ppxscal/embedding_network huggingface dataset:
Sorting Genomes by Reversals and Translocations
Authors: Xiao Yin, Daming Zhu
Venue: Proceedings of the 2009 Asia-Pacific Conference on Information Processing - Volume 02 (2009)

Reversal and translocation are both common rearrangement events in the evolution of mammalian species. Given two multi-chromosomal genomes A and B, the problem of sorting by reversals and translocations (SBRT) is to find a shortest sequence of reversals and translocations that transforms A into B. This problem is currently solved by a reduction to the problem of sorting by reversals (SBR), where each reversal simulates either a reciprocal translocation or an internal reversal. In this paper, we present a new algorithm for SBRT that explicitly treats translocations and reversals as distinct operations, which looks more natural and simple than the previous one.
A roe-average algorithm for a granular-gas model with non-conservative terms
Authors: Hemant Kamath, Xiaoju Du
Venue: Journal of Computational Physics (2009)

A Roe-average algorithm has been derived for a granular-gas model, proposed by Goldshtein and Shapiro [Goldshtein, Shapiro, Mechanics of collisional motion of granular materials: Part 1. General hydrodynamic equations, J. Fluid Mech. 282 (1995) 75-114], which contains non-conservative terms in the Euler-like hyperbolic governing equations apart from sink terms, which arise from inelastic collision of granules and are present only in the energy equation. The non-conservative terms introduce non-isentropic effects in acoustic-wave propagation within granular media and they also contribute to the Rankine-Hugoniot relations across a discontinuity. A Roe-average algorithm, based on the same granular-gas model, was derived in the literature [V. Kamenetsky, A. Goldshtein, M. Shapiro, D. Degani, Evolution of a shock wave in a granular gas, Phys. Fluids, 12 (2000) 3036-3049] which then required the implementation of a shock-fitting technique at a discontinuity. In the present work, Roe-averaged variables have been obtained from the Rankine-Hugoniot jump relations and the non-conservative terms have been incorporated in the numerical flux formula consistent with upwind principles associated with the granular speed of sound. Results for unsteady one-dimensional granular flows, colliding with a wall, demonstrate the capability of the proposed algorithm to capture strong shocks in addition to flow features not found in molecular gases, such as a fluidized region downstream of the shock and a compacted solid-block region adjacent to the wall.
A Lower Bound for Oblivious Dimensional Routing
Authors: Andre Osterloh
Venue: Proceedings of the 15th International Euro-Par Conference on Parallel Processing (2009)

In this work we consider deterministic oblivious dimensional routing algorithms on d-dimensional meshes. In oblivious dimensional routing algorithms the path of a packet depends only on the source and destination node of the packet. Furthermore packets use a shortest path with a minimal number of bends. We present an ¿(kn (d + 1)/2) step lower bound for oblivious dimensional k-k routing algorithms on d-dimensional meshes for odd d > 1 and show that the bound is tight. 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
Impact of Grazing Excluding and Grazing on Soil Properties in Sandy Grassland in Horqin Sand Land, China
Authors: Yu-Hui He, Ha-Lin Zhao, Xin-Ping Liu
Venue: Proceedings of the 2009 International Conference on Environmental Science and Information Application Technology - Volume 02 (2009)

The restoration of degraded grassland which caused by overgrazing is directly related to land sustainable and economical development in North China. However, it is not well know that the impact of grazing excluding and continuous free grazing on soil properties in this region. In this paper, Soil physical and chemical properties under grazing excluded for 5 and 11 years and free grazing were examined in representative degraded sandy grassland. Results showed that continuous free grazing cause soil compaction, soil structure degradation, and loss of soil organic C and total N. Different period exclusion contribute to soil structure improvement, bulk density decreased, and soil fertility improvement through area protection. In addition, soil organic C and total N stocks showed a significant increasing trend from FG to 11GE. It indicated grazing excluding has important significance in soil restoration. So there is a need to develop sustainable grassland management and exclusion practices to combat the ongoing grassland degradation in the region.
Global synchronization of delay-coupled genetic oscillators
Authors: Jianlong Qiu, Jinde Cao
Venue: Neurocomputing (2009)

