ppxscal/embedding_network huggingface dataset:
Lateral gene transfer in phylogeny of azoreductase enzyme
Authors: Amit Bafana, Tapan Chakrabarti
Venue: Computational Biology and Chemistry (2008)

This paper attempts to reconstruct the phylogeny of azoreductase enzyme from different organisms and compare it with the small subunit rRNA-based phylogeny of the organisms. The two phylogenies were found to be incongruent, indicating several events of lateral transfer of azoreductase gene between phylogenetically diverse organisms. However, the phylogenetic analysis methods have several limitations and a single method may not give the true pattern. Hence, it is necessary to corroborate the results with other complementary analysis tools. We used several tools to test our hypothesis of lateral transfer and found that it was supported not only by the analysis of the whole sequences, but also by the conserved motifs detected in these sequences. There were ample evidences for lateral transfer of azoreductase gene among enteric bacteria. There were also indications that azoreductase probably evolved in prokaryotes and then it was laterally transferred to eukaryotes in multiple events, resulting in some sequence variation among eukaryotic azoreductases. Finally, profile HMMs and conserved motifs extracted from these azoreductase sequences were found to provide sensitive tools for identifying potential azoreductases from the database. The analysis techniques used in this study can be extended to other gene trees to verify their evolutionary histories.
Password Generation of OTP System using Fingerprint Features
Authors: ByungRae Cha, ChulWon Kim
Venue: Proceedings of the 2008 International Conference on Information Security and Assurance (isa 2008) (2008)

Security of internet is becoming the latest important concerns along with extensive application of the Internet. All elements that compose security system over maliciously action can display the performance though accomplish harmony of security elements perfectly. Weakness of some a part causes fatal result to whole security system. Therefore, Security systems need elaborate design and mutual coordination in each elements. In this paper, we propose the method of one time password key generation of OTP using fingerprint features. Fingerprint is powerful personal authentication factors, and it can create variable password key for one time using information of fingerprint features. And we performed a simulation for proposed password key generation method.
Paper interface to electronic medical records: a case of usage-driven technology appropriation
Authors: Elin Rønby Pedersen, Greg Wolff
Venue: Proceedings of the 7th ACM conference on Designing interactive systems (2008)

We conducted a 6-month project with a physical therapy clinic, involving equal parts ethnographic fieldwork and rapid prototyping. It differed from most reported user-informed design by having an explicit dual purpose. On the one hand, the prototype should provide significant, measurable improvements for the field site. On the other hand, the project sponsor did not intend to develop the prototype into a product but rather identify future opportunities and needs in the small-to-medium health care sector, requirements for next generation multifunction peripherals (MFPs), and business applications of existing technology. Thus, the project simultaneously investigated specific solutions for a specific work practice while looking for key technologies to address future needs. This paper provides a detailed account of the process and results, highlighting particular contingencies that come with a dual-purpose exploration, as well as the benefits of a small, focused team that "oscillates" between research and deployment.
Efficient parallel algorithms for tree-decomposition and related problems
Authors: J. Lagergren
Venue: Proceedings of the 31st Annual Symposium on Foundations of Computer Science (1990)

An efficient parallel algorithm for the tree-decomposition problem for fixed width w is presented. The algorithm runs in time O(log/sup 3/ n) and uses O(n) processors on a concurrent-read, concurrent-write parallel random access machine (CRCW PRAM). This result can be used to construct efficient parallel algorithms for three important classes of problems: MS (monadic second-order) properties, linear EMS (extended monadic second-order) extremum problems, and enumeration problems for MS properties, for graphs of tree width at most w. The sequential time complexity of the tree-composition problem for fixed w is improved, and some implications for this improvement are stated.
Latest innovation for FFT implementation using RCBNS
Authors: Sadaf Saeed, Usman Ali, Shahid A. Khan
Venue: Proceedings of the 4th WSEAS International Conference on Signal Processing, Computational Geometry & Artificial Vision (2004)

Recent research relating to complex numbers has indicated that a complex numbers can be represented by a single unit with base (-1+j) and (-1-j) in Complex Binary Number System (CBNS). Redundant Complex Binary Number System is another technique for one-unit representation. RCBNS is getting preference over CBNS due to carry-free addition, simple multiplication and direct conversion method between base-2 and base (-1+j), whereas CBNS does not provide these advantages. This paper proposes the applications of these Redundant Complex Binary Number System (RCBNS) in the implementation of Fast Fourier Transform. The proposed technique is believed to reduce computational complexity and cost of FFT implementation as compared to traditional technique used for FFT implementation. The results presented in this paper indicate that the utilization of the proposed complex binary numbers technique reduces the number of real additions involved in single butterfly, from 6-addition to 2-addition and real multiplication from 4-multiplication to 1-multiplication only.
Orthogonal latin rectangles
Authors: Roland HÄggkvist, Anders Johansson
Venue: Combinatorics, Probability and Computing (2008)

