ppxscal/embedding_network huggingface dataset:
An Automated Combination of Kernels for Predicting Protein Subcellular Localization
Authors: Cheng Soon Ong, Alexander Zien
Venue: Proceedings of the 8th international workshop on Algorithms in Bioinformatics (2008)

Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions. While many predictive computational tools have been proposed, they tend to have complicated architectures and require many design decisions from the developer.Here we utilize the multiclass support vector machine (m-SVM) method to directly solve protein subcellular localization without resorting to the common approach of splitting the problem into several binary classification problems. We further propose a general class of protein sequence kernels which considers all motifs, including motifs with gaps. Instead of heuristically selecting one or a few kernels from this family, we utilize a recent extension of SVMs that optimizes over multiple kernels simultaneously. This way, we automatically search over families of possible amino acid motifs.We compare our automated approach to three other predictors on four different datasets, and show that we perform better than the current state of the art. Further, our method provides some insights as to which sequence motifs are most useful for determining subcellular localization, which are in agreement with biological reasoning. Data files, kernel matrices and open source software are available at http://www.fml.mpg.de/raetsch/projects/protsubloc .
A Scalable Parallel Software Volume Rendering Algorithm for Large-Scale Unstructured Data
Authors: Kangjian Wangc, Yao Zheng
Venue: Proceedings of the 7th international conference on Computational Science, Part I: ICCS 2007 (2007)

In this paper, we develop a highly accurate parallel software scanned cell projection algorithm (PSSCPA) which is applicable of any classification system. This algorithm could handle both convex and non-convex meshes, and provide maximum flexibilities in applicable types of cells. Compared with previous algorithms using 3D commodity graphics hardware, it introduces no the volume decomposition and rendering artifacts in the resulting images. Finally, high resolution images generated by the algorithm are provided, and the scalability of the algorithm is demonstrated on a PC Cluster with modest parallel resources.
Seeing the Invisible and Predicting the Unexpected
Authors: Michal Irani
Venue: Proceedings of the 3rd Iberian conference on Pattern Recognition and Image Analysis, Part I (2007)

Analysis, interpretation and manipulation of complex visual data is something which humans do quite easily. We can easily recognize different instances of objects (like faces, bodies, flowers, etc.), in spite of the huge variations in their appearances.We have no problem determining that two actions are the same, even though they are performed by different people wearing different clothes against different backgrounds.Moreover, we humans can predict and make inferences about very complex static and dynamic visual information which we have never seen. We can infer about the appearance of unfamiliar places, objects and actions, as well as detect saliency and abnormalities in such data. Such complex visual tasks require sophisticated notions of visual similarity and dissimilarity.
Robust Wide Baseline Feature Point Matching Based on Scale Invariant Feature Descriptor
Authors: Sicong Yue, Qing Wang, Rongchun Zhao
Venue: Proceedings of the 4th international conference on Intelligent Computing: Advanced Intelligent Computing Theories and Applications - with Aspects of Theoretical and Methodological Issues (2008)

This paper proposed a robust point matching method for wide baseline in order to achieve a large number of correct correspondences and high accuracy. To cope with large variations of scale and rotation, a feature descriptor, that is robust to scale and view-point, is added to the feature detection phase and it is included in the equations of the correspondence matrix that is central to the matching algorithm. Furthermore, the image window for normalized cross correlation is modified with adaptive scale and orientation. At the same time we remove from the matrix all the proximity information about the distance between points' locations which is the source of mismatches. Thus, the proposed algorithm is invariant to changes of scale, rotation, light and partially invariant to viewpoint. Experimental results show that the proposed algorithm can be used for large scene variations and provide evidence of better performance.
Note: Identities via Bell matrix and Fibonacci matrix
Authors: Weiping Wang, Tianming Wang
Venue: Discrete Applied Mathematics (2008)

In this paper, we study the relations between the Bell matrix and the Fibonacci matrix, which provide a unified approach to some lower triangular matrices, such as the Stirling matrices of both kinds, the Lah matrix, and the generalized Pascal matrix. To make the results more general, the discussion is also extended to the generalized Fibonacci numbers and the corresponding matrix. Moreover, based on the matrix representations, various identities are derived.
Enabling adaptive time-based web applications with SMIL state
Authors: Jack Jansen, Dick C.A. Bulterman
Venue: Proceeding of the eighth ACM symposium on Document engineering (2008)

In this paper we examine adaptive time-based web applications (or presentations). These are interactive presentations where time dictates the major structure, and that require interactivity and other dynamic adaptation. We investigate the current technologies available to create such presentations and their shortcomings, and suggest a mechanism for addressing these shortcomings. This mechanism, SMIL State, can be used to add user-defined state to declarative time-based languages such as SMIL or SVG animation, thereby enabling the author to create control flows that are difficult to realize within the temporal containment model of the host languages. In addition, SMIL State can be used as a bridging mechanism between languages, enabling easy integration of external components into the web application.
Analytical comparison of distributed object components
Authors: Usha Batra, Deepak Dahiya, Sachin Bhardwaj
Venue: Proceedings of the 7th WSEAS International Conference on Applied Computer and Applied Computational Science (2008)

