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IEEE International Conference on Data Mining Workshops (ICDM Workshops)

作者： Jim Jing-Yan Wang Xin Gao Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia

Trypanosma brucei (T. Brucei) is an important pathogen agent of African trypanosomiasis. The flagellum is an essential and multifunctional organelle of T. Brucei, thus it is very important to recognize the flagellar proteins from T. Brucei proteins for the purposes of both biological research and drug design. In this paper, we investigate computationally recognizing flagellar proteins in T. Brucei by pattern recognition methods. It is argued that an optimal decision function can be obtained as the difference of probability functions of flagella protein and the non-flagellar protein for the purpose of flagella protein recognition. We propose to learn a multi-kernel classification function to approximate this optimal decision function, by minimizing the information loss of such approximation which is measured by the Kull back - Leibler (KL) divergence. An iterative multi-kernel classifier learning algorithm is developed to minimize the KL divergence for the problem of T. Brucei flagella protein recognition, experiments show its advantage over other T. Brucei flagellar protein recognition and multi-kernel learning methods.

关键词： Proteins Kernel Vectors Training Feature extraction Approximation methods Loss measurement

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An empirical evaluation of bufferbloat in IEEE 802.11n wireless networks

An empirical evaluation of bufferbloat in IEEE 802.11n wirel...

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IEEE Conference on Wireless Communications and Networking

作者： Ahmad Showail Kamran Jamshaid Basem Shihada Computer Electrical and Mathematical Sciences and Engineering (CEMSE) Division King Abdullah University of Science and Technology Thuwal Saudi Arabia

ISBN: (纸本)9781479930845

In this paper, we analyze the impact of large, persistently-full buffers (`bufferbloat') on various network dynamics in IEEE 802.11n wireless networks. Bufferbloat has mostly been studied in the context of wired networks. We study the impact of bufferbloat on a variety of wireless network topologies, including wireless LAN (WLAN) and multi-hop wireless networks. Our results show that a single FTP transfer between two Linux wireless hosts can saturate the buffers in the network stack, leading to RTT delays exceeding 4.5 s in multi-hop configurations. We show that well-designed Aggregate MAC Protocol Data Unit (A-MPDU) MAC-layer frame aggregation can reduce RTT delays while simultaneously increasing network throughput. However, additional measures may still be required to meet the constraints of real-time flows (such as VoIP). Our experiments show that large buffers can deteriorate the fairness in rate allocation in parking lot based multi-hop networks.

关键词： Throughput Delays Topology Wireless networks Network topology IEEE 802.11n Standard

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On the outage capacity of the block fading channel at low-power regime

On the outage capacity of the block fading channel at low-po...

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IEEE International Symposium on Information Theory

作者： Zouheir Rezki Mohamed-Slim Alouini Computer Electrical and Mathematical Sciences and Engineering (CEMSE) Division King Abdullah University of Science and Technology (KAUST) Saudi Arabia

Outage performance of the M-block fading with additive white Gaussian noise (BF-AWGN) is investigated at low-power regime. We consider delay-constrained constant-rate communications with perfect channel state information (CSI) at both the transmitter and the receiver (CSI-TR), under a short-term power constraint. We show that selection diversity that allocates all the power to the strongest block is asymptotically optimal. Then, we provide a simple characterization of the outage probability in the regime of interest. We quantify the reward due to CSI-TR over the constant-rate constant-power scheme and show that this reward increases with the delay constraint. For instance, for Rayleigh fading, we find that a power gain up to 4.3 dB is achievable.

关键词： Frequency modulation Gain Manganese Information theory Rayleigh channels Reliability

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Quick Mining of Isomorphic Exact Large Patterns from Large Graphs

Quick Mining of Isomorphic Exact Large Patterns from Large G...

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IEEE International Conference on Data Mining Workshops (ICDM Workshops)

作者： Islam Almasri Xin Gao Nina Fedoroff Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia Biological and Environmental Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia

The applications of the sub graph isomorphism search are growing with the growing number of areas that model their systems using graphs or networks. Specifically, many biological systems, such as protein interaction networks, molecular structures and protein contact maps, are modeled as graphs. The sub graph isomorphism search is concerned with finding all sub graphs that are isomorphic to a relevant query graph, the existence of such sub graphs can reflect on the characteristics of the modeled system. The most computationally expensive step in the search for isomorphic sub graphs is the backtracking algorithm that traverses the nodes of the target graph. In this paper, we propose a pruning approach that is inspired by the minimum remaining value heuristic that achieves greater scalability over large query and target graphs. Our testing on various biological networks shows that performance enhancement of our approach over existing state-of-the-art approaches varies between 6x and 53x.

