ppxscal/embedding_network huggingface dataset:
A toolkit for analysing large-scale plant small RNA datasets
Authors: Simon Moxon, Frank Schwach, Tamas Dalmay, Dan MacLean, David J. Studholme, Vincent Moulton
Venue: Bioinformatics (2008)

Summary: Recent developments in high-throughput sequencing technologies have generated considerable demand for tools to analyse large datasets of small RNA sequences. Here, we describe a suite of web-based tools for processing plant small RNA datasets. Our tools can be used to identify micro RNAs and their targets, compare expression levels in sRNA loci, and find putative trans-acting siRNA loci. Availability: The tools are freely available for use at http://srna-tools.cmp.uea.ac.uk Contact: vincent.moulton@cmp.uea.ac.uk
Residual flux-based a posteriori error estimates for finite volume and related locally conservative methods
Authors: Martin Vohral&#x00ed;k
Venue: Numerische Mathematik (2008)

We derive in this paper a posteriori error estimates for discretizations of convection&#x2013;diffusion&#x2013;reaction equations in two or three space dimensions. Our estimates are valid for any cell-centered finite volume scheme, and, in a larger sense, for any locally conservative method such as the mimetic finite difference, covolume, and other. We consider meshes consisting of simplices or rectangular parallelepipeds and also provide extensions to nonconvex cells and nonmatching interfaces. We allow for the cases of inhomogeneous and anisotropic diffusion&#x2013;dispersion tensors and of convection dominance. The estimates are established in the energy (semi)norm for a locally postprocessed approximate solution preserving the conservative fluxes and are of residual type. They are fully computable (all occurring constants are evaluated explicitly) and locally efficient (give a local lower bound on the error times an efficiency constant), so that they can serve both as indicators for adaptive refinement and for the actual control of the error. They are semi-robust in the sense that the local efficiency constant only depends on local variations in the coefficients and becomes optimal as the local P&#x00e9;clet number gets sufficiently small. Numerical experiments confirm their accuracy.
Reprint of "3D geological modelling from boreholes, cross-sections and geological maps, application over former natural gas storages in coal mines" [Comput. Geosci. 34 (2008) 278-290]
Authors: Olivier Kaufmann, Thierry Martin
Venue: Computers Geosciences (2009)

In a wide range of applications involving geological modelling, geological data available at low cost usually consist of documents such as cross-sections or geological maps and punctual data like borehole logs or outcrop descriptions. In order to build accurate 3D geological models based on this information, it is necessary to develop a methodology that takes into account the variety of available data. Such models, of the geometry of geological bodies, should also be easy to edit and update to integrate new data. This kind of model should produce a consistent representation of subsurface geology that may be a support for modelling other subsoil characteristics such as hydrogeologic or geothermic properties of the geological bodies. This paper presents a methodology developed to process geological information in this context. The aims of this methodology are comprehensive data description, effective data validation and easier model updates. Thus, special attention has been given to data structures and processing flows. The adopted methodology is implemented on a system architecture formed by a geographic information system, a geomodeler and a database communicating by file transfers. An application of this methodology, to build a 3D geological model of the subsoil over former coalmines used to store natural gas, is then presented. This model integrates the geological information available and is representative of the geological context. It is a support to the environmental follow-up needed after the end of gas-storage operations.
FINCH: evaluating reverse k-Nearest-Neighbor queries on location data
Authors: Wei Wu, Fei Yang, Chee-Yong Chan, Kian-Lee Tan
Venue: Proceedings of the VLDB Endowment (2008)

A Reverse k-Nearest-Neighbor (RkNN) query finds the objects that take the query object as one of their k nearest neighbors. In this paper we propose new solutions for evaluating RkNN queries and its variant bichromatic RkNN queries on 2-dimensional location data. We present an algorithm named INCH that can compute a RkNN query's search region (from which the query result candidates are drawn). In our RkNN evaluation algorithm called FINCH, the search region restricts the search space, and the search region is tightened each time a new result candidate is found. We also propose a method that enables us to apply any RkNN algorithm on bichromatic RkNN queries. With that, our FINCH algorithm is also used to evaluate bichromatic RkNN queries. Experiments show that our solutions are more efficient than existing algorithms.
Multi-mode energy management for multi-tier server clusters
Authors: Tibor Horvath, Kevin Skadron
Venue: Proceedings of the 17th international conference on Parallel architectures and compilation techniques (2008)