We use a greedy probabilistic method to prove that, for every ε > 0, every m × n Latin rectangle on n symbols has an orthogonal mate, where m = (1 − ε)n. That is, we show the existence of a second Latin rectangle such that no pair of the mn cells receives the same pair of symbols in the two rectangles.
Prevention of information attacks by run-time detection of self-replication in computer codes
Authors: V. Skormin A. Volynkin D. Summerville J. Moronski
Venue: Journal of Computer Security (2007)

This paper describes a novel approach for preventative protection from both known and previously unknown malicious software. It does not rely on screening the code for signatures of known viruses, but instead it detects attempts by the executable code in question to self-replicate during run time. Self-replication is the common feature of most malicious codes, allowing them to maximize their impact. This approach is an extension of the earlier developed method for detecting previously unknown viruses in script based computer codes. The paper presents a software tool implementing this technique for behavior-based run-time detection and suspension of self-replicating functionality in executable codes for Microsoft Windows operating systems.
On the design of hybrid peer-to-peer systems
Authors: Stratis Ioannidis, Peter Marbach
Venue: Proceedings of the 2008 ACM SIGMETRICS international conference on Measurement and modeling of computer systems (2008)

In this paper, we consider hybrid peer-to-peer systems where users form an unstructured peer-to-peer network with the purpose of assisting a server in the distribution of data. We present a mathematical model that we use to analyze the scalability of hybrid peer-to-peer systems under two query propagation mechanisms: the random walk and the expanding ring. In particular, we characterize how the query load at the server, the load at peers as well as the query response time scale as the number of users in the peer-to-peer network increases. We show that, under a properly designed random walk propagation mechanism, hybrid peer-to-peer systems can support an unbounded number of users while requiring only bounded resources both at the server and at individual peers. This important result shows that hybrid peer-to-peer systems have excellent scalability properties. To the best of our knowledge, this is the first time that a theoretical study characterizing the scalability of such hybrid peer-to-peer systems has been presented. We illustrate our results through numerical studies.
Long-term and session-specific user preferences in a mobile recommender system
Authors: Quang Nhat Nguyen, Francesco Ricci
Venue: Proceedings of the 13th international conference on Intelligent user interfaces (2008)

User preferences acquisition plays a very important role for recommender systems. In a previous paper, we proposed a critique-based mobile recommendation methodology exploiting both long-term and session-specific user preferences. In this paper, we evaluate the impact on the recommendation accuracy of the two kinds of user preferences. We have ran off-line experiments exploiting the log data recorded in a previous live-user evaluation, and we show here that exploiting both long-term and session-specific preferences results in a better recommendation accuracy than using a single user model component. Moreover, we show that when the simulated user behavior deviates from that dictated by the acquired user model the session-specific preferences are more useful than the long-term ones in predicting user decisions.
An Integration Approach of Healthcare Information System
Authors: Zhao Chenhui, Duan Huilong, Lu Xudong
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

Healthcare organizations today are still struggling with the integration challenges of heterogeneous information systems. Those system interfaces are not always compatible out of box, when the number of involved systems increases, complexity increases in an unmanageable way. Decentralized proprietary format data largely restricts the value of healthcare information. In this article, we present a healthcare information system integration approach based on an integration engine to address the integration problems. All the involved systems are connected to the integration engine through different interface adaptors. The integration engine takes the inbound message as the trigger event, generates outbound messages by workflow driver according to the workflow configuration file. The integration engine is also responsible for understanding the message context and converting the healthcare information into a unified format, and then storing it in the clinical data repository. Thus, it can facilitate the utilization and sharing of healthcare information.
On identification of wakes and trails at sea with IRS-P4 OCM data
Authors: S. K. Sasamal
Venue: International Journal of Remote Sensing (2007)

Ship wakes and aircraft contrails were identified in the IRS-P4 OCM data. The ship wake signatures were analysed for the observations made in shipping corridors of the Persian Gulf on 3 June 1999 and in the of the Arabian Sea on 17 February 2000. While the aircraft contrails were studied with OCM data on 17 November 1999 off Mumbai, India and 18 February 2002 in the Arabian Sea. The study of wakes and trails helped discriminating ships and aircraft location at the sea.
Human-like control strategy of a bipedal walking model
Authors: Andrej Olenšek, Zlatko Matjačić
Venue: Robotica (2008)