This paper investigates the global exponential synchronization of delay-coupled identical genetic oscillator. By constructing appropriate Lyapunov functional and using the linear matrix inequality (LMI) approach, a series of sufficient criteria, which are very easy to verify, are obtained. It is shown that these criteria improve and extend the earlier works. Finally, a population of genetic oscillators based on the Goodwin model is adopted as a numerical example to demonstrate the effectiveness of our theoretical results.
Artificial Intelligence: New Research
Authors: Randal B. Bernstein, Wesley N. Curtis
Venue:  (2009)

The modern definition of artificial intelligence (or AI) is "the study and design of intelligent agents" where an intelligent agent is a system that perceives its environment and takes actions which maximise its chances of success. AI research uses tools and insights from many fields, including computer science, psychology, philosophy, neuroscience, cognitive science, linguistics, operations research, economics, control theory, probability, optimisation and logic. AI research also overlaps such fields as robotics, control systems, scheduling, data mining, logistics, speech recognition, facial recognition and many others. This book presents recent and important research in the field.
Video semantic analysis based on structure-sensitive anisotropic manifold ranking
Authors: Jinhui Tang, Guo-Jun Qi, Meng Wang, Xian-Sheng Hua
Venue: Signal Processing (2009)

As a major family of semi-supervised learning (SSL), graph-based SSL has recently attracted considerable interest in the machine learning community along with application areas such as video semantic analysis. In this paper, we analyze the connections between graph-based SSL and partial differential equation- (PDE) based diffusion. From the viewpoint of PDE-based diffusion, the label propagation in normal graph-based SSL is isotropic accompanied with distance. However, according to the structural assumption, which is one of the two basic assumptions in graph-based SSL, we need to enhance the label propagation between the samples in the same structure while weakening the counterpart between the samples in different structures. Accordingly, we deduce a novel graph-based SSL framework, named structure-sensitive anisotropic manifold ranking (SSAniMR), from PDE-based anisotropic diffusion. Instead of using Euclidean distance only, SSAniMR takes local structural difference into account to make the label propagation anisotropic, which is intrinsically different from the isotropic label propagation process in general graph-based SSL methods. Experiments conducted on the TREC Video Retrieval Evaluation (TRECVID) dataset show that this approach significantly outperforms existing graph-based SSL methods and is effective for video semantic annotation.
Memory-Based Modeling of Seasonality for Prediction of Climatic Time Series
Authors: Daniel Nikovski, Ganesan Ramachandran
Venue: Proceedings of the 6th International Conference on Machine Learning and Data Mining in Pattern Recognition (2009)

The paper describes a method for predicting climatic time series that consist of significant annual and diurnal seasonal components and a short-term stochastic component. A memory-based method for modeling of the non-linear seasonal components is proposed that allows the application of simpler linear models for predicting short-term deviations from seasonal averages. The proposed method results in significant reduction of prediction error when predicting time series of ambient air temperature from multiple locations. Moreover, combining the statistical predictor with meteorological forecasts using linear regression or Kalman filtering further reduces prediction error to typically between 1 o C over a prediction horizon of one hour and 2.5 o C over 24 hours.
Faster Algorithms for Sampling and Counting Biological Sequences
Authors: Christina Boucher
Venue: Proceedings of the 16th International Symposium on String Processing and Information Retrieval (2009)