This paper presents an energy management policy for reconfigurable clusters running a multi-tier application, exploiting DVS together with multiple sleep states. We develop a theoretical analysis of the corresponding power optimization problem and design an algorithm around the solution. Moreover, we rigorously investigate selection of the optimal number of spare servers for each power state, a problem that has only been approached in an ad-hoc manner in current policies. To validate our results and policies, we implement them on an actual multi-tier server cluster where nodes support all power management techniques considered. Experimental results using realistic dynamic workloads based on the TPCW benchmark show that exploiting multiple sleep states results in significant additional cluster-wide energy savings up to 23% with little or no performance degradation.
Probabilistic algorithms for computing resolvent representations of regular differential ideals
Authors: Thomas Cluzeau, Evelyne Hubert
Venue: Applicable Algebra in Engineering, Communication and Computing (2008)

In a previous article (Cluzeau and Hubert in Appl Algebra Eng Commun Comput 13(5):395&#x2013;425, 2003), we proved the existence of resolvent representations for regular differential ideals. The present paper provides practical algorithms for computing such representations. We propose two different approaches. The first one uses differential characteristic decompositions whereas the second one proceeds by prolongation and algebraic elimination. Both constructions depend on the choice of a tuple over the differential base field and their success relies on the chosen tuple to be separating. The probabilistic aspect of the algorithms comes from this choice. To control it, we exhibit a family of tuples for which we can bound the probability that one of its element is separating.
Near-surface soil moisture retrieval from ASAR Wide Swath imagery using a Principal Component Analysis
Authors: X. Kong, S. R. Dorling
Venue: International Journal of Remote Sensing (2008)

The new ENVISAT Advanced Synthetic Aperture Radar (ASAR) Wide Swath Mode (WSM) data provide good potential for routinely monitoring near surface soil moisture due to the increased temporal revisit capability compared with ERS2 SAR. In this paper, we propose a Principal Components Analysis (PCA) to retrieve near-surface soil moisture from ASAR WSM data. The results demonstrate that PCA transformation can at least partially separate or group the effect factors, such as surface roughness, land cover, vegetation, and topography within the limitations of our datasets. The second principal component which was consistent with soil moisture and rainfall-runoff dynamics was representative of the soil moisture Saturation Potential Index over a large area. Validation against field measurements and against the UK Met Office Surface Exchange Scheme shows the retrieval performs with reasonable accuracy.
Interleaving Ontology Mapping for Online Semantic Annotation on Semantic Wiki
Authors: Jinhyun Ahn, Jason J. Jung, Key-Sun Choi
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 03 (2008)

We have designed a system that automatically annotates language resources online by referring to the semantic correspondences obtained from ontology mapping methods. Every time user inputs a term, triplets are created using a predefined pattern-triplet mapping table. If an unidentifiable term has been entered (i.e., triplets could not be created from it), the system suggests alternative terms from a thesaurus. An ontology mapping task is to map the triplets into background ontologies, efficiently producing a semantic wiki page whose tag vocabularies are derived from the ontologies. In practice, collaborative editing is also available without leading to semantic inconsistency between editors, by allowing them to use their own background ontologies and aligning these different background ontologies.
A new iterative method for discrete HJB equations
Authors: Shuzi Zhou, Zhanyong Zou
Venue: Numerische Mathematik (2008)

A successive relaxation iterative algorithm for discrete HJB equations is proposed. Monotone convergence has been proved for the algorithm.
Retrieval of land surface bidirectional reflectivity in the mid-infrared from MODIS channels 22 and 23
Authors: B. Tang, Z. -L. Li
Venue: International Journal of Remote Sensing (2008)

