ppxscal/embedding_network huggingface dataset:
Efficient whole-genome association mapping using local phylogenies for unphased genotype data
Authors: Zhihong Ding, Thomas Mailund, Yun S. Song
Venue: Bioinformatics (2008)

Motivation: Recent advances in genotyping technology has made data acquisition for whole-genome association study cost effective, and a current active area of research is developing efficient methods to analyze such large-scale datasets. Most sophisticated association mapping methods that are currently available take phased haplotype data as input. However, phase information is not readily available from sequencing methods and inferring the phase via computational approaches is time-consuming, taking days to phase a single chromosome. Results: In this article, we devise an efficient method for scanning unphased whole-genome data for association. Our approach combines a recently found linear-time algorithm for phasing genotypes on trees with a recently proposed tree-based method for association mapping. From unphased genotype data, our algorithm builds local phylogenies along the genome, and scores each tree according to the clustering of cases and controls. We assess the performance of our new method on both simulated and real biological datasets. Availability The software described in this article is available at http://www.daimi.au.dk/~mailund/Blossoc and distributed under the GNU General Public License. Contact: mailund@birc.au.dk
AOCI: Weaving Components in a Distributed Environment
Authors: Guido Söldner, Sven Schober, Wolfgang Schröder-Preikschat, Rüdiger Kapitza
Venue: Proceedings of the OTM 2008 Confederated International Conferences, CoopIS, DOA, GADA, IS, and ODBASE 2008. Part I on On the Move to Meaningful Internet Systems: (2008)

Mobile and embedded devices like PDAs, mobile phones, and all kinds of consumer hardware populate the world we live in. Despite the vision of ubiquitous computing and its idea of spontaneous interaction among these devices more than fifteen years ago, most of them are still isolated and restricted in their interaction capabilities. One reason for this limitation is the poor support for dynamic adaptation and evolution of software in distributed environments.This paper proposes AOCI, an Aspect-Oriented Component Infrastructure that takes the core ideas of AOP, the separation of concerns and system modularization to make them more adaptable and evolvable, to the domain of component systems. Components are usually considered as black boxes that can be combined to a complex system using their outer interfaces. In the context of our infrastructure, components export possible adaptation points, which are enriched by ontological information. This enables the application of AOP techniques without detailed knowledge about the component's internals, enabling dynamic and distributed adaptation.Our prototype is based on OSGi and provides a complete infrastructure to weave local as well as remote components. We demonstrate the feasibility of our approach by adapting the RUBiS infrastructure (a web-based bidding system) to support dynamic user-centric error detection.
Uplift and subsidence due to the 26 December 2004 Indonesian earthquake detected by SAR data
Authors: M. Chini, C. Bignami, S. Stramondo, N. Pierdicca
Venue: International Journal of Remote Sensing (2008)

The Indonesian earthquake took place on 26 December 2004 at 00:58 GMT (moment magnitude 9.3) in the Indian Ocean, offshore the west coast of Sumatra, at a depth of about 30 km. This earthquake is one of the largest of the past 100 years, comparable only with those in Chile (1960) and Alaska (1964). The earthquake originated in the subduction zone of the Indian and Burma plates, moving at a relative velocity of 6 cm/year. The aftershocks were distributed along a plate boundary of about 1000-1300 km between Sumatra and the Andaman Islands. Some hours after the earthquake a destructive tsunami followed and hit the coastlines of the surrounding regions, causing widespread destruction in Indonesia, India, Thailand and Sri Lanka. The European Space Agency (ESA) made available a data package composed of European Remote Sensing Satellite Synthetic Aperture Radar (ERS-SAR) and Environment Satellite Advanced SAR (ENVISAT-ASAR) data covering the affected area, acquired before (four acquisition dates) and after (five acquisition dates) the earthquake. A total of 26 frames were analysed. We used this dataset to evaluate the effects of the earthquake and tsunami on the human settlements and the physiographic conditions along the coast. The proposed method is based on a visual comparison between pre-and post-seismic SAR intensity images, and on an analysis of their correlation coefficients. No complex data were made available by the ESA to exploit phase coherence. Analysis of pre-and post-earthquake SAR backscattering showed wide uplift areas between the Andaman Islands and Simeulue Island, and large modifications of the coastline of Sumatra. Subsiding areas were detected along the southeast coast of Andaman up to the west coast of Nicobar Island. Tidal effects were filtered out of the SAR images to identify the consequences of the earthquake. Global Positioning System (GPS) stations in the Andaman provided results confirming the surface displacement pattern detected by SAR. The analysis enabled us to draw a boundary line separating the uplift and subsidence.
Low-Complexity Principal Component Analysis for Hyperspectral Image Compression
Authors: Qian Du, James E. Fowler
Venue: International Journal of High Performance Computing Applications (2008)