关键词： Proteins Filtering Heuristic algorithms Image color analysis Biological system modeling Scalability

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A parallel wavelet-enhanced PWTD algorithm for analyzing transient scattering from electrically very large PEC targets

A parallel wavelet-enhanced PWTD algorithm for analyzing tra...

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USNC-URSI Radio science Meeting (Joint with AP-S Symposium)

作者： Yang Liu Abdulkadir C. Yücel Hakan Bağcı Eric Michielssen Department of Electrical Engineering and Computer Science University of Michigan Ann Arbor MI USA King Abdullah University of Science and Technology Thuwal SA

Summary form only given. The computational complexity and memory requirements of classically formulated marching-on-in-time (MOT)-based surface integral equation (SIE) solvers scale as O(N t N s 2 ) and O(N s 2 ), respectively; here N t and N s denote the number of temporal and spatial degrees of freedom of the current density. The multilevel plane wave time domain (PWTD) algorithm, viz., the time domain counterpart of the multilevel fast multipole method, reduces these costs to O(N t N s log 2 N s ) and O(N s 1.5 ) (Ergin et al., IEEE Trans. Antennas Mag., 41, 39-52, 1999). Previously, PWTD-accelerated MOT-SIE solvers have been used to analyze transient scattering from perfect electrically conducting (PEC) and homogeneous dielectric objects discretized in terms of a million spatial unknowns (Shanker et al., IEEE Trans. Antennas Propag., 51, 628-641, 2003). More recently, an efficient parallelized solver that employs an advanced hierarchical and provably scalable spatial, angular, and temporal load partitioning strategy has been developed to analyze transient scattering problems that involve ten million spatial unknowns (Liu et. al., in URSI Digest, 2013). In this work, the efficiency of the abovementioned solver is further enhanced by employing local cosine wavelet compression along the temporal dimension (Coifman et. al., Comptes Rendus de l'Academie des sciences, Paris, Serie I, 312, 259-261, 1991). Local cosine wavelet bases (LCBs) consist of localized, quasibandlimited, and orthonormal cosine-like functions that are well-suited to represent many (naturally occurring/engineering) high frequency plane wave pulses in a multiresolution framework. As a result, they permit a memory reduction in PWTD solvers by only storing wavelet coefficients with magnitudes that exceed a prescribed threshold. Furthermore, the computational cost of the PWTD translation operation can be reduced by coupling the wavelet coefficients of incoming and outgoing plane waves using trans

关键词： Transient analysis Scattering Educational institutions Time-domain analysis Wavelet coefficients Computational efficiency Sparse matrices

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An FMM-FFT accelerated integral equation solver for characterizing electromagnetic wave propagation in mine tunnels and galleries loaded with conductors

An FMM-FFT accelerated integral equation solver for characte...

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USNC-URSI Radio science Meeting (Joint with AP-S Symposium)

作者： Abdulkadir C. Yücel Yang Liu Hakan Bağcı Eric Michielssen Department of Electrical Engineering and Computer Science University of Michigan Ann Arbor MI USA King Abdullah University of Science and Technology Thuwal SA

Reliable wireless communication and tracking systems in underground mines are of paramount importance to increase miners' productivity while monitoring the environmental conditions and increasing the effectiveness of rescue operations. Key to the design and optimization of such systems are electromagnetic (EM) simulation tools capable of analyzing wave propagation in electromagnetically large mine tunnels and galleries loaded with conducting cables (power, telephone) and mining equipment (trolleys, rails, carts), and potentially partially obstructed by debris from a cave-in. Current tools for simulating EM propagation in mine environments leverage (multi-) modal decompositions (Emslie et. al., IEEE Trans. Antennas Propag., 23, 192-205, 1975; Sun and Akyildiz, IEEE Trans. Commun., 58, 1758-1768, 2010), ray-tracing techniques (Zhang, IEEE Tran. Vehic. Tech., 5, 1308-1314, 2003), or full wave methods. Modal approaches and ray-tracing techniques cannot accurately account for the presence of conductors, intricate details of transmitters/receivers, wall roughness, or unstructured debris from a cave-in. Classical full-wave methods do not suffer from such restrictions. However, they require prohibitively large computational resources when applied to the analysis of electromagnetically large tunnels loaded with conductors. Recently, an efficient hybrid method of moment and transmission line solver has been developed to analyze the EM wave propagation inside tunnels loaded with conductors (Brocker et. al., in Proc IEEE AP-S Symp, pp.1,2, 2012). However, the applicability of the solver is limited to the characterization of EM wave propagation at medium frequency band.