This paper proposes a method to retrieve the land surface bidirectional reflectivity ρb in the mid-infrared (MIR) from MODIS channels 22 and 23. A split-window-like algorithm was developed to determine the MIR ground brightness temperature [image omitted]   without the contribution of the solar direct beam from ground brightness temperatures measured at two adjacent MIR channels. Comparing the actual values of ρb with those estimated using our proposed method, the root mean square error (RMSE) was determined to be 0.0022 for the solar zenith angle (SZA) at nadir. Similar results were obtained for other SZAs, indicating that the proposed method can retrieve ρb accurately. A detailed sensitivity analysis found that the effects of instrumental noise, variations in water vapour content in the atmosphere, and reasonable variations in horizontal visibility on the retrieval of ρb were negligible and an error of 1 K on the ground brightness temperature caused by the inaccuracy of atmospheric corrections can lead to a maximum error of 0.034 on the retrieved ρb. We compared the use of radiosonde data and European Centre for Median-range Weather Forecast (ECMWF) atmospheric data to perform atmospheric corrections. The results show that atmospheric corrections can be performed with ECMWF data instead of radiosonde data without losing the accuracy of the retrieved ρb. MODIS land surface temperature/emissivity product MOD11B1 data were also used to validate [image omitted]  . Comparison of [image omitted]   estimated respectively with the proposed method and with MOD11B1 data showed that the RMSE is less than 1 K for cloud-free skies.
Automated mapping of large-scale chromatin structure in ENCODE
Authors: Heng Lian, William A. Thompson, Robert Thurman, John A. Stamatoyannopoulos, William Stafford Noble, Charles E. Lawrence
Venue: Bioinformatics (2008)

Motivation: A recently developed DNaseI assay has given us our first genome-wide view of chromatin structure. In addition to cataloging DNaseI hypersensitive sites, these data allows us to more completely characterize overall features of chromatin accessibility. We employed a Bayesian hierarchical change-point model (CPM), a generalization of a hidden Markov Model (HMM), to characterize tiled microarray DNaseI sensitivity data available from the ENCODE project. Results: Our analysis shows that the accessibility of chromatin to cleavage by DNaseI is well described by a four state model of local segments with each state described by a continuous mixture of Gaussian variables. The CPM produces a better fit to the observed data than the HMM. The large posterior probability for the four-state CPM suggests that the data falls naturally into four classes of regions, which we call major and minor DNaseI hypersensitive sites (DHSs), regions of intermediate sensitivity, and insensitive regions. These classes agree well with a model of chromatin in which local disruptions (DHSs) are concentrated within larger domains of intermediate sensitivity, the accessibility islands. The CPM assigns 92% of the bases within the ENCODE regions to the insensitive regions. The 5.8% of the bases that are in regions of intermediate sensitivity are clearly enriched in functional elements, including genes and activating histone modifications, while the remaining 2.2% of the bases in hypersensitive regions are very strongly enriched in these elements. Availability: The CPM software is available upon request from the authors. Contact:jstam@stamlab.org; noble@gs.washington.edu; Charles_Lawrence@brown.edu Supplementary information: Supplementary data are available at Bioinformatics online. Source code is available at http://noble.gs.washington.edu/proj/segment.
Nonconvex economic load dispatch using an efficient real-coded genetic algorithm
Authors: Sushil Kumar, R. Naresh
Venue: Applied Soft Computing (2009)

An efficient optimisation procedure based on real-coded genetic algorithm (RCGA) is proposed for the solution of economic load dispatch (ELD) problem with continuous and nonsmooth/nonconvex cost function and with various constraints being considered. The effectiveness of the proposed algorithm has been demonstrated on different systems considering the transmission losses and valve point loading effect in thermal units. The proposed algorithm is equipped with an effective constraint handling technique, which eliminates the need for penalty parameters. For the purpose of comparison, the same problem has also been solved using binary-coded genetic algorithm (BCGA) and three other popular RCGAs. In the proposed RCGA, simulated binary crossover and polynomial mutation are used against the single point crossover and bit-flipping mutation in BCGA. It has been observed from the test results that the proposed RCGA is more efficient in terms of thermal cost minimisation and execution time for ELD problem with continuous search space than BCGA and some other popular RCGAs.
Partially controlled deployment strategies for wireless sensors
Authors: Mauro Leoncini, Giovanni Resta, Paolo Santi
Venue: Ad Hoc Networks (2009)