Principal component analysis (PCA) is an effective tool for spectral decorrelation of hyperspectral imagery, and PCAbased spectral transforms have been employed successfully in conjunction with JPEG2000 for hyperspectral image compression. However, the computational cost of determining the data-dependent PCA transform is high because of its traditional eigendecomposition implementation which requires calculation of a covariance matrix across the data. Several strategies for reducing the computation burden of PCA are explored, including both spatial and spectral subsampling in the covariance calculation as well as an iterative algorithm that circumvents determination of the covariance matrix entirely. Experimental results investigate the impacts of such low-complexity PCA on JPEG2000 compression of hyperspectral images, focusing on rate-distortion performance as well as data-analysis performance at an anomaly-detection task.
Is transactional memory an oxymoron?
Authors: Mark D. Hill
Venue: Proceedings of the VLDB Endowment (2008)

Transactional memory (TM) was invented 15 years ago [1]. Recently, however, TM activity has exploded [2], as the proliferation of multicore chips has provoked researchers to revisit support for parallel programming. Since some regard me as a TM expert, most of my talk will summarize TM's goals and implementation options, primarily by developing a taxonomy and using Wisconsin LogTM [3, 4] as a case study. In particular, I will consider TM implementations via software, hardware, and hybrids, as well as important design choices, such as how to buffer TM writes and when to detect TM conflicts. I will conclude with forward-looking comments regarding TM and database transactions. In theory, the two concepts have many similarities. In practice, however, they differ substantially. First, today's TM exclusively targets concurrency, while database transactions seek reliability first. Second, TM implementations focus in operations with caches and memory, while database transactions deal more with the more substantial access gap between memory and disks. Finally, I will speculate on cross-fertilization opportunities between TM and database transactions. I will not provide answers here, in part because you are the database experts. Nevertheless, I hope to encourage us all to ask the right questions.
Kepler/pPOD: Scientific Workflow and Provenance Support for Assembling the Tree of Life
Authors: Shawn Bowers, Timothy Mcphillips, Sean Riddle, Manish Kumar Anand, Bertram Ludäscher
Venue: Provenance and Annotation of Data and Processes: Second International Provenance and Annotation Workshop, IPAW 2008, Salt Lake City, UT, USA, June 17-18, 2008. Revised Selected Papers (2008)

The complexity of scientific workflows for analyzing biological data creates a number of challenges for current workflow and provenance systems. This complexity is due in part to the nature of scientific data (e.g., heterogeneous, nested data collections) and the programming constructs required for automation (e.g., nested workflows, looping, pipeline parallelism). We present an extended version of the Kepler scientific workflow system to address these challenges, tailored for the systematics community. Our system combines novel approaches for representing scientific data, modeling and automating complex analyses, and recording and browsing associated provenance information.
UTA-Rec: a recommender system based on multiple criteria analysis
Authors: Kleanthi Lakiotaki, Stelios Tsafarakis, Nikolaos Matsatsinis
Venue: Proceedings of the 2008 ACM conference on Recommender systems (2008)