This paper presents a two-level control strategy for bipedal walking mechanism that accounts for implicit control of push-off on the between-step control level and tracking of imposed holonomic constraints on kinematic variables via feedback control on within-step control level. The proposed control strategy was tested in a biologically inspired model with minimal set of segments that allows evolution of human-like push-off and power absorption. We investigated controller's stability characteristics by using Poincaré return map analysis in eight simulation cases and further evaluated the performance of the biped walking model in terms of how variations in torso position and gait velocity relate to push-off and power absorption. The results show that the proposed control strategy, with the same set of controller's gains, enables stable walking in a variety of chosen gait parameters and can accommodate to various trunk inclinations and gait velocities in a similar way as seen in humans.
InPhO: a system for collaboratively populating and extending a dynamic ontology
Authors: Mathias Niepert, Cameron Buckner, Jaimie Murdock, Colin Allen
Venue: Proceedings of the 8th ACM/IEEE-CS joint conference on Digital libraries (2008)

InPhO is a system that combines statistical text processing, information extraction, human expert feedback, and logic programming to populate and extend a dynamic ontology for the field of philosophy. Integrated in the editorial workflow of the Stanford Encyclopedia of Philosophy (SEP), it will provide important metadata features such as automated generation of cross-references, semantic search, and ontology driven conceptual navigation.
A Hilbert-order multiplication scheme for unstructured sparse matrices
Authors: Gundolf Haase, Manfred Liebmann, Gernot Plank
Venue: International Journal of Parallel, Emergent and Distributed Systems (2007)

We investigate a new storage format for unstructured sparse matrices based on the space-filling Hilbert curve. Numerical tests with matrix-vector multiplication show the potential of the fractal storage (FS) format in comparison to the traditional compressed row storage (CRS) format. The FS format outperforms the CRS format by up to 50% for matrix-vector multiplications with multiple right hand sides.
Rob Kling In Search of One Good Theory
Authors: Alice Robbin
Venue: The Information Society (2007)

Rob Kling's legacy is a corpus of work that exemplifies the craft of inquiry and the social enterprise of science. This article examines his contribution to social informatics through an analysis of the multiple theories, methods, and sources of evidence he relied on to make his arguments about the social life of computing and the consequences of computerization. His citation identity demonstrates that he transcended disciplinary boundaries but grounded his analysis of the political and social order in interpretive theory and critique. Kling created a working vocabulary for theorizing about computerization and social life. His sustained inquiry and critique, a very public record of his work, enthusiasm, and charisma, contributed to the penetration of his ideas and the fostering of a world-wide community of interest for a domain of study called social informatics.
Scheduling of Scientific Workflows on Data Grids
Authors: Suraj Pandey, Rajkumar Buyya
Venue: Proceedings of the 2008 Eighth IEEE International Symposium on Cluster Computing and the Grid (2008)

Selection of resources for execution of scientific workflows in data grids becomes challenging with the exponential growth of files as a result of the distribution of scientific experiments around the world. With more runs of these experiments, huge number of data-files produced can be made available from numerous resources. There is lack of work in optimal selection of data-hosts and compute resources in the presence of replicated files for scientific workflows. Foreseeing this, the thesis work aims at proposing novel workflow scheduling algorithms on data grids with large number of replicated files that incorporates practical constraintsin heterogeneous environments such as Grids.In this paper, we define the workflow scheduling problemstatement in the context of data grids, supported by motivating applications; list research issues arising from practical constraints; propose two algorithms for experimenting with the problem; report simulation results obtained as a result of preliminary studies. The results are promising enough to motivate us to research on the problem stated.
The Semantic Web: Apotheosis of Annotation, but What Are Its Semantics?
Authors: Yorick Wilks
Venue: IEEE Intelligent Systems (2008)

This article discusses what kind of entity the proposed Semantic Web (SW) is, principally by reference to the relationship of natural language structure to knowledge representation (KR). There are three distinct views on this issue. The first is that the SW is basically a renaming of the traditional AI KR task, with all its problems and challenges. The second view is that the SW will be, at a minimum, the World Wide Web with its constituent documents annotated so as to yield their content, or meaning structure, more directly. This view makes natural language processing central as the procedural bridge from texts to KR, usually via some form of automated information extraction. The third view is that the SW is about trusted databases as the foundation of a system of Web processes and services. There's also a fourth view, which is much more difficult to define and discuss: If the SW just keeps moving as an engineering development and is lucky, then real problems won't arise. This article is part of a special issue called Semantic Web Update.
Learning all optimal policies with multiple criteria
Authors: Leon Barrett, Srini Narayanan
Venue: Proceedings of the 25th international conference on Machine learning (2008)

We describe an algorithm for learning in the presence of multiple criteria. Our technique generalizes previous approaches in that it can learn optimal policies for all linear preference assignments over the multiple reward criteria at once. The algorithm can be viewed as an extension to standard reinforcement learning for MDPs where instead of repeatedly backing up maximal expected rewards, we back up the set of expected rewards that are maximal for some set of linear preferences (given by a weight vector, w). We present the algorithm along with a proof of correctness showing that our solution gives the optimal policy for any linear preference function. The solution reduces to the standard value iteration algorithm for a specific weight vector, w.
Design and Implementation of a High-Performance Microprocessor Cache Compression Algorithm
Authors: Xi Chen, Lei Yang, Haris Lekatsas, Robert P. Dick, Li Shang
Venue: Proceedings of the Data Compression Conference (2008)