In this paper we study the following problem: we are given a certain one- or two-dimensional region R to monitor and a requirement on the degree of coverage (DoC) of R to meet by a network of deployed sensors. The latter will be dropped by a moving vehicle, which can release sensors at arbitrary points within R. The node spatial distribution when sensors are dropped at a certain point is modeled by a certain probability density function F. The network designer is allowed to choose an arbitrary set of drop points, and to release an arbitrary number of sensors at each point. Given this setting, we consider the problem of determining the best performing strategy among a certain set of grid-like strategies that reflect the (one- or two-dimensional) symmetry of the region to be monitored. The best performing deployment strategy is such that: (1) the DoC requirement is fulfilled and (2) the total number of deployed nodes n is minimum. We study this problem both analytically and through simulation, under the assumption that F is the two-dimensional Normal distribution centered at the drop point. The main contribution of this paper is an in-depth study of the inter-relationships between environmental conditions, DoC requirement, and cost of the deployment.
Projective re-normalization for improving the behavior of a homogeneous conic linear system
Authors: Alexandre Belloni, Robert M. Freund
Venue: Mathematical Programming: Series A and B (2009)

In this paper we study the homogeneous conic system $$F: Ax = 0, x \in C\setminus \{0\}$$. We choose a point $$\bar s \in {\rm int}C^*$$ that serves as a normalizer and consider computational properties of the normalized system $$F_{\bar s} : Ax = 0, \bar s^T x = 1, x \in C$$. We show that the computational complexity of solving F via an interior-point method depends only on the complexity value $$\vartheta$$ of the barrier for C and on the symmetry of the origin in the image set $$H_{\bar s} := \{Ax {\bar s}^Tx = 1, x \in C\}$$, where the symmetry of 0 in $$H_{\bar s}$$ is $$ {\rm sym}(0, H_{\bar s}) := {\rm max}\{\alpha : y \in H_{\bar s} \Rightarrow -\alpha y \in H_{\bar s} \}$$. interior-point iterations. In order to improve the theoretical and practical computation of a solution of F, we next present a general theory for projective re-normalization of the feasible region $$F_{\bar s}$$ and the image set $$H_{\bar s}$$ and prove the existence of a normalizer $${\bar s}$$ such that $${\rm sym}(0,H_{\bar s}) \ge 1/m$$ provided that F has an interior solution. We develop a methodology for constructing a normalizer $${\bar s}$$ such that $${\rm sym}(0, H_{\bar s}) \ge 1/m$$ with high probability, based on sampling on a geometric random walk with associated probabilistic complexity analysis. While such a normalizer is not itself computable in strongly-polynomial-time, the normalizer will yield a conic system that is solvable in $$O(\sqrt{\vartheta}{\rm ln}(m\vartheta))$$ iterations, which is strongly-polynomial-time. Finally, we implement this methodology on randomly generated homogeneous linear programming feasibility problems, constructed to be poorly behaved. Our computational results indicate that the projective re-normalization methodology holds the promise to markedly reduce the overall computation time for conic feasibility problems; for instance we observe a 46% decrease in average IPM iterations for 100 randomly generated poorly-behaved problem instances of dimension 1,000 &#x00a0;&#x00d7;&#x00a0; 5,000.
Coding-based Join Algorithms for Structural Queries on Graph-Structured XML Document
Authors: Hongzhi Wang, Jianzhong Li, Wei Wang, Xuemin Lin
Venue: World Wide Web (2008)

