ppxscal/embedding_network huggingface dataset:
Large scale genomic sequence SVM classifiers
Authors: Sören Sonnenburg, Gunnar Rätsch, Bernhard Schölkopf
Venue: Proceedings of the 22nd international conference on Machine learning (2005)

In genomic sequence analysis tasks like splice site recognition or promoter identification, large amounts of training sequences are available, and indeed needed to achieve sufficiently high classification performances. In this work we study two recently proposed and successfully used kernels, namely the Spectrum kernel and the Weighted Degree kernel (WD). In particular, we suggest several extensions using Suffix Trees and modifications of an SMO-like SVM training algorithm in order to accelerate the training of the SVMs and their evaluation on test sequences. Our simulations show that for the spectrum kernel and WD kernel, large scale SVM training can be accelerated by factors of 20 and 4 times, respectively, while using much less memory (e.g. no kernel caching). The evaluation on new sequences is often several thousand times faster using the new techniques (depending on the number of Support Vectors). Our method allows us to train on sets as large as one million sequences.
Energy-conserving data cache placement in sensor networks
Authors: K. Shashi Prabh, Tarek F. Abdelzaher
Venue: ACM Transactions on Sensor Networks (TOSN) (2005)

Wireless sensor networks hold a very promising future. The nodes of wireless sensor networks (WSN) have a small energy supply and limited bandwidth available. Since radio communication is expensive in terms of energy consumption, the nodes typically spend most of their energy reserve on wireless communication (rather than on CPU processing) for data dissemination and retrieval. Therefore, the role of energy conserving data communication protocols and services in WSN can not be overemphasized. Caching data at locations that minimize packet transmissions in the network reduces the power consumption in the network, and hence extends its lifetime. Finding locations of the nodes for caching data to minimize communication cost corresponds to finding the nodes of a weighted Minimum Steiner tree whose edge weights depend on the edge's Euclidean length and its data traffic rate. We call this tree a Steiner Data Caching Tree (SDCT). We prove that an optimal SDCT is binary, and that at-least two of the three internal angles formed at the Steiner points are equal. We derive expressions that determine the exact location of a Steiner point for a set of three nodes based on their location and their data refresh rate requirements. Based on these (optimality) results, we present a dynamic distributed energy-conserving application-layer service for data caching and asynchronous multicast. We present the results of simulation of our service that verifies its power saving properties.
Online Segmentation of Freehand Stroke by Dynamic Programming
Authors: Liu Yin, Yu Yajie, Liu Wenyin
Venue: Proceedings of the Eighth International Conference on Document Analysis and Recognition (2005)

In this paper, a dynamic programming (DP) based approach is proposed to split a freehand stroke into the optimal number of line segments and elliptical arcs. Different from existing DP approaches, which often require a predefined fixed number and/or the templates of the result segments, our approach is actually a generic parameterized framework, which can be configured to some existing methods by fixing some of the parameters. Our key contribution is to avoid presetting of the number or templates of the segments and achieve the best tradeoff between the segment number and approximate error by using a suitable penalty function. Experiments show that our approach achieves high segmentation accuracy and can response to user's stroke input in real-time.
Multilevel Parallelism in Computational Chemistry using Common Component Architecture and Global Arrays
Authors: Manojkumar Krishnan, Yuri Alexeev, Theresa L. Windus, Jarek Nieplocha
Venue: Proceedings of the 2005 ACM/IEEE conference on Supercomputing (2005)

The development of complex scientific applications for high-end systems is a challenging task. Addressing complexity of the involved software and algorithms is becoming increasingly difficult and requires appropriate software engineering approaches to address interoperability, maintenance, and software composition challenges. At the same time, the requirements for performance and scalability to thousand processor configurations magnifies the level of difficulties facing the scientific programmer due to the variable levels of parallelism available in different algorithms or functional modules of the application. This paper demonstrates how the Common Component Architecture (CCA) and Global Arrays (GA) can be used in context of computational chemistry to express and manage multi-level parallelism through the use of processor groups. For example, the numerical Hessian calculation using three levels of parallelism in NWChem computational chemistry package outperformed the original version of the NWChem code based on single level parallelism by a factor of 90% when running on 256 processors.
Author's comments on Gr&ouml;hn, Lokki, and Takala, ICAD 2003
Authors: Matti Gröhn, Tapio Lokki, Tapio Takala
Venue: ACM Transactions on Applied Perception (TAP) (2005)

