ppxscal/embedding_network huggingface dataset:
Mining emerging massive scientific sequence data using block-wise decomposition methods
Authors: Wei Wang
Venue:  (2009)

I present efficient data mining algorithms for knowledge discovery on two types of emerging large-scale sequence-based scientific datasets: (1) static sequence data generated from SNP diversity arrays for genomic studies, and (2) dynamic sequence data collected in streaming and sensor network systems for environmental studies. The massive, noisy nature of the SNP arrays and the distributive, online nature of sensor network data pose challenging issues for knowledge discovery such as scalability, robustness, and efficiency. Despite the different characteristics of the SNP arrays and streaming sensor data, when viewed as sequences of ordered observations, both can be efficiently mined using algorithms based on block-wise decomposition methods. I present models and mining algorithms for inferring the genetic variation structure in genome-wide Single-Nucleotide Polymorphism (SNP) arrays. Genome-wide SNP arrays provide a comprehensive view of genome variation and serve as powerful resources for genetic and biomedical studies. Understanding the patterns of genetic variation in a population of individuals plays an important role in solving many genetics problems such as genealogy reconstruction and gene association studies. In this thesis, I propose data mining models and algorithms to efficiently infer genetic variation structure from the massive SNP panels of recombinant sequences resulting from meiotic recombination. I introduced the Minimum Segmentation Problem (MSP) to infer the segmentation structure of a single recombinant strain, as well as the Minimum Mosaic Problem (MMP) to infer the mosaic structure on a panel of recombinant strains. Both MSP and MMP estimate the ancestral polymorphism patterns exhibited in recombinant strains which provides important inputs for the subsequent association analysis. Efficient dynamic programming and graph algorithms based on block-wise decomposition are proposed which can solve MSP and MMP on genome-wide large-scale panels. I present efficient algorithms for mining massive streaming and sensor network data for observational sciences such as ecology and environmental studies. I proposed efficient algoirithms using block-wise synopsis construction to capture the data distribution online for the dynamic sequence data collected in the sensor network and streaming systems including clustering analysis and order-statistics computation, which is critical for real-time monitoring, anomaly detection, and other domain specific analysis. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
The $100 laptop: a cyberspace playground
Authors: Danielle Harris
Venue: ACM SIGCAS Computers and Society (2010)

One Laptop per Child (OLPC) attempts to bridge the "digital divide" between the rich and the poor, especially in third-world countries. In order to accomplish this, OLPC must introduce twenty-first century technology to the poverty-stricken, which can lead to more efficient means of education. Nicholas Negroponte, founder of OLPC, explains that in his opinion, "whatever big problem you can imagine, from world peace to the environment to hunger to poverty, the solution always includes education" (Pontin). The first step to improving education in poverty-stricken countries, according to OLPC, is providing children with an inexpensive yet functional laptop, informally known as the $100 laptop.
Differential fault analysis on Camellia
Authors: Wei Li, Dawu Gu, Juanru Li, Zhiqiang Liu, Ya Liu
Venue: Journal of Systems and Software (2010)

Camellia is a 128-bit block cipher published by NTT and Mitsubishi in 2000. On the basis of the byte-oriented model and the differential analysis principle, we propose a differential fault attack on the Camellia algorithm. Mathematical analysis and simulating experiments show that our attack can recover its 128-bit, 192-bit or 256-bit secret key by introducing 30 faulty ciphertexts. Thus our result in this study describes that Camellia is vulnerable to differential fault analysis. This work provides a new reference to the fault analysis of other block ciphers.
An optimal experimental design approach to model discrimination in dynamic biochemical systems
Authors: Dominik Skanda, Dirk Lebiedz
Venue: Bioinformatics (2010)

Motivation: Finding suitable models of dynamic biochemical systems is an important task in systems biology approaches to the biosciences. On the one hand, a correct model helps to understand the underlying mechanisms and on the other hand, one can use the model to predict the behavior of a biological system under various circumstances. Typically, before the correct model of a biochemical system is found, different hypothetical models might be reasonable and consistent with previous knowledge and available data. The main goal now is to find the best suited model out of different hypotheses. The process of falsifying inappropriate candidate models is called model discrimination. Results: We have developed a new computational tool to compute optimal experiments for biochemical kinetic systems with underlying ordinary differential equation (ODE) models for the purpose of model discrimination. We were inspired by the demands of biological experimentalists which perform one run measurement where perturbations to the system are possible. We provide a criterion which calculates the number and location of time points of optimal measurements as well as optimal initial conditions and optimal perturbations to the system. Availability: The model discrimination algorithm described here is implemented in C++ in the package ModelDiscriminationToolkit. The source code can be downloaded from http://omnibus.unifreiburg.de/~ds500/_software.html Contact: dirk.lebiedz@biologie.uni-freiburg.de Supplementary information:Supplementary data are available at Bioinformatics online. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Non-uniform self-selective coder for fuzzy rules and its application
Authors: Eva Chung-chiung Yen
Venue: Expert Systems with Applications: An International Journal (2010)