In many applications, XML documents need to be modelled as graphs. The query processing of graph-structured XML documents brings new challenges. In this paper, we design a method based on labelling scheme for structural queries processing on graph-structured XML documents. We give each node some labels, the reachability labelling scheme. By extending an interval-based reachability labelling scheme for DAG by Rakesh et al., we design labelling schemes to support the judgements of reachability relationships for general graphs. Based on the labelling schemes, we design graph structural join algorithms to answer the structural queries with only ancestor-descendant relationship efficiently. For the processing of subgraph query, we design a subgraph join algorithm. With efficient data structure, the subgraph join algorithm can process subgraph queries with various structures efficiently. Experimental results show that our algorithms have good performance and scalability.
E-Learning: A Tool for Teachers with a Disability
Authors: Olga Revilla
Venue: Proceedings of the 4th Symposium of the Workgroup Human-Computer Interaction and Usability Engineering of the Austrian Computer Society on HCI and Usability for Education and Work (2008)

Usability and accessibility in e-Learning has usually focused on the learners' experience and how to improve the learning efficiency. However, very little studies analyze the accessibility and usability issues from the teachers' point of view, especially when the teachers have one or more disabilities. Teachers with disabilities find it very difficult to manage in their off-line jobs. Therefore, it is expected that technology can make them easier to work as on-line teachers. In this paper, I will summarize which troubles Spanish teachers with disabilities at Elementary degree find out in their job and how the e-learning can improve their quality of job life.
Accuracy assessment of MODIS, NOAA and IRS data in snow cover mapping under Himalayan conditions
Authors: Sanjay K. Jain, Ajanta Goswami, A. K. Saraf
Venue: International Journal of Remote Sensing (2008)

Snow cover information is an essential parameter for a wide variety of scientific studies and management applications, especially in snowmelt runoff modelling. Until now NOAA and IRS data were widely and effectively used for snow-covered area (SCA) estimation in several Himalayan basins. The suit of snow cover products produced from MODIS data had not previously been used in SCA estimation and snowmelt runoff modelling in any Himalayan basin. The present study was conducted with the aim of assessing the accuracy of MODIS, NOAA and IRS data in snow cover mapping under Himalayan conditions. The total SCA was estimated using these three datasets for 15 dates spread over 4 years. The results were compared with ground-based estimation of snow cover. A good agreement was observed between satellite-based estimation and ground-based estimation. The influence of aspect in SCA estimation was analysed for the three satellite datasets and it was observed that MODIS produced better results. Snow mapping accuracy with respect to elevation was tested and it was observed that at higher elevation MODIS sensed more snow and proved better at mapping snow under mountain shadow conditions. At lower elevation, IRS proved better in mapping patchy snow cover due to higher spatial resolution. The temporal resolution of MODIS and NOAA data is better than IRS data, which means that the chances of getting cloud-free scenes is higher. In addition, MODIS has an automated snow-mapping algorithm, which reduces the time and errors incorporated during processing satellite data manually. Considering all these factors, it was concluded that MODIS data could be effectively used for SCA estimation under Himalayan conditions, which is a vital parameter for snowmelt runoff estimation.
Higher-Order Logic Recommender System
Authors: Linna Li, Wei Zhang
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 03 (2008)

In this paper, we present a novel and elegant hybrid recommender system called HOLCF, which use higher-order logic as data representation and integrate content and demographic information into a collaborative filtering framework by using higher-order logic distance computation approaches without the effort of feature construction. Our experiments suggest that the effective combination of various kinds of information based on higher-order logic distance computation approaches provides improved accurate recommendations than other approaches.
The implications of program genres for the design of social television systems
Authors: David Geerts, Pablo Cesar, Dick Bulterman
Venue: Proceeding of the 1st international conference on Designing interactive user experiences for TV and video (2008)

In this paper, we look at how television genres can play a role in the use of social interactive television systems (social iTV). Based on a user study of a system for sending and receiving enriched video fragments to and from a range of devices, we discuss which genres are preferred for talking while watching, talking about after watching and for sending to users with different devices. The results show that news, soap, quiz and sport are genres during which our participants talk most while watching and are thus suitable for synchronous social iTV systems. For asynchronous social iTV systems film, news, documentaries and music programs are potentially popular genres. The plot structure of certain genres influences if people are inclined to talk while watching or not, and to which device they would send a video fragment. We also discuss how this impacts the design and evaluation of social iTV systems.