关键词： Conductors Acceleration Propagation Integral equations Educational institutions Load modeling Antennas

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Fractional Dynamical Model for Neurovascular Coupling

Fractional Dynamical Model for Neurovascular Coupling

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Annual International Conference of the IEEE engineering in Medicine and Biology Society

作者： Zehor Belkhatir Taous Meriem Laleg-Kirati Computer Electricaland Mathematical Sciences and Engineering (CEMSE) King Abdullah University of Science and Technology

ISBN: (纸本)9781424479276

The neurovascular coupling is a key mechanism linking the neural activity to the hemodynamic behavior. Modeling of this coupling is very important to understand the brain function but it is at the same time very complex due to the complexity of the involved phenomena. Many studies have reported a time delay between the neural activity and the cerebral blood flow, which has been described by adding a delay parameter in some of the existing models. An alternative approach is proposed in this paper, where a fractional system is used to model the neurovascular coupling. Thanks to its non-local property, a fractional derivative is suitable for modeling the phenomena with delay. The proposed model is coupled with the first version of the well-known balloon model, which relates the cerebral blood flow to the Blood Oxygen Level Dependent (BOLD) signal measured using functional Magnetic Resonance Imaging (fMRI). Through some numerical simulations, the properties of the fractional model are explained and some preliminary comparisons to a real BOLD data set are provided.

关键词： Mathematical model Brain modeling Couplings Data models Blood Delays Numerical models

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Residual generator for cardiovascular anomalies detection

Residual generator for cardiovascular anomalies detection

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European Control Conference (ECC)

作者： Z. Belkhatir T. M. Laleg-Kirati M. Tadjine Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah university of science and technology KSA Ecole Polytechnique of Algiers Algeria

ISBN: (纸本)9781479947287

This paper discusses the possibility of using observer-based approaches for cardiovascular anomalies detection and isolation. We consider a lumped parameter model of the cardiovascular system that can be written in a form of nonlinear state-space representation. We show that residuals that are sensitive to variations in some cardiovascular parameters and to abnormal opening and closure of the valves, can be generated. Since the whole state is not easily available for measurement, we propose to associate the residual generator to a robust extended kalman filter. Numerical results performed on synthetic data are provided.

关键词： Valves Generators Mathematical model Biological system modeling Vectors Physiology Robustness

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FANTOM5 CAGE profiles of human and mouse samples

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Scientific Data 2017年第1期4卷 1-10页