The Distributed object computing is a paradigm that allows objects to be distributed across a heterogeneous network, and allows each of the components to interoperate as a unified whole. This paper compares the layered architectures of various platforms such as COM/DCOM, RMI, CORBA, SOAP supporting distributed computing. While the fundamental structure of each is similar, there are differences that can profoundly impact an application developer or the administrator of a distributed simulation exercise. This paper compares the features of these distributed technologies and provides a more desirable support for distributed computing, as compared to rest of the object or component technologies.
Towards a standard taxonomy of artifact functions
Authors: Paweł Garbacz
Venue: Applied Ontology (2006)

The aim of this paper is to provide a logically accurate and technologically sound taxonomy of artifact functions. To this end, I review one of the recent proposals of such taxonomy: the Reconciled Functional Basis. Since it turns out that this taxonomy involves some serious shortcomings, I attempt to refine it with the help of the conceptual framework of DOLCE, which is a foundational ontology in Knowledge Representation research.
Watermarking Polygonal Lines Using Fourier Descriptors
Authors: Vassilios Solachidis, Ioannis Pitas
Venue: IEEE Computer Graphics and Applications (2004)

This article presents a blind watermarking method for vector graphics images. Unlike the common watermarking methods, where the image luminance is altered, the coordinates of the polygonal curve vertices are modified in the presented method. The watermark is embedded in the Fourier descriptors of the vertices of the polygonal lines, resulting in slight alterations of the polygonal line's vertex coordinates. Due to the Fourier descriptor properties, the watermark is detectable even after rotation, translation, scaling, additive Gaussian noise, smoothing, reflection attacks, or combination of these attacks.
A Flexible and Semantic-Aware Publication Infrastructure for Web Services
Authors: Luciano Baresi, Matteo Miraz, Pierluigi Plebani
Venue: Proceedings of the 20th international conference on Advanced Information Systems Engineering (2008)

This paper presents an innovative approach for the publication and discovery of Web services. The proposal is based on two previous works: DIRE (DIstributed REgistry), for the user-centered distributed replication of service-related information, and URBE (UDDI Registry By Example), for the semantic-aware match making between requests and available services. The integrated view also exploits USQL (Unified Service Query Language) to provide users with a higher level and homogeneous means to interact with the different registries. The proposal improves background technology in different ways: we integrate USQL as high-level language to state service requests, widen user notifications based on URBE semantic matching, and apply URBE match making to all the facets with which services can be described in DIRE. All these new concepts are demonstrated on a simple scenario.
Benefits of Virtual Characters in Computer Based Learning Environments: Claims and Evidence
Authors: Agneta Gulz
Venue: International Journal of Artificial Intelligence in Education (2004)

Pedagogical theory of today gives high priority to social components of learning. Within the field of computer supported learning there are many attempts to acknowledge this. One approach involves the addition of virtual characters to electronic learning environments. Such character enhanced systems are the focus of the present article. Firstly, a systematic overview is given of pedagogical benefits that have been proposed in the literature regarding character enhancement of electronic learning environments, for example increased motivation, stimulation of particular learning activities, enhanced flow of communication and fulfillment of a need for deeper personal relationships in learning. Secondly, I examine the empirical results presented in the literature with respect to the proposed positive pedagogical effects. Based on these reviews, I finally discuss possible directions for continued research and design in the field from a pedagogical point of view. I propose a research agenda for the near future and conclude with some reflections on a longer-term perspective.
A link adaptive transport protocol for multimedia streaming applications in multi hop wireless networks
Authors: Pirabakaran Navaratnam, Haitham Cruickshank, Rahim Tafazolli
Venue: Mobile Networks and Applications (2008)

Transport layer performance in multi hop wireless networks has been greatly challenged by the intrinsic characteristics of these networks. In particular, the nature of congestion, which is mainly due to medium contention in multi hop wireless networks, challenges the performance of traditional transport protocols in such networks. In this paper, we first study the impact of medium contention on transport layer performance and then propose a new transport protocol for improving quality of service performance in multi hop wireless networks. Our proposed protocol, Link Adaptive Transport Protocol provides a systemic way of controlling transport layer offered load for multimedia streaming applications, based on the degree of medium contention information received from the network. Simulation results show that the proposed protocol provides an efficient scheme to improve quality of service performance metrics, such as end-to-end delay, jitter, packet loss rate, throughput smoothness and fairness for media streaming applications. In addition, our scheme requires few overhead and does not maintain any per-flow state table at intermediate nodes. This makes it less complex and more cost effective.
Empirical study of how personality, team processes and task characteristics relate to satisfaction and software quality
Authors: Silvia T. Acuña, Marta N. Gómez, Juan de Lara
Venue: Proceedings of the Second ACM-IEEE international symposium on Empirical software engineering and measurement (2008)