We reconsider the application scope of fuzzy rules and find the following. (1) Using spline, we can easily obtain more accurate results than those obtain by the generalized dynamic fuzzy neural network. (2) If the model is nonlinear with a disturbance term, we obtain that the checking error is very large even though the training error is small. If the model is chaotic with a disturbance term, we obtain that both the training error and checking error are very large. (3) Using a sequential algorithm as in the generalized dynamic fuzzy neural network, we would always be trapped at the local minima rather than the global minimum. Therefore we use the non-uniform self-selective coder instead and show how it works by an empirical example.
ConaMSN: A context-aware messenger using dynamic Bayesian networks with wearable sensors
Authors: Jin-Hyuk Hong, Sung-Ihk Yang, Sung-Bae Cho
Venue: Expert Systems with Applications: An International Journal (2010)

With the growth on the concern about context-aware applications, it becomes important to recognize and share user context. Even though there are some applications, it is still limited in managing simple contexts. In this paper, we propose a context-aware messenger application that exploits dynamic Bayesian networks to automatically infer a user's context and shares contextual information to enrich electronic communication. It collects various sensory information and displays representative user contexts such as emotion, stress, and activity in the form of icons in the messenger program.
Analysis of sleep EEG activity during hypopnoea episodes by least squares support vector machine employing AR coefficients
Authors: Elif Derya íbeyli, Dean Cvetkovic, Gerard Holland, Irena Cosic
Venue: Expert Systems with Applications: An International Journal (2010)

This paper presents the application of least squares support vector machines (LS-SVMs) for automatic detection of alterations in the human electroencephalogram (EEG) activities during hypopnoea episodes. The obstructive sleep apnoea hypopnoea syndrome (OSAH) means ''cessation of breath'' during the sleep hours and the sufferers often experience related changes in the electrical activity of the brain and heart. Decision making was performed in two stages: feature extraction by computation of autoregressive (AR) coefficients and classification by the LS-SVMs. The EEG signals (pre and during hypopnoea) from three electrodes (C3, C4 and O2) were used as input patterns of the LS-SVMs. The performance of the LS-SVMs was evaluated in terms of training performance and classification accuracies and the results confirmed that the proposed LS-SVM has potential in detecting changes in the human EEG activity due to hypopnoea episodes.
Brand extension of online technology products: Evidence from search engine to virtual communities and online news
Authors: Peijian Song, Cheng Zhang, Yunjie(Calvin) Xu, Lihua Huang
Venue: Decision Support Systems (2010)

Brand extension has been a subject of increasing interest and scholarly investigation for researchers in over a decade; however, little research has been directed toward understanding brand extension in the online context. The current study examines brand extension of online products and tries to find the key factors that determine the popularity of extended products in the online channels. Drawing upon the categorization theory, we propose a research model and validate it in the context of a search engine's brand extension to a virtual community service and an online news service. The findings indicate that perceived quality of a parent brand can be transferred to its extensions. Moreover, the perceived fit between the parent brand and a new product positively influences perceived quality of the extension. This study also finds that, in the online environment, the perceived tie between the existing product and the extension positively influences perceived quality of the extension. This research advances our understanding of the usage behavior between technology products sharing the same brand and provides insights into the marketing promotion strategies for IT products in electronic markets.
A study of the viability of rf mems for the implementation of a single-chip programmable rf front end for software defined radio femto cells
Authors: Richard C. Jaeger
Venue:  (2009)

