimal performance for a problem, when the structural complexity of the system is in a certain relationship with the structural complexity of the problem. The optimality condition could be used as a basic principle in the design of intelligent systems optimizing their performance in the dynamic environment.
Ontology based object categorisation for robots
Authors: Rogan Mendoza, Mary-Anne Williams
Venue: Proceedings of the 2005 Australasian Ontology Workshop - Volume 58 (2005)

Ontologies are a powerful means for expressing and haring knowledge in a meaningful way, and are becoming accepted as a viable modelling approach. The purpose of this paper is to enhance the representations used by robots by incorporating ontologies and implementing reasoning services that can exploit the information inherent within ontology based representations. Our objective is to explore the use of ontological concepts for object categorisation in agents and issues related to the grounding of ontology based representations. The research is driven by the need to make progress towards the development of a generalised solution for the grounding problem which would allow intelligent agents to achieve more adaptive behaviours.Object categorisation is important for intercommunication between agents because it plays an important role in supporting problem solving and the achievement of goals. Ontologies allow concepts to be easily shared meaningfully between agents and this can enable interoperability between multiple heterogenous systems. In order to illustrate our ideas we focus on the robot soccer domain because it is an application where agents, namely robots, must make decision, communicate and collaborate in a complex and dynamic environment.
Maintaining a Random Binary Search Tree Dynamically
Authors: Prasad Vinod, Suri Pushpa, Carsten Maple
Venue: Proceedings of the conference on Information Visualization (2006)

Binary tree is a graph, without cycle, that is frequently used in computer science for fast data access and retrieval. To ensure faster insertion and deletion, the tree height has to be kept to a minimum. A random tree starts loosing its randomness after a series of insertions and deletions and, in the worst case, a tree with n nodes, could grow up to the height of n-1. In this paper, we present modified insertion and deletion algorithms to maintain the tree in better shape dynamically. Without applying any complex rebalancing technique, or using considerable amount of space, both algorithms maintain the tree in such a way that even a series of insertions and asymmetric deletions do not cause the tree to grow beyond n/2. A comparative study of traditional and modified insert algorithms shows that for random input, the modified insert algorithm produces a tree with 20% to 30% reduction in height, forcing the average number of comparisons required for a successful search to go down by 15% to 20%.
Texture-based visualization of multi-field flow data
Authors: Victoria Interrante
Venue:  (2006)

Researchers have long been interested in developing a deeper understanding of the key physical mechanisms in fluid dynamics. Of particular interest are the complex relationships between the multiple scalar and vector quantities used to characterize scientific phenomena within the flow. Efforts to achieve a fundamental understanding of these key physical mechanisms remain limited mainly because of a lack of understanding of the nonlinear interactions that occur among the components of the flow. The goal through this work is to enable researchers to obtain a succinct, meaningful visual summary of the contents of a dataset that consists of multiple, coincident variables. This is accomplished through providing techniques that allow the creation of an image in which the important features of multiple scalar or vector fields can be understood both independently and in the context of the other fields. This research offers several new techniques for effectively using color and texture to simultaneously convey information about multiple co-located scalar and vector distributions. Specifically, we introduce: (1) color weaving, an alternative to traditional color compositing for simultaneously representing multiple distributions by allowing colors to be closely interwoven via the assignment of distinct separate hues to individual streamlines; (2) applying natural textures to streamlines to create a richly diverse set of possibilities for the visualization of multiple distributions within a flow; (3) embossing to encode the out-of-plane component of a 3D vector field defined over a 2D domain; (4) visualizing multiple 2D vector fields using strategies involving layers of disparate textures and overlapping streamlines. These methods ultimately enhance the ability to provide insight into the complicated interactions that occur within multi-field flow data.
Modeling the α-helix to β-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide Aβ(12-28): insights from all-atom molecular dynamics simulations
Authors: Fabio Simona, Guido Tiana, Ricardo A. Broglia, Giorgio Colombo
Venue: Journal of Molecular Graphics (2004)

In this paper, all-atom molecular dynamics simulations in explicit solvent are used to investigate the structural and dynamical determinants of the α-helical to β-hairpin conformational transition of the 12-28 fragment from the full length Aβ Alzheimer's peptide. The transition from α-helical to β-structure requires the peptide to populate intermediate β-bend geometries in which several mainly hydrophobic interactions are partially formed. This is followed by the sudden collapse to ordered β-hairpin structures and the simultaneous disruption of the hydrophobic side-chain interactions with a consequent increase in solvent exposure.The solvent exposure of hydrophobic side-chains belonging to a sequence of five consecutive residues in the β-hairpin defines a possible starting point for the onset of the aggregation mechanisms. Several different conformations of model oligomeric (dimeric and tetrameric) aggregates are then investigated. These simulations show that while hydrophobic contacts are important to bring together different monomers with a β-hairpin like conformation, more specific interactions such as hydrogen-bonding and coulombic interactions, should be considered necessary to provide further stabilization and ordering to the nascent fibrillar aggregates.
The computational complexity of component selection in simulation reuse
Authors: Robert G. Bartholet, David C. Brogan, Paul F. Reynolds,  Jr.
Venue: Proceedings of the 37th conference on Winter simulation (2005)