Historical background and motivation for ICAD2003 paper is presented. In addition, the research results followed up is briefly overviewed and future work is elaborated.
DMC - Distributed and Mobile Collaboration Workshop Report
Authors: Schahram Dustdar, Harald Gall, Nikolay Mehandjiev, Samir Tata
Venue: Proceedings of the 14th IEEE International Workshops on Enabling Technologies: Infrastructure for Collaborative Enterprise (2005)

The increased need for people and organizations to continue collaborating whilst changing physical location and crossing organizational boundaries has resulted in a wave of new supporting technologies, and generated interest in tackling some of the difficult research issues arsing in such a context. The latter was the subject of the Third IEEE International Workshop on Distributed and Mobile Collaboration (DMC) at WETICE 2005, summirized here. The DMC Workshop included 10 full papers on topics grouped into four areas: Web-based collaboration, Formal description and consistency checking of collaborative processes, Models and architectures for collaborative services, and P2P collaborative infrastructures. The discussions at the workshop outlined several important issues regarding the field of distributed collaborative applications.
A Distributed Middleware Solution for Context Awareness in Ubiquitous Systems
Authors: Saad Liaquat Kiani, Maria Riaz, Yonil Zhung, Sungyoung Lee, Young-Koo Lee
Venue: Proceedings of the 11th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (2005)

Context aware middleware infrastructures have traditionally been implemented with a modular approach to allow different components to work cooperatively and supply context synthesis and provision services. In this paper, we discuss the important requirements that arise when such a middleware is deployed in a distributed environment and present the design and implementation of Context Aware Middleware for Ubiquitous Systems (CAMUS1) with which the authors have attempted to meet those requirements. Issues related to distributed coordination within the middleware in terms of component discovery and management and multiple context domains are also discussed.
Trading Precision for Stability in Congestion Control with Probabilistic Packet Marking
Authors: Jonathan Shapiro, C. V. Hollot, Don Towsley
Venue: Proceedings of the 13TH IEEE International Conference on Network Protocols (2005)

In pricing-based congestion control protocols it is common to assume that the rate of congestion feedback from the network is limited to a single bit per packet. To obtain a precise estimate of available bandwidth (as summarized by the congestion price) under the single-bit constraint, a session must consider feedback contained in a number of recently received packets. As more packets are considered, however, the estimate includes increasingly older information about the network state. We study this tradeoff between the quality and timeliness of feedback using controltheoretic approach, modelling the ¿memory¿ incorporated into the price estimate as additional feedback delay. We show through analysis that obtaining arbitrary precision in the estimated price causes control instability, making it more difficult for a session to track its targeted optimal rate. Through continuous-time simulation of our model and packet-level simulations, we find that crude estimates of congestion price based on very few packets can yield good performance while allowing the session to operate far away from the boundary of instability. We also investigate the impact of estimation bias on protocol performance, showing that protocols use a form of integral control can compensate for biased price estimates.
Video search: opportunities & challenges
Authors: Ramesh Sarukkai
Venue: Proceedings of the 7th ACM SIGMM international workshop on Multimedia information retrieval (2005)

What are the evolving trends in video search? What has changed technologically after many decades of solid research and development in computer vision, image processing, information retrieval and pattern recognition to enable products that search millions of video from the Web? We attempt to highlight some of the changes that are altering the fundamental approach to video information retrieval.
The QuORRUM Protocol: Efficient Tree Repair for Qualification-Based Multicast
Authors: L. A. Flynn, H. P. Dommel
Venue: Proceedings of the Second International Conference on Quality of Service in Heterogeneous Wired/Wireless Networks (2005)

Increasing sophistication of Internet services requires more refined methods of service differentiation in the delivery of data and media flows. Earlier work on Qualityof- Service (QoS) routing has focused on the network mechanics to find the best path for admitted connections under specific QoS constraints, and to maximize global resource utilization. We look at the related notion of qualificationbased routing, where routers check on the fulfillment of one or more constraints before handling a particular packet flow. Packets are demarcated and evaluated by qualifiers in their headers, which may indicate for example an authorization level in secure transmissions, or a payment receipt for a media-on-demand application. In particular, this paper explores the coordinative processes for tree formation and repair in qualification-based multicast routing, with the goal to leverage group-centric communication for future mass media Internet applications. We introduce the QuORRUM protocol to implement qualifier-driven sparse-mode tree building and repair and show that it performs better than other protocols in terms of bandwidth usage and repair times.
Critical thinking, self-direction and online learning: a practical inquiry perspective in higher education
Authors: Thomas E. Hall
Venue:  (2005)