The RF front end circuitry makes up over 60% of the cost of a base transceiver station (BTS, also referred as Node B in 3G networks). Included in this cost is that of the Power Amplifier unit, RF filters, and the GPS unit for clock recovery and synchronization. Because of the evolving mobile wireless communications standards (2G/2.5G/3G/LTE/4G and their various implementation standards including CDMA2000, WCDMA, TD-SCDMA, WiMAX, etc), the BTS original equipment manufacturer (OEM) is faced with the monumental task of designing a BTS RF Front End for each mobile network standard that they wish to support. Moreover, the OEMs are forced to manufacture and maintain in the field all of these BTS variants. One way to address the frequency re-use and power range limitations of today's base stations is to have more base stations covering smaller geographical areas by implementing what is called a femtocell, which also implies a significant cost reduction of the RF front end. Thus the RF front end represents the single biggest opportunity for cost reduction and logistics simplification for the base station of the future: the software-defined radio based cellular femtocell. The problem is that today's BTS RF front end implementations are not programmable but fixed to work with a specific RF frequency (e.g., 1,900 MHz) for a specific mobile network standard (e.g., CDM2000 or W-CDMA). To band-aid this problem, the OEMs typically implement multiple RF front ends to give the illusion of a &ldquo;multi-band&rdquo; programmable system at twice, triple or quadruple the cost of a single-band system. RF MEMS (micro-electro-mechanical systems) is a technology that has the potential to not only help solve the BTS cost and logistic issues, but also to complement SDR architectures by providing a true low cost, high performance, programmable RF front end. Because of its potential in the implementation of low cost, high performance, programmable RF front end filters and antennas, the author is investigating the possibility of implementing a single-chip programmable RF MEMS front end for SDR-based cellular pico and femto base stations for commercialization by 2015 or earlier. This dissertation summarizes the author's findings, conclusions, and future work recommendations. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Utility driven grid scheduling framework
Authors: Purushotham Bangalore
Venue:  (2009)

The grid computing paradigm enables access to geographically and administratively distributed networked resources, and delivers functionality of those resources to individual users. Stemming from the core composition and aggregation of individual resources, the grid is primarily characterized by the heterogeneity it offers. Although such heterogeneity is often considered a feature, it also presents an obstacle in terms of application execution patterns and expectations (in terms of job runtime, resource utilization, and/or user Quality of Service (QoS)). Typical users have little or no knowledge about the concrete requirements their application imposes on such resources and thus have to stumble through a sea of options and uncertainties when submitting a job, leading to inefficient use of available resources.In order to alleviate the user from having to understand existing dependencies and make low-level decisions, a grid metascheduling framework has been devised that enables automated application- and user-oriented job metascheduling. In order to enable application-oriented metascheduling, a set of core grid services, Application Information Services (AIS), were designed and developed to provide application metaschedulers with relevant information regarding each application's execution requirements and preferences. With such information, a metascheduler is capable of automatically realizing more job-to-resource mappings. In order to enable user-oriented metascheduling, a novel mode of user-scheduler interaction has been devised that builds on top of AIS. The model is realized in terms of two-way communication between a user and the scheduler enabling strict focus on an individual user and their current job. Overall, this dissertation makes contributions regarding efficiency of use and ease of access for grid resources.Results of grid job metaschedulers implementing the devised framework are shown as capable of consuming application-specific data in a manner that leverages existing heterogeneity and, in turn, automatically deliver effective application-to-resource mappings. Results achieved are two-fold: (1) behavior of application jobs across grid resources has been significantly improved in terms of job execution control, capable of increasing resource utilization and achieving significant runtime reduction (up to 50%), and (2) each job submission is being tailored specifically to an individual user and their respective job, delivering significantly higher QoS to the user.Keywords: grid, application-oriented job scheduling, Application Information Services, job execution space, user-scheduler interaction The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Correspondence: Comments on "Adaptive ILC for a class of discrete-time systems with iteration-varying trajectory and random initial condition"
Authors: Jing Li, Junmin Li, Weisheng Chen
Venue: Automatica (Journal of IFAC) (2010)

This note points out some errors in the proof of the asymptotic learning convergence of the tracking error in Chi, Hou and Xu [Chi, R.H., Hou, Z.S., & Xu, J.X. (2008) Adaptive ILC for a class of discrete-time systems with iteration-varying trajectory and random initial condition. Automatica, 44(8), 2207-2213].
How significant is a protein structure similarity with TM-score = 0.5?
Authors: Jinrui Xu, Yang Zhang
Venue: Bioinformatics (2010)