Simulation composability has been much more difficult to realize than some initially imagined. We believe that success lies in explicit considerations for the adaptability of components. In this paper we show that the complexity of optimal component selection for adaptable components is NP-complete. However, our approach allows for the efficient adaptation of components to construct a complex simulation in the most flexible manner while allowing the greatest opportunity to meet all requirements, all the while reducing time and costs. We demonstrate that complexity can vary from polynomial, to NP, and even to exponential as a function of seemingly simple decisions made about the nature of dependencies among components. We generalize these results to show that regardless of the types or reasons for dependencies in component selection, just their mere existence makes this problem very difficult to solve optimally.
Virtual Repository Supporting Integration of Pluginable Resources
Authors: Kamil Kuliberda, Piotr Blaszczyk, Grzegorz Balcerzak, Krzysztof Kaczmarski, Radoslaw Adamus, Kazimierz Subieta
Venue: Proceedings of the 17th International Conference on Database and Expert Systems Applications (2006)

The paper describes a dynamic integration mechanism for a virtual repository that transparently integrates distributed, heterogeneous and redundant resources. The repository is based on combination of a P2P network, object-oriented databases, a query language SBQL and virtual updateable views defined and used in SBQL. It is currently implemented as a prototype under .NET in C#. We also discuss a solution for an independent virtual P2P network integrating resources stored in databases and a novel global index mechanism.
Analysis of a multiobjective evolutionary algorithm on the 0-1 knapsack problem
Authors: Rajeev Kumar, Nilanjan Banerjee
Venue: Theoretical Computer Science (2006)

Multiobjective Evolutionary Algorithms (MOEAs) are increasingly being used for effectively solving many real-world problems, and many empirical results are available. However, theoretical analysis is limited to a few simple toy functions. In this work, we select the well-known knapsack problem for the analysis. The multiobjective knapsack problem in its general form is NP-complete. Moreover, the size of the set of Pareto-optimal solutions can grow exponentially with the number of items in the knapsack. Thus, we formalize a (1 + ε)-approximate set of the knapsack problem and attempt to present a rigorous running time analysis of a MOEA to obtain the formalized set. The algorithm used in the paper is based on a restricted mating pool with a separate archive to store the remaining population; we call the algorithm a Restricted Evolutionary Multiobjective Optimizer (REMO). We also analyze the running time of REMO on a special bi-objective linear function, known as LOTZ (Leading Ones : Trailing Zeros), whose Pareto set is shown to be a subset of the knapsack. An extension of the analysis to the Simple Evolutionary Multiobjective Optimizer (SEMO) is also presented. A strategy based on partitioning of the decision space into fitness layers is used for the analysis.
A comparison of two different formulations for arc routing problems on mixed graphs
Authors: Angel Corberán, Enrique Mota, José M. Sanchis
Venue: Computers and Operations Research (2006)

Arc routing problems on mixed graphs have been modelled in the literature either using just one variable per edge or associating to each edge two variables, each one representing its traversal in the corresponding direction. In this paper, and using the mixed general routing problem as an example, we compare theoretical and computationally both formulations as well as the lower bounds obtained from them using Linear Programming based methods. Extensive computational experiments, including some big and newly generated random instances, are presented.
Introducing Auction Scheme to Route Allocation to Prolong the Lifetime of Ad-Hoc Networks
Authors: Kenji TEI, Hiromi MUTO, Yoshiaki FUKAZAWA, Shinichi HONIDEN
Venue: Proceedings of the International Conference on Computational Inteligence for Modelling Control and Automation and International Conference on Intelligent Agents Web Technologies and International Commerce (2006)

Prolonging a network lifetime is one of crucial issues of message routing protocol in mobile ad-hoc networks (MANETs), because MANETs consist of mobile devices powered by batteries. Previous routing protocols focus on route selection by a message sender to balance message forwarding load. However, in this approach, message routes determined by different senders cannot be coordinated, because each sender selects its message route independently. In this paper, we propose an auction-based route allocation scheme where message routes are determined by auctions between message senders and forwarders, and apply the route allocation scheme to the Dynamic Source Routing protocol. Simulation results show the DSR protocol with our allocation scheme can prolong the network lifetime comparing with the routing protocol proposed in the previous works.
Intelligent Electronic Navigational Aids: A New Approach
Authors: Costin Barbu, Maura Lohrenz, Geary Layne
Venue: Proceedings of the 5th International Conference on Machine Learning and Applications (2006)