UTARec, a Recommender System that incorporates Multiple Criteria Analysis methodologies is presented. The system's performance and capability of addressing certain shortfalls of existing Recommender Systems is demonstrated in the case of movie recommendations. UTARec's accuracy is measured in terms of Kendall's tau and ROC curve analysis and is also compared to a Multiple Rating Collaborative Filtering (MRCF) approach. The results indicate that the proposed Multiple Criteria Analysis methodology can certainly improve the recommendation process by producing highly accurate results, from a user oriented perspective.
MP1: languages for safety-critical software: issues and assessment
Authors: Ben Brosgol
Venue: ACM SIGAda Ada Letters (2008)

Level - Intermediate. This intermediate-level tutorial is aimed at people with a technical background in software development. No previous experience with safety-critical standards is required. Some familiarity with one or more of C, C++, Ada, or Java would be useful. Safety-critical systems (whose anomalous behavior could cause catastrophic or major failure involving loss of life) are becoming increasingly prevalent. Standards such as DO-178B, originally developed for commercial avionics, are attracting attention in other segments. The requirement to comply with such standards imposes constraints (on quality assurance, traceability, etc.) much beyond what is typical for Commercial-Off-The-Shelf Software. One of the major decisions that affects safety certification is the choice of programming language(s). Specific language features, either by their presence of absence, may make certification easier or harder. (Practicalities such as tool support and programmer experience are of course also important but are outside the scope of the tutorial). This tutorial first summarizes existing safety standards, with a focus on DO-178B, and explains how they affect the requirements on a programming language. It specifically addresses the challenges imposed by Object-Oriented Technology and summarizes the work currently underway on DO-178C. The tutorial then assesses three language technologies - C (including C++), Ada, and Java - with respect to suitability for meeting these requirements through appropriate subsetting. MISRA C, SPARK, and the in-progress Safety-Critical Java Technology are specifically identified and reviewed.
Decentralized adaptive fuzzy control for a class of nonlinear systems
Authors: A. Errahmani, H. Ouakka, M. Benyakhlef, I. Boumhidi
Venue: WSEAS Transactions on Systems and Control (2007)

In this paper, stable direct and indirect decentralized adaptive fuzzy controls are proposed for a class of large-scale nonlinear systems with the strong interconnected. The feedback and adaptive mechanisms for each subsystem depend only upon local measurements to provide asymptotic tracking of a reference trajectory. In both approaches, the proposed controllers are used to approximate the unknown subsystems. In addition, each subsystem is able to adaptively compensate for interconnections without known bounds. Simulation results are given to illustrate the tracking performance of the proposed methods.
Merging Event-Driven Process Chains
Authors: Florian Gottschalk, Wil M. Aalst, Monique H. Jansen-Vullers
Venue: Proceedings of the OTM 2008 Confederated International Conferences, CoopIS, DOA, GADA, IS, and ODBASE 2008. Part I on On the Move to Meaningful Internet Systems: (2008)

While business processes are typically handled differently among companies, many of them are variations of a common process like procurement or invoicing. To gain synergy effects from corporate mergers, process analysts align such processes by identifying and seamlessly integrating overlapping process parts. To support this, we present in this paper an approach that merges two business process models which are depicted as Event-driven Process Chains into a single process model which can serve as a starting point for further process optimization. The approach has been implemented in the ProM process mining framework and can thus be used together with a wide range of other process mining and analysis techniques.
A supervised Bayesian method for cerebrovascular segmentation
Authors: Jutao Hao, Minglu Li
Venue: WSEAS Transactions on Signal Processing (2007)