A set of sequences S is pairwise bounded if the Hamming distance between any pair of sequences in S is at most 2d. The Consensus Sequence problem aims to discern between pairwise bounded sets that have a consensus, and if so, finding one such sequence s *, and those that do not. This problem is closely related to the motif-recognition problem, which abstractly models finding important subsequences in biological data. We give an efficient algorithm for sampling pairwise bounded sets, referred to as MarkovSampling, and show it generates pairwise bounded sets uniformly at random. We illustrate the applicability of MarkovSampling to efficiently solving motif-recognition instances. Computing the expected number of motif sets has been a long-standing open problem in motif-recognition [1,3]. We consider the related problem of counting the number of pairwise bounded sets, give new bounds on number of pairwise bounded sets, and present an algorithmic approach to counting the number of pairwise bounded sets.
Perceived Usefulness and Perceived Ease-of-Use of Ambient Intelligence Applications in Office Environments
Authors: Carsten Röcker
Venue: Proceedings of the 1st International Conference on Human Centered Design: Held as Part of HCI International 2009 (2009)

This paper describes a multi-national study evaluating the perceived usefulness and perceived ease of use of Ambient Intelligence (AmI) applications in office environments. In a first step, existing usage scenarios were analyzed to identify characteristic functionalities and application domains. The identified core functionalities were integrated into a representative and coherent evaluation scenario, which was presented to a target user population in a questionnaire-based study. The results of the study indicate, that the participants regard the described Ambient Intelligence functionalities as rather useful and easy to use. Nevertheless, moderate overall ratings for both factors show, that the acceptance of AmI technologies is not as high as often argued.
Workshop Organizers' Message
Authors: Wei Wang, Baihua Zheng
Venue: Database Systems for Advanced Applications: DASFAA 2009 International Workshops: BenchmarX, MCIS, WDPP, PPDA, MBC, PhD, Brisbane, Australia, April 20 - 23, 2009 (2009)

The DASFAA PhD workshop will be held in Brisbane, Australia on 22 April, 2009, in conjunction with the DASFAA 2009 conference. The workshop is the first in its series and aims to bring together PhD students working on topics related to the DASFAA conference series. It will offer PhD students the opportunity to present, discuss, and receive feedback on their research in a constructive and international atmosphere.The workshop has attracted six submissions. The submissions are highly diversified, coming from Australia, Cananda, Japan, and Mexico. All submissions were peer reviewed by three program committee members. The program committee selected three (short) papers for inclusion in the proceeding. The accepted papers covered important research topics and novel applications on Database, Data Mining, and Web Services.
A High Performance Cluster File System with Standard Network File System Interface
Authors: Jun Lu, Bin Du, Yi Zhu, Ly Ren, Daiw Li
Venue: Proceedings of the 2009 International Forum on Information Technology and Applications - Volume 01 (2009)

The Cluster technology can organize many cheap servers to cluster, and obtain the high performance. The traditional cluster file systems although can achieve high performance, but these systems all require to modify the software on client. This requirement make these systems can not be widely applied. This paper provides a novel high performance cluster file system with standard network file system access interface: CFS-SI. CFS-SI has following characters: (1) CFS-SI unitizes the advantage of cluster file system, and can adequately use the network bandwidth and the storage capability; (2) CFS-SI use the load balance to improve the performance based on IP spoof technology; (3) CFS-SI can give standard network file system access interface to client and do no require any software modification to client. The experiment in this paper shows that CFS-SI can not only inherit the excellence of normal cluster file system, but also can provide high performance for file operation.
Analysis and system combination of phrase- and N-gram-based statistical machine translation systems
Authors: Marta R. Costa-jussà, Josep M. Crego, David Vilar, José A. R. Fonollosa, José B. Mariño, Hermann Ney
Venue: Human Language Technologies 2007: The Conference of the North American Chapter of the Association for Computational Linguistics; Companion Volume, Short Papers on XX (2007)

In the framework of the Tc-Star project, we analyze and propose a combination of two Statistical Machine Translation systems: a phrase-based and an N-gram-based one. The exhaustive analysis includes a comparison of the translation models in terms of efficiency (number of translation units used in the search and computational time) and an examination of the errors in each system's output. Additionally, we combine both systems, showing accuracy improvements.
A nonlinear compromise scheme in multicriteria evaluation and optimization problems
Authors: A. N. Voronin
Venue: Cybernetics and Systems Analysis (2009)