Due to the proliferation of computer-mediated courses in higher education and the importance placed on promoting self-direction and higher-order critical thinking skills in our college and university classrooms, there is need to investigate theoretical frameworks with the potential to explain and shape online learning practice. The purpose of this study was to investigate the extent of higher-level critical thinking exhibited by two groups of graduate students enrolled in the same online course approximately one year apart. Central elements of the study's self-directed learning design were student control of the learning environment, critically reflective thought, and learner responsibility. The researcher used a process of qualitative content analysis to study and code the posted discourse of 37 graduate students to determine their exhibited level of higher-order critical thinking in the domain of cognitive presence. Garrison's model of practical inquiry provided the theoretical basis for data collection. The content analysis coding process was implemented using a pretest-posttest, nonequivalent control group study design. The research emphasis of this study was unique in that it was from an adult self-directed learning paradigm. Student control of the learning environment, critically reflective thought, and learner responsibility were all central elements of this study's instructional design. Study findings indicated that students tend to operate at the lower levels of critical thinking and only progress through higher levels when challenged to do so by the instructor. In this study, experimental group students were impacted by the planned intervention to the point that the frequency of their higher order critical thinking comments improved. This indicates that learners can be self-directed and apply new learning strategies, increasing their level of critical thinking when challenged to do so. Among researcher recommendations was that faculty should be provided with the professional development opportunities necessary to assist them in learning instructional strategies and design techniques that have been developed to foster higher-level critical thinking in the classroom whether that classroom is face-to-face or computer-mediated. This study suggested that the Practical Inquiry Model can be an appropriate instructional tool to be considered for incorporation into faculty development activities.
There can still be only one: independent animation production for the lonely
Authors: Steve Rittler
Venue: ACM SIGGRAPH 2004 Course Notes (2004)

This course is designed to introduce the participant to professional digital production procedures used in the animation industry and their application for use by individuals or small groups. Participants will learn the logical order of production, organization, scheduling, and available sources that they will need in order to plan, execute and distribute an independently produced animation piece. This is a strategic-planning course, not a software or technique course. Participants will learn how to use their own existing skills and talents in an organized and effective manner that will help them to achieve the best results from their work.Participants will learn pre-production concepts and techniques that will allow them to focus on creative aspects of their projects and to avoid time-consuming scheduling mistakes that will cripple production. From concept to design, storyboard to animatic, participants will learn the smartest ways to work, which will save them time, money and heartache as they seek to realize their particular vision. Scheduling, resource management and copyright issues will be explored and discussed in the production segment of the class, aimed at keeping the artist on track for project completion while taking care of minute details that could lead to major legal and logistical roadblocks. In the post-production segment, the final edit, output issues, credits and final submission to animation festivals will be addressed, leaving the participant with a clear, organized plan of execution for his or her piece. With more careful organization, animators can concentrate on the creative aspects of their work and not get bogged down in unforeseen details.
Classification Models for Historical Manuscript Recognition
Authors: S. L. Feng, R. Manmatha
Venue: Proceedings of the Eighth International Conference on Document Analysis and Recognition (2005)

This paper investigates different machine learning models to solve the historical handwritten manuscript recognition problem. In particular, we test and compare support vector machines, conditional maximum entropy models and Naive Bayes with kernel density estimates and explore their behaviors and properties when solving this problem. We focus on a whole word problem to avoid having to do character segmentation which is difficult with degraded handwritten documents. Our results on a publicly available standard dataset of 20 pages of George Washington's manuscripts show that Naive Bayes with Gaussian kernel density estimates significantly outperforms the other models and prior work using hidden Markov models on this heavily unbalanced dataset.
User Guidance: From Theory to Practice, the Case of Visual Data Mining
Authors: Edwige Fangseu Badjio, Francois Poulet
Venue: Proceedings of the 17th IEEE International Conference on Tools with Artificial Intelligence (2005)