In this paper, we present a supervised statistical-based cerebrovascular segmentation method from Time-Of-Flight MRA. The novelty of this method is that rather than model the dataset over the entire intensity range, we at first use a low threshold to eliminate the lowest intensity region, and then use two uniform distributions to model the middle and high intensity regions, respectively. Subsequently, in order to overcome the intensity overlap between subcutaneous fat and arteries, a high order multiscale features based energy function is introduced to enhance the segmentation. Comparing with those sole intensity based segmentation method the newly proposed algorithm can solve the problem of the regional intensity variation of TOF-MRA well and improve the quality of segmentation. The experimental results also show that the proposed method can provide a better quality segmentation than sole intensity information used method.
Research on MPPT and single-stage grid-connected for photovoltaic system
Authors: Jui-Liang Yang, Ding-Tsair Su, Ying-Shing Shiao
Venue: WSEAS TRANSACTIONS on SYSTEMS (2008)

This paper proposes a grid-connected photovoltaic (PV) system that is consisted of a boost converter with maximum power tracking, battery charge controller, inverter, and the related control circuits. A sliding mode controller is designed for controlling the boost converter to output the maximum power of the solar cells. A control strategy is proposed of a Maximum Power Point Tracking (MPPT) impendence adapter coupling a photovoltaic generator to a battery. The proposed strategy is based on the sliding mode control theory of continuing systems to permit a direct control of power converter. The PV generator price is even relatively high, so the user is interested of the optimal coupling of PV generator to electromechanical loads. In fact, this system uses the optimal coupling in order to have maximum power during the whole operating period. A grid-connected inverter is designed to transform the maximum output power into the load and utility. The real power control is using zero-cross and phase-lock circuits that control the inverter output voltage which is phase lead and synchronized with the utility. A digital circuit is used to detect the phase angles of the load voltage and current to control the inverter output amplitude to achieve the reactive power load compensation. A monitor circuit is designed to detect the voltage and frequency variation in the utility. When the photovoltaic system encounters a voltage and frequency deviation, the monitor circuit immediately disconnects the photovoltaic system from the utility to prevent the island effect. The proposed system is implemented by using OP amplifiers and micro controller (PIC16F877A). Both the simulation and experimental results using MATLAB show the sliding mode controller for maximum power tracking has good performance. The phase and amplitude control experiments achieve the real and reactive power control. The island effect experiments demonstrate evidence of the solar cell system protection ability illustrating the proposed grid-connected photovoltaic system has good operating performance.
mlegp
Authors: Garrett M. Dancik, Karin S. Dorman
Venue: Bioinformatics (2008)

Summary: Gaussian processes (GPs) are flexible statistical models commonly used for predicting output from complex computer codes. As such, GPs are well suited for the analysis of computer models of biological systems, which have been traditionally difficult to analyze due to their high-dimensional, non-linear and resource-intensive nature. We describe an R package, mlegp, that fits GPs to computer model outputs and performs sensitivity analysis to identify and characterize the effects of important model inputs. Availability: http://www.biomath.org/mlegp Contact: kdorman@iastate.edu Supplementary information: See http://www.biomath.org/mlegp for a user manual and examples.
On Dimensionality of Embedding Space in Multidimensional Scaling
Authors: Julius Žilinskas
Venue: Informatica (2008)

Multidimensional scaling is a technique for exploratory analysis of multidimensional data widely usable in different applications. By means of this technique the image points in a low-dimensional embedding space can be found whose inter-point distances fit the given dissimilarities between the considered objects. In this paper dependence of relative visualization error on the dimensionality of embedding space is investigated. Both artificial and practical data sets have been used. The images in three-dimensional embedding space normally show the structural properties of sets of considered objects with acceptable accuracy, and widening of applications of stereo screens makes three-dimensional visualization very attractive.
Fault-tolerant stream processing using a distributed, replicated file system
Authors: YongChul Kwon, Magdalena Balazinska, Albert Greenberg
Venue: Proceedings of the VLDB Endowment (2008)