The concept of a nonlinear compromise scheme in multicriteria problems of evaluation and optimization is presented. It is shown that the problem is to approximate correctly the utility function and construct a substantial mathematical model (scalar convolution) adequate to the given situation to solve various multicriteria problems. In analysis problems, this convolution is an objective function. Its extremization results in a compromise-optimal vector of arguments. An illustrative example is given.
Seeded discovery of base relations in large corpora
Authors: Nicholas Andrews, Naren Ramakrishnan
Venue: Proceedings of the Conference on Empirical Methods in Natural Language Processing (2008)

Relationship discovery is the task of identifying salient relationships between named entities in text. We propose novel approaches for two sub-tasks of the problem: identifying the entities of interest, and partitioning and describing the relations based on their semantics. In particular, we show that term frequency patterns can be used effectively instead of supervised NER, and that the p-median clustering objective function naturally uncovers relation exemplars appropriate for describing the partitioning. Furthermore, we introduce a novel application of relationship discovery: the unsupervised identification of protein-protein interaction phrases.
Biodegradation of Synthetic High Phenol Contamination Wastewater by an Immersed Membrane Bioreactor
Authors: Yun Wu, Hongwei Zhang
Venue: Proceedings of the 2009 International Conference on Environmental Science and Information Application Technology - Volume 02 (2009)

Phenol is a highly toxic and carcinogenic compound and its biological treatment has been broadly agreed that it is economical, practical and it leads to a complete removal of phenol (degraded to inorganic, CO2 H2O etc.). The effect of acclimated activated sludge in the phenol biodegradation has been studied. First, the batch acclimated period have been performed gradually by elevated the activated sludge tolerance to the concentration of phenol from 100 mg·L-1 to 2000 mg·L-1 as carbon source. Subsequently, the immersed membrane bioreactor had been conducted to verify the feasibility of biodegradable high concentration of phenol (2000 mg·L-1), using acclimated activated sludge. The phenol and COD removal efficiency were respective 99.98% and 98.29%, at HRT 18h and F/M 0.29 kg COD·kg MLSS-1·d-1. The results proved the ability of the immersed MBR to tackle with synthetic high strength of phenol wastewater.
TH-CDP: An Efficient Block Level Continuous Data Protection System
Authors: Yonghong Sheng, Dongsheng Wang, JinYang He, DaPeng Ju
Venue: Proceedings of the 2009 IEEE International Conference on Networking, Architecture, and Storage (2009)

Traditional data protection technologies, such as remote mirroring, snapshot and backup, cannot completely solve virus attack, user error problems. Continuous data protection (CDP), capturing all data writes at file or block level, is an enabling technology to storage systems against malicious attacks or user mistakes, because it allows each block data to be undoable. Most of existing data protection systems or prototypes are not real CDP ones because there is a data exposure between subsequent snapshots. Therefore they provide less granular recovery points. In addition, some products work either at file system level or at application level which lack general purpose. This paper presents the design, implementation, and performance of a new block level continuous data protection system, TH-CDP. Besides providing the basic functions of true CDP, TH-CDP provides virtual volume image at any point in time without affecting the production system. Another distinctive feature of TH-CDP is its checkpointing mechanism. By encapsulating the checkpoint information into I/O request packet queue, TH-CDP can take checkpoints without temporarily halting normal business processing or any incoming request. In addition, TH-CDP uses log-structured technique to store changed block data on raw disk, thereby speeding up both data writing and space recycling. Extensive experiments on file systems, databases using IOzone, and TPC-C benchmark show that TH-CDP can effectively improve the convenience of checkpointing and recovery assurance process. Under the circumstances of the changed block data up to 20 times of the original data size, the 100% sequence read speed of the oldest virtual volume image version is nearly 1/3 to 1/4 compared to the normal iSCSI volume.
Explaining Anomalous Responses to Treatment in the Intensive Care Unit
Authors: Laura Moss, Derek Sleeman, Malcolm Booth, Malcolm Daniel, Lyndsay Donaldson, Charlotte Gilhooly, Martin Hughes, Malcolm Sim, John Kinsella
Venue: Proceedings of the 12th Conference on Artificial Intelligence in Medicine: Artificial Intelligence in Medicine (2009)