This paper analyses the relationships between personality, team processes, task characteristics, product quality and satisfaction in software development teams. The data analysed here were gathered from a sample of 35 teams of students (105 participants) from a Spanish university. These teams applied an adaptation of an agile methodology, eXtreme Programming (XP), to develop the same software product. We found that the teams with the highest job satisfaction are precisely the ones whose members score highest for the personality factors agreeableness and conscientiousness. The satisfaction levels are also higher when the members can decide how to develop and organize their work. On the other hand, the level of satisfaction and cohesion drops the more conflict there is between the team members. Finally, the teams exhibit a significant positive correlation between the personality factor extroversion and software product quality.
The Reuse of Grammars with Embedded Semantic Actions
Authors: Terence Parr
Venue: Proceedings of the 2008 The 16th IEEE International Conference on Program Comprehension (2008)

Reusing syntax specifications without embedded arbitrary semantic actions is straightforward because the semantic analysis phases of new applications can feed off trees or other intermediate structures constructed by the pre-existing parser. The presence of arbitrary embedded semantic actions, however, makes reuse difficult with existing mechanisms such as grammar inheritance and modules. This short paper proposes a mechanism based upon prototype grammars that automatically pushes changes from prototypes to derived grammars even in the presence of semantic actions. The prototype mechanism alone would be unsuitable for creating a new grammar from multiple pre-existing grammars. When combined with grammar composition, however, the prototype mechanism would improve grammar reuse because imported pre-existing grammars could be altered to suit each new application.
Integrating Biomedical Publications with Existing Metadata
Authors: Nikolay Nikolov, Peter Stoehr
Venue: Proceedings of the 2008 21st IEEE International Symposium on Computer-Based Medical Systems (2008)

Currently biomedical literature is largely disconnected from its metadata. While there are freely accessible centralised metadata repositories the publications themselves are split among a large number of repositories. We address this problem by harvesting freely accessible biomedical publications from the web and integrating them with the corresponding metadata. The system involves title recognition applied on the harvested publications using knowledge-based algorithm and a fuzzy match between the extracted title and the metadata records using edit distance metric. So far we were able to locate +300.000 publications on the web and achieve +96% precision and nearly 85% recall on a random sample of 250 documents harvested from the web.
On Optimizing Subclass Discriminant Analysis Using a Pre-clustering Technique
Authors: Sang-Woon Kim
Venue: Proceedings of the 13th Iberoamerican congress on Pattern Recognition: Progress in Pattern Recognition, Image Analysis and Applications (2008)

Subclass Discriminant Analysis (SDA) [10] is a dimensionality reduction method that has been proven to be successful for different types of class distributions. The advantage of SDA is that since it does not treat the class-conditional distributions as uni-modal ones, the nonlinearly separable problems can be handled as linear ones. The problem with this strategy, however, is that to estimate the number of subclasses needed to represent the distribution of each class, i.e., to find out the best partition, all possible solutions should be verified. Therefore, this approach leads to an associated high computational cost. In this paper, we propose a method that optimizes the computational burden of SDA-based classification by simply reducing the number of classes to be examined through choosing a few classes of the training set prior to the execution of SDA. To select the classes to be partitioned, the intra-set distance is employed as a criterion and a k-means clustering is performed to divide them. Our experimental results for an artificial data set and two face databases demonstrate that the processing CPU-time of the optimized SDA could be reduced dramatically without sacrificing either the classification accuracy or the computational complexity.
MSPtool: A Versatile Tool for Mass Spectrometry Data Preprocessing
Authors: Francesco Gullo, Giovanni Ponti, Andrea Tagarelli, Giuseppe Tradigo, Pierangelo Veltri
Venue: Proceedings of the 2008 21st IEEE International Symposium on Computer-Based Medical Systems (2008)

Preprocessing mass spectrometry (MS) data has been recognized as a crucial preliminary phase in order to perform data management and knowledge discovery tasks on mass spectra. The huge dimensionality and heterogeneity of MS data make mandatory the use of tools that are able to guide the user in the MS preprocessing task. However, most MS preprocessing tools are typically designed to perform only some preprocessing steps and are strictly coupled with MS data analysis modules. In this paper, we present Mass Spectra Preprocessing tool (MSPtool), a user-friendly versatile tool for preprocessing MS data. MSPtool provides the user with a wide set of MS preprocessing steps by means of an easy-to-use graphical interface. Also, this tool has been embedded in a time-series-based framework for MS data clustering.
A Novel Method for Fast Estimating the Number of Wideband Sources
Authors: Heng-li Zhang, Yong-jun Zhao
Venue: Proceedings of the 2008 Congress on Image and Signal Processing, Vol. 5 - Volume 05 (2008)

