ppxscal/embedding_network huggingface dataset:
Plant growth monitoring and potential drought risk assessment by means of Earth observation data
Authors: K. Richter, P. Rischbeck, J. Eitzinger, W. Schneider, F. Suppan, P. Weihs
Venue: International Journal of Remote Sensing (2008)

The potential of hyperspectral imagery for the determination of drought risk zones, responsible for heterogeneous plant growth due to different soil compositions, was assessed at the field scale. The research was carried out in the Marchfeld region, an agricultural, flat area east of Vienna, Austria, during June 2005 by means of an airborne imaging spectrometer (HyMap). The inversion of a radiative transfer model by using a look-up-table (LUT) approach was performed to retrieve canopy parameters, indicators of plant growth, such as leaf area index (LAI), chlorophyll content and a soil reflectance factor (ALFA). To quantify ALFA with respect to its relationship to soil surface water content, the soil reflectance was measured at different levels of known soil water conditions. Finally, a cluster analysis was performed using the parameters estimated from the model inversion to explain plant growth variability, quantified by means of measured yield. The results were compared with a simple Normalized Differenced Vegetation Index (NDVI) approach to evaluate the contribution of hyperspectral data to vegetation monitoring. Areas characterizing different levels of drought risk could be determined by both methods with a similar performance.
Cancer outlier detection based on likelihood ratio test
Authors: Jianhua Hu
Venue: Bioinformatics (2008)

Motivation: Microarray experiments can be used to help study the role of chromosomal translocation in cancer development through cancer outlier detection. The aim is to identify genes that are up-or down-regulated in a subset of cancer samples in comparison to normal samples. Results: We propose a likelihood-based approach which targets detecting the change of point in mean expression intensity in the group of cancer samples. A desirable property of the proposed approach is the availability of theoretical significance-level results. Simulation studies showed that the performance of the proposed approach is appealing in terms of both detection power and false discovery rate. And the real data example also favored the likelihood-based approach in terms of the biological relevance of the results. Availability: R code to implement the proposed method in the statistical package R is available at: http://odin.mdacc.tmc.edu/~jhhu/cod-analysis/. Contact: jhu@mdanderson.org Supplementary information:Supplementary data are available at Bioinformatics online.
Comparison of Agent-Based and Population-Based Simulations of Displacement of Crime
Authors: Tibor Bosse, Charlotte Gerritsen, Mark Hoogendoorn, S. Waqar Jaffry, Jan Treur
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 02 (2008)

Within Criminology, the process of crime displacement is usually explained by referring to the interaction of three types of agents: criminals, passers-by, and guardians. Most existing simulation models of this process are agent-based. However, when the number of agents considered becomes large, population-based simulation has computational advantages over agent-based simulation. This paper presents both an agent-based and a population-based simulation model of crime displacement, and reports a comparative evaluation of the two models. In addition, an approach is put forward to analyse the behaviour of both models by means of formal techniques.
Evaluating talking heads for smart home systems
Authors: Christine Kühnel, Benjamin Weiss, Ina Wechsung, Sascha Fagel, Sebastian Möller
Venue: Proceedings of the 10th international conference on Multimodal interfaces (2008)

In this paper we report the results of a user study evaluating talking heads in the smart home domain. Three noncommercial talking head components are linked to two freely available speech synthesis systems, resulting in six different combinations. The influence of head and voice components on overall quality is analyzed as well as the correlation between them. Three different ways to assess overall quality are presented. It is shown that these three are consistent in their results. Another important result is that in this design speech and visual quality are independent of each other. Furthermore, a linear combination of both quality aspects models overall quality of talking heads to a good degree.
Evaluation of remote sensing of vegetation fluorescence by the analysis of diurnal cycles
Authors: J. Amoros-Lopez, L. Gomez-Chova, J. Vila-Frances, L. Alonso, J. Calpe, J. Moreno, S. del Valle-Tascon
Venue: International Journal of Remote Sensing (2008)

Chlorophyll fluorescence (ChF) emission is a direct indicator of the photosynthetic activity of vegetation, which is a key parameter of the carbon cycle. This paper analyses chlorophyll fluorescence evolution at leaf level during a complete diurnal cycle in simulated and natural conditions, for two species under different stress conditions. Absolute spectral radiance of the ChF emission is obtained allowing a quantitative derivation of the fluorescence yield of the ChF, which correlates well with established fluorescence instruments. The studied cases show that the ChF emission is mainly driven by the photosynthetic active radiation during the whole cycle, but the fluorescence yield is severely reduced during the central hours of the day when the plant is under stress due to light and heat. Results show that the Fraunhofer Line Discriminator method is an accurate way of retrieving quantitative values of ChF from remote sensing sensors at 760 nm and suggest that the mid-morning period is the best time of the day to maximize signal levels while identifying vegetation stress state.
Penalised spline support vector classifiers: computational issues
Authors: John T. Ormerod, M. P. Wand, Inge Koch
Venue: Computational Statistics (2008)