We present two modulesfor users' guidance in visual data mining (VDW domain which use artificial intelligence. User guidance refers to the available ways to advise, orient, instruct, and inform the users throughout their interactions with a computer. The first module allows recommending best available data mining algorithms to users and the second module aims at reducing attributes and/or data items in very large data sets to be visually mined.
Properties of Numeric Codes for the Scheme of Random Subspaces RSC
Authors: D. A. Rachkovskii, S. V. Slipchenko, E. M. Kussul, T. N. Baidyk
Venue: Cybernetics and Systems Analysis (2005)

Properties of coarse coding obtained by using the random subspace coding (RSC) scheme with random hyperrectangular receptive fields are considered. Characteristics of codes are provided such as the dimensionality of receptive fields, code density at various points of the input space, code overlapping, and others. The results of theoretical analysis are illustrated by experiments with high-dimensional codes.
Transformations for Abstractions
Authors: Eelco Visser
Venue: Proceedings of the Fifth IEEE International Workshop on Source Code Analysis and Manipulation (2005)

The transformation language Stratego provides highlevel abstractions for implementation of a wide range of transformations. Our aim is to integrate transformation in the software development process and make it available to programmers. This requires the transformations provided by the programming environment to be extensible. This paper presents a case study in the implementation of extensible programming environments using Stratego, by developing a small collection of language extensions and several typical transformations for these languages.
Rule-based Middle-level Character Detection for Simplifying Thai Document Layout Analysis
Authors: Chaiyakorn Yingsaeree, Asanee Kawtrakul
Venue: Proceedings of the Eighth International Conference on Document Analysis and Recognition (2005)

Although research interest in machine printed Thai character recognition has been an intense research area in the past decade, there are only a few results available for Thai document layout analysis. In addition, directly using the method proposed for other languages with Thai documents is not possible since Thai documents have a unique characteristic (i.e., Thai characters can be placed in four different levels). This paper proposed an approach to eliminate that characteristic by removing nonmiddle-level characters from the image based on heuristic rules derived from Thai language properties: nonmiddle-level characters are usually smaller than middle-level characters, and the gap between each level is smaller than the gap between two consecutive lines. After removed, one can use any existing methods with Thai documents without any modification. The experimental results show that the proposed method can effectively remove nonmiddle-level characters from 200 test images with 99.46% accuracy even when the image contains various font sizes.
B-CWB: Bilingual Comparative Web Browser Based on Content-Synchronization and Viewpoint Retrieval
Authors: Akiyo Nadamoto, Qiang Ma, Katsumi Tanaka
Venue: World Wide Web (2005)

We propose a new way of browsing bilingual web sites through concurrent browsing with automatic similar-content synchronization and viewpoint retrieval facilities. Our prototype browser system is called the Bilingual Comparative Web Browser (B-CWB) and it concurrently presents bilingual web pages in a way that enables their contents to be automatically synchronized. The B-CWB allows users to browse multiple web news sites concurrently and compare their viewpoint of news articles written in different languages (English and Japanese). Our viewpoint retrieval is based on similar and different detection. We described categorizing pages in terms of viewpoint: the entire similarity, the content difference, and subject difference. Content synchronization means that user operation (scrolling or clicking) on one web page does not necessarily invoke the same operations on the other web page to preserve similarity of content between the multiple web pages. For example, scrolling a web page may invoke passage-level viewpoint retrieval on the other web page. Clicking a web page (and obtaining a new web page) invokes page-level viewpoint retrieval within the other site's pages through the use of an English-Japanese dictionary.
PALM: a computational framework for assembling high-performance computing applications
Authors: Samuel Buis, Andrea Piacentini, Damien Déclat
Venue: Concurrency and Computation: Practice Experience (2006)

The PALM project aims to implement a general tool allowing the easy integration of high-performance computing applications in a flexible and evolutive way. It was originally designed for oceanographic data assimilation algorithms, but its application domain extends to multiple scientific applications. In the framework of PALM, applications are split into elementary components that can exchange data. The main features of PALM are the dynamic launching of the coupled components, the full independence of the components from the application algorithm, the parallel data exchanges with redistribution and the separation of the physics from the algebraic manipulations performed by the PALM algebra toolbox. Copyright &copy; 2005 John Wiley & Sons, Ltd.