Intelligent devices, with smart clutter management capabilities, can enhance a user's situational awareness under adverse conditions. Two approaches to assist a user with target detection and clutter analysis are presented, and suggestions on how these tools could be integrated with an electronic chart system are further detailed. The first tool, which can assist a user in finding a target partially obscured by display clutter, is a multiple-view generalization of AdaBoost. The second technique determines a meaningful measure of clutter in electronic displays by clustering features in both geospatial and color space. The clutter metric correlates with preliminary, subjective, clutter ratings. The user can be warned if display clutter is a potential hazard to performance. Synthetic and real data sets are used for performance evaluation of the proposed technique compared with recent classifier fusion strategies.
Segmenting Customers from Population to Individuals: Does 1-to-1 Keep Your Customers Forever?
Authors: Tianyi Jiang, Alexander Tuzhilin
Venue: IEEE Transactions on Knowledge and Data Engineering (2006)

There have been various claims made in the marketing community about the benefits of 1-to-1 marketing versus traditional customer segmentation approaches and how much they can improve understanding of customer behavior. However, few rigorous studies exist that systematically compare these approaches. In this paper, we conducted such a study and compared the predictive performance of aggregate, segmentation, and 1-to-1 marketing approaches across a broad range of experimental settings, such as multiple segmentation levels, multiple real-world marketing data sets, multiple dependent variables, different types of classifiers, different segmentation techniques, and different predictive measures. Our experiments show that both 1-to-1 and segmentation approaches significantly outperform aggregate modeling. Reaffirming anecdotal evidence of the benefits of 1-to-1 marketing, our experiments show that the 1-to-1 approach also dominates the segmentation approach for the frequently transacting customers. However, our experiments also show that segmentation models taken at the best granularity levels dominate 1-to-1 models when modeling customers with little transactional data using effective clustering methods. In addition, the peak performance of segmentation models are reached at the finest granularity levels, skewed towards the 1-to-1 case. This finding adds support for the microsegmentation approach and suggests that 1-to-1 marketing may not always be the best solution.
Hierarchical variable ordering for distributed constraint optimization
Authors: John Davin, Pragnesh Jay Modi
Venue: Proceedings of the fifth international joint conference on Autonomous agents and multiagent systems (2006)

The Multiagent Agreement Problem (MAP) is a special form of Distributed Constraint Optimization (DCOP) that requires agents to choose values for variables to satisfy not only their own constraints, but also equality constraints with other agents. We introduce the AdoptMVA algorithm, an extension of the existing Adopt algorithm, designed to take advantage of MAP domains where agents often control multiple variables. We also propose an approach to agent ordering which leverages known ordering techniques from the centralized and distributed constraint satisfaction literature and applies them to MAPs. By combining ordering at the agent level with orderings at the variable level, we hope to obtain efficient global orderings. While the contributions discussed in this paper are applicable to general DCOPs, we focus our evaluation on MAPs because we feel it is a significant problem class worthy of specific attention.
Identifying domain-specific defect classes using inspections and change history
Authors: Taiga Nakamura, Lorin Hochstein, Victor R. Basili
Venue: Proceedings of the 2006 ACM/IEEE international symposium on Empirical software engineering (2006)

We present an iterative, reading-based methodology for analyzing defects in source code when change history is available. Our bottom-up approach can be applied to build knowledge of recurring defects in a specific domain, even if other sources of defect data such as defect reports and change requests are unavailable, incomplete or at the wrong level of abstraction for the purposes of the defect analysis. After defining the methodology, we present the results of an empirical study where our method was applied to analyze defects in parallel programs which use the MPI (Message Passing Interface) library to express parallelism. This library is often used in the domain of high performance computing, where there is much discussion but little empirical data about the frequency and severity of defect types. Preliminary results indicate the methodology is feasible and can provide insights into the nature of real defects. We present the results, derived hypothesis, and lessons learned.
Resources, dynamic capabilities and performance in a dynamic environment: perceptions in Taiwanese IT enterprises
Authors: Lei-Yu Wu
Venue: Information and Management (2006)

This paper presents the results of an analysis of resources, dynamic capabilities and performance in a dynamic environment. The author used data from 244 Taiwanese information technology firms and found that, in an unstable environment, resources, whether from the firm itself or from associated support firms, did not directly influence performance. Instead, resources influenced performance through exercising dynamic capabilities. Furthermore, this effort showed that information technology firm performance can be directly assessed by examining the innovation speed, market response speed, production efficiency, and production flexibility of a firm.