Estimating the number of sources impinging on an array of sensors is a well known and well investigated problem. Based on the rotational invariance property between two identical subarrays, using the Lanczos algorithm to fast compute the analysis filterbank of multi-stage wiener filter, a novel method for fast estimating the number of wideband sources is proposed in this paper. Unlike the traditional number estimator, the new method does not require an estimate of the covariance matrix or its eigen-decomposition, so it avoids computationally intensive eigen-decomposition and the complexity is greatly decreased. The computer simulations show the availability and efficacy of the method.
Application of a Massively Multi-Agent System to Internet Routing Management
Authors: Osamu Akashi, Kensuke Fukuda, Satoshi Kurihara, Toshio Hirotsu, Toshiharu Sugawara
Venue: Massively Multi-Agent Technology: AAMAS Workshops, MMAS 2006, LSMAS 2006, and CCMMS 2007 Hakodate, Japan, May 9, 2006 Honolulu, HI, USA, May 15, 2007 Selected and Revised Papers (2008)

Diagnosing the anomalies of inter-AS (autonomous system) routing and flexibly controlling its behavior to adapt to environmental changes are difficult, because this information changes spatially and temporally over different administrative domains. Multi-agent-based systems that coincide with this control architecture have been applied to these domains, but the number of deployed agents is small and more accurate analysis taking into consideration the actual Internet structure is desirable. To enable better analysis, cooperation among tens of thousands of agents is needed. This paper proposes a cooperative routing management system, called NetManager-M, which enables detailed analysis by using massively deployed agents on the Internet. NetManager-M can diagnose the routing flows around suspicious areas through cooperation among dynamically organized agents. This cooperation, which is conducted based on the current and previous routing topology, enables monitoring of routing update messages at neighboring observation points and the identification of the causes of problems in more detail. This system is thus an effective means of detailed analysis for typical scenarios of inter-AS routing failures.
Locational Awareness on the Internet
Authors: Franz Leberl
Venue: Proceedings of the 10th international conference on Visual Information Systems: Web-Based Visual Information Search and Management (2008)

In March 2005, at the occasion of his 50th birthday, Bill Gates went public with his "Virtual Earth Vision" for local search in the Internet and stated:"You'll be walking around in downtown London and be able to see the shops, the stores, see what the traffic is like. Walk in a shop and navigate the merchandise. Not in the flat, 2D interface that we have on the web today, but in a virtual reality walkthrough."This implies an enormous advance in computing power, communications bandwidth, miniaturization of computing, increase of storage capacity and in the ability to model the human habitat (the Earth) in great detail in 3 dimensions, with photographic realism and at very low cost per data unit. Action followed this declaration by Bill Gates, and the transition of a then-10-year old Microsoft business segment called "Map Point" into a new Virtual Earth Business Unit was kicked off.
Learning Assessment Model in Web-Learning Based on Rough Set
Authors: Yan Li, Chen Yang
Venue: Proceedings of the 7th international conference on Computational Science, Part III: ICCS 2007 (2007)

Assessment is a powerful technique for improving Web-Learning achievement. In this paper we outline a learning assessment model to assessment learning effect for improving learning efficiency. This learning assessment model is based on the rough set theory. In Web-Learning process, learners' data are collected. And, the model used attribute reduction to reduce many factors that in the learning process. It found the key factors which affect the learning effect. Then, the association rules among factors have been concluded. Finally, this learning assessment model is experimented at Jianghan University.
An Effective Automated Approach to Specialization of Code
Authors: Minhaj Ahmad Khan, H. -P. Charles, D. Barthou
Venue: Languages and Compilers for Parallel Computing: 20th International Workshop, LCPC 2007, Urbana, IL, USA, October 11-13, 2007, Revised Selected Papers (2007)

Application performance is heavily dependent on the compiler optimizations. Modern compilers rely largely on the information made available to them at the time of compilation. In this regard, specializing the code according to input values is an effective way to communicate necessary information to the compiler.However, the static specialization suffers from possible code explosion and dynamic specialization requires runtime compilation activities that may degrade the overall performance of the application.This article proposes an automated approach for specializing code that is able to address both the problems of code size increase and the overhead of runtime activities. We first obtain optimized code through specialization performed at static compile time and then generate a template that can work for a large set of values through runtime specialization.Our experiments show significant improvement for different SPEC benchmarks on Itanium-II(IA-64) and Pentium-IV processors using icc and gcc compilers.