The Intensive Care Unit (ICU) provides treatment to critically ill patients. When a patient does not respond as expected to such treatment it can be challenging for clinicians, especially junior clinicians, as they may not have the relevant experience to understand the patient's anomalous response. Datasets for 10 patients from Glasgow Royal Infirmary's ICU have been made available to us. We asked several ICU clinicians to review these datasets and to suggest sequences which include anomalous or unusual reactions to treatment. Further, we then asked two ICU clinicians if they agreed with their colleagues' assessments, and if they did to provide possible explanations for these anomalous sequences. Subsequently we have developed a system which is able to replicate the clinicians' explanations based on the knowledge contained in its several ontologies; further the system can suggest additional explanations which will be evaluated by the senior consultant.
Model-lite planning for the web age masses: the challenges of planning with incomplete and evolving domain models
Authors: Subbarao Kambhampati
Venue: Proceedings of the 22nd national conference on Artificial intelligence - Volume 2 (2007)

The automated planning community has traditionally focused on the efficient synthesis of plans given a complete domain theory. In the past several years, this line of work met with significant successes, and the future course of the community seems to be set on efficient planning with even richer models. While this line of research has its applications, there are also many domains and scenarios where the first bottleneck is getting the domain model at any level of completeness. In these scenarios, the modeling burden automatically renders the planning technology unusable. To counter this, I will motivate model-lite planning technology aimed at reducing the domain-modeling burden (possibly at the expense of reduced functionality), and outline the research challenges that need to be addressed to realize it.
Robust periodic planning and execution for autonomous spacecraft
Authors: Barney Pell, Erann Gat, Ron Keesing, Nicola Muscettola, Ben Smith
Venue: Proceedings of the Fifteenth international joint conference on Artifical intelligence - Volume 2 (1997)

The New Millennium Remote Agent (NMRA) will be the first on-board AI system to control an actual spacecraft. The spacecraft domain raises a number of challenges for planning and execution, ranging from extended agency and long-term planning to dynamic recoveries and robust concurrent execution, all in the presence of tight real-time deadlines, changing goals, scarce resource constraints, and a wide variety of possible failures. NMRA is one of the first systems to integrate closed-loop planning and execution of concurrent temporal plans. It is also the first autonomous system that will be able to achieve a sustained, multi-stage, multiyear mission without communication or guidance from earth.
Self-consistent solution of cosmological radiation-hydrodynamics and chemical ionization
Authors: Daniel R. Reynolds, John C. Hayes, Pascal Paschos, Michael L. Norman
Venue: Journal of Computational Physics (2009)

We consider a PDE system comprising compressible hydrodynamics, flux-limited diffusion radiation transport and chemical ionization kinetics in a cosmologically-expanding universe. Under an operator-split framework, the cosmological hydrodynamics equations are solved through the piecewise parabolic method, as implemented in the Enzo community hydrodynamics code. The remainder of the model, including radiation transport, chemical ionization kinetics, and gas energy feedback, form a stiff coupled PDE system, which we solve using a fully-implicit inexact Newton approach, and which forms the crux of this paper. The inner linear Newton systems are solved using a Schur complement formulation, and employ a multigrid-preconditioned conjugate gradient solver for the inner Schur systems. We describe this approach and provide results on a suite of test problems, demonstrating its accuracy, robustness, and scalability to very large problems.