We study computational issues for support vector classification with penalised spline kernels. We show that, compared with traditional kernels, computational times can be drastically reduced in large problems making such problems feasible for sample sizes as large as ~106. The optimisation technology known as interior point methods plays a central role. Penalised spline kernels are also shown to allow simple incorporation of low-dimensional structure such as additivity. This can aid both interpretability and performance.
On the difficulty of finding the nearest peer in p2p systems
Authors: Vivek Vishnumurthy, Paul Francis
Venue: Proceedings of the 8th ACM SIGCOMM conference on Internet measurement (2008)

Finding the nearest peer, in terms of latency, is an important problem in many Internet applications. In this paper, we argue that existing solutions, which only examine inter-peer latencies as part of their operation will find it costly, in certain commonly occurring scenarios, to discover the nearest peer in P2P systems. The difficulty arises out of the way the PoP access networks are laid out in the Internet, where a single PoP (point of presence) belonging to an ISP provides connectivity to numerous client networks. This setup makes a group of peers all appear roughly the same distance from each other, leading to inefficiencies in the existing solutions. In this paper, we use large-scale measurements to show that the problematic topology does occur, use simulations of the Meridian closest-server algorithm to show that the condition does indeed lead to difficulty in finding the exact-closest peer, and propose solutions.
Searching for trends of change through exploratory data analysis of time series of remotely sensed images of SW Europe and NW Africa
Authors: Agustin Lobo, Philippe Maisongrande
Venue: International Journal of Remote Sensing (2008)

Time series of remotely sensed imagery have proven to be a valuable tool to study the dynamics of the Earth surface. Some important features have been put in evidence in time series of greenness (measured as Normalized Difference Vegetation Index (NDVI)) fields at global and continental scales, and linked to changes in atmospheric variables and/or direct human impact. Analysing the same kind of information at regional scales is more challenging, as the increased detail implies increased complexity. We present a case of study of visualization coupled to statistical analysis based on Empirical Orthogonal Functions (EOF) of the seasonal pattern of greenness in SW Europe (52° N, 11° W to 30° N, 5° E) between 1999 and 2003. Our goal was to determine whether trends could be identified in the inter-annual change of some regions. We have found that for most of the area of study, inter-annual change in seasonal pattern of greenness consisted of an oscillation along a linear trajectory on the plane defined by the first two EO components. Nevertheless, a few scattered sites and two larger regions show trends, as both the direction and the sense of the inter-annual changes remained consistent from year to year during the period of study. Considering the dependency of the seasonal course of greenness on annual patterns of temperature and precipitation, the extent covered by these areas and the diversity of land cover that they include strongly suggest a response to changes in the seasonal patterns of key atmospheric variables for the same period. While the period of study is short, the particular response of these regions deserves further attention, including the analysis of longer series of NDVI and other satellite products, as well as the exploration of the actual relationships to atmospheric variables.
Anisotropic filtering of multidimensional rotational trajectories as a generalization of 2D diffusion process
Authors: Bartosz Jablonski
Venue: Multidimensional Systems and Signal Processing (2008)

Information about the rotation of an object can be described by different representations, e.g. Euler angles, rotation matrices or quaternions. The latter representation is being intensively exploited in many applications, because of the compact description and interesting properties. In the paper the filtering method for rotational trajectories is proposed. We generalize anisotropic diffusion process defined for two dimensional images, taking into consideration specific properties of rotational motion. Filtering of trajectories in Euclidean space has already been researched in detail using different approaches. However, the straightforward application of well known filtering methods for the rotational space fails to produce appropriate results. We propose a new algorithm for processing trajectories directly in four dimensional space of unit quaternions. In the paper practical examples of the process, theoretical properties and numerical evaluation of the algorithm are presented.
Removing exponential backoff from TCP
Authors: Amit Mondal, Aleksandar Kuzmanovic
Venue: ACM SIGCOMM Computer Communication Review (2008)