Motivation: Protein structure similarity is often measured by root mean squared deviation, global distance test score and template modeling score (TM-score). However, the scores themselves cannot provide information on how significant the structural similarity is. Also, it lacks a quantitative relation between the scores and conventional fold classifications. This article aims to answer two questions: (i) what is the statistical significance of TM-score? (ii) What is the probability of two proteins having the same fold given a specific TM-score? Results: We first made an all-to-all gapless structural match on 6684 non-homologous single-domain proteins in the PDB and found that the TM-scores follow an extreme value distribution. The data allow us to assign each TM-score a P-value that measures the chance of two randomly selected proteins obtaining an equal or higher TM-score. With a TM-score at 0.5, for instance, its P-value is 5.5 × 10-7, which means we need to consider at least 1.8 million random protein pairs to acquire a TM-score of no less than 0.5. Second, we examine the posterior probability of the same fold proteins from three datasets SCOP, CATH and the consensus of SCOP and CATH. It is found that the posterior probability from different datasets has a similar rapid phase transition around TM-score=0.5. This finding indicates that TM-score can be used as an approximate but quantitative criterion for protein topology classification, i.e. protein pairs with a TM-score >0.5 are mostly in the same fold while those with a TM-score <0.5 are mainly not in the same fold. Contact: zhng@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
A driver fatigue recognition model based on information fusion and dynamic Bayesian network
Authors: Guosheng Yang, Yingzi Lin, Prabir Bhattacharya
Venue: Information Sciences: an International Journal (2010)

We propose a driver fatigue recognition model based on the dynamic Bayesian network, information fusion and multiple contextual and physiological features. We include features such as the contact physiological features (e.g., ECG and EEG), and apply the first-order Hidden Markov Model to compute the dynamics of the Bayesian network at different time slices. The experimental validation shows the effectiveness of the proposed system; also it indicates that the contact physiological features (especially ECG and EEG) are significant factors for inferring the fatigue state of a driver.
The impact of tree structures on the performance of zerotree-based wavelet video codecs
Authors: Athar Ali Moinuddin, Ekram Khan, Mohammed Ghanbari
Venue: Image Communication (2010)

In this paper we analyze the impact of tree structures on the performance of zerotree-based wavelet video codecs. Since zerotree approach is based on aggregation of insignificant coefficients in trees, therefore design of a tree structure is the key issue for a better performance. We have considered six different tree structures with characteristics varying from a simple to relatively complex and composite tree structures to code the luminance-chrominance components of a video sequence. Their performances are compared in terms of average number of bits generated per bitplane, number of coded bitplanes for a given bit budget, rate-distortion performance, memory requirements and computational complexity. We observe that in general more complex and longer trees do not necessarily improve the coding efficiency. However, the tree structures encapsulating more elements per tree are memory efficient. Therefore, the rate-distortion performance, memory requirements and computational complexities need to be traded-off while selecting a particular tree structure. It is also observed that the additional improvement due to optional entropy coding is also tree structure dependent. Further, the simulation results show that by designing an efficient tree structure, depending on the picture content, the performance of a video coder can be improved by up to 2.0dB, while reducing the computational complexity by 45-60% as well as the memory requirements by almost 29-35%. Compared to the standard JPEG2000 (for intra-frame), tree-based coders are found to be efficient in terms of coding and complexity, particularly at lower bit rates.
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Authors: Thomas D. Wu, Serban Nacu
Venue: Bioinformatics (2010)

Motivation: Next-generation sequencing captures sequence differences in reads relative to a reference genome or transcriptome, including splicing events and complex variants involving multiple mismatches and long indels. We present computational methods for fast detection of complex variants and splicing in short reads, based on a successively constrained search process of merging and filtering position lists from a genomic index. Our methods are implemented in GSNAP (Genomic Short-read Nucleotide Alignment Program), which can align both single-and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short-and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state. Results: In comparison testing, GSNAP has speeds comparable to existing programs, especially in reads of ≥70 nt and is fastest in detecting complex variants with four or more mismatches or insertions of 1–9 nt and deletions of 1–30 nt. Although SNP tolerance does not increase alignment yield substantially, it affects alignment results in 7–8% of transcriptional reads, typically by revealing alternate genomic mappings for a read. Simulations of bisulfite-converted DNA show a decrease in identifying genomic positions uniquely in 6% of 36 nt reads and 3% of 70 nt reads. Availability: Source code in C and utility programs in Perl are freely available for download as part of the GMAP package at http://share.gene.com/gmap. Contact: twu@gene.com The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player