Researchers have proposed using hardware data compression units within the memory hierarchies of microprocessors in order to improve performance, energy efficiency, and functionality. However, most past work, and in particular work on cache compression, has made unsubstantiated assumptions about the performance, power consumption, and area overheads of the required compression hardware. We present a lossless compression algorithm that has been designed for on-line memory hierarchy compression, and cache compression in particular. We reduced our algorithm to a register transfer level hardware implementation, permitting performance, power consumption, and area estimation. The results of experiments comparing our work to previous work are presented.
Evaluations of emitter clogging in drip irrigation by two-phase flow simulations and laboratory experiments
Authors: Wei Qingsong, Lu Gang, Liu Jie, Shi Yusheng, Dong Wenchu, Huang Shuhuai
Venue: Computers and Electronics in Agriculture (2008)

Emitter clogging will affect greatly the irrigation efficiency and the running cost of a drip irrigation system. If there is an effective method to predict the emitter clogging, the lost will be reduced to a minimum. A solid-liquid two-phase turbulent model describing the flow within drip emitters was studied. Then, the moving trace and depositing feature of suspending solids in emitter channels were obtained by computational fluid dynamics (CFD) based on the turbulent model established, which provided some visual and direct evidences for predicting the clogging performance of drip emitters. The three types of emitters with novel channel form, including eddy drip-arrows, pre-depositing drippers and round-flow drip-tapes, developed by us were used in this study. The simulation results showed that the solids moved along a helical path in the eddy drip-arrow, but no obvious deposition existed in its interior channel. In the pre-depositing dripper, some solids concentrated in the parts of ''depositing pones''. In the round-flow drip-tape, a small number of solids adhered to the out-edges of every channel corner, which was a potential factor for the occurrence of emitter clogging. To verify the predictions from the CFD simulations, series of ''short-cycle'' clogging tests for the three emitters were conducted in laboratory. The statistical data of discharge variation caused by emitter clogging were in good agreement with the two-phase flow CFD simulations.
Personalized Shopping Assistance Service at Ubiquitous Shop Space
Authors: Somkiat Sae-Ueng, Sineenard Pinyapong, Akihiro Ogino, Toshikazu Kato
Venue: Proceedings of the 22nd International Conference on Advanced Information Networking and Applications - Workshops (2008)

We have been developing an experimental prototype system - Ubiquitous Shop Space, an application of personal information assistance in a shopping context, (1) to find items of users’ interest and/or preferences through data observed from users’ behaviors in a ubiquitous information environment, (2)to automatically build a user preference model, and (3) to apply the model and provide suitable information service in the real world. In this paper, we study personal behavior from a log file that has been recorded by RFID and camera sensors. Utilizing ubiquitous sensors, we apply three types of observation scopes to model each user’s preference. They are microscopic, mezzoscopic, and macroscopic observation scopes. We have proposed the behavior analysis, algorithms, and combined content-based and collaborative filtering to retrieve information. We provide consumer-friendly services which are based on personal behavior log data. Our system can inject suitable and controlled messages to a user to build up his precise preference model without putting any stress on him.
AI Developers: Stand Up and Be Counted!
Authors: Richard Ellis
Venue: IEEE Intelligent Systems (2008)

The British Computer Society Specialist Group on Artificial Intelligence's Machine Intelligence Prize has attracted a wide range of entries spanning the gamut of AI applications and technologies, from air traffic control to art and from neural nets to robotics. Several entries are described. Last year's winner, the Painting Fool, produces fascinating, visually arresting portraits. The Machine Intelligence Prize, along with three other AI competitions described here, offer fertile ground for innovative AI ideas to grow and bear fruit.
Bus encoding for simultaneous delay and energy optimization
Authors: Jingyi Zhang, Qing Wu, Qinru Qiu
Venue: Proceeding of the 13th international symposium on Low power electronics and design (2008)

In this paper we propose two bus encoding algorithms that optimize both bus delay and energy dissipation based on the probabilistic characteristics of data on data buses. The first algorithm minimizes the crosstalk transitions by inserting temporal redundancy and achieves optimal energy. The second algorithm reduces crosstalk more aggressively to achieve optimal bus delay by mapping the original data to low-energy opposite-transition-forbidden codes. Experimental results show that they outperform the existing heuristic bus encoding algorithms by 15.7% to 58.8% in average energy dissipation and 11.4% to 58.4% in average delay.