作者： Noguchi, Shuhei Arakawa, Takahiro Fukuda, Shiro Furuno, Masaaki Hasegawa, Akira Hori, Fumi Ishikawa-Kato, Sachi Kaida, Kaoru Kaiho, Ai Kanamori-Katayama, Mutsumi Kawashima, Tsugumi Kojima, Miki Kubosaki, Atsutaka Manabe, Ri-Ichiroh Murata, Mitsuyoshi Nagao-Sato, Sayaka Nakazato, Kenichi Ninomiya, Noriko Nishiyori-Sueki, Hiromi Noma, Shohei Saijyo, Eri Saka, Akiko Sakai, Mizuho Simon, Christophe Suzuki, Naoko Tagami, Michihira Watanabe, Shoko Yoshida, Shigehiro Arner, Peter Axton, Richard A. Babina, Magda Kenneth Baillie, J. Barnett, Timothy C. Beckhouse, Anthony G. Blumenthal, Antje Bodega, Beatrice Bonetti, Alessandro Briggs, James Brombacher, Frank Carlisle, Ailsa J. Clevers, Hans C. Davis, Carrie A. Detmar, Michael Dohi, Taeko Edge, B. Albert S. Edinger, Matthias Ehrlund, Anna Ekwall, Karl Endoh, Mitsuhiro Enomoto, Hideki Eslami, Afsaneh Fagiolini, Michela Fairbairn, Lynsey Farach-Carson, Mary C. Faulkner, Geoffrey J. Ferrai, Carmelo Fisher, Malcolm E. Forrester, Lesley M. Fujita, Rie Furusawa, Jun-Ichi Geijtenbeek, Teunis B. Gingeras, Thomas Goldowitz, Daniel Guhl, Sven Guler, Reto Gustincich, Stefano Ha, Thomas J. Hamaguchi, Masahide Hara, Mitsuko Hasegawa, Yuki Herlyn, Meenhard Heutink, Peter Hitchens, Kelly J. Hume, David A. Ikawa, Tomokatsu Ishizu, Yuri Kai, Chieko Kawamoto, Hiroshi Kawamura, Yuki I. Kempfle, Judith S. Kenna, Tony J. Kere, Juha Khachigian, Levon M. Kitamura, Toshio Klein, Sarah Peter Klinken, S. Knox, Alan J. Kojima, Soichi Koseki, Haruhiko Koyasu, Shigeo Lee, Weonju Lennartsson, Andreas MacKay-Sim, Alan Mejhert, Niklas Mizuno, Yosuke Morikawa, Hiromasa Morimoto, Mitsuru Moro, Kazuyo Morris, Kelly J. Motohashi, Hozumi Mummery, Christine L. Nakachi, Yutaka Nakahara, Fumio Nakamura, Toshiyuki Nakamura, Yukio Nozaki, Tadasuke Ogishima, Soichi Ohkura, Naganari Ohno, Hiroshi Ohshima, Mitsuhiro Okada-Hatakeyama, Mariko Okazaki, Yasushi Orlando, Valerio Ovchinnikov, Dmitry A. Passier, Robert Patrikakis, Margaret Pombo, Ana Pradhan-Bhatt, Swati Qin, Xian-Yang Rehli, Michael Rizzu, Patrizia Roy, S Division of Genomic Technologies RIKEN Center for Life Science Technologies Yokohama Kanagawa 230-0045 Japan RIKEN Omics Science Center Yokohama Kanagawa 230-0045 Japan Department of Medicine Karolinska Institutet Stockholm 14186 Sweden Karolinska University Hospital Center for Metabolism and Endocrinology Stockholm 14186 Sweden Scottish Centre for Regenerative Medicine University of Edinburgh 5 Little France Drive Edinburgh EH164UU United Kingdom Department of Dermatology and Allergy Charite University Medicine Berlin Charitéplatz 1 Berlin 10117 Germany Roslin Institute and Royal School of Veterinary Studies University of Edinburgh Edinburgh EH259RG United Kingdom Australian Infectious Diseases Research Centre University of Queensland St Lucia 4072 QLD Australia School of Chemistry and Molecular Biosciences University of Queensland St Lucia 4072 QLD Australia Bio-Rad Laboratories Pty Ltd Hercules 94547 CA United States University of Queensland Diamantina Institute University of Queensland Woolloongabba 4102 QLD Australia IRCCS Fondazione Santa Lucia Via del Fosso di Fiorano 64 Rome 00143 Italy Australian Institute for Bioengineering and Nanotechnology University of Queensland Brisbane St Lucia 4072 QLD Australia Division of Immunology Institute of Infectious Diseases and Molecular Medicine University of Cape Town Anzio Road Observatory 7925 South Africa Immunology of Infectious Diseases Faculty of Health Sciences South African Medical Research Council University of Cape Town Anzio Road 7925 South Africa International Centre for Genetic Engineering and Biotechnology Cape Town Component Anzio Road 7925 South Africa Hubrecht Institute Royal Netherlands Academy of Arts and Sciences Uppsalalaan 8 3584 Netherlands University Medical Centre Utrecht Postbus 85500 Utrecht 3508 Netherlands Genomics Cold Spring Harbor Laboratory Cold Spring Harbor New York 11797 NY United States Institute of Pharmaceutical Sciences ETH Zurich Vladi

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

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Exploring Mixed Membership Stochastic Block Models via Non-negative Matrix Factorization

Exploring Mixed Membership Stochastic Block Models via Non-n...

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IEEE International Conference on Data Mining Workshops (ICDM Workshops)

作者： Chengbin Peng Ka-Chun Wong Computer Electrical and Mathematical Sciences & Engineering King Abdullah University of Science and Technology Thuwal Kingdom of Saudi Arabia Department of Computer Science University of Toronto Toronto Canada

ISBN: (纸本)9781479942732

Many real-world phenomena can be modeled by networks in which entities and connections are represented by nodes and edges respectively. When certain nodes are highly connected with each other, those nodes forms a cluster, which is called community in our context. It is usually assumed that each node belongs to one community only, but evidences in biology and social networks reveal that the communities often overlap with each other. In other words, one node can probably belong to multiple communities. In light of that, mixed membership stochastic block models (MMB) have been developed to model those networks with overlapping communities. Such a model contains three matrices: two incidence matrices indicating in and out connections and one probability matrix. When the probability of connections for nodes between communities are significantly small, the parameter inference problem to this model can be solved by a constrained non-negative matrix factorization (NMF) algorithm. In this paper, we explore the connection between the two models and propose an algorithm based on NMF to infer the parameters of MMB. The proposed algorithms can detect overlapping communities regardless of knowing or not the number of communities. Experiments show that our algorithm can achieve a better community detection performance than the traditional NMF algorithm.

关键词： Communities Inference algorithms Stochastic processes Bayes methods Clustering algorithms Computational modeling Symmetric matrices

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