The well-accepted wisdom is that TCP's exponential backoff mechanism, introduced by Jacobson 20 years ago, is essential for preserving the stability of the Internet. In this paper, we show that removing exponential backoff from TCP altogether can be done without inducing any stability side-effects. We introduce the implicit packet conservation principle and show that as long as the endpoints uphold this principle, they can only improve their end-to-end performance relative to the exponential backoff case. By conducting large-scale simulations, modeling, and network experiments in Emulab and the Internet using a kernel-level FreeBSD TCP implementation, realistic traffic distributions, and complex network topologies, we demonstrate that TCP's binary exponential backoff mechanism can be safely removed. Moreover, we show that insuitability of TCP's exponential backoff is fundamental, i.e., independent from the currently-dominant Internet traffic properties or bottleneck capacities. Surprisingly, our results indicate that a path to incrementally deploying the change does exist.
TRACE, a graphical tool for the acquisition and detection of signal patterns
Authors: A. Otero, P. Félix, S. Barro
Venue: Expert Systems with Applications: An International Journal (2009)

In this work we present TRACE, a tool for projecting the description of a signal pattern, obtained directly from an expert in the application domain, onto a computational model, and automatically identifying the pattern over a recording of the temporal evolution of a physical system. Knowledge acquisition and the visualization of results from detection are based on visual metaphors that enable experts to simply and intuitively describe patterns and identify them over a signal recording. TRACE has been used in the domains of mobile robotics and patient supervision in the intensive care units, with highly satisfactory results. The multivariable fuzzy temporal profile model (MFTP), which supports the tool, describes a signal pattern as a network of fuzzy constraints between a set of points from the evolution of the system which are especially relevant for experts. The constraint network formalism permits a single pattern to be described as a set of increments, temporal durations and slopes between the relevant points of the system's evolution. Thanks to the use of fuzzy logic, the vagueness and uncertainty that are characteristic of human knowledge can be captured by means of the representation of imprecise values for the aforementioned parameters.
A recursive architecture for hierarchical grid resource management
Authors: Eduardo Huedo, Rubén S. Montero, Ignacio M. Llorente
Venue: Future Generation Computer Systems (2009)

Grid resource management has been traditionally limited to just two levels of hierarchy, namely local resource managers and metaschedulers. This results in a non-manageable, and thus not scalable, architecture, where each metascheduler has to be able to access thousands of resources, which also implies having a detailed knowledge about their interfaces and configuration. This paper presents a recursive architecture allowing an arbitrary number of levels in the hierarchy. This way, resources can be arranged in different ways-for example, following organizational boundaries or aggregating them by similarity-while hiding the access details. An implementation of this architecture is shown, as well as its benefits in terms of autonomy, scalability, deployment and security. The proposed implementation is based on existing interfaces, allowing for standardization.
Model-based prediction of sequence alignment quality
Authors: Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka
Venue: Bioinformatics (2008)

Motivation: Multiple sequence alignment (MSA) is an essential prerequisite for many sequence analysis methods and valuable tool itself for describing relationships between protein sequences. Since the success of the sequence analysis is highly dependent on the reliability of alignments, measures for assessing the quality of alignments are highly requisite. Results: We present a statistical model-based alignment quality score. Unlike other quality scores, it does not require several parallel alignments for the same set of sequences or additional structural information. Our quality score is based on measuring the conservation level of reference alignments in Homstrad. Reference sequences were realigned with the Mafft, Muscle and Probcons alignment programs, and a sum-of-pairs (SP) score was used to measure the quality of the realignments. Statistical modelling of the SP score as a function of conservation level and other alignment characteristics makes it possible to predict the SP score for any global MSA. The predicted SP scores are highly correlated with the correct SP scores, when tested on the Homstrad and SABmark databases. The results are comparable to that of multiple overlap score (MOS) and better than those of normalized mean distance (NorMD) and normalized iRMSD (NiRMSD) alignment quality criteria. Furthermore, the predicted SP score is able to detect alignments with badly aligned or unrelated sequences. Availability: The method is freely available at http://www.mtt.fi/AlignmentQuality/ Contact: virpi.ahola@mtt.fi Supplementary information:Supplementary data are available at Bioinformatics online.
Deriving input syntactic structure from execution
Authors: Zhiqiang Lin, Xiangyu Zhang
Venue: Proceedings of the 16th ACM SIGSOFT International Symposium on Foundations of software engineering (2008)

Program input syntactic structure is essential for a wide range of applications such as test case generation, software debugging and network security. However, such important information is often not available (e.g., most malware programs make use of secret protocols to communicate) or not directly usable by machines (e.g., many programs specify their inputs in plain text or other random formats). Furthermore, many programs claim they accept inputs with a published format, but their implementations actually support a subset or a variant. Based on the observations that input structure is manifested by the way input symbols are used during execution and most programs take input with top-down or bottom-up grammars, we devise two dynamic analyses, one for each grammar category. Our evaluation on a set of real-world programs shows that our technique is able to precisely reverse engineer input syntactic structure from execution.
Shape from silhouettes based on a centripetal pentahedron model
Authors: Xin Liu, Hongxun Yao, Xilin Chen, Wen Gao
Venue: Graphical Models (2008)