We present SGuard, a new fault-tolerance technique for distributed stream processing engines (SPEs) running in clusters of commodity servers. SGuard is less disruptive to normal stream processing and leaves more resources available for normal stream processing than previous proposals. Like several previous schemes, SGuard is based on rollback recovery [18]: it checkpoints the state of stream processing nodes periodically and restarts failed nodes from their most recent checkpoints. In contrast to previous proposals, however, SGuard performs checkpoints asynchronously: i.e., operators continue processing streams during the checkpoint thus reducing the potential disruption due to the checkpointing activity. Additionally, SGuard saves the checkpointed state into a new type of distributed and replicated file system (DFS) such as GFS [22] or HDFS [9], leaving more memory resources available for normal stream processing. To manage resource contention due to simultaneous checkpoints by different SPE nodes, SGuard adds a scheduler to the DFS. This scheduler coordinates large batches of write requests in a manner that reduces individual checkpoint times while maintaining good overall resource utilization. We demonstrate the effectiveness of the approach through measurements of a prototype implementation in the Borealis [2] open-source SPE using HDFS [9] as the DFS.
Energy distribution modeling of car body deformation using LPV representations and fuzzy reasoning
Authors: István Á. Harmati, László Szeidl, András Rövid, Péter Várlaki
Venue: WSEAS TRANSACTIONS on SYSTEMS (2008)

The main aim of the paper is to introduce a novel method - based on fuzzy control and linear parameter varying (LPV) system representation transformable into HOSVD based Canonical form - for modeling deformation processes with respect to the distribution of the absorbed kinetic energy. Modeling such kind of processes requires many uncertain input parameters. Using the proposed concept we are able to handle them and keep the complexity of the models low by using higher order singular value decomposition (HOSVD) technique.
Modelling situation awareness for Context-aware Decision Support
Authors: Yu-Hong Feng, Teck-Hou Teng, Ah-Hwee Tan
Venue: Expert Systems with Applications: An International Journal (2009)

Situation awareness modelling is popularly used in the command and control domain for situation assessment and decision support. However, situation models in real-world applications are typically complex and not easy to use. This paper presents a Context-aware Decision Support (CaDS) system, which consists of a situation model for shared situation awareness modelling and a group of entity agents, one for each individual user, for focused and customized decision support. By incorporating a rule-based inference engine, the entity agents provide functions including event classification, action recommendation, and proactive decision making. The implementation and the performance of the proposed system are demonstrated through a case study on a simulated command and control application.
Uniform sensing protocol for autonomous rechargeable sensor networks
Authors: Volodymyr Pryyma, Ladislau Bölöni, Damla Turgut
Venue: Proceedings of the 11th international symposium on Modeling, analysis and simulation of wireless and mobile systems (2008)

Autonomous rechargeable sensor networks are becoming a feasible solution to many real world applications. In this paper, we propose a Uniform Sensing Protocol for autonomous rechargeable sensor networks. Our protocol aims to provide uniformly distributed sensing throughout the entire life-time of the network, thus increasing the overall network reliability. It considers the amount of available energy in the environment as well as the probability of encountering a specific number of threats. Using these parameters, each node estimates its own active period, such that uniform sensing is established. We compare the performance of our protocol with static and dynamic active time slot approaches. The simulation results show that the Uniform Sensing Protocol generates fewer failures and has a significantly longer mean time to failure than the other two schemes.
A method for cross-calibrating geostationary and polar orbiting satellite sensors in the infrared windows
Authors: M. O. Kolawole
Venue: International Journal of Remote Sensing (2008)

The forward radiative transfer routine has been used to remove the artefact caused by modulation on meteorological satellite-sensor responses. This paper describes a direct method where images observed by the infrared channels aboard the Multi-functional Transport Satellite (MTSAT-1R) and Fengyun-2C (FY-2C) geostationary satellites are compared with those by the Advanced Very High Resolution Radiometer (AVHRR) sensor aboard the National Oceanic and Atmospheric Administration (NOAA) polar-orbiting satellites. The calibration differences between the polar orbiting and the geostationary satellites are found to be within 1 K of each other.