In this paper we present a novel volumetric shape from silhouette (SfS) algorithm based on a centripetal pentahedron model (pent-model). The pent-model is an object-centered volumetric model composed of a set of pentahedrons cut from the centripetal triangular pyramids, which together partition the 3D space. The SfS algorithm first computes the pyramids by constructing a geodesic sphere. These pyramids are then projected onto the image planes of all cameras. The intersections between the projected pyramids and the silhouettes, which are a set of hexagons, are computed. This process can be performed very efficiently with pre-computed polar silhouette graphs (PSGs) and reduced PSGs. The hexagons are then back-projected into the 3D space, where the intersections are calculated and the pent-model is derived. After that, a mesh surface model can be extracted by marching pentahedrons. Our algorithm has the combined advantages of robustness, speediness and preciseness. Experimental results based on both synthetic images and real photos are presented.
Modelling the giant, Zn-Pb-Ag Century deposit, Queensland, Australia
Authors: L. Feltrin, J. G. McLellan, N. H. S. Oliver
Venue: Computers Geosciences (2009)

This paper presents a combination of geometric reconstructions of the Century Zn-Pb-Ag deposit, and finite-difference modelling of coupled deformation and fluid flow. Our intention is to demonstrate that these computer-based applications represent a new approach in testing ore genesis models. We use a ''visiometric'' approach, utilising GoCad 3D structural and property modelling. Computer visualisation is applied to reveal metal zonations, fault distributions and timing, stratigraphic influence on zoning, and the nature and extent of metal redistribution during basin evolution and deformation. We also examine possible links between fluid flow, deformation, and mass transfer using the numerical code FLAC3D. Numerical modelling results suggest that subsurface fluid flow during basin inversion is compartmentalised, being focussed within more permeable fault zones, thus accounting for the secondary redistribution of base metals identified using the 3D reconstructions. However, the results do not explain the broad metal zonation observed. Both the spatial and numerical models suggest that Century is syngenetic, with further diagenesis and deformation producing 1-100m-scale (re)mobilisation.
Multiagent Technology Solutions for Planning in Ambient Intelligence
Authors: Nicola Gatti, Francesco Amigoni, Marco Rolando
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 02 (2008)

The coordination of devices during the execution of services in AmI systems is of paramount importance. Effective solutions are based on planning techniques and multiagent technologies. Literature focuses on the analysis of the most appropriate planner and leaves open the technological issues. In this paper we show the limitations of the multiagent state-of-the-art technologies and we design a multiagent system for planning in AmI applications.
TRITON
Authors: Martin Prokop, Jan Adam, Zdeněk Kříž, Michaela Wimmerová, Jaroslav Koča
Venue: Bioinformatics (2008)

Summary: The new version of the TRITON program provides user-friendly graphical tools for modeling protein mutants using the external program MODELLER and for docking ligands into the mutants using the external program AutoDock. TRITON can now be used to design ligand-binding proteins, to study protein–ligand binding mechanisms or simply to dock any ligand to a protein. Availability: Executable files of TRITON are available free of charge for academic users at http://ncbr.chemi.muni.cz/triton/ Contact: triton@chemi.muni.cz Supplementary information: Supplementary data are available at Bioinformatics online.
Novel driving method for BLDCM from standstill to high speeds
Authors: Wang Hua-bin, Liu He-ping
Venue: WSEAS TRANSACTIONS on SYSTEMS (2008)

A novel approach is proposed which can drive an interior permanent magnet (IPM) brushless DC motor (BLDCM) smoothly from standstill to high speeds without position or speed sensors. At standstill, initial rotor position is estimated by using the inductance variation due to the magnet position. In rotating condition, indirect inductance method was implemented for BLDCM with H_PWM-L_PWM modulation scheme at very low speeds; When the motor speed is beyond a certain speed where the back EMF is enough, the sensorless algorithm for rotor position detection is switched to the back EMF method to drive the IPM BLDCM with H_PWM-L_ON modulation scheme. The validity of the proposed method is verified through Experimental results.
Expertise Analysis in a Question Answer Portal for Author Ranking
Authors: Lin Chen, Richi Nayak
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 01 (2008)

An online question answering (QA) portal provides users a way to socialize and help each other to solve problems. The majority of the online question answer systems use user-feedback to rank users’ answers. This way of ranking is inefficient as it involves ongoing efforts by the users and is subjective. Currently researchers have utilized link analysis of user interactions for this task. However, this is not accurate in some circumstances. A detailed structural analysis of an online QA portal is conducted in this paper. A novel approach based on users’ reputation reflecting the usage patterns is proposed to rank and recommend the user answers. The method is compared with a popular link topology analysis method, HITS. The result of the proposed method is promising.